All modules for which code is available
-- oaklib.converters.data_model_converter -
- oaklib.converters.obo_graph_to_cx_converter -
- oaklib.converters.obo_graph_to_fhir_converter -
- oaklib.converters.obo_graph_to_obo_format_converter -
- oaklib.datamodels.search +
- oaklib.datamodels.search
- oaklib.datamodels.text_annotator
- oaklib.implementations.aggregator.aggregator_implementation -
- oaklib.implementations.funowl.funowl_implementation -
- oaklib.implementations.gilda -
- oaklib.implementations.obograph.obograph_implementation -
- oaklib.implementations.ols.ols_implementation -
- oaklib.implementations.ontobee.ontobee_implementation -
- oaklib.implementations.owlery.owlery_implementation -
- oaklib.implementations.pantherdb.pantherdb_implementation -
- oaklib.implementations.pronto.pronto_implementation -
- oaklib.implementations.simpleobo.simple_obo_implementation -
- oaklib.implementations.sparql.sparql_implementation -
- oaklib.implementations.sqldb.sql_implementation -
- oaklib.implementations.ubergraph.ubergraph_implementation
- oaklib.interfaces.association_provider_interface
- oaklib.interfaces.basic_ontology_interface -
- oaklib.interfaces.class_enrichment_calculation_interface
- oaklib.interfaces.differ_interface -
- oaklib.interfaces.dumper_interface
- oaklib.interfaces.mapping_provider_interface
- oaklib.interfaces.obograph_interface
- oaklib.interfaces.owl_interface @@ -117,7 +99,6 @@
- oaklib.interfaces.summary_statistics_interface
- oaklib.interfaces.text_annotator_interface
- oaklib.interfaces.validator_interface -
- oaklib.selector
- semsql.sqla.semsql
- Predicates -
- Commands
-
-
- runoak
-
-
- aliases -
- ancestors -
- annotate -
- apply -
- apply-obsolete -
- apply-taxon-constraints -
- associations -
- associations-counts -
- associations-matrix -
- axioms -
- cache-clear -
- cache-ls -
- definitions -
- descendants -
- diff -
- diff-associations -
- diff-terms -
- diff-via-mappings -
- disjoints -
- dump -
- enrichment -
- expand-subsets -
- extract -
- fill-table -
- generate-definitions -
- generate-disjoints -
- generate-lexical-replacements -
- generate-logical-definitions -
- generate-synonyms -
- info -
- information-content -
- labels -
- languages -
- leafs -
- lexmatch -
- lint -
- logical-definitions -
- mappings -
- migrate-curies -
- normalize -
- obsoletes -
- ontologies -
- ontology-metadata -
- ontology-versions -
- paths -
- prefixes -
- query -
- relationships -
- rollup -
- roots -
- search -
- set-apikey -
- siblings -
- similarity -
- similarity-pair -
- singletons -
- statistics -
- subsets -
- synonymize -
- taxon-constraints -
- term-categories -
- term-metadata -
- term-subsets -
- terms -
- termset-similarity -
- transform -
- tree -
- validate -
- validate-definitions -
- validate-mappings -
- validate-multiple -
- viz -
-
+ - runoak
- Commands
- Datamodels @@ -259,5953 +182,6 @@
- --v, --verbose -
- --q, --quiet, --no-quiet -
- ---stacktrace, --no-stacktrace -
If set then show full stacktrace on error
--
-
- Default: -
-False
-
- ---save-as <save_as> -
For commands that mutate the ontology, this specifies where changes are saved to
-- ---autosave, --no-autosave -
For commands that mutate the ontology, this determines if these are automatically saved in place
--
-
- Default: -
-False
-
- ---named-prefix-map <named_prefix_map> -
the name of a prefix map, e.g. obo, prefixcc
-- ---prefix <prefix> -
prefix=expansion pair
-- ---metamodel-mappings <metamodel_mappings> -
overrides for metamodel properties such as rdfs:label
-- ---import-depth <import_depth> -
Maximum depth in the import tree to traverse. Currently this is only used by the pronto adapter
-- --g, --associations <associations> -
Location of ontology associations
-- --G, --associations-type <associations_type> -
Syntax of associations input
-- --l, --preferred-language <preferred_language> -
Preferred language for labels and lexical elements
-- ---other-languages <other_languages> -
Additional languages for labels and lexical elements
-- ---requests-cache-db <requests_cache_db> -
If specified, all http requests will be cached to this sqlite file
-- --W, --wrap-adapter <wrap_adapter> -
Wrap the input adapter using another adapter (e.g. llm or semsimian).
-- --i, --input <input> -
input implementation specification. This is either a path to a file, or an ontology selector
-- --I, --input-type <input_type> -
Input format. Permissible values vary depending on the context
-- --a, --add <add> -
additional implementation specification.
-- ---merge, --no-merge -
Merge all inputs specified using –add
--
-
- Default: -
-False
-
- ---profile, --no-profile -
If set, will profile the command
--
-
- Default: -
-False
-
- ---obo-model, --no-obo-model -
If true, assume the OBO synonym datamodel, including provenancem synonym types
-- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --M, --graph-traversal-method <graph_traversal_method> -
Whether formal entailment or graph walking should be used.
--
-
- Options: -
HOP | ENTAILMENT
-
-
- --O, --output-type <output_type> -
Desired output type
-- ---statistics, --no-statistics -
For each ancestor, show statistics.
--
-
- Default: -
-False
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --W, --matches-whole-text, --no-W, --no-matches-whole-text -
if true, then only show matches that span the entire input text
--
-
- Default: -
-False
-
- ---include-aliases, --no-include-aliases -
Include alias maps in output.
--
-
- Default: -
-False
-
- ---text-file <text_file> -
Text file to annotate. Each newline separated entry is a distinct text.
-- --L, --lexical-index-file <lexical_index_file> -
path to lexical index. This is recreated each time unless –no-recreate is passed
-- --A, --match-column <match_column> -
name of column to match on (if the input is tsv/csv)
-- --m, --model <model> -
Name of trained model to use for annotation, e.g. ‘en_ner_craft_md’.
-- --x, --exclude-tokens <exclude_tokens> -
Text file or list of tokens to filter from input prior to annotation. If passed as text file, each newline separated entry is a distinct text.
-- --R, --rules-file <rules_file> -
path to rules file. Conforms to https://w3id.org/oak/mapping-rules
-- --C, --configuration-file <configuration_file> -
path to config file. Conforms to https://w3id.org/oak/text-annotator
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -WORDS -
Optional argument(s)
-for some ontologies, CURIEs may not work, instead specify a full URI surrounded by <>s
-only a subset of KGCL commands are supported by each backend
-- --o, --output <output> -
- ---changes-output <changes_output> -
output file for KGCL changes
-- ---changes-input <changes_input> -
Path to an input changes file
-- ---changes-format <changes_format> -
Format of the changes file (json or kgcl)
-- ---dry-run, --no-dry-run -
if true, only perform the parse of KCGL and do not apply
--
-
- Default: -
-False
-
- ---expand, --no-expand -
if true, expand complex changes to atomic changes
--
-
- Default: -
-True
-
- ---ignore-invalid-changes, --no-ignore-invalid-changes -
if true, ignore invalid changes, e.g. obsoletions of dependent entities
--
-
- Default: -
-False
-
- ---contributor <contributor> -
CURIE for the person contributing the patch
-- --O, --output-type <output_type> -
Desired output type
-- ---overwrite, --no-overwrite -
If set, any changes applied will be saved back to the input file/source
-- -COMMANDS -
Optional argument(s)
-- --o, --output <output> -
- ---expand, --no-expand -
if true, expand complex changes to atomic changes
--
-
- Default: -
-True
-
- ---ignore-invalid-changes, --no-ignore-invalid-changes -
if true, ignore invalid changes, e.g. obsoletions of dependent entities
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --E, --evolution-file <evolution_file> -
path to file containing gains and losses
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --M, --graph-traversal-method <graph_traversal_method> -
Whether formal entailment or graph walking should be used.
--
-
- Options: -
HOP | ENTAILMENT
-
-
- -CONSTRAINTS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---if-absent <if_absent> -
determines behavior when the value is not present or is empty.
--
-
- Options: -
absent-only | present-only
-
-
- --S, --set-value <set_value> -
the value to set for all terms for the given property.
-- ---add-closure-fields, --no-add-closure-fields -
Add closure fields to the output
--
-
- Default: -
-False
-
- ---association-predicates <association_predicates> -
A comma-separated list of predicates for the association relation
-- --Q, --terms-role <terms_role> -
How to interpret query terms.
--
-
- Default: -
-object
-- Options: -
subject | object | both
-
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---add-closure-fields, --no-add-closure-fields -
Add closure fields to the output
--
-
- Default: -
-False
-
- ---association-predicates <association_predicates> -
A comma-separated list of predicates for the association relation
-- --Q, --terms-role <terms_role> -
How to interpret query terms.
--
-
- Default: -
-object
-- Options: -
subject | object | both
-
-
- --L, --limit <limit> -
Limit the number of results
--
-
- Default: -
-10
-
- --F, --filter <filter> -
Additional filters in K=V format
-- ---min-facet-count <min_facet_count> -
Minimum count for a facet to be included
--
-
- Default: -
-1
-
- ---group-by <group_by> -
Group by subject or object
--
-
- Default: -
-object
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---association-predicates <association_predicates> -
A comma-separated list of predicates for the association relation
-- --Q, --terms-role <terms_role> -
How to interpret query terms.
--
-
- Default: -
-object
-- Options: -
subject | object | both
-
-
- ---include-entities, --no-include-entities -
Include entities (e.g. genes) in the output, otherwise just the counts
--
-
- Default: -
-True
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---axiom-type <axiom_type> -
Type of axiom, e.g. SubClassOf
-- ---about <about> -
CURIE that the axiom is about
-- ---references <references> -
CURIEs that the axiom references
-- -TERMS -
Optional argument(s)
-- ---days-old <days_old> -
Clear anything more than this number of days old
--
-
- Default: -
-100
-
- --o, --output <output> -
Output file, e.g. obo file
-- --D, --display <display> -
A comma-separated list of display options. Use ‘all’ for all
-- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- ---if-absent <if_absent> -
determines behavior when the value is not present or is empty.
--
-
- Options: -
absent-only | present-only
-
-
- ---additional-metadata, --no-additional-metadata -
if true then fetch additional metadata about statements stored as OWL reification
--
-
- Default: -
-False
-
- --S, --set-value <set_value> -
the value to set for all terms for the given property.
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- -TERMS -
Optional argument(s)
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --M, --graph-traversal-method <graph_traversal_method> -
Whether formal entailment or graph walking should be used.
--
-
- Options: -
HOP | ENTAILMENT
-
-
- --D, --display <display> -
A comma-separated list of display options. Use ‘all’ for all
-- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --X, --other-ontology <other_ontology> -
other ontology
-- ---simple, --no-simple -
perform a quick difference showing only terms that differ
--
-
- Default: -
-False
-
- ---statistics, --no-statistics -
show summary statistics only
--
-
- Default: -
-False
-
- ---change-type <change_type> -
filter by KGCL change type (e.g. ‘ClassCreation’, ‘EdgeDeletion’)
-- ---group-by-property <group_by_property> -
group summaries by a metadata property, e.g. rdfs:isDefinedBy
-- ---group-by-obo-namespace, --no-group-by-obo-namespace -
shortcut for –group-by-property oio:hasOBONamespace (note this is distinct from the ID namespace)
--
-
- Default: -
-False
-
- ---group-by-defined-by, --no-group-by-defined-by -
shortcut for –group-by-property rdfs:isDefinedBy. This may be inferred from prefix if not set explicitly
--
-
- Default: -
-False
-
- ---group-by-prefix, --no-group-by-prefix -
shortcut for –group-by-property sh:prefix. Groups by the prefix of the CURIE
--
-
- Default: -
-False
-
- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---old-date <old_date> -
Old date, in YYYY-MM-DD format
-- ---new-date <new_date> -
Old date, in YYYY-MM-DD format
-- --g, --associations <associations> -
associations
-- --X, --other-associations <other_associations> -
other associations
-- ---group-by <group_by> -
One of: publications; primary_knowledge_source
-- ---other-ontology <other_ontology> -
other ontology
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --S, --source <source> -
ontology prefixes e.g. HP, MP
-- ---mapping-input <mapping_input> -
File of mappings in SSSOM format. If not provided then mappings in ontology(ies) are used
-- --X, --other-input <other_input> -
Additional input file
-- ---other-input-type <other_input_type> -
Type of additional input file
-- ---intra, --no-intra -
If true, then all sources are in the main input ontology
--
-
- Default: -
-False
-
- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- ---include-identity-mappings, --no-include-identity-mappings -
Use identity relation as mapping; use this for two versions of the same ontology
--
-
- Default: -
-False
-
- ---filter-category-identical, --no-filter-category-identical -
Do not report cases where a relationship has not changed
--
-
- Default: -
-False
-
- ---bidirectional, --no-bidirectional -
Show diff from both left and right perspectives
--
-
- Default: -
-True
-
- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- ---named-classes-only, --no-named-classes-only -
Only show disjointness axioms between two named classes.
--
-
- Default: -
-False
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Path to output file
-- --O, --output-type <output_type> -
Desired output type
-- --c, --config-file <config_file> -
Config file for additional params. Presently used by fhirjson only.
-- ---enforce-canonical-ordering, --no-enforce-canonical-ordering -
Forces the serialization to be in canonical order, which is useful for diffing
--
-
- Default: -
-False
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---ontology-only, --no-ontology-only -
If true, perform a pseudo-enrichment analysis treating each term as an association to itself.
--
-
- Default: -
-False
-
- ---cutoff <cutoff> -
The cutoff for the p-value; any p-values greater than this are not reported.
--
-
- Default: -
-0.05
-
- --U, --sample-file <sample_file> -
Required file containing input list of entity IDs (e.g. gene IDs)
-- --B, --background-file <background_file> -
file containing background list of entity IDs (e.g. gene IDs)
-- ---association-predicates <association_predicates> -
A comma-separated list of predicates for the association relation
-- ---filter-redundant, --no-filter-redundant -
If true, filter out redundant terms
-- ---allow-labels, --no-allow-labels -
If true, allow labels as well as CURIEs in the input files
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- -SUBSETS -
Optional argument(s)
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --o, --output <output> -
Path to output file
-- ---dangling, --no-dangling -
If True, allow dangling edges in the output
--
-
- Default: -
-False
-
- ---include-metadata, --no-include-metadata -
If True, include term metadata such as definitions, synonyms
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-id – the unique identifier of the element
-label – the rdfs:label of the element
-definition – the definition of the element
-mappings – mappings for the element
-ancestors – ancestors for the element (this can be parameterized)
-Pass in a YAML structure (on command line or in a YAML file) listing relations
-Pass in a LinkML data definitions YAML file
-- classes:
-
-
- Person:
-
-
- attributes:
-
-
- id:
identifier: true
-
-- name:
slot_uri: rdfs:label
-
-
-
-
-TODO: allow for an option that will perform fuzzy matches of labels
-TODO: reverse lookup is not provided for all fields, such as definitions
-TODO: add an option to detect inconsistencies
-TODO: add logical for obsoletion/replaced by
-TODO: use most optimized method for whichever backend
-- ---allow-missing, --no-allow-missing -
Allow some dependent values to be blank, post-processing
--
-
- Default: -
-False
-
- ---missing-value-token <missing_value_token> -
Populate all missing values with this token
-- ---schema <schema> -
Path to linkml schema
-- ---delimiter <delimiter> -
Delimiter between columns in input and output
--
-
- Default: -
`` ``
-
-
- ---comment <comment> -
Comment indicator at the beginning of a row.
--
-
- Default: -
-#
-
- ---relation <relation> -
Serialized YAML string corresponding to a normalized relation between two columns
-- ---relation-file <relation_file> -
Path to YAML file corresponding to a list of normalized relation between two columns
-- ---autolabel, --no-autolabel -
Autolabel columns
--
-
- Default: -
-False
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TABLE_FILE -
Required argument
-- ---style-hints <style_hints> -
Description of style for definitions
-- ---apply-patch, --no-apply-patch -
Apply KGCL syntax.
--
-
- Default: -
-False
-
- ---patch <patch> -
Path to where patch file will be written.
-- ---patch-format <patch_format> -
Output syntax for patches.
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --O, --output-type <output_type> -
Desired output type
-- --M, --min-descendants <min_descendants> -
Minimum number of descendants for a class to have to be considered a candidate.
--
-
- Default: -
-3
-
- ---exclude-existing, --no-exclude-existing -
Do not report duplicates with existing disjointness axioms.
--
-
- Default: -
-True
-
- -TERMS -
Optional argument(s)
-- --R, --rules-file <rules_file> -
path to rules file. Conforms to rules_datamodel. e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
-- --Y, --rules-expression <rules_expression> -
YAML encoding of a rules expression
-- ---apply-patch, --no-apply-patch -
Apply KGCL syntax generated based on the synonymizer rules file.
--
-
- Default: -
-False
-
- ---patch <patch> -
Path to where patch file will be written.
-- ---patch-format <patch_format> -
Output syntax for patches.
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --P, --patterns-file <patterns_file> -
path to patterns file
-- ---show-extract, --no-show-extract -
Show the original extracted object.
--
-
- Default: -
-False
-
- ---parse, --no-parse -
Parse the input terms according to the patterns.
--
-
- Default: -
-True
-
- ---fill, --no-fill -
If true, fill in descendant logical definitions.
--
-
- Default: -
-False
-
- ---analyze, --no-analyze -
Analyze consistency of logical definitions (in progress).
--
-
- Default: -
-False
-
- ---unmelt, --no-unmelt -
Use a wide table for display.
--
-
- Default: -
-False
-
- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --R, --rules-file <rules_file> -
Required path to rules file. Conforms to rules_datamodel. e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
-- ---apply-patch, --no-apply-patch -
Apply KGCL syntax generated based on the synonymizer rules file.
--
-
- Default: -
-False
-
- ---patch <patch> -
Path to where patch file will be written.
-- ---patch-format <patch_format> -
Output syntax for patches.
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --D, --display <display> -
A comma-separated list of display options. Use ‘all’ for all
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---use-associations, --no-use-associations -
Use associations to calculate IC
--
-
- Default: -
-False
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --D, --display <display> -
A comma-separated list of display options. Use ‘all’ for all
-- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- ---pivot-languages, --no-pivot-languages -
include one column per language
-- ---all-languages, --no-all-languages -
if source is multi-lingual, show all languages rather than just default
-- ---if-absent <if_absent> -
determines behavior when the value is not present or is empty.
--
-
- Options: -
absent-only | present-only
-
-
- --S, --set-value <set_value> -
the value to set for all terms for the given property.
-- -TERMS -
Optional argument(s)
-https://incatools.github.io/ontology-access-kit/interfaces/basic.html# -oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.leafs
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---filter-obsoletes, --no-filter-obsoletes -
If set, results will exclude obsoletes
--
-
- Default: -
-True
-
create a lexical index, keyed by normalized strings of labels, synonyms
-report all pairs of entities that have the same key
-- --R, --rules-file <rules_file> -
path to rules file. Conforms to rules_datamodel. e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
-- ---add-labels, --no-add-labels -
Populate empty labels with URI fragments or CURIE local IDs, for ontologies that use semantic IDs
--
-
- Default: -
-False
-
- --L, --lexical-index-file <lexical_index_file> -
path to lexical index. This is recreated each time unless –no-recreate is passed
-- ---recreate, --no-recreate -
if true and lexical index is specified, always recreate, otherwise load from index
--
-
- Default: -
-True
-
- ---ensure-strict-prefixes, --no-ensure-strict-prefixes -
Clean prefix map and mappings before generating an output.
--
-
- Default: -
-False
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
- ---report-format <report_format> -
Output format for reporting proposed/applied changes
-- ---dry-run, --no-dry-run -
If true, nothing will be modified by executing command
-- --O, --output-type <output_type> -
Desired output type
-- definedClassId: PATO:0045071
genusIds: -- PATO:0001439 -restrictions: -- fillerId: PATO:0000461
--
-propertyId: RO:0015010
-
-Each property/predicate is a column
-For repeated properties, columns of the form prop_1, prop_2, … are generated
-- ---unmelt, --no-unmelt -
Flatten to a wide table
--
-
- Default: -
-False
-
- ---matrix-axes <matrix_axes> -
If specified, transform results to matrix using these row and column axes. Examples: d,p; f,g
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---if-absent <if_absent> -
determines behavior when the value is not present or is empty.
--
-
- Options: -
absent-only | present-only
-
-
- --S, --set-value <set_value> -
the value to set for all terms for the given property.
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --M, --maps-to-source <maps_to_source> -
Return only mappings with subject or object source equal to this
-- ---mapper <mapper> -
A selector for an adapter that is to be used for the main lookup operation
-- -TERMS -
Optional argument(s)
-- ---replace, --no-replace -
If true, will update in place
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- -CURIE_PAIRS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --M, --maps-to-source <maps_to_source> -
Required Return only mappings with subject or object source equal to this
-- -TERMS -
Optional argument(s)
-- ---include-merged, --no-include-merged -
Include merged terms in output
--
-
- Default: -
-True
-
- ---show-migration-relationships, --no-show-migration-relationships -
Show migration relationships (e.g. replaced_by, consider)
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---all, --no-all -
If true, show all ontologies. Use in place of passing an explicit list
--
-
- Default: -
-False
-
- -ONTOLOGIES -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- ---all, --no-all -
If true, show all ontologies. Use in place of passing an explicit list
--
-
- Default: -
-False
-
- -ONTOLOGIES -
Optional argument(s)
-- ---target <target> -
end point of path
-- ---narrow, --no-narrow -
If true then output path is written a list of terms
--
-
- Default: -
-False
-
- ---viz, --no-viz -
If true then generate a path graph from output
--
-
- Default: -
-False
-
- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---exclude-predicates <exclude_predicates> -
A comma-separated list of predicates to exclude
-- --O, --output-type <output_type> -
Desired output type
-- ---directed, --no-directed -
only show directed paths
--
-
- Default: -
-False
-
- ---include-predicates, --no-include-predicates -
show predicates between nodes
--
-
- Default: -
-False
-
- ---predicate-weights <predicate_weights> -
key-value pairs specified in YAML where keys are predicates or shorthands and values are weights
-- --S, --stylemap <stylemap> -
a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
-- --C, --configure <configure> -
overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
-- --o, --output <output> -
Path to output file
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
- ---used-only, --no-used-only -
If True, show only prefixes used in ontology
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --q, --query <query> -
Main query, specified in adapter-specific language (SQL, SPARQL)
-- --L, --label-fields <label_fields> -
Comma-separated list of fields to use as labels
-- --P, --prefixes <prefixes> -
Comma-separated list of prefixes to expand
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---direction <direction> -
direction of traversal over edges, which up is subject to object, down is object to subject.
--
-
- Options: -
up | down | both
-
-
- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- ---if-absent <if_absent> -
determines behavior when the value is not present or is empty.
--
-
- Options: -
absent-only | present-only
-
-
- --S, --set-value <set_value> -
the value to set for all terms for the given property.
-- ---include-entailed, --no-include-entailed -
Include entailed indirect relationships
--
-
- Default: -
-False
-
- ---include-tbox, --no-include-tbox -
Include class-class relationships (subclass and existentials)
--
-
- Default: -
-True
-
- ---include-abox, --no-include-abox -
Include instance relationships (class and object property assertions)
--
-
- Default: -
-True
-
- ---include-metadata, --no-include-metadata -
Include metadata (axiom annotations)
--
-
- Default: -
-False
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- ---object-group <object_group> -
An object ID to group by. If a comma separated list of IDs is provided, the first one is interpreted as a top-level grouping and the remaining IDs are interpreted as sub-groups within.
-- -TERMS -
Optional argument(s)
-https://incatools.github.io/ontology-access-kit/interfaces/basic.html# -oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.roots
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --P, --has-prefix <has_prefix> -
filter based on a prefix, e.g. OBI
-- --O, --output-type <output_type> -
Desired output type
-- --A, --annotated-roots, --no-annotated-roots, --no-A -
If true, use annotated roots, if present
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- --e, --endpoint <endpoint> -
Required Name of endpoint, e.g. bioportal
-- -KEYVAL -
Required argument
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- -TERMS -
Optional argument(s)
-via a file
-via explicit lists of terms or queries
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---set1-file <set1_file> -
ID file for set1
-- ---set2-file <set2_file> -
ID file for set2
-- ---min-jaccard-similarity <min_jaccard_similarity> -
Minimum value for jaccard score
-- ---min-ancestor-information-content <min_ancestor_information_content> -
Minimum value for information content
-- --o, --output <output> -
path to output
-- ---main-score-field <main_score_field> -
Score used for summarization
--
-
- Default: -
-phenodigm_score
-
- ---information-content-file <information_content_file> -
File containing information content for each term
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- -TERMS -
Optional argument(s)
-https://incatools.github.io/ontology-access-kit/interfaces/basic.html# -oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.singletons
-- --o, --output <output> -
Output file, e.g. obo file
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---filter-obsoletes, --no-filter-obsoletes -
If set, results will exclude obsoletes
--
-
- Default: -
-True
-
by a collection of branch roots
-by a metadata property (e.g. oio:hasOBONamespace, rdfs:isDefinedBy)
-by prefix (e.g. GO, PR, CL, OBI)
-- --O, --output-type <output_type> -
Desired output type
--
-
- Options: -
obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
-
-
- ---group-by-property <group_by_property> -
group summaries by a metadata property, e.g. rdfs:isDefinedBy
-- ---group-by-obo-namespace, --no-group-by-obo-namespace -
shortcut for –group-by-property oio:hasOBONamespace (note this is distinct from the ID namespace)
--
-
- Default: -
-False
-
- ---group-by-prefix, --no-group-by-prefix -
shortcut for –group-by-property sh:prefix. Groups by the prefix of the CURIE
--
-
- Default: -
-False
-
- ---group-by-defined-by, --no-group-by-defined-by -
shortcut for –group-by-property rdfs:isDefinedBy. This may be inferred from prefix if not set explicitly
--
-
- Default: -
-False
-
- ---include-residuals, --no-include-residuals -
If true include an OTHER category for terms that do not have the property
-- --X, --compare-with <compare_with> -
Compare with another ontology
-- --P, --has-prefix <has_prefix> -
filter based on a prefix, e.g. OBI
-- --o, --output <output> -
Output file, e.g. obo file
-- -BRANCHES -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --R, --rules-file <rules_file> -
path to rules file. Conforms to rules_datamodel. e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
-- ---apply-patch, --no-apply-patch -
Apply KGCL syntax generated based on the synonymizer rules file.
--
-
- Default: -
-False
-
- ---patch <patch> -
Output patch file containing KGCL commands.
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-https://incatools.github.io/ontology-access-kit/src/oaklib.utilities.taxon.taxon_constraints_utils
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --M, --graph-traversal-method <graph_traversal_method> -
Whether formal entailment or graph walking should be used.
--
-
- Options: -
HOP | ENTAILMENT
-
-
- --A, --all, --no-A, --no-all -
if specified then perform for all terms
--
-
- Default: -
-False
-
- ---include-redundant, --no-include-redundant -
if specified then include redundant taxon constraints from ancestral subjects
--
-
- Default: -
-False
-
- ---direct, --no-direct -
only include directly asserted taxon constraints
--
-
- Default: -
-False
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---category-system <category_system> -
Example: biolink, cob, bfo, dbpedia, …
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- ---additional-metadata, --no-additional-metadata -
if true then fetch additional metadata about statements stored as OWL reification
--
-
- Default: -
-False
-
- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- ---filter-obsoletes, --no-filter-obsoletes -
If set, results will exclude obsoletes
--
-
- Default: -
-True
-
- --o, --output <output> -
Output file, e.g. obo file
-- ---owl-type <owl_type> -
only include entities of this type, e.g. owl:Class, rdf:Property
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- ---information-content-file <information_content_file> -
File containing information content for each term
-- -TERMS -
Optional argument(s)
-- --o, --output <output> -
Path to output file
-- --O, --output-type <output_type> -
Desired output type
-- --c, --config-file <config_file> -
Config file for additional transform params.
-- --t, --transform <transform> -
Required Name of transformation to apply.
-- -TERMS -
Optional argument(s)
--
-
- [] ENVO:00000247 ! volcano
-
-
-
-
- [i] ENVO:00000403 ! shield volcano
-
-
[i] ENVO:00000372 ! pyroclastic shield volcano
-
-
-[i] ENVO:00000407 ! subglacial volcano
-
-
-- ---down, --no-down -
traverse down
--
-
- Default: -
-False
-
- ---gap-fill, --no-gap-fill -
If set then find the minimal graph that spans all input curies
--
-
- Default: -
-False
-
- ---add-mrcas, --no-add-mrcas -
If set then extend input seed list to include all pairwise MRCAs
--
-
- Default: -
-False
-
- --S, --stylemap <stylemap> -
a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
-- --C, --configure <configure> -
overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
-- ---max-hops <max_hops> -
Trim nodes that are equal to or greater than this distance from terms
-- ---skip <skip> -
Exclude paths that contain this node
-- ---root <root> -
Use this node or nodes as roots
-- --D, --display <display> -
A comma-separated list of display options. Use ‘all’ for all
-- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- ---cutoff <cutoff> -
maximum results to report for any (type, predicate) pair
--
-
- Default: -
-50
-
- ---skip-structural-validation, --no-skip-structural-validation -
If true, main structural validation checks are skipped
--
-
- Default: -
-False
-
- ---skip-ontology-rules, --no-skip-ontology-rules -
If true, ontology rules are skipped
--
-
- Default: -
-True
-
- --R, --rule <rule> -
A rule to run. Can be specified multiple times. If not specified, all rules are run.
-- --o, --output <output> -
Output file, e.g. obo file
-- --O, --output-type <output_type> -
Desired output type
-- -TERMS -
Optional argument(s)
-- ---skip-text-annotation, --no-skip-text-annotation -
If true, do not parse text annotations
--
-
- Default: -
-False
-
- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Output file, e.g. obo file
-- -TERMS -
Optional argument(s)
-- ---autolabel, --no-autolabel -
If set, results will automatically have labels assigned
--
-
- Default: -
-True
-
- --O, --output-type <output_type> -
Desired output type
-- ---adapter-mapping <adapter_mapping> -
Multiple prefix=selector pairs, e.g. –adapter-mapping uberon=db/uberon.db
-- --o, --output <output> -
Output file, e.g. obo file
-- --C, --configuration-file <configuration_file> -
Path to a configuration file. This is typically a YAML file, but may be a JSON file
-- -TERMS -
Optional argument(s)
-- ---cutoff <cutoff> -
maximum results to report for any (type, predicate) pair
--
-
- Default: -
-50
-
- --s, --schema <schema> -
Path to schema (if you want to override the bundled OMO schema)
-- --o, --output <output> -
Output file, e.g. obo file
-- -DBS -
Optional argument(s)
-- ---view, --no-view -
if view is set then open the image after rendering
--
-
- Default: -
-True
-
- ---down, --no-down -
traverse down
--
-
- Default: -
-False
-
- ---gap-fill, --no-gap-fill -
If set then find the minimal graph that spans all input curies
--
-
- Default: -
-False
-
- ---add-mrcas, --no-add-mrcas -
If set then extend input seed list to include all pairwise MRCAs
--
-
- Default: -
-False
-
- --S, --stylemap <stylemap> -
a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
-- --C, --configure <configure> -
overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
-- ---max-hops <max_hops> -
Trim nodes that are equal to or greater than this distance from terms
-- ---meta, --no-meta -
Add metadata object to graph nodes, including xrefs, definitions
--
-
- Default: -
-False
-
- --p, --predicates <predicates> -
A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
-- --O, --output-type <output_type> -
Desired output type
-- --o, --output <output> -
Path to output file
-- -TERMS -
Optional argument(s)
-
All modules for which code is available
Source code for oaklib.converters.data_model_converter
-from abc import ABC, abstractmethod
-from dataclasses import dataclass
-from typing import Callable, Optional
-
-import curies
-
-from oaklib.datamodels.ontology_metadata import Any
-from oaklib.types import CURIE
-
-
-
-[docs]
-@dataclass(eq=False)
-class DataModelConverter(ABC):
- """
- Base class for all inter-data model converters.
-
- Do not use this directly: use one of the subclasses.
- """
-
- curie_converter: curies.Converter = None
- """Converts between CURIEs and URIs"""
-
- labeler: Callable[[CURIE], Optional[str]] = None
- """A function that returns a label for a given CURIE"""
-
- enforce_canonical_ordering: Optional[bool] = None
- """If True, will enforce canonical ordering of keys in the output"""
-
- def __hash__(self):
- return hash(str(self))
-
-
-[docs]
- @abstractmethod
- def convert(self, source: Any, target: Any = None, **kwargs) -> Any:
- """
- Converts from a source object to a target object.
-
- Individual subclasses will map this to a specific subtype.
-
- :param source:
- :param target: Optional. If passed, modified in place
- :param kwargs: Additional arguments
- :return:
- """
- raise NotImplementedError
-
-
-
-[docs]
- @abstractmethod
- def dump(self, source: Any, target: str = None, **kwargs) -> None:
- """
- Dumps a source object to a target file.
-
- :param source:
- :param target:
- :return:
- """
- raise NotImplementedError
-
-
-
Source code for oaklib.converters.obo_graph_to_cx_converter
-import json
-import sys
-from dataclasses import dataclass
-from typing import Dict, Union
-
-from ndex2 import NiceCXNetwork
-
-from oaklib.converters.data_model_converter import DataModelConverter
-from oaklib.datamodels.obograph import Graph, GraphDocument
-from oaklib.types import CURIE
-
-
-
-[docs]
-@dataclass
-class OboGraphToCXConverter(DataModelConverter):
- """Converts from OboGraph to OBO Format."""
-
-
-[docs]
- def dump(self, source: Union[GraphDocument, Graph], target: str = None, **kwargs) -> None:
- """
- Dump an OBO Graph Document to CX
-
- :param source:
- :param target:
- :return:
- """
- obj = self.convert(source)
- if target is None:
- file = sys.stdout
- else:
- file = open(target, "w", encoding="UTF-8")
- json.dump(obj, file, indent=2, sort_keys=False)
-
-
-
-[docs]
- def convert(self, source: Union[GraphDocument, Graph], target: Dict = None, **kwargs) -> Dict:
- """
- Convert an OBO Graph Document to a CX Dictionary.
-
- :param source:
- :param target: if None, one will be created
- :return:
- """
- cxn = NiceCXNetwork()
- if isinstance(source, GraphDocument):
- graphs = source.graphs
- else:
- graphs = [source]
- cxn.set_name(graphs[0].id)
- pm = {}
- for g in graphs:
- for pe in g.prefixes.values():
- pm[pe.prefix] = pe.expansion
- cxn.set_context(pm)
- node_id_map = {}
- for g in graphs:
- for n in g.nodes:
- n_iid = cxn.create_node(n.lbl, node_represents=self._id(n.id))
- node_id_map[n.id] = n_iid
- if n.meta:
- if n.meta.synonyms:
- # cx does not appear to allow repeated attributes, so we join synonyms
- cxn.add_node_attribute(
- n_iid, "altname", "; ".join([s.val for s in n.meta.synonyms])
- )
- for e in g.edges:
- s = node_id_map.get(e.sub, None)
- t = node_id_map.get(e.obj, None)
- if not s or not t:
- continue
- cxn.create_edge(s, t, self._id(e.pred))
- doc = cxn.to_cx()
- return doc
-
-
- def _id(self, uri: CURIE) -> CURIE:
- if not self.curie_converter:
- return uri
- return self.curie_converter.compress(uri, passthrough=True)
-
-
Source code for oaklib.converters.obo_graph_to_fhir_converter
-"""
-OboGraph to FHIR Converter
-
-Resources
-- Updates issue: https://github.com/INCATools/ontology-access-kit/issues/369
-- Conversion examples: https://drive.google.com/drive/folders/1lwGQ63_fedfWlGlRemq8OeZhZsvIXN01
-"""
-
-import logging
-from dataclasses import dataclass
-from typing import Any, Dict, List, Tuple, Union
-
-import rdflib
-from linkml_runtime.dumpers import json_dumper
-
-from oaklib.converters.data_model_converter import DataModelConverter
-from oaklib.datamodels.fhir import (
- CodeSystem,
- CodeSystemProperty,
- Coding,
- Concept,
- ConceptDesignation,
- ConceptProperty,
-)
-from oaklib.datamodels.obograph import Edge, Graph, GraphDocument, Node
-from oaklib.datamodels.vocabulary import (
- HAS_BROAD_SYNONYM,
- HAS_EXACT_SYNONYM,
- HAS_NARROW_SYNONYM,
- HAS_RELATED_SYNONYM,
-)
-from oaklib.types import CURIE, URI
-from oaklib.utilities.obograph_utils import index_graph_edges_by_subject
-
-TRIPLE = Tuple[rdflib.URIRef, rdflib.URIRef, Any]
-
-DIRECT_PREDICATE_MAP = {
- "is_a": "parent",
-}
-
-SCOPE_MAP = {
- "hasBroadSynonym": HAS_BROAD_SYNONYM,
- "hasExactSynonym": HAS_EXACT_SYNONYM,
- "hasNarrowSynonym": HAS_NARROW_SYNONYM,
- "hasRelatedSynonym": HAS_RELATED_SYNONYM,
-}
-
-SCOPE_DISPLAY = {
- "hasBroadSynonym": "has broad synonym",
- "hasExactSynonym": "has exact synonym",
- "hasNarrowSynonym": "has narrow synonym",
- "hasRelatedSynonym": "has related synonym",
-}
-
-
-
-[docs]
-@dataclass
-class OboGraphToFHIRConverter(DataModelConverter):
- """
- Converts from OboGraph to FHIR.
-
- - An ontology is mapped to a FHIR `CodeSystem <https://build.fhir.org/codesystem.html>`_.
- - Each node in the OboGraph is converted to a _FHIR Concept_.
- - Each CURIE/URI in the OboGraph is treated as a CURIE when it becomes a packages (e.g. "HP:0000001")
-
- - Each edge in the OboGraph is converted to a _FHIR ConceptProperty_ if the `include_all_predicates` param is
- True. Otherwise, will only convert edges if the predicate is in the `DIRECT_PREDICATE_MAP`.
- - Each synonym in the OboGraph is converted to a _FHIR ConceptDesignation_.
-
- - The synonym predicate is mapped to a _FHIR Coding_, using the `SCOPE_MAP`.
-
- To run on the command line:
-
- runoak --prefix my_prefix=my_expansion -i obograph:my-ont.json dump -O fhirjson -o my-ont.fhir.json
-
- Here the input is an OboGraph JSON file. You can also specify:
-
- - OWL as sqlite
- - OBO Format
-
- """
-
-
-[docs]
- def dump(
- self,
- source: GraphDocument,
- target: str = None,
- **kwargs,
- ) -> None:
- """
- Dump an OBO Graph Document to a FHIR CodeSystem.
-
- :param source: Source serialization.
- :param target: Target serialization.
- :param kwargs: Additional keyword arguments passed to :ref:`convert`.
- """
- cs = self.convert(
- source,
- **kwargs,
- )
- json_str = json_dumper.dumps(cs, inject_type=False)
- if target is None:
- print(json_str)
- else:
- with open(target, "w", encoding="UTF-8") as f:
- f.write(json_str)
-
-
- # todo: id/url: any way to try to ascertain ID or URL if not passed? and warn if not determined?
-
-[docs]
- def convert(
- self,
- source: GraphDocument,
- target: CodeSystem = None,
- code_system_id: str = None,
- code_system_url: str = None,
- include_all_predicates: bool = True,
- native_uri_stems: List[str] = None,
- use_curies_native_concepts: bool = False,
- use_curies_foreign_concepts: bool = True,
- predicate_period_replacement: bool = False,
- **kwargs,
- ) -> CodeSystem:
- """
- Convert an OBO Graph Document to a FHIR CodingSystem
-
- To use:
-
- >>> from oaklib.converters.obo_graph_to_fhir_converter import OboGraphToFHIRConverter
- >>> from oaklib.datamodels.obograph import GraphDocument
- >>> from linkml_runtime.dumpers import json_dumper
- >>> from linkml_runtime.loaders import json_loader
- >>> converter = OboGraphToFHIRConverter()
- >>> graph = json_loader.load("tests/input/hp_test.json", target_class=GraphDocument)
- >>> code_system = converter.convert(graph)
- >>> print(json_dumper.dumps(code_system))
- <BLANKLINE>
- ...
- "concept": [
- {
- "code": "HP:0012639",
- "display": "Abnormal nervous system morphology",
- "definition": "A structural anomaly of the nervous system.",
- "designation": [
- ...
-
- :param code_system_id: The packages system ID to use for identification on the server uploaded to.
- See: https://hl7.org/fhir/resource-definitions.html#Resource.id
- :param code_system_url: Canonical URL for the packages system.
- See: https://hl7.org/fhir/codesystem-definitions.html#CodeSystem.url
- :param native_uri_stems: A list of URI stems that will be used to determine whether a
- concept is native to the CodeSystem. (not implemented)
- For example, for OMIM, the following URI stems are native:
- https://omim.org/entry/, https://omim.org/phenotypicSeries/PS
- :param include_all_predicates: Include the maximal amount of predicates.
- Changes the default behavior from only
- exporting: IS_A (rdfs:subClassOf)
- :param use_curies_native_concepts: FHIR conventionally uses codes for references to
- concepts that are native to a given CodeSystem. With this option,
- references will be CURIEs instead. (not implemented)
- :param use_curies_foreign_concepts: Typical FHIR CodeSystems do not contain any
- concepts that are not native to that CodeSystem. In cases where they
- do appear, this converter defaults to URIs
- for references, unless this flag is present, in which case the converter
- will attempt to construct CURIEs. (not implemented)
- :param predicate_period_replacement: Predicates URIs populated into `CodeSystem.concept.property.packages`
- and `CodeSystem.concept.property.packages`, but the HAPI FHIR server
- has a bug in which periods '.' cause errors. If this flag is present,
- periods will be replaced with underscores '_'.
- :return: FHIR CodeSystem object
- """
- if target is None:
- target = CodeSystem()
- target.resourceType = CodeSystem.__name__
- for g in source.graphs:
- self._convert_graph(
- g,
- target=target,
- include_all_predicates=include_all_predicates,
- native_uri_stems=native_uri_stems,
- use_curies_native_concepts=use_curies_native_concepts,
- use_curies_foreign_concepts=use_curies_foreign_concepts,
- predicate_period_replacement=predicate_period_replacement,
- )
- target.id = code_system_id
- if not code_system_id:
- del target.id
- if code_system_id:
- target.url = code_system_url
- return target
-
-
-
-[docs]
- def code(self, uri: CURIE) -> str:
- """
- Convert a packages.
-
- This is a wrapper onto curie_converter.compress
-
- :param uri: URI or CURIE to convert
- :return: CURIE
- """
- if not self.curie_converter:
- return uri
- return self.curie_converter.compress(uri, passthrough=True)
-
-
- def _convert_graph(
- self,
- source: Graph,
- target: CodeSystem,
- include_all_predicates: bool = True,
- native_uri_stems: List[str] = None,
- use_curies_native_concepts: bool = False,
- use_curies_foreign_concepts: bool = True,
- predicate_period_replacement: bool = False,
- ) -> CodeSystem:
- target.id = source.id
- edges_by_subject = index_graph_edges_by_subject(source)
- logging.info(f"Converting graph to obo: {source.id}, nodes={len(source.nodes)}")
- self.predicates_to_export = set()
- # CodeSystem.concept
- for n in source.nodes:
- logging.debug(f"Converting node {n.id}")
- self._convert_node(
- n,
- index=edges_by_subject,
- target=target,
- include_all_predicates=include_all_predicates,
- native_uri_stems=native_uri_stems,
- use_curies_native_concepts=use_curies_native_concepts,
- use_curies_foreign_concepts=use_curies_foreign_concepts,
- predicate_period_replacement=predicate_period_replacement,
- )
- # CodeSystem.property
- # todo's
- # i. packages: mostly URIs, which don't conform to [^\s]+(\s[^\s]+)* (https://hl7.org/fhir/datatypes.html#code)
- # ii. description: can get, but tedious; downloading and caching and looking up in source ontologies
- # iii. type: ideally Coding (https://build.fhir.org/datatypes.html#Coding). The property value is a packages
- # defined in an external packages system. This may be used for translations, but is not the intent.
- # https://hl7.org/fhir/codesystem-concept-property-type.htm
- target.property = [
- CodeSystemProperty(code=x, uri=x, type="packages") for x in self.predicates_to_export
- ]
- return target
-
- def _convert_node(
- self,
- source: Node,
- index: Dict[Union[URI, CURIE], List[Edge]],
- target: CodeSystem,
- include_all_predicates: bool = True,
- native_uri_stems: List[str] = None,
- use_curies_native_concepts: bool = False,
- use_curies_foreign_concepts: bool = True,
- predicate_period_replacement: bool = False,
- ) -> Concept:
- """Converts a node to a FHIR Concept. Also collects predicates to be included in CodeSystem.property."""
- # TODO: Use new flags
- # self.uri(source.id) # <--- self.uri does not exist
- # self.packages is actually a curie. change to self.curie and add a self.packages func?
- _id = self.code(source.id)
- logging.debug(f"Converting node {_id} from {source}")
- concept = Concept(code=_id, display=source.lbl)
- target.concept.append(concept)
- if source.meta:
- self._convert_meta(source, concept)
- for e in index.get(source.id, []):
- obj = self.code(e.obj)
- logging.debug(
- f"Converting edge {e.pred} {e.obj} // include_all={include_all_predicates}"
- )
- if include_all_predicates or e.pred in DIRECT_PREDICATE_MAP:
- pred: str = DIRECT_PREDICATE_MAP.get(e.pred, e.pred)
- if predicate_period_replacement:
- pred = pred.replace(".", "_")
- concept.property.append(ConceptProperty(code=pred, valueCode=obj))
- self.predicates_to_export.add(pred)
- else:
- logging.debug(f"Skipping edge {e}")
- return concept
-
- def _convert_meta(self, source: Node, concept: Concept):
- meta = source.meta
- if meta.definition:
- concept.definition = meta.definition.val
- for synonym in meta.synonyms:
- synonym_pred_code = self.code(synonym.pred)
- concept.designation.append(
- ConceptDesignation(
- # language=synonym.lang,
- use=Coding(
- system="oio",
- code=synonym_pred_code,
- display=SCOPE_DISPLAY.get(synonym.pred),
- ),
- value=synonym.val,
- )
- )
-
-
Source code for oaklib.converters.obo_graph_to_obo_format_converter
-import logging
-import sys
-from dataclasses import dataclass
-from io import BytesIO, StringIO
-from typing import Any, Dict, List, Tuple
-
-import rdflib
-
-from oaklib.converters.data_model_converter import DataModelConverter
-from oaklib.datamodels.obograph import Edge, Graph, GraphDocument, Node
-from oaklib.datamodels.vocabulary import IS_A, SYNONYM_PRED_TO_SCOPE_MAP
-from oaklib.implementations.simpleobo.simple_obo_parser import (
- TAG_DEFINITION,
- TAG_INTERSECTION_OF,
- TAG_INVERSE_OF,
- TAG_IS_A,
- TAG_NAME,
- TAG_RELATIONSHIP,
- TAG_SUBSET,
- TAG_SYNONYM,
- TAG_XREF,
- OboDocument,
- Stanza,
-)
-from oaklib.types import CURIE
-from oaklib.utilities.oboformat_utils import subset_to_shorthand
-from oaklib.utilities.obograph_utils import index_graph_edges_by_subject
-
-TRIPLE = Tuple[rdflib.URIRef, rdflib.URIRef, Any]
-
-DIRECT_PREDICATE_MAP = {
- "is_a": TAG_IS_A,
- IS_A: TAG_IS_A, # sometime obographs use the predicate rather than shorthand
- "subPropertyOf": TAG_IS_A,
- "inverseOf": TAG_INVERSE_OF,
-}
-
-typedef_type_map = {
- "CLASS": "Term",
- "PROPERTY": "Typedef",
-}
-
-
-def _escape(s: str) -> str:
- return s.replace('"', '\\"').replace("\n", "\\n")
-
-
-
-[docs]
-@dataclass
-class OboGraphToOboFormatConverter(DataModelConverter):
- """Converts from OboGraph to OBO Format."""
-
- use_shorthand: bool = True
-
-
-[docs]
- def dump(self, source: GraphDocument, target: str = None, **kwargs) -> None:
- """
- Dump an OBO Graph Document to a FHIR CodeSystem
-
- :param source:
- :param target:
- :return:
- """
- obodoc = self.convert(source)
- if target is None:
- obodoc.dump(sys.stdout)
- else:
- with open(target, "w", encoding="UTF-8") as f:
- obodoc.dump(f)
-
-
-
-[docs]
- def dumps(self, source: GraphDocument, **kwargs) -> str:
- """
- Dump an OBO Graph Document to a string
-
- :param source:
- :return:
- """
- obodoc = self.convert(source)
- io = StringIO()
- obodoc.dump(io)
- return io.getvalue()
-
-
-
-[docs]
- def as_bytes_io(self, source: GraphDocument, **kwargs) -> BytesIO:
- """
- Dump an OBO Graph Document to a string
-
- :param source:
- :return:
- """
- s = self.dumps(source)
- return BytesIO(s.encode("UTF-8"))
-
-
-
-[docs]
- def convert(self, source: GraphDocument, target: OboDocument = None, **kwargs) -> OboDocument:
- """
- Convert an OBO Format Document.
-
- :param source:
- :param target: if None, one will be created
- :return:
- """
- if target is None:
- target = OboDocument()
- for g in source.graphs:
- logging.info(f"Converting graph {g.id}, nodes: {len(g.nodes)}, edges: {len(g.edges)}")
- self._convert_graph(g, target=target)
- logging.info(f"Converted {len(target.stanzas)} stanzas")
- return target
-
-
- def _id(self, uri_or_curie: CURIE) -> CURIE:
- if not self.curie_converter:
- return uri_or_curie
- return self.curie_converter.compress(uri_or_curie, passthrough=True)
-
- def _predicate_id(self, uri_or_curie: CURIE, target: OboDocument) -> CURIE:
- curie = self._id(uri_or_curie)
- return target.curie_to_shorthand_map.get(curie, curie)
-
- def _convert_graph(self, source: Graph, target: OboDocument) -> OboDocument:
- edges_by_subject = index_graph_edges_by_subject(source)
- for n in source.nodes:
- if n.type == "PROPERTY" and n.lbl:
- shorthand = n.lbl.replace(" ", "_")
- target.curie_to_shorthand_map[self._id(n.id)] = shorthand
- for n in source.nodes:
- logging.debug(f"Converting node {n.id}")
- self._convert_node(n, index=edges_by_subject, target=target, graph=source)
- for lda in source.logicalDefinitionAxioms:
- defined_class_id = self._id(lda.definedClassId)
- if defined_class_id not in target.stanzas:
- target.add_stanza(Stanza(id=defined_class_id, type="Term"))
- stanza = target.stanzas[defined_class_id]
- for g in lda.genusIds:
- obj = self._id(g)
- stanza.add_tag_value(TAG_INTERSECTION_OF, obj)
- for r in lda.restrictions:
- filler = self._id(r.fillerId)
- pred = self._id(r.propertyId)
- stanza.add_tag_value_pair(TAG_INTERSECTION_OF, pred, filler)
- return target
-
- def _convert_node(
- self,
- source: Node,
- index: Dict[CURIE, List[Edge]],
- target: OboDocument,
- graph: Graph = None,
- ) -> None:
- id = self._id(source.id)
- shorthand_xref = None
- if id in target.curie_to_shorthand_map:
- shorthand_xref = id
- id = target.curie_to_shorthand_map[id]
- logging.debug(f"Converting node {id} from {source}")
- t = source.type
- # if not t:
- # logging.warning(f"No type for {id}")
- # return
- if id.startswith("oio:"):
- return
- typedef_type = typedef_type_map.get(t, None)
- if not typedef_type:
- return
- stanza = Stanza(id=id, type=typedef_type)
- target.add_stanza(stanza)
- if source.lbl:
- stanza.add_tag_value(TAG_NAME, source.lbl)
- if source.meta:
- self._convert_meta(source, target=stanza)
- if shorthand_xref:
- stanza.add_tag_value(TAG_XREF, shorthand_xref)
- for e in index.get(source.id, []):
- obj = self._id(e.obj)
- obj_lbl = None
- if graph:
- nodes = [n for n in graph.nodes if n.id == e.obj]
- if nodes:
- obj_lbl = nodes[0].lbl
- if obj_lbl:
- cmt = f" ! {obj_lbl}"
- else:
- cmt = ""
- pred = self._predicate_id(e.pred, target)
- if e.pred in DIRECT_PREDICATE_MAP:
- stanza.add_tag_value(DIRECT_PREDICATE_MAP[e.pred], f"{obj}{cmt}")
- else:
- stanza.add_tag_value(TAG_RELATIONSHIP, f"{pred} {obj}{cmt}")
- return
-
- def _convert_meta(self, source: Node, target: Stanza):
- meta = source.meta
- logging.debug(f"ADDING DEF {target}")
- if meta.definition:
- xrefs = ", ".join(meta.definition.xrefs)
- target.add_tag_value(TAG_DEFINITION, f'"{_escape(meta.definition.val)}" [{xrefs}]')
- if meta.xrefs:
- for x in meta.xrefs:
- target.add_tag_value(TAG_XREF, x.val)
- for x in meta.subsets:
- target.add_tag_value(TAG_SUBSET, subset_to_shorthand(x))
- for s in meta.synonyms:
- xrefs = ", ".join(s.xrefs)
- scope = SYNONYM_PRED_TO_SCOPE_MAP[f"oio:{s.pred}"]
- target.add_tag_value(TAG_SYNONYM, f'"{_escape(s.val)}" {scope} [{xrefs}]')
-
-
Source code for oaklib.implementations.funowl.funowl_implementation
-import logging
-from dataclasses import dataclass
-from typing import Any, Iterable, List, Mapping, Optional
-
-import rdflib
-from funowl import (
- IRI,
- AnnotationAssertion,
- Axiom,
- Declaration,
- ObjectSomeValuesFrom,
- OntologyDocument,
- SubClassOf,
-)
-from funowl.converters.functional_converter import to_python
-from funowl.writers.FunctionalWriter import FunctionalWriter
-from kgcl_schema.datamodel import kgcl
-
-from oaklib.datamodels.vocabulary import (
- DEPRECATED_PREDICATE,
- HAS_DEFINITION_CURIE,
- HAS_EXACT_SYNONYM,
- IS_A,
- LABEL_PREDICATE,
-)
-from oaklib.interfaces import SearchInterface
-from oaklib.interfaces.basic_ontology_interface import LANGUAGE_TAG
-from oaklib.interfaces.owl_interface import OwlInterface, ReasonerConfiguration
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.types import CURIE, PRED_CURIE
-
-
-
-[docs]
-@dataclass
-class FunOwlImplementation(OwlInterface, PatcherInterface, SearchInterface):
- """
- An experimental partial implementation of :ref:`OwlInterface`
-
- Wraps FunOWL
-
- `<https://github.com/hsolbrig/funowl>`_
-
- """
-
- ontology_document: OntologyDocument = None
-
- def __post_init__(self):
- if self.ontology_document is None:
- resource = self.resource
- if resource is None or resource.local_path is None:
- doc = OntologyDocument()
- else:
- logging.info(f"Loading {resource.local_path} into FunOwl")
- doc = to_python(str(resource.local_path))
- self.ontology_document = doc
- if self.functional_writer is None:
- self.functional_writer = FunctionalWriter()
- for prefix in doc.prefixDeclarations.as_prefixes():
- self.functional_writer.bind(prefix.prefixName, prefix.fullIRI)
-
- @property
- def _ontology(self):
- return self.ontology_document.ontology
-
- def entity_iri_to_curie(self, entity: IRI) -> CURIE:
- uri = entity.to_rdf(self.functional_writer.g)
- return self.uri_to_curie(str(uri), use_uri_fallback=True)
-
- def curie_to_entity_iri(self, curie: CURIE) -> IRI:
- return IRI(self.curie_to_uri(curie))
-
- def _single_valued_assignment(self, curie: CURIE, property: CURIE) -> Optional[str]:
- labels = [a.value for a in self.annotation_assertion_axioms(curie, property=property)]
- if labels:
- if len(labels) > 1:
- logging.warning(f"Multiple labels for {curie} = {labels}")
- val = labels[0]
- rdf_v = val.to_rdf(self.functional_writer.g)
- if isinstance(rdf_v, rdflib.Literal):
- return rdf_v.value
- else:
- raise ValueError(f"Label must be literal, not {val}")
-
- def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- return self._single_valued_assignment(curie, HAS_DEFINITION_CURIE)
-
- def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> str:
- labels = [
- a.value for a in self.annotation_assertion_axioms(curie, property=LABEL_PREDICATE)
- ]
- if labels:
- if len(labels) > 1:
- logging.warning(f"Multiple labels for {curie} = {labels}")
- label = labels[0]
- rdf_v = label.to_rdf(self.functional_writer.g)
- if isinstance(rdf_v, rdflib.Literal):
- return rdf_v.value
- else:
- raise ValueError(f"Label must be literal, not {label}")
-
- def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
- for ax in self._ontology.axioms:
- if isinstance(ax, Declaration):
- uri = ax.v.full_uri(self.functional_writer.g)
- try:
- yv = self.uri_to_curie(str(uri))
- except ValueError:
- logging.warning(
- "could not compress URI %s with functional writer context %s",
- uri,
- list(self.functional_writer.g.namespaces()),
- )
- continue
- else:
- yield yv
-
- def axioms(self, reasoner: Optional[ReasonerConfiguration] = None) -> Iterable[Axiom]:
- ont = self._ontology
- for axiom in ont.axioms:
- yield axiom
-
- def set_axioms(self, axioms: List[Axiom]) -> None:
- self._ontology.axioms = axioms
-
- def dump(self, path: str = None, syntax: str = None, **kwargs):
- if syntax is None or syntax == "ofn":
- out = self.ontology_document.to_functional(self.functional_writer)
- elif syntax == "ttl" or syntax == "turtle":
- g = rdflib.Graph()
- self.ontology_document.to_rdf(g)
- out = g.serialize(format="ttl")
- else:
- out = str(self.ontology_document)
- if path is None:
- print(out)
- elif isinstance(path, str):
- with open(path, "w", encoding="UTF-8") as file:
- file.write(str(out))
- else:
- path.write(str(out))
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: PatcherInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _set_annotation_predicate_value(self, subject: CURIE, property: CURIE, value: Any):
- for axiom in self.annotation_assertion_axioms(subject, property):
- self._ontology.axioms.remove(axiom)
- self._ontology.axioms.append(
- AnnotationAssertion(
- subject=self.curie_to_entity_iri(subject),
- property=self.curie_to_entity_iri(property),
- value=value,
- )
- )
-
- def apply_patch(
- self,
- patch: kgcl.Change,
- activity: kgcl.Activity = None,
- metadata: Mapping[PRED_CURIE, Any] = None,
- configuration: kgcl.Configuration = None,
- ) -> Optional[kgcl.Change]:
- if isinstance(patch, kgcl.NodeChange):
- about = patch.about_node
- if isinstance(patch, kgcl.NodeRename):
- self._set_annotation_predicate_value(about, LABEL_PREDICATE, patch.new_value)
- elif isinstance(patch, kgcl.NodeTextDefinitionChange):
- self._set_annotation_predicate_value(about, HAS_DEFINITION_CURIE, patch.new_value)
- elif isinstance(patch, kgcl.NewSynonym):
- self._ontology.axioms.append(
- AnnotationAssertion(
- subject=about,
- property=self.curie_to_entity_iri(HAS_EXACT_SYNONYM),
- value=patch.new_value,
- )
- )
- elif isinstance(patch, kgcl.NodeObsoletion):
- self._set_annotation_predicate_value(about, DEPRECATED_PREDICATE, value=True)
- elif isinstance(patch, kgcl.NodeDeletion):
- raise NotImplementedError("Deletions not supported yet")
- elif isinstance(patch, kgcl.NodeCreation):
- self._set_annotation_predicate_value(about, LABEL_PREDICATE, patch.name)
- elif isinstance(patch, kgcl.NameBecomesSynonym):
- label = self.label(about)
- self.apply_patch(
- kgcl.NodeRename(id=f"{patch.id}-1", about_node=about, new_value=patch.new_value)
- )
- self.apply_patch(
- kgcl.NewSynonym(id=f"{patch.id}-2", about_node=about, new_value=label)
- )
- else:
- raise NotImplementedError(f"Cannot handle patches of type {type(patch)}")
- elif isinstance(patch, kgcl.EdgeChange):
- about = patch.about_edge
- subject = self.curie_to_uri(patch.subject)
- object = self.curie_to_uri(patch.object)
- if isinstance(patch, kgcl.EdgeCreation):
- if patch.predicate == IS_A or patch.predicate == "is_a":
- self._ontology.axioms.append(SubClassOf(subject, object))
- else:
- predicate = self.curie_to_entity_iri(patch.predicate)
- self._ontology.axioms.append(
- SubClassOf(subject, ObjectSomeValuesFrom(predicate, object))
- )
- else:
- raise NotImplementedError(f"Cannot handle patches of type {type(patch)}")
- else:
- raise NotImplementedError(f"Cannot handle patches of type {type(patch)}")
- return patch
-
-
Source code for oaklib.implementations.gilda
-"""A text annotator based on Gilda."""
-
-import logging
-from dataclasses import dataclass
-from typing import TYPE_CHECKING, Iterator
-
-from oaklib.datamodels.text_annotator import TextAnnotation, TextAnnotationConfiguration
-from oaklib.interfaces import TextAnnotatorInterface
-from oaklib.interfaces.text_annotator_interface import TEXT, nen_annotation
-
-if TYPE_CHECKING:
- import gilda
-
-__all__ = [
- "GildaImplementation",
-]
-
-
-
-[docs]
-@dataclass
-class GildaImplementation(TextAnnotatorInterface):
- """
- Perform named entity normalization on text strings with Gilda [gyori2021]_.
-
- .. [gyori2021] Benjamin M Gyori, Charles Tapley Hoyt, Albert Steppi (2021)
- `Gilda: biomedical entity text normalization with machine-learned
- disambiguation as a service <https://doi.org/10.1093/bioadv/vbac034>`_,
- *Bioinformatics Advances*, Volume 2, Issue 1, 2022, vbac034,
- """
-
- grounder: "gilda.Grounder" = None
- """A grounder used by Gilda.
-
- This is instantiated in one of the following ways:
-
- 1. It can be passed directly during instantiation of the
- :class:`GildaImplementation` class.
- 2. If not passed and this implementation's ``slug`` attribute is set
- to a path to a gzipped term TSV file, it gets instantiated with the
- custom index
- 3. Otherwise, it gets instantiated with the default Gilda term index
- """
-
- def __post_init__(self):
- if self.grounder is None:
- from gilda.grounder import Grounder
-
- # The slug corresponds to the path to a gzipped terms TSV
- # when parsed from a descriptor like ``gilda:<path>` via
- # :func:`get_resource_from_shorthand`. If no <path> was
- # given, then this will default to the default Gilda index
- try:
- self.grounder = Grounder(terms=self.resource.slug)
- except AttributeError: # i.e., there's no slug
- logging.warning("Gilda grounder will use default term index.")
- self.grounder = Grounder()
-
- def annotate_text(
- self, text: TEXT, configuration: TextAnnotationConfiguration = None
- ) -> Iterator[TextAnnotation]:
- """
- Implements annotate_text from text_annotator_interface by calling the
- `annotate` endpoint using gilda client.
-
- :param text: Text to be annotated.
- :param configuration: Text annotation configuration.
- :yield: A generator function that returns annotated results.
- """
- if not configuration:
- raise NotImplementedError("Missing text annotation configuration")
- if configuration.matches_whole_text:
- yield from self._ground(text)
- else:
- yield from self._gilda_annotate(text)
-
- def _gilda_annotate(self, text: str) -> Iterator[TextAnnotation]:
- from gilda.ner import annotate
-
- for match_text, match, start, end in annotate(text, grounder=self.grounder):
- yield TextAnnotation(
- subject_start=start,
- subject_end=end,
- subject_label=match_text,
- object_id=match.term.get_curie(),
- object_label=match.term.entry_name,
- matches_whole_text=start == 0 and end == len(text),
- )
-
- def _ground(self, text: str) -> Iterator[TextAnnotation]:
- for match in self.grounder.ground(text):
- yield nen_annotation(
- text=text,
- object_id=match.term.get_curie(),
- object_label=match.term.entry_name,
- )
-
-
Source code for oaklib.implementations.obograph.obograph_implementation
-import logging
-import re
-from collections import defaultdict
-from copy import deepcopy
-from dataclasses import dataclass
-from typing import Any, Dict, Iterable, Iterator, List, Mapping, Optional, Tuple, Union
-
-import sssom_schema as sssom
-from kgcl_schema.datamodel import kgcl
-from linkml_runtime.dumpers import json_dumper
-from linkml_runtime.loaders import json_loader
-
-from oaklib.converters.obo_graph_to_rdf_owl_converter import SCOPE_MAP
-from oaklib.datamodels import obograph
-from oaklib.datamodels.obograph import (
- Edge,
- Graph,
- GraphDocument,
- LogicalDefinitionAxiom,
- Meta,
- Node,
-)
-from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
-from oaklib.datamodels.vocabulary import (
- EQUIVALENT_CLASS,
- HAS_DBXREF,
- INVERSE_OF,
- IS_A,
- LABEL_PREDICATE,
- OWL_CLASS,
- OWL_OBJECT_PROPERTY,
- SUBPROPERTY_OF,
-)
-from oaklib.interfaces.basic_ontology_interface import (
- ALIAS_MAP,
- LANGUAGE_TAG,
- RELATIONSHIP,
- RELATIONSHIP_MAP,
-)
-from oaklib.interfaces.differ_interface import DifferInterface
-from oaklib.interfaces.dumper_interface import DumperInterface
-from oaklib.interfaces.merge_interface import MergeInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.interfaces.rdf_interface import RdfInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.resource import OntologyResource
-from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE, URI
-from oaklib.utilities.axioms.logical_definition_utilities import (
- logical_definition_matches,
-)
-from oaklib.utilities.basic_utils import pairs_as_dict
-
-RDFLIB_FORMAT_MAP = {
- "ttl": "ttl",
- "n3": "n3",
- "rdfxml": "xml",
- "xml": "xml",
- "owl": "xml",
-}
-
-
-
-[docs]
-@dataclass
-class OboGraphImplementation(
- ValidatorInterface,
- DifferInterface,
- RdfInterface,
- OboGraphInterface,
- SearchInterface,
- PatcherInterface,
- DumperInterface,
- MergeInterface,
-):
- """
- OBO Graphs JSON backed implementation.
-
- This implementation works off of an in-memory GraphDocument object.
-
- To use:
-
- .. packages :: python
-
- >>> from oaklib import get_adapter
- >>> oi = get_adapter('obograph:tests/input/go-nucleus.json')
- >>> for node_id in oi.entities():
- ... print(node_id, oi.label(node_id))
- <BLANKLINE>
- ...
- GO:0043226 organelle
- ...
- """
-
- obograph_document: GraphDocument = None
- _relationship_index_cache: Dict[CURIE, List[RELATIONSHIP]] = None
-
- def __post_init__(self):
- if self.obograph_document is None:
- resource = self.resource
- if resource and resource.local_path:
- gd = json_loader.load(str(resource.local_path), target_class=GraphDocument)
- else:
- gd = GraphDocument()
- self.obograph_document = gd
-
- def uri_to_curie(
- self, uri: URI, strict: bool = False, use_uri_fallback=True
- ) -> Optional[CURIE]:
- # TODO: use a map
- if uri == "is_a":
- return IS_A
- elif uri == "subPropertyOf":
- return SUBPROPERTY_OF
- elif uri == "inverseOf":
- return INVERSE_OF
- elif uri == EQUIVALENT_CLASS:
- return EQUIVALENT_CLASS
- else:
- return super().uri_to_curie(uri, strict=strict, use_uri_fallback=use_uri_fallback)
-
- def store(self, resource: OntologyResource = None) -> None:
- if resource is None:
- resource = self.resource
- od = self.obograph_document
- if resource.local:
- if resource.slug:
- json_dumper.dump(od, resource.slug)
- else:
- print(json_dumper.dumps(od))
- else:
- raise NotImplementedError(f"Cannot dump to {resource}")
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: BasicOntologyInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _tuple_to_curies(self, t: Tuple) -> Tuple:
- return tuple([self.uri_to_curie(x) for x in t])
-
- def _all_relationships(self) -> Iterator[RELATIONSHIP]:
- logging.info("Commencing indexing")
- od = self.obograph_document
- for g in od.graphs:
- for e in g.edges:
- yield self._tuple_to_curies((e.sub, e.pred, e.obj))
- for ens in g.equivalentNodesSets:
- for n1 in ens.nodeIds:
- for n2 in ens.nodeIds:
- if n1 != n2:
- # directionality is lost in OboGraph representation
- yield self._tuple_to_curies((n1, EQUIVALENT_CLASS, n2))
-
- def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
- od = self.obograph_document
- for g in od.graphs:
- for n in g.nodes:
- if filter_obsoletes and n.meta and n.meta.deprecated:
- continue
- if owl_type:
- t = n.type
- if t:
- if t == "CLASS" and owl_type != OWL_CLASS:
- continue
- if t == "PROPERTY" and owl_type != OWL_OBJECT_PROPERTY:
- continue
- yield self.uri_to_curie(n.id)
-
- def obsoletes(self) -> Iterable[CURIE]:
- od = self.obograph_document
- for g in od.graphs:
- for n in g.nodes:
- if n.meta.deprecated:
- yield n.id
-
- # TODO: abstract into separate standalone package
- def _get_subset_curie(self, curie: str) -> str:
- if "#" in curie:
- return curie.split("#")[-1]
- else:
- return curie
-
- def _node_subsets(self, node: Node) -> List[SUBSET_CURIE]:
- if node.meta:
- return [self._get_subset_curie(s) for s in node.meta.subsets]
- else:
- return []
-
- def _entire_graph(self) -> Graph:
- if len(self.obograph_document.graphs) > 1:
- raise ValueError("Multiple graphs")
- return self.obograph_document.graphs[0]
-
- def _nodes(self) -> Iterator[Node]:
- for g in self.obograph_document.graphs:
- for n in g.nodes:
- yield n
-
- def _node(self, curie: CURIE, strict=False) -> Optional[Node]:
- node: Optional[Node] = None
- for g in self.obograph_document.graphs:
- for n in g.nodes:
- # TODO: make this more efficient
- if self.uri_to_curie(n.id) == curie:
- # handle duplicates
- if node:
- if node.lbl:
- if strict:
- raise ValueError(f"Multiple nodes with id {curie}")
- else:
- # previously encountered node was dangling/stub;
- # replace
- node = n
- else:
- node = n
- if node:
- node = deepcopy(node)
- node.id = self.uri_to_curie(node.id)
- return node
- else:
- if strict:
- raise ValueError(f"No such node {curie}")
-
- def _meta(self, curie: CURIE, strict=False) -> Optional[Meta]:
- n = self._node(curie, strict=strict)
- if n:
- return n.meta
-
- def ontologies(self) -> Iterable[CURIE]:
- return [g.id for g in self.obograph_document.graphs]
-
- def subsets(self) -> Iterable[CURIE]:
- raise NotImplementedError
-
- def subset_members(self, subset: SUBSET_CURIE) -> Iterable[CURIE]:
- od = self.obograph_document
- for g in od.graphs:
- for n in g.nodes:
- if subset in self._node_subsets(n):
- yield n
-
- def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- if lang:
- raise NotImplementedError("Language tags not supported")
- if curie == IS_A:
- return "subClassOf"
- n = self._node(curie)
- if n:
- return n.lbl
-
- def set_label(self, curie: CURIE, label: str, lang: Optional[LANGUAGE_TAG] = None) -> bool:
- if lang:
- raise NotImplementedError("Language tags not supported")
- n = self._node(curie, True)
- n.lbl = label
- return True
-
- def curies_by_label(self, label: str) -> List[CURIE]:
- return [self.uri_to_curie(n.id) for n in self._nodes() if n.lbl == label]
-
- def create_entity(
- self,
- curie: CURIE,
- label: Optional[str] = None,
- relationships: Optional[RELATIONSHIP_MAP] = None,
- type: Optional[str] = None,
- **kwargs,
- ) -> CURIE:
- g = self._entire_graph()
- g.nodes.append(Node(curie, lbl=label, type=type))
- for p, objs in relationships:
- for obj in objs:
- g.edges.append(Edge(curie, p, obj))
- return curie
-
- def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- if lang:
- raise NotImplementedError("Language tags not supported")
- m = self._meta(curie)
- if m:
- return m.definition.val
-
- def comments(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
- for curie in curies:
- m = self._meta(curie)
- if m:
- for v in m.comments:
- yield curie, v
-
- def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
- meta = self._meta(curie)
- m = defaultdict(list)
- lbl = self.label(curie)
- if lbl:
- m[LABEL_PREDICATE] = [lbl]
- if meta is not None:
- for syn in meta.synonyms:
- pred = SCOPE_MAP.get(syn.pred, None)
- m[pred].append(syn.val)
- return m
-
- # TODO: DRY
- def relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_tbox: bool = True,
- include_abox: bool = True,
- include_entailed: bool = False,
- exclude_blank: bool = True,
- ) -> Iterator[RELATIONSHIP]:
- ei = self.edge_index
- if include_entailed:
- raise NotImplementedError("Entailment not supported for pronto")
- yield from ei.edges(
- subjects=subjects,
- predicates=predicates,
- objects=objects,
- )
-
- # TODO: DRY
- def outgoing_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None, entailed=False
- ) -> Iterator[Tuple[PRED_CURIE, CURIE]]:
- for s, p, o in self.relationships([curie], predicates, include_entailed=entailed):
- if s == curie:
- yield p, o
-
- # TODO: DRY
- def outgoing_relationship_map(self, *args, **kwargs) -> RELATIONSHIP_MAP:
- return pairs_as_dict(self.outgoing_relationships(*args, **kwargs))
-
- # TODO: DRY
- def incoming_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None, entailed=False
- ) -> Iterator[Tuple[PRED_CURIE, CURIE]]:
- for s, p, o in self.relationships(None, predicates, [curie], include_entailed=entailed):
- if o == curie:
- yield p, s
-
- # TODO: DRY
- def incoming_relationship_map(self, *args, **kwargs) -> RELATIONSHIP_MAP:
- return pairs_as_dict(self.incoming_relationships(*args, **kwargs))
-
- # TODO: DRY
- def basic_search(self, search_term: str, config: SearchConfiguration = None) -> Iterable[CURIE]:
- # TODO: move up, avoid repeating packages
- if config is None:
- config = SearchConfiguration()
- matches = []
- mfunc = None
- if config.syntax == SearchTermSyntax(SearchTermSyntax.STARTS_WITH):
- mfunc = lambda label: str(label).startswith(search_term)
- elif config.syntax == SearchTermSyntax(SearchTermSyntax.REGULAR_EXPRESSION):
- prog = re.compile(search_term)
- mfunc = lambda label: prog.search(label)
- elif config.is_partial:
- mfunc = lambda label: search_term in str(label)
- else:
- mfunc = lambda label: label == search_term
- search_all = SearchProperty(SearchProperty.ANYTHING) in config.properties
- logging.info(f"SEARCH={search_term}")
- for t in self.entities():
- lbl = self.label(t)
- logging.debug(f"T={t} // {config}")
- if (
- search_all
- or SearchProperty(SearchProperty.LABEL)
- or config.properties not in config.properties
- ):
- if lbl and mfunc(lbl):
- matches.append(t)
- logging.info(f"Name match to {t}")
- continue
- if search_all or SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
- if mfunc(t):
- matches.append(t)
- logging.info(f"identifier match to {t}")
- continue
- if search_all or SearchProperty(SearchProperty.ALIAS) in config.properties:
- for syn in self.entity_aliases(t):
- if mfunc(syn):
- logging.info(f"Syn match to {t}")
- matches.append(t)
- continue
- for m in matches:
- yield m
-
- def simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- meta = self._meta(curie, strict=False)
- if meta:
- # TODO: SKOS
- for x in meta.xrefs:
- yield HAS_DBXREF, x.val
-
- def dump(self, path: str = None, syntax: str = "json", **kwargs):
- logging.info(f"Dumping graph to {path} syntax: {syntax}")
- if syntax == "json" or syntax == "obojson":
- if path is None:
- print(json_dumper.dumps(self.obograph_document))
- else:
- json_dumper.dump(self.obograph_document, to_file=str(path))
- else:
- super().dump(path, syntax, **kwargs)
-
- def save(
- self,
- ):
- logging.info("Committing and flushing changes")
- self.dump(self.resource.slug)
-
- def load_graph(self, graph: Graph, replace: True) -> None:
- if not replace:
- raise NotImplementedError
- self.obograph_document = GraphDocument(graphs=[graph])
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MappingsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def sssom_mappings(
- self, curies: Optional[Union[CURIE, Iterable[CURIE]]] = None, source: Optional[str] = None
- ) -> Iterable[sssom.Mapping]:
- raise NotImplementedError()
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def node(
- self, curie: CURIE, strict=False, include_metadata=False, expand_curies=False
- ) -> obograph.Node:
- return self._node(curie)
-
- def as_obograph(self) -> Graph:
- return self._entire_graph()
-
- def logical_definitions(
- self,
- subjects: Iterable[CURIE] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- **kwargs,
- ) -> Iterable[LogicalDefinitionAxiom]:
- if subjects:
- subjects = list(subjects)
- for g in self.obograph_document.graphs:
- for ldef in g.logicalDefinitionAxioms:
- if logical_definition_matches(
- ldef, subjects=subjects, predicates=predicates, objects=objects
- ):
- yield ldef
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SearchInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: PatcherInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def different_from(self, entity: CURIE, other_ontology: DifferInterface) -> bool:
- raise NotImplementedError
-
- def migrate_curies(self, curie_map: Mapping[CURIE, CURIE]) -> None:
- raise NotImplementedError
-
- def apply_patch(
- self,
- patch: kgcl.Change,
- activity: kgcl.Activity = None,
- metadata: Mapping[PRED_CURIE, Any] = None,
- configuration: kgcl.Configuration = None,
- ) -> kgcl.Change:
- raise NotImplementedError
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OwlInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def transitive_object_properties(self) -> Iterable[CURIE]:
- # TODO: obographs datamodel needs to be expanded to support this
- pass
-
- def simple_subproperty_of_chains(self) -> Iterable[Tuple[CURIE, List[CURIE]]]:
- for g in self.obograph_document.graphs:
- for pca in g.propertyChainAxioms:
- yield self.uri_to_curie(pca.predicateId), [
- self.uri_to_curie(p) for p in pca.chainPredicateIds
- ]
-
-
Source code for oaklib.implementations.ols.ols_implementation
-from collections import ChainMap
-from dataclasses import dataclass, field
-from typing import Any, ClassVar, Dict, Iterable, Iterator, List, Tuple, Union
-
-import requests
-from ols_client import Client, EBIClient, TIBClient
-from sssom_schema import Mapping
-
-from oaklib.constants import TIMEOUT_SECONDS
-from oaklib.datamodels import oxo
-from oaklib.datamodels.oxo import ScopeEnum
-from oaklib.datamodels.search import SearchConfiguration, SearchProperty
-from oaklib.datamodels.text_annotator import TextAnnotation
-from oaklib.datamodels.vocabulary import IS_A, SEMAPV
-from oaklib.implementations.ols.constants import SEARCH_CONFIG
-from oaklib.implementations.ols.oxo_utils import load_oxo_payload
-from oaklib.interfaces.basic_ontology_interface import PREFIX_MAP
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface
-from oaklib.types import CURIE, PRED_CURIE
-
-__all__ = [
- # Abstract classes
- "BaseOlsImplementation",
- # Concrete classes
- "OlsImplementation",
- "TIBOlsImplementation",
-]
-
-ANNOTATION = Dict[str, Any]
-SEARCH_ROWS = 50
-
-oxo_pred_mappings = {
- ScopeEnum.EXACT.text: "skos:exactMatch",
- ScopeEnum.BROADER.text: "skos:broadMatch",
- ScopeEnum.NARROWER.text: "skos:narrowMatch",
- ScopeEnum.RELATED.text: "skos:closeMatch",
-}
-
-
-@dataclass
-class BaseOlsImplementation(TextAnnotatorInterface, SearchInterface, MappingProviderInterface):
- """
- Implementation over OLS and OxO APIs
- """
-
- ols_client_class: ClassVar[type[Client]]
- label_cache: Dict[CURIE, str] = field(default_factory=lambda: {})
- base_url = "https://www.ebi.ac.uk/spot/oxo/api/mappings"
- _prefix_map: Dict[str, str] = field(default_factory=lambda: {})
- focus_ontology: str = None
- client: Client = field(init=False)
-
- def __post_init__(self):
- self.client = self.ols_client_class()
- if self.focus_ontology is None:
- if self.resource:
- self.focus_ontology = self.resource.slug
-
- def add_prefix(self, curie: str, uri: str):
- [pfx, local] = curie.split(":", 1)
- if pfx not in self._prefix_map:
- self._prefix_map[pfx] = uri.replace(local, "")
-
- def prefix_map(self) -> PREFIX_MAP:
- return ChainMap(super().prefix_map(), self._prefix_map)
-
- def labels(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
- for curie in curies:
- yield curie, self.label_cache[curie]
-
- def annotate_text(self, text: str) -> Iterator[TextAnnotation]:
- raise NotImplementedError
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def ancestors(
- self, start_curies: Union[CURIE, List[CURIE]], predicates: List[PRED_CURIE] = None
- ) -> Iterable[CURIE]:
- func = self.client.iter_hierarchical_ancestors
- if predicates:
- if predicates == [IS_A]:
- func = self.client.iter_ancestors
- elif IS_A not in predicates:
- raise NotImplementedError(f"OLS always include {IS_A}, you selected: {predicates}")
- if not isinstance(start_curies, list):
- start_curies = [start_curies]
- ancs = set()
- ontology = self.focus_ontology
- for curie in start_curies:
- iri = self.curie_to_uri(curie)
- records = func(ontology=ontology, iri=iri)
- ancs.update(record["obo_id"] for record in records)
- return list(ancs)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SearchInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def basic_search(
- self, search_term: str, config: SearchConfiguration = SEARCH_CONFIG
- ) -> Iterable[CURIE]:
- query_fields = set()
- # Anything not covered by these conditions (i.e. query_fields set remains empty)
- # will cause the queryFields query param to be left off and all fields to be queried
- if SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
- query_fields.update(["iri", "obo_id"])
- if SearchProperty(SearchProperty.LABEL) in config.properties:
- query_fields.update(["label"])
- if SearchProperty(SearchProperty.ALIAS) in config.properties:
- query_fields.update(["synonym"])
- if SearchProperty(SearchProperty.DEFINITION) in config.properties:
- query_fields.update(["description"])
- if SearchProperty(SearchProperty.INFORMATIVE_TEXT) in config.properties:
- query_fields.update(["description"])
-
- params = {
- "type": "class",
- "local": "true",
- "fieldList": "iri,label",
- "rows": config.limit if config.limit is not None else SEARCH_ROWS,
- "start": 0,
- "exact": (
- "true" if (config.is_complete is True or config.is_partial is False) else "false"
- ),
- }
- if len(query_fields) > 0:
- params["queryFields"] = ",".join(query_fields)
- if self.focus_ontology:
- params["ontology"] = self.focus_ontology.lower()
-
- for record in self.client.search(search_term, params=params):
- curie = self.uri_to_curie(record["iri"])
- self.label_cache[curie] = record["label"]
- yield curie
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MappingsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def get_sssom_mappings_by_curie(self, curie: Union[str, CURIE]) -> Iterator[Mapping]:
- result = requests.get(self.base_url, params=dict(fromId=curie), timeout=TIMEOUT_SECONDS)
- obj = result.json()
- container = load_oxo_payload(obj)
- return self.convert_payload(container)
-
- def convert_payload(self, container: oxo.Container) -> Iterator[Mapping]:
- oxo_mappings = container._embedded.mappings
- for oxo_mapping in oxo_mappings:
- oxo_s = oxo_mapping.fromTerm
- oxo_o = oxo_mapping.toTerm
- mapping = Mapping(
- subject_id=oxo_s.curie,
- subject_label=oxo_s.label,
- subject_source=oxo_s.datasource.prefix if oxo_s.datasource else None,
- predicate_id=oxo_pred_mappings[str(oxo_mapping.scope)],
- mapping_justification=SEMAPV.UnspecifiedMatching.value,
- object_id=oxo_o.curie,
- object_label=oxo_o.label,
- object_source=oxo_o.datasource.prefix if oxo_o.datasource else None,
- mapping_provider=oxo_mapping.datasource.prefix,
- )
- self.add_prefix(oxo_s.curie, oxo_s.uri)
- self.add_prefix(oxo_o.curie, oxo_o.uri)
- yield mapping
-
- # def fill_gaps(self, msdoc: MappingSetDocument, confidence: float = 1.0) -> int:
- # curie_map = curie_to_uri_map(msdoc)
- # # inv_map = {v: k for k, v in curie_map.items()}
- # n = 0
- # for curie, uri in curie_map.items():
- # pfx, _ = curie.split(":", 2)
- # ancs = self.get_ancestors(uri, ontology=pfx.lower())
- # logging.debug(f"{curie} ANCS = {ancs}")
- # for anc in ancs:
- # if anc in curie_map:
- # m = Mapping(
- # subject_id=curie,
- # object_id=anc,
- # predicate_id="rdfs:subClassOf",
- # confidence=confidence,
- # match_type=MatchTypeEnum.HumanCurated,
- # )
- # logging.info(f"Gap filled link: {m}")
- # msdoc.mapping_set.mappings.append(m)
- # n += 1
- # return n
-
-
-
-[docs]
-class OlsImplementation(BaseOlsImplementation):
- """Implementation for the EBI OLS instance."""
-
- ols_client_class = EBIClient
-
-
-
-class TIBOlsImplementation(BaseOlsImplementation):
- """Implementation for the TIB Hannover OLS instance."""
-
- ols_client_class = TIBClient
-
Source code for oaklib.implementations.ontobee.ontobee_implementation
-from dataclasses import dataclass
-from typing import Optional
-
-from oaklib.implementations.sparql.abstract_sparql_implementation import (
- AbstractSparqlImplementation,
-)
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.interfaces.search_interface import SearchInterface
-
-ONTOBEE_MERGED_GRAPH_PREFIX = "http://purl.obolibrary.org/obo/merged/"
-
-
-
-[docs]
-@dataclass
-class OntobeeImplementation(
- AbstractSparqlImplementation, SearchInterface, MappingProviderInterface, OboGraphInterface
-):
- """
- An OAK adapter that standardizes access to the Ontobee sparql endpoint.
-
- Ontobee is the default linked data server for most OBO Foundry library ontologies.
- Ontobee has also been used for many non-OBO ontologies.
-
- To access this use the ``ontobee:`` :term:`Input Selector`:
-
- - ``ontobee:`` - the default ontobee endpoint
- - ``ontobee:uberon`` - the uberon subgraph on ontobee
-
- This adapter implements:
-
- - :ref:`basic_ontology_interface`
- - :ref:`search_interface`
- - :ref:`mapping_provider_interface`
- - :ref:`obograph_interface`
-
- .. note ::
-
- To see the full range of methods implemented, see the documentation for the interfaces above.
-
- An OntobeeImplementation can be initialized directly:
-
- >>> from oaklib.implementations import OntobeeImplementation
- >>> oi = OntobeeImplementation()
-
- The default ontobee endpoint will be assumed
-
- Alternatively, use a selector:
-
- >>> from oaklib import get_adapter
- >>> oi = get_adapter("ontobee:")
-
- Or to access a specific ontology, such as the Vaccine Ontology:
-
- >>> oi = get_adapter("ontobee:vo")
-
- After that you can use any of the methods that OntoBee implements; e.g.
-
- >>> from oaklib.datamodels.vocabulary import IS_A
- >>> # uncomment to test
- >>> # for a in oi.ancestors("UBERON:0002398", predicates=[IS_A]):
- >>> # print(a)
-
- Command Line
- ------------
-
- .. code-block:: bash
-
- $ runoak -i ontobee:uberon ancestors -p i UBERON:0002398
-
- Notes
- -----
- This is a specialization the :ref:`sparql` implementation to
- allow access for ontologies on the `Ontobee <https://www.ontobee.org/>`_ linked data server.
-
- See: `<https://www.ontobee.org/>`_
-
- """
-
- def _default_url(self) -> str:
- return "http://sparql.hegroup.org/sparql"
-
- @property
- def named_graph(self) -> Optional[str]:
- if self.resource.slug is None:
- return None
- else:
- return f"{ONTOBEE_MERGED_GRAPH_PREFIX}{self.resource.slug.upper()}"
-
-
Source code for oaklib.implementations.owlery.owlery_implementation
-from dataclasses import dataclass
-
-from oaklib.implementations.sparql.abstract_sparql_implementation import (
- AbstractSparqlImplementation,
-)
-from oaklib.interfaces.owl_interface import OwlInterface
-
-
-
-[docs]
-@dataclass
-class OwleryImplementation(OwlInterface, AbstractSparqlImplementation):
- """
- Wraps an owlery endpoint
-
- See `<https://github.com/phenoscape/owlery>`_
-
- .. warning ::
-
- Not implemented
- """
-
-
Source code for oaklib.implementations.pantherdb.pantherdb_implementation
-"""PantherDB implementation for OAK."""
-
-import logging
-from collections import defaultdict
-from dataclasses import dataclass
-from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union
-
-import requests_cache
-import sssom
-from sssom.constants import SEMAPV
-from sssom_schema import Mapping
-
-from oaklib.datamodels.association import Association
-from oaklib.datamodels.class_enrichment import ClassEnrichmentResult
-from oaklib.datamodels.item_list import ItemList
-from oaklib.datamodels.vocabulary import (
- BIOLOGICAL_PROCESS,
- CELLULAR_COMPONENT,
- MOLECULAR_FUNCTION,
- SKOS_EXACT_MATCH,
-)
-from oaklib.interfaces import (
- MappingProviderInterface,
- OboGraphInterface,
- SearchInterface,
-)
-from oaklib.interfaces.association_provider_interface import (
- AssociationProviderInterface,
-)
-from oaklib.interfaces.class_enrichment_calculation_interface import (
- ClassEnrichmentCalculationInterface,
-)
-from oaklib.types import CURIE, PRED_CURIE
-
-logger = logging.getLogger(__name__)
-
-
-GENE_REQUESTS_CACHE = ".panther_requests_cache"
-
-
-BASE_URL = "https://pantherdb.org/services/oai/pantherdb"
-
-
-
-[docs]
-@dataclass
-class PantherDBImplementation(
- ClassEnrichmentCalculationInterface,
- MappingProviderInterface,
- OboGraphInterface,
- AssociationProviderInterface,
- SearchInterface,
-):
- """
- PantherDB implementation for OAK.
-
- This implementation provides access to PantherDB data and services.
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("pantherdb:9606")
- >>> for assoc in adapter.associations(["UniProtKB:P04217"]):
- ... print(assoc.object)
- <BLANKLINE>
- ...
- GO:0005576
- ...
-
- In general this Adapter needs to be instantiated with a taxon_id,
- which is the NCBI Taxon ID for the species of interest.
-
- If your input IDs are all HGNC gene IDs, this is inferred automatically.
-
- Note that currently the PantherDB API doesn't distinguish between HGNC and NCBIGene IDs.
- Although you as the client will pass in CURIEs, only the numeric part is used, so matches
- may be more permissive than expected.
-
- """
-
- _requests_session: requests_cache.CachedSession = None
-
- requires_associations = False
- taxon_id: Optional[int] = None
- use_protein_ids: bool = True
-
- def __post_init__(self):
- slug = self.resource.slug
- if slug:
- slug = slug.replace("pantherdb:", "")
- self.taxon_id = int(slug)
-
- def requests_session(self):
- if self._requests_session is None:
- self._requests_session = requests_cache.CachedSession(GENE_REQUESTS_CACHE)
- return self._requests_session
-
- def _convert_gene_curies(
- self, curies: List[CURIE], expected_taxa: Optional[int] = None
- ) -> Dict[int, Dict[CURIE, str]]:
- taxon2ids = defaultdict(dict)
- for curie in curies:
- taxon_id = self.taxon_id
- [pfx, local_id] = curie.split(":")
- if pfx == "HGNC":
- taxon_id = 9606
- if not taxon_id:
- raise ValueError(f"Could not determine taxon for {curie}")
- taxon2ids[taxon_id][curie] = local_id
- if expected_taxa is not None:
- if len(taxon2ids) != expected_taxa:
- raise ValueError(f"Expected {expected_taxa} taxa, got {len(taxon2ids)}")
- return taxon2ids
-
- def _convert_gene_curies_single_taxon(
- self, curies: List[CURIE]
- ) -> Tuple[int, Dict[CURIE, str]]:
- taxon2ids = self._convert_gene_curies(curies, expected_taxa=1)
- taxon_id, id_pairs = list(taxon2ids.items())[0]
- return taxon_id, id_pairs
-
- def associations(
- self,
- subjects: Iterable[CURIE] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- property_filter: Dict[PRED_CURIE, Any] = None,
- subject_closure_predicates: Optional[List[PRED_CURIE]] = None,
- predicate_closure_predicates: Optional[List[PRED_CURIE]] = None,
- object_closure_predicates: Optional[List[PRED_CURIE]] = None,
- include_modified: bool = False,
- **kwargs,
- ) -> Iterator[Association]:
- """
- Get associations from PantherDB.
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("pantherdb:9606")
- >>> for assoc in adapter.associations(["UniProtKB:P04217"]):
- ... print(assoc.object)
- <BLANKLINE>
- ...
- GO:0005576
- ...
-
- :param subjects:
- :param predicates:
- :param objects:
- :param property_filter:
- :param subject_closure_predicates:
- :param predicate_closure_predicates:
- :param object_closure_predicates:
- :param include_modified:
- :param kwargs:
- :return:
- """
- if subjects and not isinstance(subjects, list):
- subjects = list(subjects)
- if objects and not isinstance(objects, list):
- objects = list(objects)
- if objects:
- raise ValueError("PantherDB does not support term-based queries")
- taxon2ids = self._convert_gene_curies(subjects)
- yield from self._functional_annotations(taxon2ids)
- yield from self._homologs(taxon2ids, homolog_type="O")
-
- def _curie_from_accession(self, gene: Union[Dict, str]):
- if isinstance(gene, str):
- acc = gene
- else:
- acc = gene["accession"]
- [sp, gene_curie, prot_curie] = acc.split("|")
- if self.use_protein_ids:
- return prot_curie.replace("=", ":")
- else:
- return gene_curie.replace("=", ":")
-
- def _functional_annotations(
- self,
- taxon2ids: Dict[int, Dict[CURIE, str]],
- ) -> Iterator[Association]:
- session = self.requests_session()
- for taxon_id, curie2id in taxon2ids.items():
- ids_str = ",".join(curie2id.values())
- r = session.get(
- f"{BASE_URL}/geneinfo", params={"geneInputList": ids_str, "organism": taxon_id}
- )
- r.raise_for_status()
- results = r.json()
- genes = results["search"]["mapped_genes"]["gene"]
- if not isinstance(genes, list):
- genes = [genes]
- for gene in genes:
- subject = self._curie_from_accession(gene)
- atl = gene["annotation_type_list"]
- content = atl.get("content", None)
- for adt in atl["annotation_data_type"]:
- if "content" in adt:
- content = adt["content"]
- pfx = ""
- if content == BIOLOGICAL_PROCESS:
- predicate = "biolink:involved_in"
- elif content == MOLECULAR_FUNCTION:
- predicate = "biolink:has_function"
- elif content == CELLULAR_COMPONENT:
- predicate = "biolink:located_in"
- elif content == "ANNOT_TYPE_ID_REACTOME_PATHWAY":
- predicate = "biolink:involved_in"
- pfx = "REACT:"
- else:
- continue
- annlist = adt["annotation_list"]
- anns = annlist["annotation"]
- if not isinstance(anns, list):
- anns = [anns]
- for ann in anns:
- obj = pfx + ann["id"]
- yield Association(
- subject=subject,
- predicate=predicate,
- object=obj,
- object_label=ann["name"],
- )
-
- def _homologs(
- self,
- taxon2ids: Dict[int, Dict[CURIE, str]],
- homolog_type: str = "O",
- ) -> Iterator[Association]:
- session = self.requests_session()
- for taxon_id, curie2id in taxon2ids.items():
- ids_str = ",".join(curie2id.values())
- r = session.get(
- f"{BASE_URL}/ortholog/matchortho",
- params={"geneInputList": ids_str, "organism": taxon_id},
- )
- r.raise_for_status()
- results = r.json()
- for m in results["search"]["mapping"]["mapped"]:
- subject = self._curie_from_accession(m["gene"])
- object = self._curie_from_accession(m["target_gene"])
- yield Association(
- subject=subject,
- predicate="biolink:homologous_to",
- object=object,
- )
-
- def ontologies(self) -> Iterable[CURIE]:
- yield "infores:pantherdb"
-
- def sssom_mappings(
- self, curies: Optional[Union[CURIE, Iterable[CURIE]]] = None, source: Optional[str] = None
- ) -> Iterable[sssom.Mapping]:
- if isinstance(curies, CURIE):
- curies = [curies]
- else:
- curies = list(curies)
- session = self.requests_session()
- objects = set()
- subjects = set()
- taxon2ids = self._convert_gene_curies(curies)
- for taxon_id, curie2id in taxon2ids.items():
- ids_str = ",".join(curie2id.values())
- logger.info(f"Fetching mappings for {ids_str} in {taxon_id}")
- r = session.get(
- f"{BASE_URL}/geneinfo", params={"geneInputList": ids_str, "organism": taxon_id}
- )
- r.raise_for_status()
- results = r.json()
- logger.debug(f"Got results {results}")
- genes = results["search"]["mapped_genes"]["gene"]
- if not isinstance(genes, list):
- genes = [genes]
- for gene in genes:
- acc = gene["accession"]
- [sp, gene_curie, prot_curie] = acc.split("|")
- gene_curie = gene_curie.replace("=", ":")
- prot_curie = prot_curie.replace("=", ":")
- m = sssom.Mapping(
- subject_id=gene_curie,
- predicate_id=SKOS_EXACT_MATCH,
- object_id=prot_curie,
- mapping_justification=str(SEMAPV.ManualMappingCuration.value),
- )
- # inject_mapping_sources(m)
- logger.debug(f"Got mapping {m}")
- yield m
- subjects.add(gene_curie)
- objects.add(prot_curie)
- for curie in curies:
- if curie not in subjects:
- logging.warning(f"Could not find any mappings for {curie}")
-
- def inject_mapping_labels(self, mappings: Iterable[Mapping]) -> None:
- return
-
- def enriched_classes(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- item_list: Optional[ItemList] = None,
- predicates: Iterable[CURIE] = None,
- object_closure_predicates: Optional[List[PRED_CURIE]] = None,
- background: Iterable[CURIE] = None,
- hypotheses: Iterable[CURIE] = None,
- cutoff=0.05,
- autolabel=False,
- filter_redundant=False,
- sort_by: str = None,
- direction="greater",
- ) -> Iterator[ClassEnrichmentResult]:
- if subjects and item_list:
- raise ValueError("Only one of subjects or item_list may be provided")
- if subjects is None:
- if not item_list:
- raise ValueError("Either subjects or item_list must be provided")
- if not item_list.itemListElements:
- raise ValueError("item_list must not be empty")
- subjects = item_list.itemListElements
- subjects = list(subjects)
- taxon_id, subject_idmap = self._convert_gene_curies_single_taxon(subjects)
- subject_ids_str = ",".join(subject_idmap.values())
- session = self.requests_session()
- r = session.get(
- f"{BASE_URL}/enrich/overrep",
- params={
- "geneInputList": subject_ids_str,
- "organism": taxon_id,
- "annotDataSet": "GO:0008150",
- },
- )
- r.raise_for_status()
- results = r.json()["results"]["result"]
- for result in results:
- if result["pValue"] > cutoff:
- break
- # TODO: all fields
- term = result["term"]
- yield ClassEnrichmentResult(
- class_id=term["id"],
- class_label=term["label"],
- p_value=result["pValue"],
- false_discovery_rate=result["fdr"],
- sample_count=result["number_in_list"],
- background_count=result["number_in_reference"],
- )
-
-
Source code for oaklib.implementations.pronto.pronto_implementation
-import logging
-import re
-import shutil
-import sys
-import tempfile
-
-# https://github.com/althonos/pronto/issues/173
-import warnings
-from collections import defaultdict
-from dataclasses import dataclass
-from typing import Any, Dict, Iterable, Iterator, List, Mapping, Optional, Tuple, Union
-
-import pronto
-import sssom_schema as sssom
-from deprecated import deprecated
-from kgcl_schema.datamodel import kgcl
-from linkml_runtime.dumpers import json_dumper
-from pronto import LiteralPropertyValue, Ontology, ResourcePropertyValue, Term
-
-from oaklib.converters.obo_graph_to_obo_format_converter import (
- OboGraphToOboFormatConverter,
-)
-from oaklib.datamodels import obograph
-from oaklib.datamodels.obograph import Edge, Graph, GraphDocument
-from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
-from oaklib.datamodels.vocabulary import (
- CONSIDER_REPLACEMENT,
- DEPRECATED_PREDICATE,
- EQUIVALENT_CLASS,
- HAS_DBXREF,
- HAS_OBO_NAMESPACE,
- HAS_OBSOLESCENCE_REASON,
- IS_A,
- LABEL_PREDICATE,
- OIO_SUBSET_PROPERTY,
- OIO_SYNONYM_TYPE_PROPERTY,
- OWL_CLASS,
- OWL_OBJECT_PROPERTY,
- OWL_VERSION_INFO,
- SCOPE_TO_SYNONYM_PRED_MAP,
- SEMAPV,
- SKOS_CLOSE_MATCH,
- SKOS_MATCH_PREDICATES,
- TERM_REPLACED_BY,
- TERMS_MERGED,
-)
-from oaklib.inference.relation_graph_reasoner import RelationGraphReasoner
-from oaklib.interfaces import TextAnnotatorInterface
-from oaklib.interfaces.basic_ontology_interface import (
- ALIAS_MAP,
- DEFINITION,
- LANGUAGE_TAG,
- METADATA_MAP,
- PRED_CURIE,
- RELATIONSHIP,
- RELATIONSHIP_MAP,
-)
-from oaklib.interfaces.class_enrichment_calculation_interface import (
- ClassEnrichmentCalculationInterface,
-)
-from oaklib.interfaces.differ_interface import DifferInterface
-from oaklib.interfaces.dumper_interface import DumperInterface
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.merge_interface import MergeInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.interfaces.obolegacy_interface import OboLegacyInterface
-from oaklib.interfaces.owl_interface import OwlInterface
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.interfaces.rdf_interface import RdfInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
-from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
-from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
-from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.resource import OntologyResource
-from oaklib.types import CURIE, SUBSET_CURIE
-from oaklib.utilities.axioms.logical_definition_utilities import (
- logical_definition_matches,
-)
-from oaklib.utilities.kgcl_utilities import tidy_change_object
-from oaklib.utilities.mapping.sssom_utils import inject_mapping_sources
-
-warnings.filterwarnings("ignore", category=pronto.warnings.SyntaxWarning, module="pronto")
-
-
-def _synonym_scope_pred(s: pronto.Synonym) -> str:
- scope = s.scope.upper()
- if scope in SCOPE_TO_SYNONYM_PRED_MAP:
- return SCOPE_TO_SYNONYM_PRED_MAP[scope]
- else:
- raise ValueError(f"Unknown scope: {scope}")
-
-
-
-[docs]
-@dataclass
-class ProntoImplementation(
- ValidatorInterface,
- RdfInterface,
- OboGraphInterface,
- OboLegacyInterface,
- SearchInterface,
- MappingProviderInterface,
- PatcherInterface,
- DifferInterface,
- # AssociationProviderInterface,
- ClassEnrichmentCalculationInterface,
- SemanticSimilarityInterface,
- TextAnnotatorInterface,
- SummaryStatisticsInterface,
- TaxonConstraintInterface,
- DumperInterface,
- MergeInterface,
- OwlInterface,
-):
- """
- An adapter that standardizes access to OBO Format files by wrapping the Pronto library.
-
- `Pronto <https://github.com/althonos/pronto/>`_ is a high-performance parsing library
- for parsing obo format 1.4 and other formats.
-
- Input Selector
- --------------
-
- This adapter uses the ``pronto:`` :term:`Input Selector`; e.g.
-
- - ``pronto:path/to/my/file``
- - ``pronto:https://example.com/my/file``
- - ``prontolib:go`
-
- Examples
- --------
- >>> from oaklib.implementations import ProntoImplementation
- >>> resource = OntologyResource(slug='go-nucleus.obo', directory='tests/input', local=True)
- >>> adapter = ProntoImplementation(resource)
-
- Or use a selector:
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("pronto:tests/input/go-nucleus.obo")
-
- Then you can use any of the methods implemented by pronto
-
- >>> rels = adapter.relationships(['GO:0005773'])
- >>> for _s, p, o in rels:
- ... print(f' {p} {o} ! {adapter.label(o)}')
- rdfs:subClassOf GO:0043231 ! intracellular membrane-bounded organelle
- BFO:0000050 GO:0005737 ! cytoplasm
-
- .. warning::
-
- pronto uses the fastobo library for loading ontologies. This follows a strict
- interpretation of obo format, and some ontologies may fail to load.
- In these cases, consider an alternative implementation
-
- Alternatives:
-
- - use the :ref:`simple_obo_implementation`
- - convert to an OWL representation using ROBOT
- - convert to a JSON representation using ROBOT and use :ref:`obograph_implementation`
-
- """
-
- wrapped_ontology: Ontology = None
- _relationship_index_cache: Dict[CURIE, List[RELATIONSHIP]] = None
- _alt_id_to_replacement_map: Dict[CURIE, List[CURIE]] = None
-
- def __post_init__(self):
- if self.wrapped_ontology is None:
- resource = self.resource
- logging.info(f"Pronto using resource: {resource}")
- kwargs = {}
- if resource and resource.import_depth is not None:
- kwargs["import_depth"] = resource.import_depth
- if resource is None:
- ontology = Ontology()
- elif resource.local:
- if resource.local_path:
- ontology = Ontology(str(resource.local_path), **kwargs)
- else:
- ontology = Ontology()
- else:
- ontology = Ontology.from_obo_library(resource.slug, **kwargs)
- self.wrapped_ontology = ontology
- for prefix, expansion in ontology.metadata.idspaces.items():
- self.prefix_map()[prefix] = expansion[0]
-
- @classmethod
- @deprecated("old style")
- def create(cls, resource: OntologyResource = None) -> "ProntoImplementation":
- return ProntoImplementation(resource=resource)
-
- def _all_relationships(self) -> Iterator[RELATIONSHIP]:
- for s in self.entities(filter_obsoletes=False):
- term = self._entity(s)
- if isinstance(term, Term):
- # only "Terms" in pronto have relationships
- for o in term.superclasses(distance=1):
- if o.id != s:
- yield s, IS_A, o.id
- for rel_type, parents in term.relationships.items():
- p = self._get_pronto_relationship_type_curie(rel_type)
- try:
- for o in parents:
- yield s, p, o.id
- except KeyError:
- pass
- if term.equivalent_to:
- for o in term.equivalent_to.ids:
- # symmetric
- yield s, EQUIVALENT_CLASS, o
- yield o, EQUIVALENT_CLASS, s
-
- def _all_entailed_relationships(self):
- reasoner = RelationGraphReasoner(self)
- yield from reasoner.entailed_edges()
-
- def store(self, resource: OntologyResource = None) -> None:
- if resource is None:
- resource = self.resource
- ontology = self.wrapped_ontology
- if resource.local:
- if resource.slug:
- with open(str(resource.local_path), "wb") as f:
- ontology.dump(f, format=resource.format)
- else:
- ontology.dump(sys.stdout.buffer, format=resource.format)
- else:
- raise NotImplementedError(f"Cannot dump to {resource}")
-
- def load_graph(self, graph: Graph, replace: True) -> None:
- if replace:
- converter = OboGraphToOboFormatConverter()
- gd = GraphDocument(graphs=[graph])
- io = converter.as_bytes_io(gd)
- ont = Ontology(io)
- self.wrapped_ontology = ont
- self._relationship_index_cache = None
- self._alt_id_to_replacement_map = None
- return
- for n in graph.nodes:
- if n.id == IS_A:
- pass
- else:
- self.create_entity(n.id, n.lbl, type=n.type)
- for e in graph.edges:
- self.add_relationship(e.sub, e.pred, e.obj)
-
- @deprecated("Use this when we fix https://github.com/fastobo/fastobo/issues/42")
- def load_graph_using_jsondoc(self, graph: Graph, replace: True) -> None:
- tf = tempfile.NamedTemporaryFile()
- tf_name = "/tmp/tf.json" # noqa
- gd = GraphDocument(graphs=[graph])
- json_dumper.dump(gd, to_file=tf_name)
- tf.flush()
- ont = Ontology(tf_name)
- if replace:
- self.wrapped_ontology = ont
- else:
- raise NotImplementedError
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: BasicOntologyInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _entity(self, curie: CURIE, strict=False):
- for r in self.wrapped_ontology.relationships():
- # TODO: use OboLegacyInterface
- # see https://owlcollab.github.io/oboformat/doc/obo-syntax.html#4.4.1
- # pronto gives relations shorthand IDs for RO and BFO, as it is providing
- # oboformat as a level of abstraction. We want to map these back to the CURIEs
- if r.id == curie:
- return r
- if curie.startswith("RO:") or curie.startswith("BFO:"):
- if any(x for x in r.xrefs if x.id == curie):
- return r
- if curie in self.wrapped_ontology:
- return self.wrapped_ontology[curie]
- else:
- if strict:
- raise ValueError(f"No such CURIE: {curie}")
- return None
-
- def _create(self, curie: CURIE, exist_ok=True):
- if curie in self.wrapped_ontology:
- return self.wrapped_ontology[curie]
- else:
- return self.wrapped_ontology.create_term(curie)
-
- def _create_pred(self, curie: CURIE, exist_ok=True):
- if curie in self.wrapped_ontology.relationships():
- return self.wrapped_ontology.get_relationship(curie)
- else:
- return self.wrapped_ontology.create_relationship(curie)
-
- def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
- for t in self.wrapped_ontology.terms():
- if filter_obsoletes and t.obsolete:
- continue
- if owl_type and owl_type != OWL_CLASS:
- continue
- yield t.id
- # note what Pronto calls "relationship" is actually "relationship type"
- for t in self.wrapped_ontology.relationships():
- if filter_obsoletes and t.obsolete:
- continue
- if owl_type and owl_type != OWL_OBJECT_PROPERTY:
- continue
- curie = self._get_pronto_relationship_type_curie(t)
- yield curie
- for t in self.wrapped_ontology.synonym_types():
- if owl_type and owl_type != OIO_SYNONYM_TYPE_PROPERTY:
- continue
- yield t.id
- for t in self.wrapped_ontology.metadata.subsetdefs:
- if owl_type and owl_type != OIO_SUBSET_PROPERTY:
- continue
- yield t.name
- if not owl_type or owl_type == OWL_CLASS:
- # note that in the case of alt_ids, metadata such as
- # original owl_type is lost. We assume that the original
- # owl_type was OWL_CLASS
- if not filter_obsoletes:
- for s in self._get_alt_id_to_replacement_map().keys():
- yield s
-
- def ontologies(self) -> Iterable[CURIE]:
- yield self.wrapped_ontology.metadata.ontology
-
- def ontology_metadata_map(self, ontology: CURIE) -> METADATA_MAP:
- m = {}
- meta = self.wrapped_ontology.metadata
- ont_id = meta.ontology
- if meta.data_version:
- m[OWL_VERSION_INFO] = [f"obo:{ont_id}/{meta.data_version}{ont_id}.owl"]
- return m
-
- def owl_types(self, entities: Iterable[CURIE]) -> Iterable[Tuple[CURIE, CURIE]]:
- subset_names = [s.name for s in self.wrapped_ontology.metadata.subsetdefs]
- syntype_ids = [s.id for s in self.wrapped_ontology.synonym_types()]
- for curie in entities:
- if curie in self.wrapped_ontology.terms():
- yield curie, OWL_CLASS
- elif curie in self.wrapped_ontology.relationships():
- yield curie, OWL_OBJECT_PROPERTY
- elif curie in syntype_ids:
- yield curie, OIO_SYNONYM_TYPE_PROPERTY
- elif curie in subset_names:
- yield curie, OIO_SUBSET_PROPERTY
- else:
- yield curie, None
-
- def obsoletes(self, include_merged=True) -> Iterable[CURIE]:
- for t in self.wrapped_ontology.terms():
- if t.obsolete:
- yield t.id
- # note what Pronto calls "relationship" is actually "relationship type"
- for t in self.wrapped_ontology.relationships():
- if t.obsolete:
- yield t.id
- if include_merged:
- for a in self._get_alt_id_to_replacement_map().keys():
- yield a
-
- def subsets(self) -> Iterable[CURIE]:
- reported = set()
- for s in self.wrapped_ontology.metadata.subsetdefs:
- reported.add(s.name)
- yield s.name
- # also yield implicit subsets
- subsets = set()
- for t in self.wrapped_ontology.terms():
- subsets.update(t.subsets)
- for subset in subsets:
- if subset not in reported:
- yield subset
-
- def subset_members(self, subset: SUBSET_CURIE) -> Iterable[CURIE]:
- for t in self.wrapped_ontology.terms():
- if subset in t.subsets:
- yield t.id
-
- def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> str:
- t = self._entity(curie)
- if t:
- return t.name
- else:
- if curie == IS_A:
- return "subClassOf"
- else:
- return None
-
- def set_label(self, curie: CURIE, label: str, lang: Optional[LANGUAGE_TAG] = None) -> bool:
- t = self._entity(curie)
- if t:
- curr = t.name
- if curr != label:
- t.name = label
- return True
- else:
- return False
- else:
- raise ValueError(f"No such ID: {curie}")
-
- def curies_by_label(self, label: str) -> List[CURIE]:
- return [t.id for t in self.wrapped_ontology.terms() if t.name == label]
-
- def _get_pronto_relationship_type_curie(self, rel_type: pronto.Relationship) -> CURIE:
- for x in rel_type.xrefs:
- if x.id.startswith("BFO:") or x.id.startswith("RO:"):
- return x.id
- for x in rel_type.xrefs:
- if x.id.startswith("http"):
- compacted = self.uri_to_curie(x.id)
- return compacted
- return rel_type.id
-
- def relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_tbox: bool = True,
- include_abox: bool = True,
- include_entailed: bool = False,
- exclude_blank: bool = True,
- ) -> Iterator[RELATIONSHIP]:
- ei = self.edge_index
- if include_entailed:
- ei = self.entailed_edge_index
- yield from ei.edges(
- subjects=subjects,
- predicates=predicates,
- objects=objects,
- )
-
- def outgoing_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None, entailed=False
- ) -> Iterator[Tuple[PRED_CURIE, CURIE]]:
- for _s, p, o in self.relationships([curie], predicates, include_entailed=entailed):
- yield p, o
-
- def create_entity(
- self,
- curie: CURIE,
- label: Optional[str] = None,
- relationships: Optional[RELATIONSHIP_MAP] = None,
- type: Optional[str] = None,
- replace=False,
- ) -> CURIE:
- ont = self.wrapped_ontology
- t = self._entity(curie, False)
- if t:
- if replace:
- t = None
- if not t:
- if not type or type == "CLASS":
- t = ont.create_term(curie)
- elif type == "PROPERTY":
- t = ont.create_relationship(curie)
- else:
- raise ValueError(f"Pronto cannot handle type of {type} for {curie}")
- t.name = label
- if relationships:
- for pred, fillers in relationships.items():
- for filler in fillers:
- self.add_relationship(curie, pred, filler)
- logging.info(f"Created: {curie}")
- return curie
-
- def add_relationship(self, curie: CURIE, predicate: PRED_CURIE, filler: CURIE):
- t = self._entity(curie)
- filler_term = self._create(filler)
- if predicate == IS_A:
- t.superclasses().add(filler_term)
- else:
- predicate_term = self._create_pred(predicate)
- if predicate_term not in t.relationships.keys():
- t.relationships[predicate_term] = []
- t.relationships[predicate_term].add(filler_term)
- self._clear_relationship_index()
-
- def remove_relationship(self, curie: CURIE, predicate: Optional[PRED_CURIE], filler: CURIE):
- t = self._entity(curie)
- filler_term = self._entity(filler)
- if not predicate or predicate == IS_A:
- t.superclasses().remove(filler_term)
- else:
- predicate_term = self._create_pred(predicate)
- t.relationships[predicate_term].remove(filler_term)
- self._clear_relationship_index()
-
- def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- e = self._entity(curie)
- return str(e.definition) if e and e.definition else None
-
- def definitions(
- self,
- curies: Iterable[CURIE],
- include_metadata=False,
- include_missing=False,
- lang: Optional[LANGUAGE_TAG] = None,
- ) -> Iterator[DEFINITION]:
- for curie in curies:
- e = self._entity(curie)
- if not e:
- continue
- defn = e.definition
- if not defn and not include_missing:
- continue
- metadata = {}
- if include_metadata:
- metadata[HAS_DBXREF] = []
- for x in defn.xrefs:
- metadata[HAS_DBXREF].append(x.id)
- yield curie, defn, metadata
-
- def comments(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
- for curie in curies:
- e = self._entity(curie)
- if e:
- yield curie, e.comment
-
- def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
- t = self._entity(curie)
- if t is None:
- return {}
- m = defaultdict(list)
- m[LABEL_PREDICATE] = [t.name]
- for s in t.synonyms:
- pred = _synonym_scope_pred(s)
- m[pred].append(s.description)
- return m
-
- def simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- t = self._entity(curie)
- if t is None:
- return
- for s in t.xrefs:
- yield HAS_DBXREF, s.id
- for s in t.annotations:
- rel = self._entity(s.property)
- if ":" in s.property:
- pred = s.property
- else:
- pred = self._get_pronto_relationship_type_curie(rel)
- if pred in SKOS_MATCH_PREDICATES:
- if isinstance(s, LiteralPropertyValue):
- v = s.literal
- yield pred, v
- elif isinstance(s, ResourcePropertyValue):
- yield pred, s.resource
-
- def entity_metadata_map(self, curie: CURIE) -> METADATA_MAP:
- t = self._entity(curie)
- m = defaultdict(list)
- _alt_id_map = self._get_alt_id_to_replacement_map()
- if t:
- for ann in t.annotations:
- if isinstance(ann, LiteralPropertyValue):
- m[ann.property].append(ann.literal)
- elif isinstance(ann, ResourcePropertyValue):
- m[ann.property].append(ann.resource)
- if t.replaced_by:
- for x in t.replaced_by:
- m[TERM_REPLACED_BY].append(x.id)
- if t.consider:
- for x in t.consider:
- m[CONSIDER_REPLACEMENT].append(x.id)
- if t.obsolete:
- m[DEPRECATED_PREDICATE].append(True)
- if t.namespace:
- m[HAS_OBO_NAMESPACE].append(t.namespace)
- if curie in _alt_id_map:
- m[TERM_REPLACED_BY] += _alt_id_map[curie]
- m[DEPRECATED_PREDICATE].append(True)
- m[HAS_OBSOLESCENCE_REASON].append(TERMS_MERGED)
- self.add_missing_property_values(curie, m)
- return dict(m)
-
- def _get_alt_id_to_replacement_map(self) -> Dict[CURIE, List[CURIE]]:
- if self._alt_id_to_replacement_map is None:
- self._alt_id_to_replacement_map = defaultdict(list)
- for e in self.entities():
- t = self._entity(e)
- if t and t.alternate_ids:
- for a in t.alternate_ids:
- self._alt_id_to_replacement_map[a].append(e)
- return self._alt_id_to_replacement_map
-
- def create_subontology(self, curies: List[CURIE]) -> "ProntoImplementation":
- subontology = Ontology()
- for curie in curies:
- t = self._entity(curie)
- subontology.create_term(curie)
- t2 = subontology[curie]
- t2.name = t.name
- # TODO - complete object
- return ProntoImplementation(wrapped_ontology=subontology)
-
- def clone(self, resource: Any) -> None:
- shutil.copyfile(self.resource.slug, resource.slug)
- return type(self)(resource)
-
- def dump(
- self, path: str = None, syntax: str = "obo", enforce_canonical_ordering=False, **kwargs
- ):
- if syntax is None:
- syntax = "obo"
- if syntax in ["obo", "json"]:
- if enforce_canonical_ordering:
- raise NotImplementedError("enforce_canonical_ordering not implemented for pronto")
- # TODO: simplify the logic here; not clear why pronto wants a binary file
- if isinstance(path, str):
- with open(path, "wb") as file:
- self.wrapped_ontology.dump(file, format=syntax)
- else:
- if path == sys.stdout:
- print(self.wrapped_ontology.dumps(format=syntax))
- else:
- self.wrapped_ontology.dump(path, format=syntax)
- else:
- super().dump(path, syntax, **kwargs)
-
- def save(
- self,
- ):
- logging.info("Committing and flushing changes")
- self.dump(self.resource.slug)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MappingsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def sssom_mappings(
- self, curies: Optional[Union[CURIE, Iterable[CURIE]]] = None, source: Optional[str] = None
- ) -> Iterable[sssom.Mapping]:
- if isinstance(curies, CURIE):
- curies = [curies]
- elif curies is None:
- curies = list(self.entities())
- else:
- curies = list(curies)
- # mappings where curie is the subject:
- for curie in curies:
- for pred, obj in self.simple_mappings_by_curie(curie):
- m = sssom.Mapping(
- subject_id=curie,
- predicate_id=pred,
- object_id=obj,
- mapping_justification=sssom.EntityReference(SEMAPV.UnspecifiedMatching.value),
- )
- inject_mapping_sources(m)
- if source and m.object_source != source and m.subject_source != source:
- continue
- yield m
- # mappings where curie is the object:
- # TODO: use a cache to avoid re-calculating
- for e in self.entities():
- t = self._entity(e)
- if t:
- for x in t.xrefs:
- if x.id in curies:
- m = sssom.Mapping(
- subject_id=e,
- predicate_id=SKOS_CLOSE_MATCH,
- object_id=x.id,
- mapping_justification=sssom.EntityReference(
- SEMAPV.UnspecifiedMatching.value
- ),
- )
- inject_mapping_sources(m)
- if source and m.object_source != source and m.subject_source != source:
- continue
- yield m
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def node(self, curie: CURIE, strict=False, include_metadata=False) -> obograph.Node:
- t = self._entity(curie)
- if t is None:
- return obograph.Node(id=curie)
- else:
- meta = obograph.Meta()
- if isinstance(t, pronto.Relationship):
- t_id = self._get_pronto_relationship_type_curie(t)
- typ = "PROPERTY"
- else:
- t_id = t.id
- typ = "CLASS"
- if include_metadata:
- if t.definition:
- defn_xrefs = [x.id for x in t.definition.xrefs]
- meta.definition = obograph.DefinitionPropertyValue(
- val=t.definition, xrefs=defn_xrefs
- )
- if t.xrefs:
- meta.xrefs = [obograph.XrefPropertyValue(val=x.id) for x in t.xrefs]
- if t.subsets:
- meta.subsets = [x for x in t.subsets]
- if isinstance(t, pronto.Relationship):
- for x in t.xrefs:
- if x.id.startswith("RO:") or x.id.startswith("BFO:"):
- t_id = x.id
- for s in t.synonyms:
- pred = SCOPE_TO_SYNONYM_PRED_MAP[s.scope].replace("oio:", "")
- synonym_type = s.type.id if s.type else None
- meta.synonyms.append(
- obograph.SynonymPropertyValue(
- val=s.description,
- pred=pred,
- synonymType=synonym_type,
- xrefs=[x.id for x in s.xrefs],
- )
- )
- return obograph.Node(id=t_id, lbl=t.name, type=typ, meta=meta)
-
- def as_obograph(self, expand_curies=False) -> Graph:
- om = self.wrapped_ontology.metadata
- entities = set(self.entities(filter_obsoletes=False, owl_type=OWL_CLASS))
- # entities.extend(self.entities(filter_obsoletes=False, owl_type=OWL_OBJECT_PROPERTY))
- nodes = [self.node(curie) for curie in entities]
- nodes = [n for n in nodes if n.lbl or n.meta]
- edges = [
- Edge(sub=r[0], pred="is_a" if r[1] == IS_A else r[1], obj=r[2])
- for r in self.relationships()
- ]
- ldefs = list(self.logical_definitions(entities))
- graph_id = om.ontology
- if not graph_id:
- graph_id = self.resource.slug
- return Graph(id=graph_id, nodes=nodes, edges=edges, logicalDefinitionAxioms=ldefs)
-
- def synonym_property_values(
- self, subject: Union[CURIE, Iterable[CURIE]]
- ) -> Iterator[Tuple[CURIE, obograph.SynonymPropertyValue]]:
- if isinstance(subject, CURIE):
- subject = [subject]
- for curie in subject:
- e = self._entity(curie)
- if e:
- for s in e.synonyms:
- pred = _synonym_scope_pred(s).replace("oio:", "")
- xrefs = [x.id for x in s.xrefs]
- t = s.type.id if s.type else None
- spv = obograph.SynonymPropertyValue(
- pred=pred, val=s.description, xrefs=xrefs, synonymType=t
- )
- yield curie, spv
-
- def logical_definitions(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- **kwargs,
- ) -> Iterable[obograph.LogicalDefinitionAxiom]:
- if not subjects:
- subjects = self.entities()
- for s in subjects:
- term = self._entity(s)
- if term and term.intersection_of:
- ldef = obograph.LogicalDefinitionAxiom(definedClassId=s)
- for ix in term.intersection_of:
- if isinstance(ix, Term):
- ldef.genusIds.append(ix.id)
- else:
- (rel, filler) = ix
- rel = self._get_pronto_relationship_type_curie(rel)
- er = obograph.ExistentialRestrictionExpression(
- propertyId=rel, fillerId=filler.id
- )
- ldef.restrictions.append(er)
- if logical_definition_matches(ldef, predicates=predicates, objects=objects):
- yield ldef
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SearchInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def basic_search(self, search_term: str, config: SearchConfiguration = None) -> Iterable[CURIE]:
- if config is None:
- config = SearchConfiguration()
- matches = []
- mfunc = None
- if config.syntax == SearchTermSyntax(SearchTermSyntax.STARTS_WITH):
- mfunc = lambda label: str(label).startswith(search_term)
- elif config.syntax == SearchTermSyntax(SearchTermSyntax.REGULAR_EXPRESSION):
- prog = re.compile(search_term)
- mfunc = lambda label: prog.search(label)
- elif config.is_partial:
- mfunc = lambda label: search_term in str(label)
- else:
- mfunc = lambda label: label == search_term
- search_all = SearchProperty(SearchProperty.ANYTHING) in config.properties
- logging.info(f"SEARCH={search_term}")
- for t in self.wrapped_ontology.terms():
- logging.debug(f"T={t} // {config}")
- if (
- search_all
- or SearchProperty(SearchProperty.LABEL)
- or config.properties not in config.properties
- ):
- if t.name and mfunc(t.name):
- matches.append(t.id)
- logging.info(f"Name match to {t.id}")
- continue
- if search_all or SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
- if mfunc(t.id):
- matches.append(t.id)
- logging.info(f"identifier match to {t.id}")
- continue
- if (
- search_all
- or SearchProperty(SearchProperty.REPLACEMENT_IDENTIFIER) in config.properties
- ):
- if t.replaced_by:
- for r in t.replaced_by:
- if mfunc(t.id):
- matches.append(r.id)
- logging.info(f"replaced_by match to {t.id}")
- continue
- if t.alternate_ids:
- for a in t.alternate_ids:
- if mfunc(a):
- matches.append(t.id)
- logging.info(f"alternate_id match to {t.id}")
- continue
- if search_all or SearchProperty(SearchProperty.ALIAS) in config.properties:
- for syn in t.synonyms:
- if mfunc(syn.description):
- logging.info(f"Syn match to {t.id}")
- matches.append(t.id)
- continue
- if search_all or SearchProperty(SearchProperty.MAPPED_IDENTIFIER) in config.properties:
- for x in t.xrefs:
- if mfunc(x.id):
- logging.info(f"Mapping match to {t.id}")
- matches.append(t.id)
- continue
- # if search_all or SearchProperty(SearchProperty.REPLACEMENT_IDENTIFIER) in config.properties:
- # if search_term in self._get_alt_id_to_replacement_map():
- # matches.append(self._get_alt_id_to_replacement_map()[search_term])
- for m in matches:
- yield m
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: PatcherInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def migrate_curies(self, curie_map: Dict[CURIE, CURIE]) -> None:
- pass
-
- def apply_patch(
- self,
- patch: kgcl.Change,
- activity: kgcl.Activity = None,
- metadata: Mapping[PRED_CURIE, Any] = None,
- configuration: kgcl.Configuration = None,
- ) -> Optional[kgcl.Change]:
- tidy_change_object(patch)
- if isinstance(patch, kgcl.NodeRename):
- self.set_label(patch.about_node, patch.new_value)
- elif isinstance(patch, kgcl.NodeObsoletion):
- t = self._entity(patch.about_node, strict=True)
- t.obsolete = True
- if isinstance(patch, kgcl.NodeObsoletionWithDirectReplacement):
- t.replaced_by = [self._entity(patch.has_direct_replacement)]
- elif isinstance(patch, kgcl.NodeDeletion):
- t = self._entity(patch.about_node, strict=True)
- raise NotImplementedError
- elif isinstance(patch, kgcl.NodeCreation):
- # TODO: decide which field to use in KGCL
- if patch.about_node:
- self.create_entity(patch.about_node, patch.name)
- else:
- self.create_entity(patch.node_id, patch.name)
- elif isinstance(patch, kgcl.SynonymReplacement):
- t = self._entity(patch.about_node, strict=True)
- for syn in t.synonyms:
- if syn.description == patch.old_value:
- syn.description = patch.new_value
- elif isinstance(patch, kgcl.NewTextDefinition):
- t = self._entity(patch.about_node, strict=True)
- xrefs = t.definition.xrefs if t.definition else []
- t.definition = pronto.Definition(patch.new_value, xrefs=xrefs)
- elif isinstance(patch, kgcl.NodeTextDefinitionChange):
- t = self._entity(patch.about_node, strict=True)
- xrefs = t.definition.xrefs if t.definition else []
- t.definition = pronto.Definition(patch.new_value, xrefs=xrefs)
- elif isinstance(patch, kgcl.NewSynonym):
- t = self._entity(patch.about_node, strict=True)
- # Get scope from patch.qualifier
- # rather than forcing all synonyms to be related.
- scope = str(patch.qualifier.value).upper() if patch.qualifier else "RELATED"
- t.add_synonym(description=patch.new_value, scope=scope)
- elif isinstance(patch, kgcl.AddNodeToSubset):
- t = self._entity(patch.about_node, strict=True)
- t.subsets = t.subsets.union({patch.in_subset})
- elif isinstance(patch, kgcl.RemoveNodeFromSubset):
- t = self._entity(patch.about_node, strict=True)
- t.subsets = t.subsets.difference({patch.in_subset})
- elif isinstance(patch, kgcl.EdgeCreation):
- self.add_relationship(patch.subject, patch.predicate, patch.object)
- elif isinstance(patch, kgcl.EdgeDeletion):
- self.remove_relationship(patch.subject, patch.predicate, patch.object)
- elif isinstance(patch, kgcl.RemoveSynonym):
- t = self._entity(patch.about_node, strict=True)
- synonym_to_remove = [
- syn for syn in t._data().synonyms if syn.description == patch.old_value
- ][0]
- t._data().synonyms.discard(synonym_to_remove)
- else:
- raise NotImplementedError(f"cannot handle KGCL type {type(patch)}")
- return patch
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OwlInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def transitive_object_properties(self) -> Iterable[CURIE]:
- for t in self.wrapped_ontology.relationships():
- if t.transitive:
- yield self._get_pronto_relationship_type_curie(t)
-
- def simple_subproperty_of_chains(self) -> Iterable[Tuple[CURIE, List[CURIE]]]:
- for t in self.wrapped_ontology.relationships():
- try:
- if t.holds_over_chain:
- subp = self._get_pronto_relationship_type_curie(t)
- r1, r2 = t.holds_over_chain
- p1 = self._get_pronto_relationship_type_curie(r1)
- p2 = self._get_pronto_relationship_type_curie(r2)
- yield subp, [p1, p2]
- except KeyError as e:
- logging.warning(f"could not find chain relationships for {t}: {e}")
-
-
Source code for oaklib.implementations.simpleobo.simple_obo_implementation
-import logging
-import re
-import shutil
-import sys
-from collections import defaultdict
-from dataclasses import dataclass
-from pathlib import Path
-from typing import (
- Any,
- Dict,
- Iterable,
- Iterator,
- List,
- Mapping,
- Optional,
- TextIO,
- Tuple,
- Union,
-)
-
-import sssom_schema as sssom
-from kgcl_schema.datamodel import kgcl
-
-from oaklib.converters.obo_graph_to_obo_format_converter import (
- OboGraphToOboFormatConverter,
-)
-from oaklib.datamodels import obograph
-from oaklib.datamodels.obograph import (
- Edge,
- ExistentialRestrictionExpression,
- Graph,
- GraphDocument,
- LogicalDefinitionAxiom,
- SynonymPropertyValue,
-)
-from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
-from oaklib.datamodels.vocabulary import (
- CONSIDER_REPLACEMENT,
- CONTRIBUTOR,
- CREATED,
- CREATOR,
- DEPRECATED_PREDICATE,
- EQUIVALENT_CLASS,
- HAS_DBXREF,
- HAS_OBO_NAMESPACE,
- HAS_OBSOLESCENCE_REASON,
- INVERSE_OF,
- IS_A,
- LABEL_PREDICATE,
- OIO_CREATED_BY,
- OIO_CREATION_DATE,
- OIO_SUBSET_PROPERTY,
- OIO_SYNONYM_TYPE_PROPERTY,
- OWL_CLASS,
- OWL_OBJECT_PROPERTY,
- OWL_VERSION_IRI,
- RDFS_DOMAIN,
- RDFS_RANGE,
- SCOPE_TO_SYNONYM_PRED_MAP,
- SEMAPV,
- SKOS_CLOSE_MATCH,
- SUBPROPERTY_OF,
- TERM_REPLACED_BY,
- TERMS_MERGED,
-)
-from oaklib.implementations.simpleobo.simple_obo_parser import (
- TAG_ALT_ID,
- TAG_COMMENT,
- TAG_CONSIDER,
- TAG_CREATED_BY,
- TAG_CREATION_DATE,
- TAG_DATA_VERSION,
- TAG_DEFINITION,
- TAG_DOMAIN,
- TAG_EQUIVALENT_TO,
- TAG_HOLDS_OVER_CHAIN,
- TAG_ID_SPACE,
- TAG_INVERSE_OF,
- TAG_IS_A,
- TAG_IS_OBSOLETE,
- TAG_IS_TRANSITIVE,
- TAG_NAME,
- TAG_NAMESPACE,
- TAG_ONTOLOGY,
- TAG_PROPERTY_VALUE,
- TAG_RANGE,
- TAG_RELATIONSHIP,
- TAG_REPLACED_BY,
- TAG_SUBSET,
- TAG_SUBSETDEF,
- TAG_SYNONYM,
- TAG_SYNONYMTYPEDEF,
- TAG_XREF,
- OboDocument,
- Stanza,
- _synonym_scope_pred,
- parse_obo_document,
-)
-from oaklib.inference.relation_graph_reasoner import RelationGraphReasoner
-from oaklib.interfaces import TextAnnotatorInterface
-from oaklib.interfaces.basic_ontology_interface import (
- ALIAS_MAP,
- LANGUAGE_TAG,
- METADATA_MAP,
- RELATIONSHIP,
- RELATIONSHIP_MAP,
-)
-from oaklib.interfaces.differ_interface import DiffConfiguration, DifferInterface
-from oaklib.interfaces.dumper_interface import DumperInterface
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.merge_interface import MergeInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.interfaces.obolegacy_interface import PRED_CODE, OboLegacyInterface
-from oaklib.interfaces.owl_interface import OwlInterface
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.interfaces.rdf_interface import RdfInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
-from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
-from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
-from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.resource import OntologyResource
-from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE
-from oaklib.utilities.axioms.logical_definition_utilities import (
- logical_definition_matches,
-)
-from oaklib.utilities.kgcl_utilities import generate_change_id, tidy_change_object
-from oaklib.utilities.mapping.sssom_utils import inject_mapping_sources
-
-
-def _is_isa(x: str):
- return x == IS_A or x.lower() == "is_a" or x.lower() == "isa"
-
-
-
-[docs]
-@dataclass
-class SimpleOboImplementation(
- ValidatorInterface,
- DifferInterface,
- RdfInterface,
- OboGraphInterface,
- OboLegacyInterface,
- SearchInterface,
- MappingProviderInterface,
- PatcherInterface,
- SummaryStatisticsInterface,
- SemanticSimilarityInterface,
- TaxonConstraintInterface,
- TextAnnotatorInterface,
- DumperInterface,
- MergeInterface,
- OwlInterface,
-):
- """
- Simple OBO-file backed implementation
-
- This implementation is incomplete and is intended primarily as a Patcher implementation
-
- This can be abandoned when pronto is less strict
- """
-
- obo_document: OboDocument = None
- _relationship_index_cache: Dict[CURIE, List[RELATIONSHIP]] = None
- _alt_id_to_replacement_map: Dict[CURIE, List[CURIE]] = None
- _uses_legacy_properties: bool = None
-
- def __post_init__(self):
- if self.obo_document is None:
- resource = self.resource
- if resource and resource.local_path:
- logging.info(f"Creating doc for {resource}")
- self.obo_document = parse_obo_document(resource.local_path)
- if "edit.obo" in str(resource.local_path) and self.auto_relax_axioms is None:
- # TODO: in future ontology modules should explicitly set this in the metadata
- logging.info(
- f"Auto-setting auto_relax_axioms based on name: {resource.local_path}"
- )
- self.auto_relax_axioms = True
- else:
- self.obo_document = OboDocument()
- for prefix, expansion in self.obo_document.header.pair_values(TAG_ID_SPACE):
- self.prefix_map()[prefix] = expansion
-
- def store(self, resource: OntologyResource = None) -> None:
- if resource is None:
- resource = self.resource
- od = self.obo_document
- if resource.local:
- if resource.slug:
- with open(str(resource.local_path), "w", encoding="UTF-8") as f:
- od.dump(f)
- else:
- od.dump(sys.stdout.buffer)
- else:
- raise NotImplementedError(f"Cannot dump to {resource}")
-
- def load_graph(self, graph: Graph, replace: True) -> None:
- if not replace:
- raise NotImplementedError("Cannot merge obograph")
- converter = OboGraphToOboFormatConverter()
- self.obo_document = OboDocument()
- gd = GraphDocument(graphs=[graph])
- converter.convert(gd, self.obo_document)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: BasicOntologyInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _all_relationships(self) -> Iterator[RELATIONSHIP]:
- logging.info("Commencing indexing")
- n = 0
- entities = list(self.entities(filter_obsoletes=False))
- for s in entities:
- t = self._stanza(s, strict=False)
- if t is None:
- # alt_ids
- continue
- is_relation = t.type == "Typedef"
- for v in t.simple_values(TAG_IS_A):
- n += 1
- if is_relation:
- yield s, SUBPROPERTY_OF, self.map_shorthand_to_curie(v)
- else:
- yield s, IS_A, v
- for tag, prop in [
- (TAG_INVERSE_OF, INVERSE_OF),
- (TAG_DOMAIN, RDFS_DOMAIN),
- (TAG_RANGE, RDFS_RANGE),
- ]:
- for v in t.simple_values(tag):
- n += 1
- yield s, prop, self.map_shorthand_to_curie(v)
- for v in t.simple_values(TAG_EQUIVALENT_TO):
- n += 1
- yield s, EQUIVALENT_CLASS, v
- yield v, EQUIVALENT_CLASS, s
- for p, v in t.pair_values(TAG_RELATIONSHIP):
- yield s, self.map_shorthand_to_curie(p), v
- # for p, v in t.intersection_of_tuples():
- # n += 1
- # yield s, self._get_relationship_type_curie(p), v
- logging.info(f"Indexed {n} relationships")
- if self.auto_relax_axioms:
- n = 0
- logging.info("Auto-relaxing axioms")
- for ldef in self.logical_definitions(entities):
- for p in ldef.genusIds:
- yield ldef.definedClassId, IS_A, p
- n += 1
- for r in ldef.restrictions:
- yield ldef.definedClassId, r.propertyId, r.fillerId
- n += 1
- logging.info(f"Relaxed {n} relationships")
-
- def _all_entailed_relationships(self):
- reasoner = RelationGraphReasoner(self)
- yield from reasoner.entailed_edges()
-
- def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
- od = self.obo_document
- for s_id, s in od.stanzas.items():
- if filter_obsoletes:
- if s.get_boolean_value(TAG_IS_OBSOLETE):
- continue
- if (
- owl_type is None
- or (owl_type == OWL_CLASS and s.type == "Term")
- or (owl_type == OWL_OBJECT_PROPERTY and s.type == "Typedef")
- ):
- if s.type == "Typedef":
- yield self.map_shorthand_to_curie(s_id)
- else:
- yield s_id
- if not owl_type or owl_type == OWL_CLASS:
- # note that in the case of alt_ids, metadata such as
- # original owl_type is lost. We assume that the original
- # owl_type was OWL_CLASS
- if not filter_obsoletes:
- for s in self._get_alt_id_to_replacement_map().keys():
- yield s
- if not owl_type or owl_type == OIO_SUBSET_PROPERTY:
- for v in od.header.simple_values(TAG_SUBSETDEF):
- yield v
- if not owl_type or owl_type == OIO_SYNONYM_TYPE_PROPERTY:
- for v in od.header.simple_values(TAG_SYNONYMTYPEDEF):
- yield v
-
- def owl_types(self, entities: Iterable[CURIE]) -> Iterable[Tuple[CURIE, CURIE]]:
- od = self.obo_document
- for curie in entities:
- s = self._stanza(curie, False)
- if s is None:
- if curie in self.subsets():
- yield curie, OIO_SUBSET_PROPERTY
- elif curie in od.header.simple_values(TAG_SYNONYMTYPEDEF):
- yield curie, OIO_SYNONYM_TYPE_PROPERTY
- else:
- yield curie, None
- else:
- if s.type == "Term":
- yield curie, OWL_CLASS
- elif s.type == "Typedef":
- yield curie, OWL_OBJECT_PROPERTY
- else:
- raise ValueError(f"Unknown stanza type: {s.type}")
-
- def obsoletes(self, include_merged=True) -> Iterable[CURIE]:
- od = self.obo_document
- for s in od.stanzas.values():
- if s.get_boolean_value(TAG_IS_OBSOLETE):
- yield s.id
- if include_merged:
- for s in self._get_alt_id_to_replacement_map().keys():
- yield s
-
- def subsets(self) -> Iterable[CURIE]:
- od = self.obo_document
- for s in od.header.simple_values(TAG_SUBSETDEF):
- yield s
-
- def subset_members(self, subset: SUBSET_CURIE) -> Iterable[CURIE]:
- od = self.obo_document
- for s in od.stanzas.values():
- if subset in s.simple_values(TAG_SUBSET):
- yield s.id
-
- def terms_subsets(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, SUBSET_CURIE]]:
- for curie in curies:
- s = self._stanza(curie, False)
- if s:
- for subset in s.simple_values(TAG_SUBSET):
- yield curie, subset
-
- def ontologies(self) -> Iterable[CURIE]:
- od = self.obo_document
- for v in od.header.simple_values(TAG_ONTOLOGY):
- yield v
-
- def ontology_metadata_map(self, ontology: CURIE) -> METADATA_MAP:
- m = defaultdict(list)
- m["id"] = [ontology]
- omo_map = {
- TAG_DATA_VERSION: OWL_VERSION_IRI,
- }
- header = self.obo_document.header
- for tv in header.tag_values:
- tag = tv.tag
- if tag in omo_map:
- p = omo_map[tag]
- val = tv.value
- if p == OWL_VERSION_IRI:
- val = f"obo:{ontology}/{val}{ontology}.owl"
- m[p].append(val)
- return dict(m)
-
- def _stanza(self, curie: CURIE, strict=True) -> Optional[Stanza]:
- stanza = self.obo_document.stanzas.get(curie, None)
- if stanza is None:
- alt_curie = self.map_curie_to_shorthand(curie)
- if alt_curie and alt_curie != curie:
- stanza = self.obo_document.stanzas.get(alt_curie)
- if strict and not stanza:
- raise ValueError(f"No such stanza {curie}")
- return stanza
-
- def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- if lang:
- raise NotImplementedError("Language tags not supported")
- s = self._stanza(curie, False)
- if s:
- return s.singular_value(TAG_NAME)
- else:
- if curie == IS_A:
- return "subClassOf"
- else:
- return None
-
- def set_label(self, curie: CURIE, label: str, lang: Optional[LANGUAGE_TAG] = None) -> bool:
- if lang:
- raise NotImplementedError("Language tags not supported")
- s = self._stanza(curie, False)
- s.set_singular_tag(TAG_NAME, label)
- return True
-
- def curies_by_label(self, label: str) -> List[CURIE]:
- return [
- s.id
- for s in self.obo_document.stanzas.values()
- if s.singular_value(TAG_NAME, False) == label
- ]
-
- def _lookup(self, label_or_curie: str) -> CURIE:
- if ":" in label_or_curie and " " not in label_or_curie:
- return label_or_curie
- else:
- candidates = self.curies_by_label(label_or_curie)
- if len(candidates) != 1:
- raise ValueError(f"{label_or_curie} => {candidates}")
- return candidates[0]
-
- def create_entity(
- self,
- curie: CURIE,
- label: Optional[str] = None,
- relationships: Optional[RELATIONSHIP_MAP] = None,
- type: Optional[str] = None,
- replace=False,
- ) -> CURIE:
- if type is None or type == OWL_CLASS:
- type = "Term"
- elif type == OWL_OBJECT_PROPERTY:
- type = "Typedef"
- else:
- raise ValueError(f"Cannot handle type: {type}")
- stanza = self._stanza(curie, False)
- if stanza:
- if replace:
- stanza = None
- if not stanza:
- stanza = Stanza(id=curie, type=type)
- stanza.add_tag_value(TAG_NAME, label)
- self.obo_document.add_stanza(stanza)
- if relationships:
- for pred, fillers in relationships.items():
- for filler in fillers:
- self.add_relationship(curie, pred, filler)
-
- def add_relationship(self, curie: CURIE, predicate: PRED_CURIE, filler: CURIE, **kwargs):
- t = self._stanza(curie)
- if predicate == IS_A:
- t.add_tag_value(TAG_IS_A, filler, **kwargs)
- else:
- predicate_code = self.map_curie_to_shorthand(predicate)
- t.add_tag_value_pair(TAG_RELATIONSHIP, predicate_code, filler, **kwargs)
- self._clear_relationship_index()
-
- def remove_relationship(self, curie: CURIE, predicate: Optional[PRED_CURIE], filler: CURIE):
- t = self._stanza(curie)
- if not predicate or predicate == IS_A:
- t.remove_simple_tag_value(TAG_IS_A, filler)
- else:
- predicate_code = self.map_curie_to_shorthand(predicate)
- t.remove_pairwise_tag_value(TAG_RELATIONSHIP, predicate_code, filler)
- self._clear_relationship_index()
-
- def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- s = self._stanza(curie, strict=False)
- if s:
- return s.quoted_value(TAG_DEFINITION)
-
- def comments(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
- for curie in curies:
- s = self._stanza(curie)
- if s:
- yield curie, s.singular_value(TAG_COMMENT)
-
- def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
- s = self._stanza(curie, strict=False)
- if s is None:
- return {}
- m = defaultdict(list)
- lbl = self.label(curie)
- if lbl:
- m[LABEL_PREDICATE] = [lbl]
- for st in s.synonyms():
- syn, pred, _type, _xrefs = st
- pred = _synonym_scope_pred(pred)
- m[pred].append(syn)
- return m
-
- def synonym_property_values(
- self, subject: Union[CURIE, Iterable[CURIE]]
- ) -> Iterator[Tuple[CURIE, SynonymPropertyValue]]:
- if isinstance(subject, str):
- subject = [subject]
- for curie in subject:
- for p, vs in self.entity_alias_map(curie).items():
- if p == LABEL_PREDICATE:
- continue
- for v in vs:
- yield curie, SynonymPropertyValue(pred=p.replace("oio:", ""), val=v)
-
- def map_shorthand_to_curie(self, rel_code: PRED_CODE) -> PRED_CURIE:
- """
- Maps either a true relationship type CURIE or a shorthand packages to a CURIE.
-
- See `section 5.9 <https://owlcollab.github.io/oboformat/doc/obo-syntax.html#5.9>`_
-
- :param rel_code:
- :return:
- """
- for _, x in self.simple_mappings_by_curie(rel_code):
- if x.startswith("BFO:") or x.startswith("RO:"):
- return x
- if ":" not in rel_code and ":" in x:
- return x
- return rel_code
-
- def map_curie_to_shorthand(self, rel_type: PRED_CURIE) -> PRED_CODE:
- """
- Reciprocal of `_get_relationship_type_curie`
-
- :param rel_type:
- :return:
- """
- if rel_type:
- is_core = rel_type.startswith("BFO:") or rel_type.startswith("RO:")
- for s in self.obo_document.stanzas.values():
- if s.type == "Typedef":
- for x in s.simple_values(TAG_XREF):
- if x == rel_type:
- if is_core or ":" not in s.id:
- return s.id
- return rel_type
-
- def relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_tbox: bool = True,
- include_abox: bool = True,
- include_entailed: bool = False,
- exclude_blank: bool = True,
- ) -> Iterator[RELATIONSHIP]:
- ei = self.edge_index
- if include_entailed:
- ei = self.entailed_edge_index
- yield from ei.edges(
- subjects=subjects,
- predicates=predicates,
- objects=objects,
- )
-
- def basic_search(self, search_term: str, config: SearchConfiguration = None) -> Iterable[CURIE]:
- # TODO: move up, avoid repeating packages
- if config is None:
- config = SearchConfiguration()
- matches = []
- mfunc = None
- if config.syntax == SearchTermSyntax(SearchTermSyntax.STARTS_WITH):
- mfunc = lambda label: str(label).startswith(search_term)
- elif config.syntax == SearchTermSyntax(SearchTermSyntax.REGULAR_EXPRESSION):
- prog = re.compile(search_term)
- mfunc = lambda label: prog.search(label)
- elif config.is_partial:
- mfunc = lambda label: search_term in str(label)
- else:
- mfunc = lambda label: label == search_term
- search_all = SearchProperty(SearchProperty.ANYTHING) in config.properties
- logging.info(f"SEARCH={search_term}")
- for t in self.entities(filter_obsoletes=False):
- lbl = self.label(t)
- logging.debug(f"T={t} // {config}")
- if (
- search_all
- or SearchProperty(SearchProperty.LABEL)
- or config.properties not in config.properties
- ):
- if lbl and mfunc(lbl):
- matches.append(t)
- logging.info(f"Name match to {t}")
- continue
- if search_all or SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
- if mfunc(t):
- matches.append(t)
- logging.info(f"identifier match to {t}")
- continue
- if (
- search_all
- or SearchProperty(SearchProperty.REPLACEMENT_IDENTIFIER) in config.properties
- ):
- s = self._stanza(t, strict=False)
- if s:
- for r in s.simple_values(TAG_REPLACED_BY):
- if mfunc(t):
- matches.append(r)
- logging.info(f"replaced_by match to {t}")
- continue
- for a in s.simple_values(TAG_ALT_ID):
- if mfunc(a):
- matches.append(t)
- logging.info(f"alternate_id match to {t}")
- continue
- if search_all or SearchProperty(SearchProperty.ALIAS) in config.properties:
- for syn in self.entity_aliases(t):
- if mfunc(syn):
- logging.info(f"Syn match to {t}")
- matches.append(t)
- continue
- if search_all or SearchProperty(SearchProperty.MAPPED_IDENTIFIER) in config.properties:
- for x in self.simple_mappings_by_curie(t):
- if mfunc(x):
- logging.info(f"Syn match to {t}")
- matches.append(t)
- continue
- for m in matches:
- yield m
-
- def simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- t = self._stanza(curie, strict=False)
- if t:
- for v in t.simple_values(TAG_XREF):
- yield HAS_DBXREF, v
-
- def entity_metadata_map(self, curie: CURIE) -> METADATA_MAP:
- t = self._stanza(curie, strict=False)
- _alt_id_map = self._get_alt_id_to_replacement_map()
- m = defaultdict(list)
- if t:
- for tag, mkey in [
- (TAG_REPLACED_BY, TERM_REPLACED_BY),
- (TAG_CONSIDER, CONSIDER_REPLACEMENT),
- (TAG_NAMESPACE, HAS_OBO_NAMESPACE),
- (TAG_IS_OBSOLETE, DEPRECATED_PREDICATE),
- (TAG_CREATION_DATE, OIO_CREATION_DATE),
- (TAG_CREATED_BY, OIO_CREATED_BY),
- ]:
- for v in t.simple_values(tag):
- if tag == TAG_IS_OBSOLETE:
- v = True if v == "true" else False
- m[mkey].append(v)
- for pv in t.property_values():
- m[self.map_shorthand_to_curie(pv[0])].append(pv[1])
- if curie in _alt_id_map:
- m[TERM_REPLACED_BY] += _alt_id_map[curie]
- m[DEPRECATED_PREDICATE].append(True)
- m[HAS_OBSOLESCENCE_REASON].append(TERMS_MERGED)
- self.add_missing_property_values(curie, m)
- return dict(m)
-
- def _get_alt_id_to_replacement_map(self) -> Dict[CURIE, List[CURIE]]:
- if self._alt_id_to_replacement_map is None:
- self._alt_id_to_replacement_map = defaultdict(list)
- for e in self.entities():
- t = self._stanza(e, False)
- if t:
- for a in t.simple_values(TAG_ALT_ID):
- self._alt_id_to_replacement_map[a].append(e)
- return self._alt_id_to_replacement_map
-
- def clone(self, resource: OntologyResource) -> "SimpleOboImplementation":
- shutil.copyfile(self.resource.slug, resource.slug)
- return type(self)(resource)
-
- def dump(self, path: Union[str, TextIO] = None, syntax: str = "obo", **kwargs):
- if syntax is None or syntax == "obo":
- if isinstance(path, str) or isinstance(path, Path):
- logging.info(f"Saving to {path}")
- with open(path, "w", encoding="UTF-8") as file:
- self.obo_document.dump(file)
- else:
- self.obo_document.dump(path)
- else:
- super().dump(path, syntax=syntax)
-
- def save(
- self,
- ):
- logging.info("Committing and flushing changes")
- self.dump(self.resource.slug)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MappingsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def get_sssom_mappings_by_curie(self, curie: Union[str, CURIE]) -> Iterator[sssom.Mapping]:
- s = self._stanza(curie, strict=False)
- if s:
- for x in s.simple_values(TAG_XREF):
- m = sssom.Mapping(
- subject_id=curie,
- predicate_id=SKOS_CLOSE_MATCH,
- object_id=x,
- mapping_justification=sssom.EntityReference(SEMAPV.UnspecifiedMatching.value),
- )
- inject_mapping_sources(m)
- yield m
- # TODO: use a cache to avoid re-calculating
- for _, stanza in self.obo_document.stanzas.items():
- if len(stanza.simple_values(TAG_XREF)) > 0:
- for x in stanza.simple_values(TAG_XREF):
- if x == curie:
- m = sssom.Mapping(
- subject_id=stanza.id,
- predicate_id=SKOS_CLOSE_MATCH,
- object_id=curie,
- mapping_justification=SEMAPV.UnspecifiedMatching.value,
- )
- inject_mapping_sources(m)
- yield m
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def node(self, curie: CURIE, strict=False, include_metadata=False) -> obograph.Node:
- t = self._stanza(curie, strict=False)
- if t is None:
- return obograph.Node(id=curie)
- else:
- types = self.owl_type(curie)
- if OWL_CLASS in types:
- typ = "CLASS"
- elif OWL_OBJECT_PROPERTY in types:
- typ = "PROPERTY"
- else:
- typ = None
- meta = obograph.Meta()
- if include_metadata:
- for s in t.simple_values(TAG_SUBSET):
- meta.subsets.append(s)
- defn = self.definition(curie)
- if defn:
- meta.definition = obograph.DefinitionPropertyValue(val=defn)
- for _, syn in self.synonym_property_values([curie]):
- meta.synonyms.append(syn)
- for _, subset in self.terms_subsets([curie]):
- meta.subsets.append(subset)
- return obograph.Node(id=curie, lbl=self.label(curie), type=typ, meta=meta)
-
- def as_obograph(self, expand_curies=False) -> Graph:
- def expand(curie: CURIE) -> CURIE:
- if expand_curies:
- uri = self.curie_to_uri(curie, strict=False)
- return uri if uri is not None else curie
- else:
- return curie
-
- entities = list(self.entities())
- nodes = [self.node(expand(curie)) for curie in entities]
- edges = [
- Edge(sub=expand(r[0]), pred=expand(r[1]), obj=expand(r[2]))
- for r in self.relationships()
- ]
- ldefs = list(self.logical_definitions(entities))
- return Graph(id="TODO", nodes=nodes, edges=edges, logicalDefinitionAxioms=ldefs)
-
- def logical_definitions(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- **kwargs,
- ) -> Iterable[LogicalDefinitionAxiom]:
- if subjects is None:
- subjects = self.entities()
- for s in subjects:
- t = self._stanza(s, strict=False)
- if not t:
- continue
- ldef_tuples = t.intersection_of_tuples()
- if ldef_tuples:
- ldef = LogicalDefinitionAxiom(definedClassId=s)
- for m1, m2 in ldef_tuples:
- if m2:
- ldef.restrictions.append(
- ExistentialRestrictionExpression(
- propertyId=self.map_shorthand_to_curie(m1), fillerId=m2
- )
- )
- else:
- ldef.genusIds.append(m1)
- if logical_definition_matches(ldef, predicates=predicates, objects=objects):
- yield ldef
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SearchInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: DifferInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def diff(
- self,
- other_ontology: DifferInterface,
- configuration: DiffConfiguration = None,
- **kwargs,
- ) -> Iterator[kgcl.Change]:
- if configuration is None:
- configuration = DiffConfiguration()
- if not isinstance(other_ontology, SimpleOboImplementation):
- raise ValueError("Can only diff SimpleOboImplementation")
- stanzas1 = self.obo_document.stanzas
- stanzas2 = other_ontology.obo_document.stanzas
- all_ids = set(stanzas1.keys()).union(stanzas2.keys())
- for id in all_ids:
- yield from self._diff_stanzas(stanzas1.get(id, None), stanzas2.get(id, None))
-
- def _diff_stanzas(
- self, stanza1: Optional[Stanza], stanza2: Optional[Stanza]
- ) -> Iterator[kgcl.Change]:
- def _id():
- return generate_change_id()
-
- node_is_deleted = False
- if stanza1 is None and stanza2 is None:
- raise ValueError("Both stanzas are None")
- if stanza1 is None:
- stanza1 = Stanza(id=stanza2.id, type=stanza2.type)
- if stanza2.type == "Term":
- yield kgcl.ClassCreation(id=_id(), about_node=stanza2.id)
- elif stanza2.type == "Typedef":
- yield kgcl.NodeCreation(id=_id(), about_node=stanza2.id)
- else:
- raise ValueError(f"Unknown stanza type: {stanza2.type}")
- if stanza2 is None:
- stanza2 = Stanza(id=stanza1.id, type=stanza1.type)
- if stanza1.type == "Term":
- yield kgcl.NodeDeletion(id=_id(), about_node=stanza1.id)
- else:
- yield kgcl.NodeDeletion(id=_id(), about_node=stanza1.id)
- node_is_deleted = True
- if stanza1 == stanza2:
- return
- if stanza1.type != stanza2.type:
- raise ValueError(f"Stanza types differ: {stanza1.type} vs {stanza2.type}")
- t1id = stanza1.id
- t2id = stanza2.id
- logging.info(f"Diffing: {t1id} vs {t2id}")
-
- def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
- d = defaultdict(set)
- for tv in stanza.tag_values:
- d[tv.tag].add(tv.value)
- return d
-
- tv_dict1 = _tv_dict(stanza1)
- tv_dict2 = _tv_dict(stanza2)
- all_tags = set(tv_dict1.keys()).union(tv_dict2.keys())
- for tag in all_tags:
- vals1 = tv_dict1.get(tag, [])
- vals2 = tv_dict2.get(tag, [])
- vals1list = list(vals1)
- vals2list = list(vals2)
- tvs1 = [tv for tv in stanza1.tag_values if tv.tag == tag]
- tvs2 = [tv for tv in stanza2.tag_values if tv.tag == tag]
- if vals1 == vals2:
- continue
- logging.info(f"Difference in {tag}: {vals1} vs {vals2}")
- if tag == TAG_NAME:
- if node_is_deleted:
- continue
- if vals1 and vals2:
- yield kgcl.NodeRename(
- id=_id(), about_node=t1id, new_value=vals2list[0], old_value=vals1list[0]
- )
- elif vals1:
- yield kgcl.NodeDeletion(id=_id(), about_node=t1id)
- else:
- yield kgcl.ClassCreation(id=_id(), about_node=t2id, name=vals2list[0])
- elif tag == TAG_DEFINITION:
- if node_is_deleted:
- continue
- # TODO: provenance changes
- td1 = stanza1.quoted_value(TAG_DEFINITION)
- td2 = stanza2.quoted_value(TAG_DEFINITION)
- if vals1 and vals2:
- yield kgcl.NodeTextDefinitionChange(
- id=_id(), about_node=t1id, new_value=td2, old_value=td1
- )
- elif vals1:
- yield kgcl.RemoveTextDefinition(id=_id(), about_node=t1id, old_value=td1)
- else:
- yield kgcl.NewTextDefinition(id=_id(), about_node=t2id, new_value=td2)
- elif tag == TAG_IS_OBSOLETE:
- if node_is_deleted:
- continue
- if vals1 and not vals2:
- yield kgcl.NodeUnobsoletion(id=_id(), about_node=t1id)
- elif not vals1 and vals2:
- replaced_by = stanza2.simple_values(TAG_REPLACED_BY)
- if replaced_by:
- yield kgcl.NodeObsoletionWithDirectReplacement(
- id=_id(), about_node=t2id, has_direct_replacement=replaced_by[0]
- )
- else:
- yield kgcl.NodeObsoletion(id=_id(), about_node=t2id)
- elif tag == TAG_SUBSET:
- if node_is_deleted:
- continue
- subsets1 = stanza1.simple_values(TAG_SUBSET)
- subsets2 = stanza2.simple_values(TAG_SUBSET)
- for subset in subsets1:
- if subset not in subsets2:
- yield kgcl.RemoveNodeFromSubset(id=_id(), about_node=t1id, in_subset=subset)
- for subset in subsets2:
- if subset not in subsets1:
- yield kgcl.AddNodeToSubset(id=_id(), about_node=t2id, in_subset=subset)
- elif tag == TAG_IS_A:
- isas1 = stanza1.simple_values(TAG_IS_A)
- isas2 = stanza2.simple_values(TAG_IS_A)
- for isa in isas1:
- if isa not in isas2:
- yield kgcl.EdgeDeletion(id=_id(), subject=t1id, predicate=IS_A, object=isa)
- for isa in isas2:
- if isa not in isas1:
- yield kgcl.EdgeCreation(id=_id(), subject=t2id, predicate=IS_A, object=isa)
- elif tag == TAG_RELATIONSHIP:
- rels1 = stanza1.pair_values(TAG_RELATIONSHIP)
- rels2 = stanza2.pair_values(TAG_RELATIONSHIP)
- for p, v in rels1:
- p_curie = self.map_shorthand_to_curie(p)
- if (p, v) not in rels2:
- yield kgcl.EdgeDeletion(id=_id(), subject=t1id, predicate=p_curie, object=v)
- for p, v in rels2:
- p_curie = self.map_shorthand_to_curie(p)
- if (p, v) not in rels1:
- yield kgcl.EdgeCreation(id=_id(), subject=t2id, predicate=p_curie, object=v)
- elif tag == TAG_SYNONYM:
- if node_is_deleted:
- continue
- # TODO: make this sensitive to annotation changes; for now we truncate the tuple
- syns1 = [tv.as_synonym()[0:2] for tv in tvs1]
- syns2 = [tv.as_synonym()[0:2] for tv in tvs2]
- for syn in syns1:
- if syn not in syns2:
- yield kgcl.RemoveSynonym(id=_id(), about_node=t1id, old_value=syn[0])
- for syn in syns2:
- if syn not in syns1:
- pred = SCOPE_TO_SYNONYM_PRED_MAP[syn[1]]
- yield kgcl.NewSynonym(
- id=_id(), about_node=t2id, new_value=syn[0], predicate=pred
- )
-
- def different_from(self, entity: CURIE, other_ontology: DifferInterface) -> bool:
- t1 = self._stanza(entity, strict=False)
- if t1:
- t2 = other_ontology._stanza(entity, strict=False)
- if t2:
- return str(t1) != str(t2)
- return True
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: PatcherInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def migrate_curies(self, curie_map: Mapping[CURIE, CURIE]) -> None:
- od = self.obo_document
- for t in od.stanzas.values():
- t.replace_token(curie_map)
- od.reindex()
- self._rebuild_relationship_index()
-
- @property
- def uses_legacy_properties(self) -> bool:
- if self._uses_legacy_properties is not None:
- return self._uses_legacy_properties
- for s in self.obo_document.stanzas.values():
- for tv in s.tag_values:
- if tv.tag in [TAG_CREATED_BY, TAG_CREATION_DATE]:
- self._uses_legacy_properties = True
- return True
- return False
-
- def set_uses_legacy_properties(self, value: bool) -> None:
- self._uses_legacy_properties = value
-
- def add_contributors(self, curie: CURIE, agents: List[CURIE]) -> None:
- t = self._stanza(curie, strict=True)
- for agent in agents:
- t.add_tag_value_pair(TAG_PROPERTY_VALUE, CONTRIBUTOR, agent)
-
- def set_creator(self, curie: CURIE, agent: CURIE, date: Optional[str] = None) -> None:
- t = self._stanza(curie, strict=True)
- if self._uses_legacy_properties:
- t.set_singular_tag(TAG_CREATED_BY, agent)
- else:
- t.add_tag_value_pair(TAG_PROPERTY_VALUE, CREATOR, agent)
- if date:
- self.set_creation_date(curie, date)
-
- def set_creation_date(self, curie: CURIE, date: str) -> None:
- t = self._stanza(curie, strict=True)
- if self._uses_legacy_properties:
- t.set_singular_tag(TAG_CREATION_DATE, date)
- else:
- t.add_tag_value_pair(TAG_PROPERTY_VALUE, CREATED, date)
-
- def apply_patch(
- self,
- patch: kgcl.Change,
- activity: kgcl.Activity = None,
- metadata: Mapping[PRED_CURIE, Any] = None,
- configuration: kgcl.Configuration = None,
- ) -> kgcl.Change:
- od = self.obo_document
- tidy_change_object(patch)
- logging.debug(f"Applying {patch}")
- modified_entities = []
- if isinstance(patch, kgcl.NodeRename):
- # self.set_label(patch.about_node, _clean(patch.new_value))
- self.set_label(patch.about_node, patch.new_value)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.NodeObsoletion):
- t = self._stanza(patch.about_node, strict=True)
- t.set_singular_tag(TAG_IS_OBSOLETE, "true")
- if isinstance(patch, kgcl.NodeObsoletionWithDirectReplacement):
- t.set_singular_tag(TAG_REPLACED_BY, patch.has_direct_replacement)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.NodeDeletion):
- try:
- del od.stanzas[patch.about_node]
- except KeyError:
- logging.error(f"CURIE {patch.about_node} does not exist in the OBO file provided.")
- elif isinstance(patch, kgcl.NodeCreation):
- self.create_entity(patch.about_node, patch.name)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.ClassCreation):
- self.create_entity(patch.about_node, patch.name)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.SynonymReplacement):
- t = self._stanza(patch.about_node, strict=True)
- n = 0
- for tv in t.tag_values:
- if tv.tag == TAG_SYNONYM:
- syn = tv.as_synonym()
- if syn[0] == patch.old_value:
- tv.replace_quoted_part(patch.new_value)
- n += 1
- if not n:
- raise ValueError(f"Failed to find synonym {patch.old_value} for {t.id}")
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.AddNodeToSubset):
- t = self._stanza(patch.about_node, strict=True)
- t.add_tag_value(TAG_SUBSET, patch.in_subset)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.RemoveNodeFromSubset):
- t = self._stanza(patch.about_node, strict=True)
- t.remove_simple_tag_value(TAG_SUBSET, patch.in_subset)
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.NewTextDefinition):
- t = self._stanza(patch.about_node, strict=True)
- t.add_quoted_tag_value(TAG_DEFINITION, patch.new_value.strip("'"), xrefs=[])
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.RemoveTextDefinition):
- t = self._stanza(patch.about_node, strict=True)
- for tv in t.tag_values:
- if tv.tag == TAG_DEFINITION:
- # This is a remove_definition request
- t.remove_tag_quoted_value(TAG_DEFINITION, t._quoted_value(tv.value))
- elif isinstance(patch, kgcl.NodeTextDefinitionChange):
- t = self._stanza(patch.about_node, strict=True)
- for tv in t.tag_values:
- if tv.tag == TAG_DEFINITION:
- tv.replace_quoted_part(patch.new_value.strip("'"))
- elif isinstance(patch, kgcl.NewSynonym):
- t = self._stanza(patch.about_node, strict=True)
- # Get scope from patch.qualifier
- # rather than forcing all synonyms to be related.
- if isinstance(patch.qualifier, str):
- scope = patch.qualifier.upper()
- else:
- scope = str(patch.qualifier.value).upper() if patch.qualifier else "RELATED"
- v = patch.new_value.replace('"', '\\"')
- t.add_tag_value(TAG_SYNONYM, f'"{v}" {scope} []')
- modified_entities.append(patch.about_node)
- elif isinstance(patch, kgcl.RemoveSynonym):
- t = self._stanza(patch.about_node, strict=True)
- # scope = str(patch.qualifier.value).upper() if patch.qualifier else "RELATED"
- v = patch.old_value.strip(
- '"'
- ) # Handling a bug where quotes are accidentally introduced.
- t.remove_tag_quoted_value(TAG_SYNONYM, v)
- elif isinstance(patch, kgcl.EdgeCreation):
- description = patch.change_description
- self.add_relationship(
- patch.subject, patch.predicate, patch.object, description=description
- )
- modified_entities.append(patch.subject)
- elif isinstance(patch, kgcl.EdgeDeletion):
- self.remove_relationship(patch.subject, patch.predicate, patch.object)
- elif isinstance(patch, kgcl.NodeMove):
- logging.warning(f"Cannot handle {patch}")
- elif isinstance(patch, kgcl.PredicateChange):
- e = patch.about_edge
- subject = self._lookup(e.subject)
- object = self._lookup(e.object)
- t = self._stanza(subject, strict=True)
- if _is_isa(patch.old_value):
- t.remove_simple_tag_value(TAG_IS_A, object)
- else:
- pred = self.map_curie_to_shorthand(patch.old_value)
- t.remove_pairwise_tag_value(TAG_RELATIONSHIP, pred, object)
- if _is_isa(patch.new_value):
- t.add_tag_value(TAG_IS_A, object)
- else:
- t.add_tag_value(TAG_RELATIONSHIP, f"{patch.new_value} {object}")
- self._clear_relationship_index()
- modified_entities.append(subject)
- else:
- raise NotImplementedError(f"cannot handle KGCL type {type(patch)}")
- if patch.contributor:
- self.add_contributors(patch.about_node, [patch.contributor])
- modified_entities.append(patch.about_node)
- for e in modified_entities:
- stanza = self._stanza(e, strict=True)
- stanza.normalize_order()
- return patch
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OwlInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def transitive_object_properties(self) -> Iterable[CURIE]:
- od = self.obo_document
- for s_id, s in od.stanzas.items():
- if s.type == "Typedef":
- if s.get_boolean_value(TAG_IS_TRANSITIVE, False):
- yield self.map_shorthand_to_curie(s_id)
-
- def simple_subproperty_of_chains(self) -> Iterable[Tuple[CURIE, List[CURIE]]]:
- od = self.obo_document
- for s_id, s in od.stanzas.items():
- if s.type == "Typedef":
- for p1, p2 in s.pair_values(TAG_HOLDS_OVER_CHAIN):
- curie = self.map_shorthand_to_curie(s_id)
- yield curie, [self.map_shorthand_to_curie(p1), self.map_shorthand_to_curie(p2)]
-
-
Source code for oaklib.implementations.sparql.sparql_implementation
-from dataclasses import dataclass
-from typing import List, Optional
-
-import rdflib
-
-from oaklib import BasicOntologyInterface
-from oaklib.implementations.sparql.abstract_sparql_implementation import (
- AbstractSparqlImplementation,
-)
-from oaklib.interfaces import TextAnnotatorInterface
-from oaklib.interfaces.association_provider_interface import (
- AssociationProviderInterface,
-)
-from oaklib.interfaces.differ_interface import DifferInterface
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.merge_interface import MergeConfiguration, MergeInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.interfaces.rdf_interface import RdfInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
-from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
-
-
-
-[docs]
-@dataclass
-class SparqlImplementation(
- AbstractSparqlImplementation,
- AssociationProviderInterface,
- RdfInterface,
- DifferInterface,
- SearchInterface,
- MappingProviderInterface,
- OboGraphInterface,
- PatcherInterface,
- SemanticSimilarityInterface,
- TextAnnotatorInterface,
- TaxonConstraintInterface,
- MergeInterface,
-):
- """
- Wraps any local or remote sparql endpoint
- """
-
- def __post_init__(self):
- if self.graph is None:
- resource = self.resource
- # print(resource)
- if resource.url:
- super(SparqlImplementation, self).__post_init__()
- else:
- graph = rdflib.Graph()
- if resource is not None:
- graph.parse(str(resource.local_path), format=resource.format)
- self.graph = graph
-
- def merge(
- self,
- sources: List[BasicOntologyInterface],
- configuration: Optional[MergeConfiguration] = None,
- **kwargs,
- ):
- """
- Merges from multiple sources into current adapter.
-
- :param sources:
- :param configuration:
- :param kwargs:
- :return:
- """
- if not configuration:
- configuration = MergeConfiguration()
- if not self.graph:
- raise NotImplementedError("Cannot merge into a read-only graph")
- for source in sources:
- if not isinstance(source, RdfInterface):
- raise NotImplementedError("Cannot merge from non-sparql source")
- for t in source.all_rdflib_triples():
- self.graph.add(t)
-
-
Source code for oaklib.implementations.sqldb.sql_implementation
-import logging
-import math
-import re
-import shutil
-import typing
-from collections import defaultdict
-from dataclasses import dataclass, field
-from operator import or_
-from pathlib import Path
-from typing import (
- Any,
- Dict,
- Iterable,
- Iterator,
- List,
- Optional,
- Set,
- Tuple,
- Type,
- Union,
-)
-
-import rdflib
-import semsql.builder.builder as semsql_builder
-import sqlalchemy.orm
-from kgcl_schema.datamodel import kgcl
-from linkml_runtime import SchemaView
-from linkml_runtime.dumpers import json_dumper
-from linkml_runtime.utils.introspection import package_schemaview
-from linkml_runtime.utils.metamodelcore import URIorCURIE
-from semsql.sqla.semsql import ( # HasMappingStatement,
- AnnotationPropertyNode,
- Base,
- ClassNode,
- DeprecatedNode,
- Edge,
- EntailedEdge,
- HasSynonymStatement,
- HasTextDefinitionStatement,
- IriNode,
- NamedIndividualNode,
- Node,
- NodeIdentifier,
- ObjectPropertyNode,
- OntologyNode,
- OwlAxiomAnnotation,
- OwlDisjointClassStatement,
- OwlEquivalentClassStatement,
- OwlSomeValuesFrom,
- Prefix,
- RdfFirstStatement,
- RdfRestStatement,
- RdfsLabelStatement,
- RdfsSubclassOfStatement,
- RdfTypeStatement,
- Statements,
- TermAssociation,
- TransitivePropertyNode,
-)
-from sqlalchemy import and_, create_engine, delete, distinct, func, insert, text, update
-from sqlalchemy.orm import aliased, sessionmaker
-from sssom_schema import Mapping
-
-import oaklib.datamodels.ontology_metadata as om
-import oaklib.datamodels.validation_datamodel as vdm
-from oaklib.constants import OAKLIB_MODULE
-from oaklib.datamodels import obograph, ontology_metadata
-from oaklib.datamodels.association import Association
-from oaklib.datamodels.obograph import (
- DisjointClassExpressionsAxiom,
- ExistentialRestrictionExpression,
- LogicalDefinitionAxiom,
-)
-from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
-from oaklib.datamodels.similarity import TermPairwiseSimilarity
-from oaklib.datamodels.summary_statistics_datamodel import (
- ContributorStatistics,
- FacetedCount,
- GroupedStatistics,
- UngroupedStatistics,
-)
-from oaklib.datamodels.vocabulary import (
- ALL_CONTRIBUTOR_PREDICATES,
- ALL_MATCH_PREDICATES,
- DEPRECATED_PREDICATE,
- DISJOINT_WITH,
- ENTITY_LEVEL_DEFINITION_PREDICATES,
- EQUIVALENT_CLASS,
- HAS_DBXREF,
- HAS_DEFINITION_CURIE,
- HAS_EXACT_SYNONYM,
- HAS_OBSOLESCENCE_REASON,
- HAS_SYNONYM_TYPE,
- IN_CATEGORY_PREDS,
- IN_SUBSET,
- INVERSE_OF,
- IS_A,
- LABEL_PREDICATE,
- OBSOLETION_RELATIONSHIP_PREDICATES,
- OWL_CLASS,
- OWL_META_CLASSES,
- OWL_NAMED_INDIVIDUAL,
- OWL_NOTHING,
- OWL_PROPERTY_CHAIN_AXIOM,
- OWL_THING,
- OWL_VERSION_IRI,
- PREFIX_PREDICATE,
- RDF_TYPE,
- RDFS_COMMENT,
- RDFS_DOMAIN,
- RDFS_LABEL,
- RDFS_RANGE,
- SEMAPV,
- STANDARD_ANNOTATION_PROPERTIES,
- SUBPROPERTY_OF,
- SYNONYM_PREDICATES,
- TERM_REPLACED_BY,
- TERMS_MERGED,
- omd_slots,
-)
-from oaklib.implementations.sqldb import SEARCH_CONFIG
-from oaklib.interfaces import SubsetterInterface, TextAnnotatorInterface
-from oaklib.interfaces.association_provider_interface import EntityNormalizer
-from oaklib.interfaces.basic_ontology_interface import (
- ALIAS_MAP,
- DEFINITION,
- LANGUAGE_TAG,
- METADATA_MAP,
- METADATA_STATEMENT,
- PRED_CURIE,
- PREFIX_MAP,
- RELATIONSHIP,
- BasicOntologyInterface,
-)
-from oaklib.interfaces.class_enrichment_calculation_interface import (
- ClassEnrichmentCalculationInterface,
-)
-from oaklib.interfaces.differ_interface import DifferInterface
-from oaklib.interfaces.dumper_interface import DumperInterface
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.merge_interface import MergeInterface
-from oaklib.interfaces.metadata_interface import MetadataInterface
-from oaklib.interfaces.obograph_interface import GraphTraversalMethod, OboGraphInterface
-from oaklib.interfaces.owl_interface import OwlInterface
-from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.interfaces.relation_graph_interface import RelationGraphInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
-from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
-from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
-from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.types import CATEGORY_CURIE, CURIE, SUBSET_CURIE
-from oaklib.utilities.axioms.logical_definition_utilities import (
- logical_definition_matches,
-)
-from oaklib.utilities.format_utilities import (
- OBOGRAPHS_SYNTAX_ALIAS_MAP,
- RDFLIB_SYNTAX_ALIAS_MAP,
-)
-from oaklib.utilities.graph.relationship_walker import walk_down, walk_up
-from oaklib.utilities.identifier_utils import (
- string_as_base64_curie,
- synonym_type_code_from_curie,
-)
-
-__all__ = [
- "get_range_xsd_type",
- "regex_to_sql_like",
- "SqlImplementation",
-]
-
-from oaklib.utilities.iterator_utils import chunk
-from oaklib.utilities.mapping.sssom_utils import inject_mapping_sources
-
-SUBJECT_REL_KEY = Tuple[CURIE, Optional[List[PRED_CURIE]], Tuple]
-
-
-class SqlSchemaError(Exception):
- """Raised when there are issues with the version of the SQL DDL uses"""
-
- pass
-
-
-class ViewNotFoundError(SqlSchemaError):
- """Raised when a SQL view is not found"""
-
- pass
-
-
-def _is_blank(curie: CURIE) -> bool:
- return curie and curie.startswith("_:")
-
-
-def _python_value(val: Any, datatype: CURIE = None) -> Any:
- if datatype == "xsd:integer":
- return int(val)
- elif datatype == "xsd:float":
- return float(val)
- elif datatype == "xsd:boolean":
- return bool(val)
- else:
- return val
-
-
-def get_range_xsd_type(sv: SchemaView, rng: str) -> Optional[URIorCURIE]:
- t = sv.get_type(rng)
- if t.uri:
- return t.uri
- elif t.typeof:
- return get_range_xsd_type(sv, t.typeof)
- else:
- raise ValueError(f"No xsd type for {rng}")
-
-
-def regex_to_sql_like(regex: str) -> str:
- """
- convert a regex to a LIKE
-
- * ``.*`` => ``%``
- * ``.`` => ``_``
- * ``^`` => ``%`` (at start of string)
- * ``$`` => ``%`` (at end of string)
-
- TODO: implement various different DBMS flavors
- https://stackoverflow.com/questions/20794860/regex-in-sql-to-detect-one-or-more-digit
-
- :param regex:
- :return:
- """
- for c in r"()[]{}|":
- if c in regex:
- raise NotImplementedError(
- f"Regex engine not implemented for SQL and cannot parse char {c} in {regex}"
- )
- like = regex.replace(".*", "%")
- like = like.replace(".", "_")
- if like.startswith("^"):
- like = like[1:]
- else:
- like = f"%{like}"
- if like.endswith("$"):
- like = like[0:-1]
- else:
- like = f"{like}%"
- logging.info(f"Translated {regex} => LIKE {like}")
- return like
-
-
-def _is_quoted_url(curie: CURIE):
- return curie.startswith("<")
-
-
-def _remove_uri_quotes(curie: CURIE):
- if _is_quoted_url(curie):
- return curie[1:-1]
- else:
- return curie
-
-
-
-[docs]
-@dataclass
-class SqlImplementation(
- RelationGraphInterface,
- OboGraphInterface,
- ValidatorInterface,
- SearchInterface,
- SubsetterInterface,
- MappingProviderInterface,
- PatcherInterface,
- SemanticSimilarityInterface,
- MetadataInterface,
- DifferInterface,
- # AssociationProviderInterface,
- ClassEnrichmentCalculationInterface,
- TaxonConstraintInterface,
- TextAnnotatorInterface,
- SummaryStatisticsInterface,
- OwlInterface,
- DumperInterface,
- MergeInterface,
-):
- """
- A :class:`OntologyInterface` implementation that wraps a SQL Relational Database.
-
- Currently this must be a SQLite database. PostgreSQL support is planned.
-
- To connect, either use SqlImplementation directly:
-
- >>> from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
- >>> from oaklib.resource import OntologyResource
- >>> adapter = SqlImplementation(OntologyResource("tests/input/go-nucleus.db"))
-
- or
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("sqlite:tests/input/go-nucleus.db")
-
- you can also load from the semantic-sql repository:
-
- >>> adapter = get_adapter("sqlite:obo:obi")
-
- The schema is assumed to follow the `semantic-sql <https://github.com/incatools/semantic-sql>`_ schema.
-
- This uses SQLAlchemy ORM Models:
-
- - :class:`Statements`
- - :class:`Edge`
-
- See Also
- --------
- - `Tutorial <https://incatools.github.io/ontology-access-kit/intro/tutorial07.html>`_
- - `SQL Implementation <https://incatools.github.io/ontology-access-kit/implementations/sqldb.html>`_
-
- """
-
- # TODO: use SQLA types
- engine: Any = None
- _session: Any = None
- _connection: Any = None
- _ontology_metadata_model: SchemaView = None
- _prefix_map: PREFIX_MAP = None
- _information_content_cache: Dict[Tuple, float] = None
- _relationships_by_subject_index: Dict[CURIE, List[RELATIONSHIP]] = None
-
- max_items_for_in_clause: int = field(default_factory=lambda: 1000)
-
- can_store_associations: bool = False
- """True if the underlying sqlite database has term_association populated."""
-
- def __post_init__(self):
- if self.engine is None:
- locator = str(self.resource.slug)
- logging.info(f"Locator: {locator}")
- if locator.startswith("obo:"):
- # easter egg feature, to be documented:
- # The selector 'sqlite:obo:ONTOLOGY' will use a pre-generated
- # sqlite db of an OBO ontology after downloading from S3.
- # Note: this can take some time
- prefix = locator[len("obo:") :]
- # Option 1 uses direct URL construction:
- url = f"https://s3.amazonaws.com/bbop-sqlite/{prefix}.db.gz"
- logging.info(f"Ensuring gunzipped for {url}")
- db_path = OAKLIB_MODULE.ensure_gunzip(url=url, autoclean=False)
- # Option 2 uses botocore to interface with the S3 API directly:
- # db_path = OAKLIB_MODULE.ensure_from_s3(s3_bucket="bbop-sqlite", s3_key=f"{prefix}.db")
- locator = f"sqlite:///{db_path}"
- if locator.endswith(".owl"):
- # this is currently an "Easter Egg" feature. It allows you to specify a locator
- # such as sqlite:/path/to/my.owl
- # then semsql will be invoked to build a sqlite db from this.
- # the same sqlite db will be reused until the timestamp of the owl file changes.
- # the catch is that EITHER the user must have BOTH rdftab and relation-graph installed, OR
- # they should be running through ODK docker
- locator = locator.replace(".owl", ".db").replace("sqlite:", "")
- logging.info(f"Building {locator} using semsql")
- semsql_builder.make(locator)
- locator = f"sqlite:///{locator}"
- else:
- path = Path(locator.replace("sqlite:///", "")).absolute()
- if not path.exists():
- raise FileNotFoundError(f"File does not exist: {path}")
- locator = f"sqlite:///{path}"
- logging.info(f"Locator, post-processed: {locator}")
- self.engine = create_engine(locator)
-
- @property
- def session(self):
- if self._session is None:
- session_cls = sessionmaker(self.engine)
- self._session = session_cls()
- return self._session
-
- @property
- def connection(self):
- if self._connection is None:
- self._connection = self.engine.connect()
- return self._connection
-
- @property
- def ontology_metadata_model(self):
- if self._ontology_metadata_model is None:
- self._ontology_metadata_model = package_schemaview(ontology_metadata.__name__)
- return self._ontology_metadata_model
-
- def is_mysql(self):
- # TODO
- return False
-
- def is_postgres(self):
- # TODO
- return False
-
- def _check_has_view(
- self, sqla_class: Type[Base], minimum_version=None, fail_if_absent=True
- ) -> bool:
- engine = self.session.get_bind()
- tn = sqla_class.__tablename__
- cn = sqla_class.__name__
- has_view = sqlalchemy.inspect(engine).has_table(tn)
- if fail_if_absent and not has_view:
- raise ViewNotFoundError(
- f"View {tn} does not exist (required semsql v{minimum_version})"
- f"""
- Potential remedies:
- (1) obtain a new ready-made copy of the database, OR
- (2) rebuild the database from source OWL, OR
- (3) add the missing table to the database using CREATE VIEW {tn} AS ...
- Using the definition in https://incatools.github.io/semantic-sql/{cn}"""
- )
- return has_view
-
- def prefix_map(self) -> PREFIX_MAP:
- if self._prefix_map is None:
- self._prefix_map = {row.prefix: row.base for row in self.session.query(Prefix)}
- return self._prefix_map
-
- def languages(self) -> Iterable[LANGUAGE_TAG]:
- for row in self.session.query(Statements.language).distinct():
- if row.language:
- yield row.language
-
- def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
- # TODO: figure out how to pass through ESCAPE at SQL Alchemy level
- # s = text('SELECT id FROM class_node WHERE id NOT LIKE "\_:%" ESCAPE "\\"') # noqa W605
- q = self.session.query(Node)
- if owl_type:
- subquery = self.session.query(RdfTypeStatement.subject).filter(
- RdfTypeStatement.object == owl_type
- )
- q = q.filter(Node.id.in_(subquery))
- if filter_obsoletes:
- obs_subq = self.session.query(DeprecatedNode.id)
- q = q.filter(Node.id.not_in(obs_subq))
- logging.info(f"Query: {q}")
- for row in q:
- if row:
- if not _is_blank(row.id) and not row.id.startswith("<urn:swrl"):
- yield row.id
-
- def owl_types(self, entities: Iterable[CURIE]) -> Iterable[Tuple[CURIE, CURIE]]:
- q = self.session.query(RdfTypeStatement).filter(RdfTypeStatement.subject.in_(entities))
- for row in q:
- yield row.subject, row.object
-
- def obsoletes(self, include_merged=True) -> Iterable[CURIE]:
- q = self.session.query(DeprecatedNode)
- if not include_merged:
- subq = (
- self.session.query(Statements.subject)
- .filter(Statements.predicate == HAS_OBSOLESCENCE_REASON)
- .filter(Statements.object == TERMS_MERGED)
- )
- q = q.filter(DeprecatedNode.id.not_in(subq))
- for row in q:
- yield row.id
-
- def obsoletes_migration_relationships(
- self, entities: Iterable[CURIE]
- ) -> Iterable[RELATIONSHIP]:
- q = (
- self.session.query(Statements)
- .filter(Statements.subject.in_(entities))
- .filter(Statements.predicate.in_(OBSOLETION_RELATIONSHIP_PREDICATES))
- )
- for row in q:
- yield row.subject, row.predicate, row.object if row.object else row.value
-
- def all_relationships(self) -> Iterable[RELATIONSHIP]:
- for row in self.session.query(Edge):
- yield row.subject, row.predicate, row.object
-
- def _add_language_filter(self, q, lang, typ: Type[Statements] = Statements):
- if lang:
- if not self.multilingual:
- logging.warning(
- f"Source does not appear to be multilingual, filtering by @{lang} may not work"
- )
- if lang == self.default_language:
- q = q.filter(typ.language.is_(None))
- else:
- q = q.filter(typ.language == lang)
- return q
-
- def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- q = self.session.query(RdfsLabelStatement.value).filter(RdfsLabelStatement.subject == curie)
- q = self._add_language_filter(q, lang, RdfsLabelStatement)
- for (lbl,) in q:
- return lbl
- if lang and lang != self.default_language:
- return self.label(curie, lang=self.default_language)
-
- def labels(
- self, curies: Iterable[CURIE], allow_none=True, lang: LANGUAGE_TAG = None
- ) -> Iterable[Tuple[CURIE, str]]:
- for curie_it in chunk(curies, self.max_items_for_in_clause):
- curr_curies = list(curie_it)
-
- has_label = set()
- q = self.session.query(RdfsLabelStatement).filter(
- RdfsLabelStatement.subject.in_(tuple(curr_curies))
- )
- q = self._add_language_filter(q, lang, RdfsLabelStatement)
- for row in q:
- yield row.subject, row.value
- has_label.add(row.subject)
- if lang and lang != self.default_language:
- # fill missing
- curies_with_no_labels = set(curr_curies) - has_label
- yield from self.labels(curies_with_no_labels, allow_none=allow_none, lang=None)
- allow_none = False
- if allow_none:
- for curie in curr_curies:
- if curie not in has_label:
- yield curie, None
-
- def multilingual_labels(
- self, curies: Iterable[CURIE], allow_none=True, langs: Optional[List[LANGUAGE_TAG]] = None
- ) -> Iterable[Tuple[CURIE, str, LANGUAGE_TAG]]:
- if isinstance(curies, str):
- logging.warning(f"multilingual_labels called with a single curie: {curies}")
- curies = [curies]
- for curie_it in chunk(curies, self.max_items_for_in_clause):
- curr_curies = list(curie_it)
-
- has_label = defaultdict(set)
- q = self.session.query(RdfsLabelStatement).filter(
- RdfsLabelStatement.subject.in_(tuple(curr_curies))
- )
- if langs is not None:
- if self.default_language in langs:
- q = q.filter(
- or_(
- RdfsLabelStatement.language.is_(None),
- RdfsLabelStatement.language.in_(langs),
- )
- )
- else:
- q = q.filter(RdfsLabelStatement.language.in_(langs))
- for row in q:
- yield row.subject, row.value, row.language
- if allow_none:
- has_label[row.subject].add(row.language)
- if allow_none:
- for curie in curr_curies:
- if curie not in has_label:
- yield curie, None, None
-
- def curies_by_label(self, label: str) -> List[CURIE]:
- q = self.session.query(RdfsLabelStatement.subject)
- q = q.filter(RdfsLabelStatement.value == label)
- return list(set([row.subject for row in q]))
-
- def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
- m = defaultdict(list)
- m[LABEL_PREDICATE] = [self.label(curie)]
- for row in self.session.query(HasSynonymStatement).filter(
- HasSynonymStatement.subject == curie
- ):
- m[row.predicate].append(row.value)
- return m
-
- def comments(
- self, curies: Iterable[CURIE], allow_none=True, lang: LANGUAGE_TAG = None
- ) -> Iterable[Tuple[CURIE, str]]:
- for curie_it in chunk(curies, self.max_items_for_in_clause):
- curr_curies = list(curie_it)
-
- has_comment = set()
- q = self.session.query(Statements).filter(Statements.subject.in_(tuple(curr_curies)))
- q = q.filter(Statements.predicate == RDFS_COMMENT)
- q = self._add_language_filter(q, lang, Statements)
- for row in q:
- yield row.subject, row.value
- has_comment.add(row.subject)
- if lang and lang != self.default_language:
- # fill missing
- curies_with_no_labels = set(curr_curies) - has_comment
- yield from self.labels(curies_with_no_labels, allow_none=allow_none, lang=None)
- allow_none = False
- if allow_none:
- for curie in curr_curies:
- if curie not in has_comment:
- yield curie, None
-
- def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
- q = self.session.query(HasTextDefinitionStatement.value).filter(
- HasTextDefinitionStatement.subject == curie
- )
- q = self._add_language_filter(q, lang, HasTextDefinitionStatement)
- for (lbl,) in q:
- return lbl
- if lang and lang != self.default_language:
- return self.definition(curie, lang=self.default_language)
-
- def definitions(
- self,
- curies: Iterable[CURIE],
- include_metadata=False,
- include_missing=False,
- lang: Optional[LANGUAGE_TAG] = None,
- ) -> Iterator[DEFINITION]:
- curies = list(curies)
- has_definition = set()
- metadata_map: Dict[Tuple[str, Optional[str]], METADATA_MAP] = defaultdict(dict)
- if include_metadata:
- # definition metadata may be axiom annotations
- for aa in self._axiom_annotations_multi(curies, predicate=HAS_DEFINITION_CURIE):
- k = (aa.subject, aa.value)
- metadata = metadata_map[k]
- if aa.annotation_predicate not in metadata:
- metadata[aa.annotation_predicate] = []
- metadata[aa.annotation_predicate].append(aa.annotation_value)
- # or direct annotations
- q = (
- self.session.query(Statements)
- .filter(Statements.predicate.in_(ENTITY_LEVEL_DEFINITION_PREDICATES))
- .filter(Statements.subject.in_(curies))
- )
- for row in q:
- # note that direct annotation is unable to distinguish between multiple definitions;
- # set to match all
- k = (row.subject, None)
- metadata = metadata_map[k]
- if row.predicate not in metadata:
- metadata[row.predicate] = []
- metadata[row.predicate].append(row.value if row.value else row.object)
- q = self.session.query(HasTextDefinitionStatement).filter(
- HasTextDefinitionStatement.subject.in_(curies)
- )
- q = self._add_language_filter(q, lang, HasTextDefinitionStatement)
- curr_curies = list(curies)
- for row in q:
- reification_metadata = metadata_map.get((row.subject, row.value), {})
- direct_metadata = metadata_map.get((row.subject, None), {})
- yield row.subject, row.value, {**reification_metadata, **direct_metadata}
- has_definition.add(row.subject)
- if lang and lang != self.default_language:
- # fill missing
- curies_with_no_defs = set(curr_curies) - has_definition
- yield from self.definitions(curies_with_no_defs, lang=None)
- if include_missing:
- for curie in curies:
- if curie not in has_definition:
- yield curie, None, None
-
- def _definitions_with_metadata(
- self, curies: Iterable[CURIE], include_missing=False
- ) -> Iterator[DEFINITION]:
- curies = list(curies)
- has_definition = set()
- q = self.session.query(HasTextDefinitionStatement)
- q.filter(HasTextDefinitionStatement.subject.in_(curies))
- q.join(HasTextDefinitionStatement.metadata)
- for row in self.session.query(HasTextDefinitionStatement).filter(
- HasTextDefinitionStatement.subject.in_(curies)
- ):
- yield row.subject, row.value, row.source, row.date
- if include_missing:
- has_definition.add(row.subject)
- if include_missing:
- for curie in curies:
- if curie not in has_definition:
- yield curie, None, None, None
-
- def entity_metadata_map(self, curie: CURIE, include_all_triples=False) -> METADATA_MAP:
- m = defaultdict(list)
- m["id"] = [curie]
- q = self.session.query(Statements)
- if not include_all_triples:
- subquery = self.session.query(RdfTypeStatement.subject).filter(
- RdfTypeStatement.object == "owl:AnnotationProperty"
- )
- annotation_properties = {row.subject for row in subquery}
- annotation_properties = annotation_properties.union(STANDARD_ANNOTATION_PROPERTIES)
- q = q.filter(Statements.predicate.in_(tuple(annotation_properties)))
- for row in q.filter(Statements.subject == curie):
- if row.value is not None:
- v = _python_value(row.value, row.datatype)
- elif row.object is not None:
- v = row.object
- else:
- v = None
- m[row.predicate].append(v)
- self.add_missing_property_values(curie, m)
- return dict(m)
-
- def entities_metadata_statements(
- self,
- curies: Iterable[CURIE],
- predicates: Optional[List[PRED_CURIE]] = None,
- include_nested_metadata=False,
- **kwargs,
- ) -> Iterator[METADATA_STATEMENT]:
- q = self.session.query(Statements)
- if not include_nested_metadata:
- subquery = self.session.query(RdfTypeStatement.subject).filter(
- RdfTypeStatement.object == "owl:AnnotationProperty"
- )
- annotation_properties = {row.subject for row in subquery}
- annotation_properties = annotation_properties.union(STANDARD_ANNOTATION_PROPERTIES)
- q = q.filter(Statements.predicate.in_(tuple(annotation_properties)))
- q = q.filter(Statements.subject.in_(curies))
- if predicates is not None:
- q = q.filter(Statements.predicate.in_(predicates))
- for row in q:
- if row.value is not None:
- v = _python_value(row.value, row.datatype)
- elif row.object is not None:
- v = row.object
- else:
- v = None
- yield row.subject, row.predicate, v, row.datatype, {}
-
- def ontologies(self) -> Iterable[CURIE]:
- for row in self.session.query(OntologyNode):
- yield row.id
-
- def ontology_versions(self, ontology: CURIE) -> Iterable[str]:
- q = self.session.query(RdfsLabelStatement).filter(RdfsLabelStatement.subject == ontology)
- q = q.filter(RdfsLabelStatement.predicate == OWL_VERSION_IRI)
- for row in q:
- yield row.object
-
- def ontology_metadata_map(self, ontology: CURIE) -> METADATA_MAP:
- return self.entity_metadata_map(ontology, include_all_triples=True)
-
- def _get_subset_curie(self, curie: str) -> str:
- if "#" in curie:
- return curie.split("#")[-1]
- else:
- return curie
-
- def _subset_uri_to_curie_map(self) -> Dict[str, CURIE]:
- m = {}
- for row in self.session.query(Statements.object).filter(Statements.predicate == IN_SUBSET):
- uri = row.object
- m[uri] = self._get_subset_curie(row.object)
- return m
-
- def _subset_curie_to_uri_map(self) -> Dict[CURIE, str]:
- m = {}
- for row in self.session.query(Statements.object, Statements.value).filter(
- Statements.predicate == IN_SUBSET
- ):
- uri = row.object
- if row.object is None:
- logging.warning(f"Subset may be incorrectly encoded as value for {row.value}")
- else:
- m[self._get_subset_curie(row.object)] = uri
- return m
-
- def subsets(self) -> Iterable[SUBSET_CURIE]:
- for s in self._subset_curie_to_uri_map().keys():
- yield s
-
- def subset_members(self, subset: SUBSET_CURIE) -> Iterable[CURIE]:
- sm = self._subset_curie_to_uri_map()
- if subset not in sm:
- raise ValueError(f"Subset {subset} not found in {sm}")
- for row in self.session.query(Statements.subject).filter(
- Statements.predicate == IN_SUBSET, Statements.object == sm[subset]
- ):
- yield self._get_subset_curie(row.subject)
-
- def terms_subsets(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, SUBSET_CURIE]]:
- for row in self.session.query(Statements).filter(
- Statements.predicate == IN_SUBSET, Statements.subject.in_(list(curies))
- ):
- yield row.subject, self._get_subset_curie(row.object)
-
- def terms_categories(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, CATEGORY_CURIE]]:
- for row in self.session.query(Statements).filter(
- Statements.predicate.in_(IN_CATEGORY_PREDS), Statements.subject.in_(list(curies))
- ):
- yield row.subject, self._get_subset_curie(row.object)
-
- def _execute(self, stmt):
- self.session.execute(stmt)
- self.session.flush()
- if self.autosave:
- self.save()
-
- def set_label(self, curie: CURIE, label: str) -> bool:
- stmt = (
- update(Statements)
- .where(and_(Statements.subject == curie, Statements.predicate == LABEL_PREDICATE))
- .values(value=label)
- )
- self._execute(stmt)
-
- def basic_search(self, search_term: str, config: SearchConfiguration = None) -> Iterable[CURIE]:
- if config is None:
- config = SEARCH_CONFIG
- if config.force_case_insensitive:
- # in sqlite, LIKEs are case insensitive
- if config.syntax:
- if config.syntax != SearchTermSyntax(SearchTermSyntax.SQL):
- raise ValueError(
- f"Cannot force case insensitive search with syntax {config.syntax}"
- )
- else:
- config.syntax = SearchTermSyntax(SearchTermSyntax.SQL)
- preds = []
- preds.append(omd_slots.label.curie)
- search_all = SearchProperty(SearchProperty.ANYTHING) in config.properties
- if search_all or SearchProperty(SearchProperty.ALIAS) in config.properties:
- preds += SYNONYM_PREDICATES
- if search_all or SearchProperty(SearchProperty.MAPPED_IDENTIFIER) in config.properties:
- preds += ALL_MATCH_PREDICATES
- view = Statements
-
- def make_query(qcol, preds, scol=view.subject):
- q = self.session.query(scol).filter(view.predicate.in_(tuple(preds)))
- if config.syntax == SearchTermSyntax(SearchTermSyntax.STARTS_WITH):
- q = q.filter(qcol.like(f"{search_term}%"))
- elif config.syntax == SearchTermSyntax(SearchTermSyntax.SQL):
- q = q.filter(qcol.like(search_term))
- elif config.syntax == SearchTermSyntax(SearchTermSyntax.REGULAR_EXPRESSION):
- if self.is_mysql():
- q = q.filter(qcol.op("regex")(search_term))
- elif self.is_postgres():
- q = q.filter(qcol.op("~")(search_term))
- else:
- q = q.filter(qcol.like(regex_to_sql_like(search_term)))
- elif config.is_partial:
- q = q.filter(qcol.like(f"%{search_term}%"))
- else:
- q = q.filter(qcol == search_term)
- return q
-
- q = make_query(view.value, preds)
- for row in q.distinct():
- if row.subject.startswith("_:"):
- continue
- yield str(row.subject)
- if search_all or SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
- q = make_query(view.subject, preds)
- for row in q.distinct():
- yield str(row.subject)
- if search_all or SearchProperty(SearchProperty.REPLACEMENT_IDENTIFIER) in config.properties:
- q = make_query(view.subject, [TERM_REPLACED_BY], view)
- for row in q.distinct():
- yield str(row.object) if row.object else str(row.value)
-
- def entailed_outgoing_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None
- ) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- return self.outgoing_relationships(curie, predicates, entailed=True)
-
- def _rebuild_relationship_index(self):
- self._relationships_by_subject_index = None
- self.precompute_lookups()
-
- def precompute_lookups(self) -> None:
- if self._relationships_by_subject_index is None:
- self._relationships_by_subject_index = {}
- logging.info("Precomputing lookups")
-
- def add(row):
- if not row.object:
- # https://github.com/INCATools/ontology-access-kit/issues/457
- logging.warning(f"Bad row: {row}")
- return
- s = row.subject
- if s not in self._relationships_by_subject_index:
- self._relationships_by_subject_index[s] = []
- self._relationships_by_subject_index[s].append((s, row.predicate, row.object))
-
- q = self.session.query(Edge.subject, Edge.predicate, Edge.object)
- for row in q:
- add(row)
- q = self.session.query(Statements.subject, Statements.predicate, Statements.object)
- q = q.filter(Statements.predicate.in_((RDF_TYPE, RDFS_DOMAIN, RDFS_RANGE, INVERSE_OF)))
- for row in q:
- add(row)
- q = self.session.query(Statements.subject, Statements.predicate, Statements.object)
- op_subq = self.session.query(ObjectPropertyNode.id)
- q = q.filter(Statements.predicate.in_(op_subq))
- for row in q:
- add(row)
-
- def relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_tbox: bool = True,
- include_abox: bool = True,
- include_entailed: bool = False,
- include_dangling: bool = True,
- exclude_blank: bool = True,
- bypass_index: bool = False,
- ) -> Iterator[RELATIONSHIP]:
- if subjects is not None:
- # materialize iterators
- subjects = list(subjects)
- if subjects and not objects and self._relationships_by_subject_index:
- # TODO: unify indexes with other implementations
- for s in subjects:
- for _, p, o in self._relationships_by_subject_index.get(s, []):
- if not o:
- raise ValueError(f"No object for {s} {p}")
- if predicates and p not in predicates:
- continue
- if not include_abox and p == RDF_TYPE:
- continue
- if self.exclude_owl_top_and_bottom and o == OWL_THING:
- continue
- if self.exclude_owl_top_and_bottom and s == OWL_NOTHING:
- continue
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- if p == RDF_TYPE and o in OWL_META_CLASSES:
- continue
- yield s, p, o
- return
- if subjects is not None and len(subjects) > self.max_items_for_in_clause:
- logging.info(
- f"Chunking {len(subjects)} subjects into subqueries to avoid large IN clauses"
- )
- for subjects_it in chunk(subjects, self.max_items_for_in_clause):
- for r in self.relationships(
- list(subjects_it),
- predicates,
- objects,
- include_tbox=include_tbox,
- include_abox=include_abox,
- include_entailed=include_entailed,
- include_dangling=include_dangling,
- exclude_blank=exclude_blank,
- ):
- yield r
- return
- if objects is not None and len(objects) > self.max_items_for_in_clause:
- logging.info(
- f"Chunking {len(objects)} objects into subqueries to avoid large IN clauses"
- )
- for objects_it in chunk(objects, self.max_items_for_in_clause):
- for r in self.relationships(
- subjects,
- predicates,
- list(objects_it),
- include_tbox=include_tbox,
- include_abox=include_abox,
- include_entailed=include_entailed,
- include_dangling=include_dangling,
- exclude_blank=exclude_blank,
- ):
- yield r
- return
- logging.debug(f"Relationships for s={subjects} p={predicates} o={objects}")
- if include_tbox:
- for s, p, o in self._tbox_relationships(
- subjects, predicates, objects, include_entailed=include_entailed
- ):
- if self.exclude_owl_top_and_bottom and o == OWL_THING:
- continue
- if self.exclude_owl_top_and_bottom and s == OWL_NOTHING:
- continue
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield s, p, o
- for s, p, o in self._equivalent_class_relationships(subjects, predicates, objects):
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield s, p, o
- if subjects or objects:
- for s, p, o in self._equivalent_class_relationships(objects, predicates, subjects):
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield o, p, s
- for s, p, o in self._rbox_relationships(subjects, predicates, objects):
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield s, p, o
- if include_abox:
- for s, p, o in self._rdf_type_relationships(subjects, predicates, objects):
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield s, p, o
- for s, p, o in self._object_property_assertion_relationships(
- subjects, predicates, objects
- ):
- if exclude_blank and (_is_blank(s) or _is_blank(o)):
- continue
- yield s, p, o
-
- def _tbox_relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_entailed: bool = False,
- include_dangling: bool = True,
- ) -> Iterator[RELATIONSHIP]:
- if include_entailed:
- tbl = EntailedEdge
- else:
- tbl = Edge
- q = self.session.query(tbl)
- if subjects:
- q = q.filter(tbl.subject.in_(tuple(subjects)))
- if predicates:
- q = q.filter(tbl.predicate.in_(tuple(predicates)))
- if objects:
- q = q.filter(tbl.object.in_(tuple(objects)))
- if not include_dangling:
- subq = self.session.query(Statements.subject)
- q = q.filter(tbl.object.in_(subq))
- logging.debug(f"Tbox query: {q}")
- for row in q:
- yield row.subject, row.predicate, row.object
-
- def _object_property_assertion_relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- ) -> Iterator[RELATIONSHIP]:
- q = self.session.query(Statements.subject, Statements.predicate, Statements.object)
- if subjects:
- q = q.filter(Statements.subject.in_(tuple(subjects)))
- if predicates:
- predicates = set(predicates).difference(
- {IS_A, RDF_TYPE, SUBPROPERTY_OF, RDFS_DOMAIN, RDFS_RANGE, INVERSE_OF}
- )
- if not predicates:
- return
- q = q.filter(Statements.predicate.in_(tuple(predicates)))
- else:
- op_subq = self.session.query(ObjectPropertyNode.id)
- q = q.filter(Statements.predicate.in_(op_subq))
- if objects:
- q = q.filter(Statements.object.in_(tuple(objects)))
- logging.debug(f"Abox query: {q}")
- for row in q:
- if not row.object:
- # edge case: see https://github.com/monarch-initiative/phenio/issues/36
- logging.warning(f"Invalid triple for S:{row.subject} P:{row.predicate}")
- continue
- yield row.subject, row.predicate, row.object
-
- def _rdf_type_relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_dangling: bool = True,
- ) -> Iterator[RELATIONSHIP]:
- if predicates and RDF_TYPE not in predicates:
- return
- q = self.session.query(Statements.subject, Statements.object).filter(
- Statements.predicate == RDF_TYPE
- )
- if subjects:
- q = q.filter(Statements.subject.in_(tuple(subjects)))
- if objects:
- q = q.filter(Statements.object.in_(tuple(objects)))
- cls_subq = self.session.query(ClassNode.id)
- q = q.filter(Statements.object.in_(cls_subq))
- logging.info(f"ClassAssertion query: {q}")
- for row in q:
- yield row.subject, RDF_TYPE, row.object
-
- def _equivalent_class_relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- ) -> Iterator[RELATIONSHIP]:
- if predicates and EQUIVALENT_CLASS not in predicates:
- return
- q = self.session.query(Statements.subject, Statements.predicate, Statements.object)
- q = q.filter(Statements.predicate == EQUIVALENT_CLASS)
- if subjects:
- q = q.filter(Statements.subject.in_(tuple(subjects)))
- if objects:
- q = q.filter(Statements.object.in_(tuple(objects)))
- cls_subq = self.session.query(ClassNode.id)
- q = q.filter(Statements.object.in_(cls_subq))
- logging.info(f"ECA query: {q}")
- for row in q:
- yield row.subject, row.predicate, row.object
-
- def _rbox_relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- ) -> Iterator[RELATIONSHIP]:
- rbox_predicates = {RDFS_DOMAIN, RDFS_RANGE, INVERSE_OF}
- if predicates:
- rbox_predicates = rbox_predicates.intersection(predicates)
- if not predicates:
- return
- q = self.session.query(Statements.subject, Statements.predicate, Statements.object)
- q = q.filter(Statements.predicate.in_(tuple(rbox_predicates)))
- if subjects:
- q = q.filter(Statements.subject.in_(tuple(subjects)))
- if objects:
- q = q.filter(Statements.object.in_(tuple(objects)))
- logging.debug(f"RBOX query: {q}")
- for row in q:
- yield row.subject, row.predicate, row.object
-
- def relationships_metadata(
- self, relationships: Iterable[RELATIONSHIP], **kwargs
- ) -> Iterator[Tuple[RELATIONSHIP, List[Tuple[PRED_CURIE, Any]]]]:
- for rel in relationships:
- anns = [(ann.predicate, ann.object) for ann in self._axiom_annotations(*rel)]
- yield rel, anns
-
- def node_exists(self, curie: CURIE) -> bool:
- return self.session.query(Statements).filter(Statements.subject == curie).count() > 0
-
- def check_node_exists(self, curie: CURIE) -> None:
- if not self.node_exists(curie):
- raise ValueError(f"Node {curie} does not exist")
-
- def simple_mappings_by_curie(
- self, curie: CURIE, bidirectional=False
- ) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- for mpg in self.sssom_mappings(curies=curie, bidirectional=bidirectional):
- yield mpg.predicate_id, mpg.object_id
-
- def query(
- self, query: str, syntax: str = None, prefixes: List[str] = None, **kwargs
- ) -> Iterator[Any]:
- q = text(query)
- resultset = self.connection.execute(q)
- m = resultset.mappings()
- for d in m:
- yield dict(d)
-
- def clone(self, resource: Any) -> None:
- if self.resource.scheme == "sqlite":
- if resource.scheme == "sqlite":
- shutil.copyfile(self.resource.slug, resource.slug)
- new_oi = type(self)(resource)
- return new_oi
- raise NotImplementedError("Can only clone sqlite to sqlite")
-
- def as_rdflib_graph(self) -> rdflib.Graph:
- g = rdflib.Graph()
- bnodes = {}
-
- uri_re = re.compile(r"^<(.*)>$")
-
- def tr(n: str, v: str = None, datatype: str = None):
- if n:
- uri_match = uri_re.match(n)
- if n.startswith("_"):
- if n not in bnodes:
- bnodes[n] = rdflib.BNode()
- return bnodes[n]
- elif uri_match:
- return rdflib.URIRef(uri_match.group(1))
- else:
- return rdflib.URIRef(self.curie_to_uri(n))
- else:
- lit = rdflib.Literal(v, datatype=datatype)
- return lit
-
- for row in self.session.query(Statements):
- s = tr(row.subject)
- p = tr(row.predicate)
- o = tr(row.object, row.value, row.datatype)
- logging.debug(f"Triple {s} {p} {o}")
- g.add((s, p, o))
- return g
-
- def dump(self, path: str = None, syntax: str = None, **kwargs):
- """
- Implements :ref:`dump`.
-
- Supported syntaxes:
-
- - ttl
- - json
-
- :param path:
- :param syntax:
- :param kwargs:
- :return:
- """
- if syntax is None:
- syntax = "ttl"
- if syntax in ["ttl", "rdfxml", "owl"]:
- if syntax in RDFLIB_SYNTAX_ALIAS_MAP:
- syntax = RDFLIB_SYNTAX_ALIAS_MAP[syntax]
- g = self.as_rdflib_graph()
- logging.info(f"Dumping to {path}")
- g.serialize(path, format=syntax)
- elif syntax in OBOGRAPHS_SYNTAX_ALIAS_MAP.keys():
- syntax = OBOGRAPHS_SYNTAX_ALIAS_MAP[syntax]
- g = self.as_obograph(expand_curies=True)
- gd = obograph.GraphDocument(graphs=[g])
- json_dumper.dump(gd, path)
- elif syntax == "sqlite":
- raise NotImplementedError
- else:
- super().dump(path, syntax)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: AssocationProviderInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def associations(self, *args, **kwargs) -> Iterator[Association]:
- if not self.can_store_associations:
- logging.info("Using base method")
- yield from super().associations(*args, **kwargs)
- return
- logging.info("Using SQL queries")
- q = self._associations_query(*args, **kwargs)
- for row_it in chunk(q):
- assocs = []
- for row in row_it:
- association = Association(
- row.subject, row.predicate, row.object, primary_knowledge_source=row.source
- )
- assocs.append(association)
- subjects = {a.subject for a in assocs}
- label_map = {s: name for s, name in self.labels(subjects)}
- for association in assocs:
- if association.subject in label_map:
- association.subject_label = label_map[association.subject]
- yield from assocs
-
- def _associations_query(
- self,
- subjects: Iterable[CURIE] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- property_filter: Dict[PRED_CURIE, Any] = None,
- subject_closure_predicates: Optional[List[PRED_CURIE]] = None,
- predicate_closure_predicates: Optional[List[PRED_CURIE]] = None,
- object_closure_predicates: Optional[List[PRED_CURIE]] = None,
- include_modified: bool = False,
- query: sqlalchemy.orm.Query = None,
- add_closure_fields: bool = False,
- **kwargs,
- ) -> Any:
- if query:
- q = query
- else:
- q = self.session.query(TermAssociation)
- if property_filter:
- raise NotImplementedError
- if subjects:
- if subject_closure_predicates:
- subquery = self.session.query(EntailedEdge.subject).filter(
- EntailedEdge.object.in_(objects)
- )
- subquery = subquery.filter(EntailedEdge.predicate.in_(subject_closure_predicates))
- logging.info(f"Object subquery: {q} // {object_closure_predicates}")
- q = q.filter(TermAssociation.subject.in_(subquery))
- else:
- q = q.filter(TermAssociation.subject.in_(tuple(subjects)))
- if predicates:
- if predicate_closure_predicates:
- raise NotImplementedError
- else:
- q = q.filter(TermAssociation.predicate.in_(tuple(predicates)))
- if objects:
- if object_closure_predicates:
- subquery = self.session.query(EntailedEdge.subject).filter(
- EntailedEdge.object.in_(objects)
- )
- subquery = subquery.filter(EntailedEdge.predicate.in_(object_closure_predicates))
- logging.info(f"Object subquery: {q} // {object_closure_predicates}")
- q = q.filter(TermAssociation.object.in_(subquery))
- else:
- q = q.filter(TermAssociation.object.in_(tuple(objects)))
- logging.info(f"_associations_query: {q}")
- return q
-
- def add_associations(
- self,
- associations: Iterable[Association],
- normalizers: List[EntityNormalizer] = None,
- **kwargs,
- ) -> bool:
- if not self.can_store_associations:
- logging.info("Using base method to store associations")
- return super().add_associations(associations, normalizers=normalizers)
- for a in associations:
- if normalizers:
- a = a.normalize(normalizers)
- if a.property_values:
- raise NotImplementedError
- stmt = insert(TermAssociation).values(
- subject=a.subject,
- predicate=a.predicate,
- object=a.object,
- source=a.primary_knowledge_source,
- )
- self._execute(stmt)
- if a.subject_label:
- stmt = insert(Statements).values(
- subject=a.subject,
- predicate=RDFS_LABEL,
- value=a.subject_label,
- )
- self._execute(stmt)
- self.session.flush()
- return True
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def node(
- self, curie: CURIE, strict=False, include_metadata=False, expand_curies=False
- ) -> obograph.Node:
- logging.debug(f"Node lookup: {curie}")
- meta = obograph.Meta()
- uri = self.curie_to_uri(curie) if expand_curies else curie
- n = obograph.Node(id=uri, meta=meta)
- q = self.session.query(Statements).filter(Statements.subject == curie)
- builtin_preds = [IS_A, DISJOINT_WITH]
- q = q.filter(Statements.predicate.not_in(builtin_preds))
- rows = list(q)
-
- def _anns_to_xrefs_and_meta(parent_pv: obograph.PropertyValue, anns: List[om.Annotation]):
- parent_pv.xrefs = [ann.object for ann in anns if ann.predicate == HAS_DBXREF]
- if isinstance(parent_pv, obograph.SynonymPropertyValue):
- synonym_types = [ann.object for ann in anns if ann.predicate == HAS_SYNONYM_TYPE]
- if len(synonym_types) > 0:
- parent_pv.synonymType = synonym_type_code_from_curie(synonym_types[0])
- if len(synonym_types) > 1:
- logging.warning(
- f"Ignoring multiple synonym types: {synonym_types} for {curie}"
- )
- pvs = [
- obograph.BasicPropertyValue(pred=ann.predicate, val=ann.object)
- for ann in anns
- if ann.predicate != HAS_DBXREF
- ]
- if pvs:
- parent_pv.meta = obograph.Meta(basicPropertyValues=pvs)
-
- for row in rows:
- if row.value is not None:
- v = row.value
- elif row.object is not None:
- v = row.object
- else:
- continue
- pred = row.predicate
- if pred == omd_slots.label.curie:
- n.lbl = v
- elif pred == RDF_TYPE:
- if v == OWL_CLASS:
- n.type = "CLASS"
- elif v in [OWL_NAMED_INDIVIDUAL]:
- n.type = "INDIVIDUAL"
- else:
- n.type = "PROPERTY"
- else:
- if include_metadata:
- anns = self._axiom_annotations(curie, pred, row.object, row.value)
- else:
- anns = []
- if pred == omd_slots.definition.curie:
- meta.definition = obograph.DefinitionPropertyValue(val=v)
- _anns_to_xrefs_and_meta(meta.definition, anns)
- elif pred in SYNONYM_PREDICATES:
- # TODO: handle in a separate util
- if pred.startswith("oio:"):
- pred = pred.replace("IAO:", "IAO_")
- scope_pred = pred.replace("oio:", "")
- else:
- scope_pred = "hasExactSynonym"
- pv = obograph.SynonymPropertyValue(pred=scope_pred, val=v)
- _anns_to_xrefs_and_meta(pv, anns)
- meta.synonyms.append(pv)
- elif pred == HAS_DBXREF:
- pv = obograph.XrefPropertyValue(val=v)
- _anns_to_xrefs_and_meta(pv, anns)
- meta.xrefs.append(pv)
- elif pred == IN_SUBSET:
- meta.subsets.append(v)
- else:
- pv = obograph.BasicPropertyValue(pred=pred, val=v)
- _anns_to_xrefs_and_meta(pv, anns)
- meta.basicPropertyValues.append(pv)
- return n
-
- def nodes(self, expand_curies=False) -> Iterator[Node]:
- """
- Yields all nodes in all graphs
-
- :param expand_curies:
- :return:
- """
- for e in self.entities():
- if not e.startswith("<"):
- n = self.node(e, include_metadata=True, expand_curies=expand_curies)
- if n.lbl:
- yield n
-
- def synonym_property_values(
- self, subject: Union[CURIE, Iterable[CURIE]]
- ) -> Iterator[Tuple[CURIE, obograph.SynonymPropertyValue]]:
- if isinstance(subject, CURIE):
- subject = [subject]
- q = self.session.query(Statements).filter(Statements.subject.in_(tuple(subject)))
- q = q.filter(Statements.predicate.in_(SYNONYM_PREDICATES))
- for row in q:
- pred = row.predicate.replace("oio:", "")
- spv = obograph.SynonymPropertyValue(pred=pred, val=row.value)
- anns = self._axiom_annotations(row.subject, row.predicate, value=row.value)
- for ann in anns:
- if ann.predicate == HAS_SYNONYM_TYPE:
- spv.synonymType = synonym_type_code_from_curie(ann.object)
- if ann.predicate == HAS_DBXREF:
- spv.xrefs.append(ann.object)
- yield row.subject, spv
-
- def _axiom_annotations(
- self, subject: CURIE, predicate: CURIE, object: CURIE = None, value: Any = None
- ) -> List[om.Annotation]:
- q = self.session.query(OwlAxiomAnnotation)
- q = q.filter(OwlAxiomAnnotation.subject == subject)
- q = q.filter(OwlAxiomAnnotation.predicate == predicate)
- if object:
- q = q.filter(OwlAxiomAnnotation.object == object)
- if value:
- q = q.filter(OwlAxiomAnnotation.value == value)
- return [
- om.Annotation(
- row.annotation_predicate,
- row.annotation_value if row.annotation_value is not None else row.annotation_object,
- )
- for row in q
- ]
-
- def _axiom_annotations_multi(
- self,
- subjects: List[CURIE],
- predicate: CURIE,
- objects: List[CURIE] = None,
- values: List[Any] = None,
- ) -> Iterator[OwlAxiomAnnotation]:
- q = self.session.query(OwlAxiomAnnotation)
- if subjects:
- q = q.filter(OwlAxiomAnnotation.subject.in_(subjects))
- q = q.filter(OwlAxiomAnnotation.predicate == predicate)
- if objects:
- q = q.filter(OwlAxiomAnnotation.object.in_(objects))
- if values:
- q = q.filter(OwlAxiomAnnotation.value.in_(values))
- for row in q:
- yield row
-
- def ancestors(
- self,
- start_curies: Union[CURIE, List[CURIE]],
- predicates: List[PRED_CURIE] = None,
- reflexive: bool = True,
- method: Optional[GraphTraversalMethod] = None,
- ) -> Iterable[CURIE]:
- if method and method == GraphTraversalMethod.HOP:
- if not isinstance(start_curies, list):
- start_curies = [start_curies]
- ancs = {o for _s, _p, o in walk_up(self, start_curies, predicates, include_abox=False)}
- if reflexive:
- ancs.update(start_curies)
- for o in ancs:
- yield o
- return
- q = self.session.query(EntailedEdge.object).distinct()
- if isinstance(start_curies, list):
- q = q.filter(EntailedEdge.subject.in_(tuple(start_curies)))
- else:
- q = q.filter(EntailedEdge.subject == start_curies)
- if predicates is not None:
- q = q.filter(EntailedEdge.predicate.in_(tuple(predicates)))
- if not reflexive:
- q = q.filter(EntailedEdge.subject != EntailedEdge.object)
- if reflexive:
- if isinstance(start_curies, list):
- yield from start_curies
- else:
- yield start_curies
- logging.debug(f"Ancestors query: {q}")
- for row in q:
- yield row.object
-
- def _multi_ancestors(
- self, start_curies: Union[CURIE, List[CURIE]], predicates: List[PRED_CURIE] = None
- ) -> Iterable[RELATIONSHIP]:
- q = self.session.query(EntailedEdge)
- if isinstance(start_curies, list):
- q = q.filter(EntailedEdge.subject.in_(tuple(start_curies)))
- else:
- q = q.filter(EntailedEdge.subject == start_curies)
- start_curies = list(start_curies)
- if predicates is not None:
- q = q.filter(EntailedEdge.predicate.in_(tuple(predicates)))
- logging.debug(f"Ancestors query, start from {start_curies}: {q}")
- for row in q:
- yield row.subject, row.predicate, row.object
-
- def descendants(
- self,
- start_curies: Union[CURIE, List[CURIE]],
- predicates: List[PRED_CURIE] = None,
- reflexive=True,
- method: Optional[GraphTraversalMethod] = None,
- ) -> Iterable[CURIE]:
- if method and method == GraphTraversalMethod.HOP:
- descs = {s for s, _p, _o in walk_down(self, start_curies, predicates)}
- for s in descs:
- yield s
- return
- q = self.session.query(EntailedEdge)
- if isinstance(start_curies, list):
- q = q.filter(EntailedEdge.object.in_(tuple(start_curies)))
- else:
- q = q.filter(EntailedEdge.object == start_curies)
- if predicates is not None:
- q = q.filter(EntailedEdge.predicate.in_(tuple(predicates)))
- if not reflexive:
- q = q.filter(EntailedEdge.subject != EntailedEdge.object)
- for row in q:
- yield row.subject
-
- def descendant_count(
- self,
- start_curies: Union[CURIE, List[CURIE]],
- predicates: List[PRED_CURIE] = None,
- reflexive=True,
- ) -> int:
- q = self.session.query(EntailedEdge.subject)
- if isinstance(start_curies, list):
- q = q.filter(EntailedEdge.object.in_(tuple(start_curies)))
- else:
- q = q.filter(EntailedEdge.object == start_curies)
- if predicates is not None:
- q = q.filter(EntailedEdge.predicate.in_(tuple(predicates)))
- if not reflexive:
- q = q.filter(EntailedEdge.subject != EntailedEdge.object)
- return q.count()
-
- def _rdf_list(self, bnode: str) -> Iterable[str]:
- for row in self.session.query(RdfFirstStatement).filter(RdfFirstStatement.subject == bnode):
- yield row.object
- for row in self.session.query(RdfRestStatement.object).filter(
- RdfRestStatement.subject == bnode
- ):
- for x in self._rdf_list(row.object):
- yield x
-
- def _ixn_definition(self, ixn: str, subject: CURIE) -> Optional[LogicalDefinitionAxiom]:
- ldef = LogicalDefinitionAxiom(definedClassId=subject)
- n = 0
- for ixn_node in self._rdf_list(ixn):
- n += 1
- if _is_blank(ixn_node):
- svfq = self.session.query(OwlSomeValuesFrom).filter(
- OwlSomeValuesFrom.id == ixn_node
- )
- svfq = list(svfq)
- if svfq:
- if len(svfq) > 1:
- raise ValueError(f"Incorrect rdf structure for equiv axioms for {ixn_node}")
- svf = svfq[0]
- ldef.restrictions.append(
- ExistentialRestrictionExpression(
- propertyId=svf.on_property, fillerId=svf.filler
- )
- )
- else:
- ldef = None
- break
- else:
- ldef.genusIds.append(ixn_node)
- if n and ldef:
- return ldef
-
- def logical_definitions(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- **kwargs,
- ) -> Iterable[LogicalDefinitionAxiom]:
- logging.info("Getting logical definitions")
- q = self.session.query(OwlEquivalentClassStatement)
- if predicates is not None:
- predicates = list(predicates)
- if objects is not None:
- objects = list(objects)
- if subjects is None:
- for ldef in self._logical_definitions_from_eq_query(q, predicates, objects):
- yield ldef
- return
- for curie_it in chunk(subjects, self.max_items_for_in_clause):
- logging.info(f"Getting logical definitions for {curie_it} from {subjects}")
- q = q.filter(OwlEquivalentClassStatement.subject.in_(tuple(curie_it)))
- for ldef in self._logical_definitions_from_eq_query(q, predicates, objects):
- yield ldef
-
- def _logical_definitions_from_eq_query(
- self,
- query,
- predicates: Iterable[PRED_CURIE] = None,
- objects: Iterable[CURIE] = None,
- ) -> Iterable[LogicalDefinitionAxiom]:
- for eq_row in query:
- ixn_q = self.session.query(Statements).filter(
- and_(
- Statements.subject == eq_row.object,
- Statements.predicate == "owl:intersectionOf",
- )
- )
- for ixn in ixn_q:
- ldef = self._ixn_definition(ixn.object, eq_row.subject)
- if ldef:
- if not logical_definition_matches(ldef, predicates=predicates, objects=objects):
- continue
- yield ldef
-
- def _node_to_class_expression(
- self, node: str
- ) -> Optional[Union[CURIE, ExistentialRestrictionExpression]]:
- if not _is_blank(node):
- return node
-
- svfq = self.session.query(OwlSomeValuesFrom).filter(OwlSomeValuesFrom.id == node)
- svfq = list(svfq)
- if svfq:
- if len(svfq) > 1:
- raise ValueError(f"Incorrect rdf structure for equiv axioms for {node}")
- svf = svfq[0]
- return ExistentialRestrictionExpression(propertyId=svf.on_property, fillerId=svf.filler)
- else:
- return None
-
- def disjoint_class_expressions_axioms(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- predicates: Iterable[PRED_CURIE] = None,
- group=False,
- **kwargs,
- ) -> Iterable[DisjointClassExpressionsAxiom]:
- logging.info("Getting disjoint class expression axioms")
- q = self.session.query(OwlDisjointClassStatement)
- if predicates is not None:
- predicates = list(predicates)
- if subjects:
- subjects = list(subjects)
- axs = []
- for da in q:
- # blank
- sx = self._node_to_class_expression(da.subject)
- ox = self._node_to_class_expression(da.object)
- allx = [sx, ox]
- allx_named = [x for x in allx if isinstance(x, str)]
- allx_exprs = [x for x in allx if isinstance(x, ExistentialRestrictionExpression)]
- allx_fillers = [x.fillerId for x in allx_exprs]
- if subjects:
- if not any(x for x in allx_named if x in subjects) and not any(
- x for x in allx_fillers if x in subjects
- ):
- continue
- if predicates:
- if not any(x for x in allx_exprs if x.propertyId in predicates):
- continue
- ax = DisjointClassExpressionsAxiom(
- classIds=allx_named,
- classExpressions=allx_exprs,
- )
- axs.append(ax)
- q = self.session.query(RdfTypeStatement.subject).filter(
- RdfTypeStatement.object == "owl:AllDisjointClasses"
- )
- for adc in q:
- class_ids = []
- class_exprs = []
- for (m,) in self.session.query(Statements.object).filter(
- and_(
- Statements.subject == adc.subject,
- Statements.predicate == "owl:members",
- )
- ):
- if isinstance(m, str):
- class_ids.append(m)
- else:
- class_exprs.append(self._node_to_class_expression(m))
- axs.append(
- DisjointClassExpressionsAxiom(
- classIds=class_ids,
- classExpressions=class_exprs,
- )
- )
- yield from axs
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: RelationGraphInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def entailed_relationships_between(self, subject: CURIE, object: CURIE) -> Iterable[PRED_CURIE]:
- preds = []
- for row in (
- self.session.query(EntailedEdge.predicate)
- .filter(EntailedEdge.subject == subject)
- .filter(EntailedEdge.object == object)
- ):
- p = row.predicate
- if p not in preds:
- yield p
- preds.append(p)
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MappingsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def sssom_mappings_by_source(self, subject_or_object_source: str = None) -> Iterable[Mapping]:
- predicates = tuple(ALL_MATCH_PREDICATES)
- base_query = self.session.query(Statements).filter(Statements.predicate.in_(predicates))
- for row in base_query:
- v = row.value if row.value is not None else row.object
- # TODO: this check is slow
- if URIorCURIE.is_valid(v):
- if row.subject.startswith("_:"):
- continue
- mpg = Mapping(
- subject_id=row.subject,
- object_id=v,
- predicate_id=row.predicate,
- mapping_justification=SEMAPV.UnspecifiedMatching.value,
- )
- inject_mapping_sources(mpg)
- if subject_or_object_source:
- # TODO: consider moving to query for efficiency
- if (
- mpg.subject_source != subject_or_object_source
- and mpg.object_source != subject_or_object_source
- ):
- continue
- yield mpg
- else:
- if self.strict:
- raise ValueError(f"not a CURIE: {v}")
-
- def sssom_mappings(
- self,
- curies: Optional[Union[CURIE, Iterable[CURIE]]] = None,
- source: Optional[str] = None,
- bidirectional=True,
- ) -> Iterator[Mapping]:
- if isinstance(curies, CURIE):
- curies = [curies]
- elif curies is not None:
- curies = list(curies)
- justification = str(SEMAPV.UnspecifiedMatching.value)
- predicates = tuple(ALL_MATCH_PREDICATES)
- base_query = self.session.query(Statements).filter(Statements.predicate.in_(predicates))
- if curies is None:
- by_subject_query = base_query
- else:
- by_subject_query = base_query.filter(Statements.subject.in_(curies))
- for row in by_subject_query:
- try:
- mpg = Mapping(
- subject_id=row.subject,
- object_id=row.value if row.value is not None else row.object,
- predicate_id=row.predicate,
- mapping_justification=justification,
- )
- except ValueError as e:
- logging.error(f"Skipping {row}; ValueError: {e}")
- continue
- inject_mapping_sources(mpg)
- if source and mpg.subject_source != source and mpg.object_source != source:
- continue
- yield mpg
- if curies is None:
- # all mappings have been returned
- return
- if bidirectional:
- # xrefs are stored as literals
- for row in base_query.filter(Statements.value.in_(curies)):
- mpg = Mapping(
- subject_id=row.subject,
- object_id=row.value,
- predicate_id=row.predicate,
- mapping_justification=justification,
- )
- inject_mapping_sources(mpg)
- if source and mpg.subject_source != source and mpg.object_source != source:
- continue
- yield mpg
- # skos mappings are stored as objects
- for row in base_query.filter(Statements.object.in_(curies)):
- mpg = Mapping(
- subject_id=row.subject,
- object_id=row.object,
- predicate_id=row.predicate,
- mapping_justification=justification,
- )
- inject_mapping_sources(mpg)
- if source and mpg.subject_source != source and mpg.object_source != source:
- continue
- yield mpg
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: ValidatorInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def validate(
- self, configuration: vdm.ValidationConfiguration = None
- ) -> Iterable[vdm.ValidationResult]:
- if configuration and configuration.schema_path:
- sv = SchemaView(configuration.schema_path)
- self._ontology_metadata_model = sv
- else:
- sv = self.ontology_metadata_model
- sv.materialize_patterns()
- for slot_name in sv.all_slots():
- for r in self._check_slot(slot_name):
- yield r
- for r in self._check_for_unknown_slots():
- yield r
-
- def _missing_value(
- self, predicate_table: Type, type_table: Type = ClassNode
- ) -> Iterable[CURIE]:
- pred_subq = self.session.query(predicate_table.subject)
- obs_subq = self.session.query(DeprecatedNode.id)
- main_q = self.session.query(type_table).join(IriNode, type_table.id == IriNode.id)
- for row in main_q.filter(type_table.id.not_in(pred_subq)).filter(
- type_table.id.not_in(obs_subq)
- ):
- yield row.id
-
- def term_curies_without_definitions(self) -> Iterable[CURIE]:
- return self._missing_value(HasTextDefinitionStatement)
-
- def term_curies_without_labels(self) -> Iterable[CURIE]:
- return self._missing_value(RdfsLabelStatement)
-
- def _check_for_unknown_slots(self) -> Iterable[vdm.ValidationResult]:
- sv = self.ontology_metadata_model
- preds = [sv.get_uri(s, expand=False) for s in sv.all_slots().values()]
- logging.info(f"Known preds: {len(preds)} -- checking for other uses")
- main_q = (
- self.session.query(Statements)
- .filter(Statements.predicate.not_in(preds))
- .join(IriNode, Statements.subject == IriNode.id)
- )
- try:
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=row.predicate,
- severity=vdm.SeverityOptions.ERROR,
- type=vdm.ValidationResultType.ClosedConstraintComponent.meaning,
- info=f"Unknown pred ({row.predicate}) = {row.object} {row.value}",
- )
- yield result
- except ValueError as e:
- logging.error(f"EXCEPTION: {e}")
-
- def _check_slot(
- self, slot_name: str, class_name: str = "Class"
- ) -> Iterable[vdm.ValidationResult]:
- """
- Validates all data with respect to a specific slot.
-
- :param slot_name:
- :param class_name:
- :return:
- """
- sv = self.ontology_metadata_model
- # for efficiency we map directly to table/view names rather
- # than querying over rdf:type; this allows for optimization via view materialization
- if class_name == "Class":
- sqla_cls = ClassNode
- elif class_name == "ObjectProperty":
- sqla_cls = ObjectPropertyNode
- elif class_name == "AnnotationProperty":
- sqla_cls = AnnotationPropertyNode
- elif class_name == "NamedIndividual":
- sqla_cls = NamedIndividualNode
- else:
- raise NotImplementedError(f"cannot handle {class_name}")
- slot = sv.induced_slot(slot_name, class_name)
- if slot.designates_type:
- logging.info(f"Ignoring type designator: {slot_name}")
- return
- logging.info(f"Validating: {slot_name}")
- predicate = sv.get_uri(slot, expand=False)
- is_used = (
- self.session.query(Statements.predicate)
- .filter(Statements.predicate == predicate)
- .first()
- is not None
- )
- pred_subq = self.session.query(Statements.subject).filter(Statements.predicate == predicate)
- obs_subq = self.session.query(DeprecatedNode.id)
- if (slot.required or slot.recommended) and not slot.identifier:
- # MinCardinality == 1
- if slot.required:
- severity = vdm.SeverityOptions.ERROR
- else:
- severity = vdm.SeverityOptions.WARNING
- logging.info(f"MinCard check: Leaving off: {slot_name} is {severity.text}")
- # exclude blank nodes
- main_q = self.session.query(sqla_cls).join(IriNode, sqla_cls.id == IriNode.id)
- main_q = main_q.filter(sqla_cls.id.not_in(pred_subq))
- main_q = main_q.filter(sqla_cls.id.not_in(obs_subq))
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.id,
- predicate=predicate,
- severity=severity,
- type=vdm.ValidationResultType.MinCountConstraintComponent.meaning,
- info=f"Missing slot ({slot_name}) for {row.id}",
- )
- yield result
- if not is_used:
- return
- if slot.pattern:
- # check values against regexes
- # NOTE: this may be slow as we have to do this in
- # packages rather than SQL. Some SQL engines have regex support,
- # and we should leverage that when it exists
- re_pattern = re.compile(slot.pattern)
- main_q = self.session.query(Statements).filter(Statements.predicate == predicate)
- for row in main_q:
- val = row.value if row.value is not None else row.object
- if val is not None:
- if not re_pattern.match(val):
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=row.predicate,
- severity=vdm.SeverityOptions.ERROR,
- type=vdm.ValidationResultType.PatternConstraintComponent.meaning,
- info=f"Pattern violation: {slot_name} = {val} does not conform to {slot.pattern}",
- )
- yield result
- if slot.deprecated:
- main_q = self.session.query(Statements.subject).filter(
- Statements.predicate == predicate
- )
- main_q = main_q.join(sqla_cls, Statements.subject == sqla_cls.id)
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=predicate,
- severity=vdm.SeverityOptions.WARNING,
- type=vdm.ValidationResultType.DeprecatedPropertyComponent.meaning,
- info=f"Deprecated slot ({slot_name}) for {row.subject}",
- )
- yield result
- if not slot.multivalued:
- # MaxCardinality == 1
- # TODO
- is_object_iri = slot.range in sv.all_classes()
- st1 = aliased(Statements)
- st2 = aliased(Statements)
- main_q = self.session.query(st1.subject).join(st2, st1.subject == st2.subject)
- main_q = main_q.filter(st1.predicate == predicate)
- main_q = main_q.filter(st2.predicate == predicate)
- if is_object_iri:
- main_q = main_q.filter(st1.object != st2.object)
- else:
- main_q = main_q.filter(st1.value != st2.value)
- main_q = main_q.join(sqla_cls, st1.subject == sqla_cls.id)
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=predicate,
- severity=vdm.SeverityOptions.ERROR,
- type=vdm.ValidationResultType.MaxCountConstraintComponent.meaning,
- info=f"Too many vals for {slot_name}",
- )
- yield result
- if slot.range:
- rng = slot.range
- rng_elements = sv.slot_applicable_range_elements(slot)
- # for now we don't handle Union or Any
- if len(rng_elements) < 2:
- logging.info(f"Datatype check: {slot_name} range is {rng_elements}")
- is_object_iri = rng in sv.all_classes()
- if is_object_iri:
- constr = Statements.object.is_(None)
- else:
- constr = Statements.value.is_(None)
- main_q = self.session.query(Statements.subject)
- main_q = main_q.join(IriNode, Statements.subject == IriNode.id)
- main_q = main_q.join(sqla_cls, Statements.subject == sqla_cls.id)
- main_q = main_q.filter(Statements.predicate == predicate, constr)
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=predicate,
- severity=vdm.SeverityOptions.ERROR,
- type=vdm.ValidationResultType.DatatypeConstraintComponent.meaning,
- info=f"Incorrect object type for {slot_name} range = {rng} should_be_iri = {is_object_iri}",
- )
- yield result
- if rng in sv.all_types():
- uri = get_range_xsd_type(sv, rng)
- # uri = rng_type.uri
- main_q = self.session.query(Statements.subject)
- main_q = main_q.join(IriNode, Statements.subject == IriNode.id)
- main_q = main_q.join(sqla_cls, Statements.subject == sqla_cls.id)
- main_q = main_q.filter(
- Statements.predicate == predicate, Statements.datatype != uri
- )
- for row in main_q:
- result = vdm.ValidationResult(
- subject=row.subject,
- predicate=predicate,
- severity=vdm.SeverityOptions.ERROR,
- type=vdm.ValidationResultType.DatatypeConstraintComponent.meaning,
- info=f"Incorrect datatype for {slot_name} expected: {uri} for {rng}",
- )
- yield result
-
- def gap_fill_relationships(
- self, seed_curies: List[CURIE], predicates: List[PRED_CURIE] = None
- ) -> Iterator[RELATIONSHIP]:
- seed_curies = tuple(seed_curies)
- q = self.session.query(EntailedEdge).filter(EntailedEdge.subject.in_(seed_curies))
- q = q.filter(EntailedEdge.object.in_(seed_curies))
- q = q.filter(EntailedEdge.subject != EntailedEdge.object)
- if predicates:
- q = q.filter(EntailedEdge.predicate.in_(tuple(predicates)))
- for row in q:
- if row.subject != row.object:
- e1 = aliased(EntailedEdge)
- e2 = aliased(EntailedEdge)
- q2 = self.session.query(e1, e2)
- q2 = q2.filter(e1.subject == row.subject)
- q2 = q2.filter(e1.object.in_(seed_curies))
- q2 = q2.filter(e1.object == e2.subject)
- q2 = q2.filter(e2.object == row.object)
- q2 = q2.filter(e1.subject != e1.object)
- q2 = q2.filter(e2.subject != e2.object)
- if predicates:
- q2 = q2.filter(e1.predicate.in_(tuple(predicates)))
- q2 = q2.filter(e2.predicate.in_(tuple(predicates)))
- redundant = False
- for e1row, e2row in q2:
- if predicates is None:
- redundant = True
- else:
- if e1row.predicate in predicates:
- if e2row.predicate in predicates or e2row.predicate == IS_A:
- redundant = True
- elif e2row.predicate in predicates:
- if e1row.predicate == IS_A:
- redundant = True
- if redundant:
- break
- if not redundant:
- yield row.subject, row.predicate, row.object
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OwlInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- def disjoint_pairs(self, subjects: Iterable[CURIE] = None) -> Iterable[Tuple[CURIE, CURIE]]:
- q = self.session.query(Statements).filter(Statements.predicate == DISJOINT_WITH)
- if subjects:
- q = q.filter(
- or_(Statements.subject.in_(tuple(subjects)), Statements.object.in_(tuple(subjects)))
- )
- for row in q:
- if not row.subject.startswith("_") and not row.object.startswith("_"):
- yield row.subject, row.object
-
- def is_disjoint(self, subject: CURIE, object: CURIE, bidirectional=True) -> bool:
- q = self.session.query(Statements).filter(Statements.predicate == DISJOINT_WITH)
- ee1 = aliased(EntailedEdge)
- ee2 = aliased(EntailedEdge)
- q = q.filter(
- ee1.subject == subject, ee1.object == Statements.subject, ee1.predicate == IS_A
- )
- q = q.filter(ee2.subject == object, ee2.object == Statements.object, ee2.predicate == IS_A)
- if q.first():
- return True
- if bidirectional:
- return self.is_disjoint(object, subject, bidirectional=False)
- return False
-
- def transitive_object_properties(self) -> Iterable[CURIE]:
- for row in self.session.query(TransitivePropertyNode.id):
- yield row[0]
-
- def simple_subproperty_of_chains(self) -> Iterable[Tuple[CURIE, List[CURIE]]]:
- q = self.session.query(Statements)
- q = q.filter(Statements.predicate == OWL_PROPERTY_CHAIN_AXIOM)
- for row in q:
- chain = list(self._rdf_list(row.object))
- yield row.subject, chain
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SemSim
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def information_content_scores(
- self,
- curies: Iterable[CURIE],
- predicates: List[PRED_CURIE] = None,
- object_closure_predicates: List[PRED_CURIE] = None,
- use_associations: bool = None,
- **kwargs,
- ) -> Iterator[Tuple[CURIE, float]]:
- curies = list(curies)
- if self.cached_information_content_map:
- yield from super().information_content_scores(curies)
- return
- if use_associations:
- logging.info("Using associations to calculate IC")
- if not self.can_store_associations:
- yield from super().information_content_scores(
- curies,
- predicates=predicates,
- object_closure_predicates=object_closure_predicates,
- use_associations=use_associations,
- **kwargs,
- )
- return
- # raise ValueError("Cannot use associations, not stored")
- q = self.session.query(EntailedEdge.object, func.count(TermAssociation.subject))
- q = q.filter(EntailedEdge.subject == TermAssociation.object)
- if curies is not None:
- q = q.filter(EntailedEdge.object.in_(curies))
- if predicates:
- q = q.filter(TermAssociation.predicate.in_(predicates))
- if object_closure_predicates:
- q = q.filter(EntailedEdge.predicate.in_(object_closure_predicates))
- q = q.group_by(EntailedEdge.object)
- logging.info(f"QUERY: {q}")
- num_nodes = (
- self.session.query(TermAssociation).distinct(TermAssociation.subject).count()
- )
- else:
- num_nodes = (
- self.session.query(EntailedEdge.subject).distinct(EntailedEdge.subject).count()
- )
- logging.info(f"Number of nodes in background set={num_nodes}")
- q = self.session.query(EntailedEdge.object, func.count(distinct(EntailedEdge.subject)))
- if predicates:
- raise ValueError(
- "predicates not valid unless use_associations=True"
- "did you mean object_closure_predicates?"
- )
- if object_closure_predicates:
- q = q.filter(EntailedEdge.predicate.in_(object_closure_predicates))
- if curies is not None:
- q = q.filter(EntailedEdge.object.in_(curies))
- q = q.group_by(EntailedEdge.object)
- yielded_owl_thing = False
- for row in q:
- curie, freq = row
- yield curie, -math.log(freq / num_nodes) / math.log(2)
- if curie == OWL_THING:
- yielded_owl_thing = True
- # inject owl:Thing, which always has zero information
- if (OWL_THING in curies or not curies) and not yielded_owl_thing:
- yield OWL_THING, 0.0
-
- def all_by_all_pairwise_similarity(
- self,
- subjects: Iterable[CURIE],
- objects: Iterable[CURIE],
- predicates: List[PRED_CURIE] = None,
- min_jaccard_similarity: Optional[float] = None,
- min_ancestor_information_content: Optional[float] = None,
- ) -> Iterator[TermPairwiseSimilarity]:
- def tuples_to_map(
- entities: List[CURIE], relationships: Iterable[RELATIONSHIP]
- ) -> Dict[CURIE, Set[CURIE]]:
- rmap = defaultdict(set)
- for r in relationships:
- rmap[r[0]].add(r[2])
- for e in entities:
- rmap[e].add(e)
- return rmap
-
- subjects = list(subjects)
- objects = list(objects)
- subjects_ancs = tuples_to_map(
- subjects, self._multi_ancestors(subjects, predicates=predicates)
- )
- objects_ancs = tuples_to_map(objects, self._multi_ancestors(objects, predicates=predicates))
- logging.info(f"SUBJECT ANCS={len(subjects_ancs)}")
- logging.info(f"OBJECT ANCS={len(objects_ancs)}")
- for s, s_ancs in subjects_ancs.items():
- for o, o_ancs in objects_ancs.items():
- logging.info(f"s={s} o={o}")
- sim = self.pairwise_similarity(
- s,
- o,
- predicates=predicates,
- subject_ancestors=list(s_ancs),
- object_ancestors=list(o_ancs),
- min_jaccard_similarity=min_jaccard_similarity,
- min_ancestor_information_content=min_ancestor_information_content,
- )
- if sim:
- yield sim
-
- def common_descendants(
- self,
- subject: CURIE,
- object: CURIE,
- predicates: List[PRED_CURIE] = None,
- include_owl_nothing: bool = False,
- ) -> Iterable[CURIE]:
- ee1 = aliased(EntailedEdge)
- ee2 = aliased(EntailedEdge)
- q = self.session.query(ee1.subject)
- q = q.filter(ee1.object == subject)
- q = q.filter(ee2.object == object)
- q = q.filter(ee1.subject == ee2.subject)
- if predicates:
- q = q.filter(ee1.predicate.in_(predicates))
- q = q.filter(ee2.predicate.in_(predicates))
- for row in q:
- if include_owl_nothing or row.subject != OWL_NOTHING:
- yield row.subject
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: PatcherInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def migrate_curies(self, curie_map: Dict[CURIE, CURIE]) -> None:
- # TODO: add an operation for this to KGCL
- for k, v in curie_map.items():
- for cls in [Statements, EntailedEdge]:
- cmd = update(cls).where(cls.subject == k).values(subject=v)
- self.session.execute(cmd)
- cmd = update(cls).where(cls.predicate == k).values(predicate=v)
- self.session.execute(cmd)
- cmd = update(cls).where(cls.object == k).values(object=v)
- self.session.execute(cmd)
- if self.autosave:
- self.save()
-
- def _set_predicate_value(
- self, subject: CURIE, predicate: PRED_CURIE, value: str, datatype: str
- ):
- stmt = delete(Statements).where(
- and_(Statements.subject == subject, Statements.predicate == predicate)
- )
- self._execute(stmt)
- stmt = insert(Statements).values(
- subject=subject, predicate=predicate, value=value, datatype=datatype
- )
- self._execute(stmt)
-
- def apply_patch(
- self,
- patch: kgcl.Change,
- activity: kgcl.Activity = None,
- metadata: typing.Mapping[PRED_CURIE, Any] = None,
- configuration: kgcl.Configuration = None,
- ) -> Optional[kgcl.Change]:
- if isinstance(patch, kgcl.NodeChange):
- about = patch.about_node
- if isinstance(patch, kgcl.NodeRename):
- self.set_label(patch.about_node, patch.new_value)
- elif isinstance(patch, kgcl.NewSynonym):
- # TODO: synonym type
- if not patch.predicate:
- patch.predicate = HAS_EXACT_SYNONYM
- self._execute(
- insert(Statements).values(
- subject=about, predicate=patch.predicate, value=patch.new_value
- )
- )
- elif isinstance(patch, kgcl.RemoveSynonym):
- q = self.session.query(Statements).filter(
- Statements.subject == about, Statements.value == patch.old_value
- )
- self._execute(
- delete(Statements).where(
- and_(
- Statements.subject == about,
- Statements.predicate.in_(SYNONYM_PREDICATES),
- Statements.value == patch.old_value,
- )
- )
- )
- elif isinstance(patch, kgcl.AddNodeToSubset):
- # TODO: implement deterministic subset mapping
- pfx = about.split(":")[0].lower()
- subset_curie = f"obo:{pfx}#{patch.in_subset}"
- self._execute(
- insert(Statements).values(
- subject=about, predicate=IN_SUBSET, object=subset_curie
- )
- )
- elif isinstance(patch, kgcl.RemoveNodeFromSubset):
- # TODO: implement deterministic subset mapping
- pfx = about.split(":")[0].lower()
- subset_curie = f"obo:{pfx}#{patch.in_subset}"
- self._execute(
- delete(Statements).where(
- and_(
- Statements.subject == about,
- Statements.predicate == IN_SUBSET,
- Statements.object == subset_curie,
- )
- )
- )
- elif isinstance(patch, kgcl.NodeObsoletion):
- self.check_node_exists(about)
- self._set_predicate_value(
- about, DEPRECATED_PREDICATE, value="true", datatype="xsd:string"
- )
- if isinstance(patch, kgcl.NodeObsoletionWithDirectReplacement):
- # TODO: allow switching between value and object
- self._set_predicate_value(
- about,
- TERM_REPLACED_BY,
- value=patch.has_direct_replacement,
- datatype="xsd:string",
- )
- elif isinstance(patch, kgcl.NodeDeletion):
- self._execute(delete(Statements).where(Statements.subject == about))
- elif isinstance(patch, kgcl.NameBecomesSynonym):
- label = self.label(about)
- self.apply_patch(
- kgcl.NodeRename(id=f"{patch.id}-1", about_node=about, new_value=patch.new_value)
- )
- self.apply_patch(
- kgcl.NewSynonym(id=f"{patch.id}-2", about_node=about, new_value=label)
- )
- elif isinstance(patch, kgcl.SynonymReplacement):
- q = self.session.query(Statements).filter(
- Statements.subject == about, Statements.value == patch.old_value
- )
- predicate = None
- for row in q:
- if predicate is None:
- predicate = row.predicate
- else:
- if predicate != row.predicate:
- if predicate in SYNONYM_PREDICATES:
- predicate = row.predicate
- else:
- raise ValueError(
- f"Multiple predicates for synonym: {about} "
- + f"syn: {patch.old_value} preds={predicate}, {row.predicate}"
- )
- logging.debug(f"replacing synonym with predicate: {predicate}")
- self._execute(
- delete(Statements).where(
- and_(
- Statements.subject == about,
- Statements.predicate == predicate,
- Statements.value == patch.old_value,
- )
- )
- )
- self._execute(
- insert(Statements).values(
- subject=about, predicate=predicate, value=patch.new_value
- )
- )
- elif isinstance(patch, kgcl.NewTextDefinition):
- q = self.session.query(Statements).filter(
- Statements.subject == about, Statements.predicate == HAS_DEFINITION_CURIE
- )
- if q.count() == 0:
- self._execute(
- insert(Statements).values(
- subject=about, predicate=HAS_DEFINITION_CURIE, value=patch.new_value
- )
- )
- else:
- self.apply_patch(
- kgcl.NodeTextDefinitionChange(subject=about, value=patch.new_value)
- )
- elif isinstance(patch, kgcl.NodeTextDefinitionChange):
- stmt = (
- update(Statements)
- .where(
- and_(
- Statements.subject == about,
- Statements.predicate == HAS_DEFINITION_CURIE,
- )
- )
- .values(value=patch.new_value)
- )
- self._execute(stmt)
- else:
- raise NotImplementedError(f"Unknown patch type: {type(patch)}")
- elif isinstance(patch, kgcl.EdgeChange):
- about = patch.about_edge
- if isinstance(patch, kgcl.EdgeCreation):
- self._execute(
- insert(Statements).values(
- subject=patch.subject, predicate=patch.predicate, object=patch.object
- )
- )
- self._rebuild_relationship_index()
- logging.warning("entailed_edge is now stale")
- elif isinstance(patch, kgcl.EdgeDeletion):
- self._execute(
- delete(Statements).where(
- and_(
- Statements.subject == patch.subject,
- Statements.predicate == patch.predicate,
- Statements.object == patch.object,
- )
- )
- )
- logging.warning("entailed_edge is now stale")
- elif isinstance(patch, kgcl.NodeMove):
- raise NotImplementedError
- # self._execute(delete(Statements).where(and_(Statements.subject==patch.subject,
- # Statements.predicate==patch.predicate,
- # Statements.object==patch.object)))
- logging.warning("entailed_edge is now stale")
- else:
- raise NotImplementedError(f"Cannot handle patches of type {type(patch)}")
- else:
- raise NotImplementedError
- if self.autosave:
- self.save()
- return patch
-
- def save(
- self,
- ):
- logging.info("Committing and flushing changes")
- self.session.commit()
- self.session.flush()
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: MetadataInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def statements_with_annotations(self, curie: CURIE) -> Iterable[om.Axiom]:
- m = self.entity_metadata_map(curie)
- q = self.session.query(OwlAxiomAnnotation)
- q = q.filter(OwlAxiomAnnotation.subject == curie)
- axiom_by_id = {}
- visited = {}
- for row in q:
- if row.value is not None:
- v = row.value
- elif row.object is not None:
- v = row.object
- else:
- raise ValueError(f"Unexpected null object/value in {row}")
- axiom_id = row.id
- if axiom_id in axiom_by_id:
- ax = axiom_by_id[axiom_id]
- else:
- ax = om.Axiom(
- annotatedSource=curie, annotatedProperty=row.predicate, annotatedTarget=v
- )
- axiom_by_id[axiom_id] = ax
- v = row.annotation_object
- if v is None:
- v = row.annotation_value
- ax.annotations.append(om.Annotation(predicate=row.annotation_predicate, object=v))
- for ax in axiom_by_id.values():
- visited[(ax.annotatedSource, ax.annotatedProperty, ax.annotatedTarget)] = True
- yield ax
- for k, vs in m.items():
- if not isinstance(vs, list):
- vs = [vs]
- for v in vs:
- if (curie, k, v) not in visited:
- if not _is_quoted_url(curie):
- ax = om.Axiom(annotatedSource=curie, annotatedProperty=k, annotatedTarget=v)
- yield ax
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: DifferInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def compare_term_in_two_ontologies(
- self, other_ontology: BasicOntologyInterface, curie: CURIE, other_curie: CURIE = None
- ) -> Any:
- if other_curie is None:
- other_curie = curie
- logging.info(f"Comparing {curie} with {other_curie}")
- if isinstance(other_ontology, SqlImplementation):
-
- def nullify_subject(row):
- return f"{row.predicate} {row.object} {row.value} {row.datatype} {row.language}"
-
- this_rows = [
- nullify_subject(row)
- for row in self.session.query(Statements).filter(Statements.subject == curie)
- ]
- other_rows = [
- nullify_subject(row)
- for row in other_ontology.session.query(Statements).filter(
- Statements.subject == other_curie
- )
- ]
- this_only = set(this_rows).difference(set(other_rows))
- other_only = set(other_rows).difference(set(this_rows))
- return this_only, other_only
- else:
- raise NotImplementedError(
- f"other ontology {other_ontology} must implement SqlInterface"
- )
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SummaryStatisticsInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- def branch_summary_statistics(
- self,
- branch_name: str = None,
- branch_roots: List[CURIE] = None,
- property_values: Dict[CURIE, Any] = None,
- include_entailed=False,
- parent: GroupedStatistics = None,
- prefixes: List[CURIE] = None,
- ) -> UngroupedStatistics:
- session = self.session
- not_in = False
- if branch_name is None:
- branch_name = "AllOntologies"
- if branch_roots is not None:
- branch_subq = session.query(EntailedEdge.subject)
- branch_subq = branch_subq.filter(EntailedEdge.predicate == IS_A)
- branch_subq = branch_subq.filter(EntailedEdge.object.in_(branch_roots))
- elif property_values is not None:
- logging.info(f"Filtering by {property_values}")
- if len(property_values) > 1:
- raise NotImplementedError("Only one property value is supported at this time")
- k, v = list(property_values.items())[0]
- if k == PREFIX_PREDICATE:
- self._check_has_view(NodeIdentifier, "0.2.5")
- branch_subq = session.query(NodeIdentifier.id)
- branch_subq = branch_subq.filter(NodeIdentifier.prefix == v)
- else:
- branch_subq = session.query(Statements.subject)
- branch_subq = branch_subq.filter(Statements.predicate == k)
- if v is None:
- not_in = True
- elif isinstance(v, list):
- branch_subq = branch_subq.filter(Statements.value.in_(v))
- else:
- branch_subq = branch_subq.filter(Statements.value == v)
- else:
- branch_subq = None
- if prefixes:
- self._check_has_view(NodeIdentifier, "0.2.5")
- branch_subq = session.query(NodeIdentifier.id)
- branch_subq = branch_subq.filter(NodeIdentifier.prefix.in_(tuple(prefixes)))
-
- def q(x):
- return session.query(x)
-
- def _filter(select_expr, filter_expr=None):
- if not filter_expr:
- filter_expr = select_expr
- q = session.query(select_expr)
- if branch_subq is not None:
- if not_in:
- q = q.filter(filter_expr.not_in(branch_subq))
- else:
- q = q.filter(filter_expr.in_(branch_subq))
- if False and prefixes:
- if len(prefixes) == 1:
- q = q.filter(filter_expr.startswith(prefixes[0]))
- else:
- self._check_has_view(NodeIdentifier, "0.2.5")
- prefix_subq = session.query(NodeIdentifier.id)
- prefix_subq = prefix_subq.filter(NodeIdentifier.prefix.in_(tuple(prefixes)))
- q = q.filter(filter_expr.in_(prefix_subq))
- return q
-
- ssc = UngroupedStatistics(branch_name)
- if not parent:
- self._add_statistics_metadata(ssc)
- obsoletion_subq = q(DeprecatedNode.id)
- text_defn_subq = q(HasTextDefinitionStatement.subject)
- logging.debug(f"Subqueries: {obsoletion_subq} {text_defn_subq}")
- logging.debug("Getting basic counts")
- ssc.class_count = _filter(ClassNode.id).distinct(ClassNode.id).count()
- ssc.named_individual_count = _filter(NamedIndividualNode.id).distinct(ClassNode.id).count()
- depr_class_query = _filter(ClassNode.id).filter(ClassNode.id.in_(obsoletion_subq))
- ssc.deprecated_class_count = depr_class_query.count()
- logging.debug(f"Calculated basic counts. Classes: {ssc.class_count}")
- merged_class_query = (
- _filter(Statements.subject)
- .filter(Statements.predicate == HAS_OBSOLESCENCE_REASON)
- .filter(Statements.object == TERMS_MERGED)
- )
- ssc.merged_class_query = merged_class_query.count()
- logging.debug(f"Calculated merged counts. Classes: {ssc.merged_class_count}")
- ssc.class_count_with_text_definitions = (
- _filter(ClassNode.id).filter(ClassNode.id.in_(text_defn_subq)).count()
- )
- ssc.object_property_count = _filter(ObjectPropertyNode.id).count()
- ssc.annotation_property_count = _filter(AnnotationPropertyNode.id).count()
- ssc.deprecated_property_count = (
- _filter(ObjectPropertyNode.id)
- .filter(ObjectPropertyNode.id.in_(obsoletion_subq))
- .count()
- )
- logging.debug(f"Calculated basic property counts. OPs: {ssc.object_property_count}")
- ssc.rdf_triple_count = _filter(Statements.subject).count()
- ssc.equivalent_classes_axiom_count = _filter(OwlEquivalentClassStatement.subject).count()
- ssc.subclass_of_axiom_count = _filter(RdfsSubclassOfStatement.subject).count()
- logging.debug(f"Calculated basic axiom counts. SCAs: {ssc.subclass_of_axiom_count}")
- subset_query = _filter(Statements.object, Statements.subject).filter(
- Statements.predicate == IN_SUBSET
- )
- ssc.subset_count = subset_query.distinct(Statements.object).count()
- subset_agg_query = session.query(
- Statements.object, func.count(Statements.subject.distinct())
- )
- subset_agg_query = subset_agg_query.filter(Statements.predicate == IN_SUBSET)
- if branch_subq:
- subset_agg_query = subset_agg_query.filter(Statements.subject.in_(branch_subq))
- for row in subset_agg_query.group_by(Statements.object):
- subset = row.object
- if subset is None:
- logging.warning("Skipping subsets modeled as strings")
- continue
- ssc.class_count_by_subset[subset] = FacetedCount(row[0], filtered_count=row[1])
- logging.debug(f"Agg count for subset {subset}: {ssc.class_count_by_subset[subset]}")
- synonym_query = q(Statements.value).filter(Statements.predicate.in_(SYNONYM_PREDICATES))
- if branch_subq:
- synonym_query = synonym_query.filter(Statements.subject.in_(branch_subq))
- ssc.synonym_statement_count = synonym_query.count()
- ssc.distinct_synonym_count = synonym_query.distinct().count()
- logging.debug(f"Calculated basic synonym counts. Statements: {ssc.synonym_statement_count}")
- synonym_agg_query = session.query(
- Statements.predicate, func.count(Statements.value.distinct())
- )
- synonym_agg_query = synonym_agg_query.filter(Statements.predicate.in_(SYNONYM_PREDICATES))
- if branch_subq:
- synonym_agg_query = synonym_agg_query.filter(Statements.subject.in_(branch_subq))
- for row in synonym_agg_query.group_by(Statements.predicate):
- pred = row.predicate
- ssc.synonym_statement_count_by_predicate[pred] = FacetedCount(
- row[0], filtered_count=row[1]
- )
- logging.debug(f"Agg count for synonym {pred}: {row}")
- edge_agg_query = session.query(Edge.predicate, func.count(Edge.subject))
- if branch_subq:
- edge_agg_query = edge_agg_query.filter(Edge.subject.in_(branch_subq))
- for row in edge_agg_query.group_by(Edge.predicate):
- ssc.edge_count_by_predicate[row.predicate] = FacetedCount(row[0], filtered_count=row[1])
- if include_entailed:
- logging.debug("Calculating entailed counts")
- entailed_edge_agg_query = session.query(
- EntailedEdge.predicate, func.count(Edge.subject)
- )
- if branch_subq:
- entailed_edge_agg_query = entailed_edge_agg_query.filter(
- Edge.subject.in_(branch_subq)
- )
- for row in entailed_edge_agg_query.group_by(EntailedEdge.predicate):
- ssc.entailed_edge_count_by_predicate[row.predicate] = FacetedCount(
- row[0], filtered_count=row[1]
- )
- logging.debug(f"Agg count for entailed edge {row}")
- match_agg_query = session.query(
- Statements.predicate, func.count(Statements.value.distinct())
- ).filter(Statements.predicate.in_(ALL_MATCH_PREDICATES))
- if branch_subq:
- match_agg_query = match_agg_query.filter(Statements.subject.in_(branch_subq))
- for row in match_agg_query.group_by(Statements.predicate):
- ssc.mapping_statement_count_by_predicate[row.predicate] = FacetedCount(
- row[0], filtered_count=row[1]
- )
- logging.debug(f"Agg count for mapping {row}")
- # non-aggregate query for matches
- match_query = session.query(Statements).filter(
- Statements.predicate.in_(ALL_MATCH_PREDICATES)
- )
- if branch_subq:
- match_query = match_query.filter(Statements.subject.in_(branch_subq))
- subject_ids_by_object_source = defaultdict(list)
- bad_ids = set()
- for row in match_query:
- subject_id = row.subject
- object_id = row.value if row.value else row.object
- if ":" not in object_id:
- if object_id not in bad_ids:
- logging.warning(f"bad mapping: {object_id}")
- bad_ids.add(object_id)
- object_source = object_id.split(":")[0]
- subject_ids_by_object_source[object_source].append(subject_id)
- for object_source, subject_ids in subject_ids_by_object_source.items():
- ssc.mapping_statement_count_by_object_source[object_source] = FacetedCount(
- object_source, filtered_count=len(subject_ids)
- )
- ssc.mapping_statement_count_subject_by_object_source[object_source] = FacetedCount(
- object_source, filtered_count=len(set(subject_ids))
- )
- logging.debug("Calculating contributor stats")
- contributor_agg_query = session.query(
- Statements.predicate,
- Statements.object,
- Statements.value,
- func.count(Statements.subject.distinct()),
- )
- contributor_agg_query = contributor_agg_query.filter(
- Statements.predicate.in_(ALL_CONTRIBUTOR_PREDICATES)
- )
- if branch_subq:
- contributor_agg_query = contributor_agg_query.filter(
- Statements.subject.in_(branch_subq)
- )
- for row in contributor_agg_query.group_by(
- Statements.predicate, Statements.object, Statements.value
- ):
- if row.object:
- contributor_id = row.object
- contributor_name = None
- else:
- contributor_id = row.value
- contributor_name = row.value
- if " " in contributor_id or ":" not in contributor_id:
- logging.debug(
- f"Ad-hoc repair of literal value for contributor: {contributor_id}"
- )
- contributor_id = string_as_base64_curie(contributor_id)
- contributor_id = _remove_uri_quotes(contributor_id)
- if contributor_id not in ssc.contributor_summary:
- ssc.contributor_summary[contributor_id] = ContributorStatistics(
- contributor_id=contributor_id, contributor_name=contributor_name
- )
- ssc.contributor_summary[contributor_id].role_counts[row.predicate] = FacetedCount(
- row.predicate, row[-1]
- )
- logging.debug(f"Agg count for contributor {row}")
- # TODO: axiom contributor stats
- self._add_derived_statistics(ssc)
- return ssc
-
- def metadata_property_summary_statistics(self, metadata_property: PRED_CURIE) -> Dict[Any, int]:
- if metadata_property == PREFIX_PREDICATE:
- d = defaultdict(int)
- for e in self.entities(filter_obsoletes=False):
- prefix = e.split(":")[0]
- d[prefix] += 1
- return dict(d)
- session = self.session
- q = session.query(Statements.value, func.count(Statements.value))
- q = q.filter(Statements.predicate == metadata_property)
- q = q.group_by(Statements.value)
- return dict(q)
-
-
Source code for oaklib.implementations.ubergraph.ubergraph_implementation
-import logging
-import math
-from collections import defaultdict
-from dataclasses import dataclass
-from enum import Enum
-from typing import Iterable, Iterator, List, Optional, Tuple, Union
-
-from rdflib import OWL, RDF, RDFS, URIRef
-
-from oaklib.datamodels import obograph
-from oaklib.datamodels.similarity import TermPairwiseSimilarity
-from oaklib.implementations.sparql.abstract_sparql_implementation import (
- AbstractSparqlImplementation,
- _as_rdf_obj,
- _sparql_values,
-)
-from oaklib.implementations.sparql.sparql_query import SparqlQuery
-from oaklib.interfaces import SubsetterInterface
-from oaklib.interfaces.basic_ontology_interface import RELATIONSHIP, RELATIONSHIP_MAP
-from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
-from oaklib.interfaces.obograph_interface import GraphTraversalMethod, OboGraphInterface
-from oaklib.interfaces.rdf_interface import TRIPLE
-from oaklib.interfaces.relation_graph_interface import RelationGraphInterface
-from oaklib.interfaces.search_interface import SearchInterface
-from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
-from oaklib.types import CURIE, PRED_CURIE
-from oaklib.utilities.graph.networkx_bridge import transitive_reduction_by_predicate
-from oaklib.utilities.semsim.similarity_utils import setwise_jaccard_similarity
-
-__all__ = [
- "RelationGraphEnum",
- "UbergraphImplementation",
-]
-
-
-
-[docs]
-class RelationGraphEnum(Enum):
- """
- triples in UG are organized into different graphs
- """
-
- ontology = "http://reasoner.renci.org/ontology"
- redundant = "http://reasoner.renci.org/redundant"
- nonredundant = "http://reasoner.renci.org/nonredundant"
- normalizedInformationContent = "http://reasoner.renci.org/vocab/normalizedInformationContent"
-
-
-
-
-[docs]
-@dataclass
-class UbergraphImplementation(
- AbstractSparqlImplementation,
- RelationGraphInterface,
- SearchInterface,
- OboGraphInterface,
- MappingProviderInterface,
- SemanticSimilarityInterface,
- SubsetterInterface,
-):
- """
- Wraps the Ubergraph sparql endpoint
-
- See: `<https://github.com/INCATools/ubergraph>`_
-
- This is a specialization of the more generic :class:`.SparqlImplementation`, which
- has knowledge of some of the specialized patterns found in Ubergraph
-
- An UbergraphImplementation can be initialed by:
-
- >>> from oaklib.implementations.ubergraph.ubergraph_implementation import UbergraphImplementation
- >>> adapter = UbergraphImplementation()
-
- or
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("ubergraph:")
-
- to use a specific ontology or named graph within ubergraph:
-
- >>> adapter = get_adapter("ubergraph:cl")
-
- """
-
- def _default_url(self) -> str:
- return "https://ubergraph.apps.renci.org/sparql"
-
- def _is_blazegraph(self) -> bool:
- """
- Currently Ubergraph uses blazegraph
- """
- return True
-
- @property
- def named_graph(self) -> Optional[str]:
- if not self.resource or self.resource.slug is None:
- return None
- else:
- ont = self.resource.slug
- if ont:
- for g in self.list_of_named_graphs():
- if f"/{ont}." in g or f"/{ont}-base" in g:
- return g
- logging.warning(f"No graph named: {ont}")
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: RelationGraph
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _get_outgoing_edges_by_curie(
- self, curie: CURIE, graph: RelationGraphEnum, predicates: List[PRED_CURIE] = None
- ) -> Iterable[Tuple[CURIE, CURIE]]:
- query_uri = self.curie_to_sparql(curie)
- query = SparqlQuery(
- select=["?p", "?o"],
- where=[f"GRAPH <{graph.value}> {{ {query_uri} ?p ?o }}", "?o a owl:Class"],
- )
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- query.where.append(f'VALUES ?p {{ {" ".join(pred_uris)} }}')
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- pred = self.uri_to_curie(row["p"]["value"])
- obj = self.uri_to_curie(row["o"]["value"])
- yield pred, obj
-
- def _get_incoming_edges_by_curie(
- self, curie: CURIE, graph: RelationGraphEnum, predicates: List[PRED_CURIE] = None
- ) -> Iterable[Tuple[CURIE, CURIE]]:
- query_uri = self.curie_to_sparql(curie)
- query = SparqlQuery(
- select=["?s", "?p"],
- where=[f"GRAPH <{graph.value}> {{ ?s ?p {query_uri} }}", "?s a owl:Class"],
- )
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- query.where.append(f'VALUES ?p {{ {" ".join(pred_uris)} }}')
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- pred = self.uri_to_curie(row["p"]["value"])
- subj = self.uri_to_curie(row["s"]["value"])
- yield pred, subj
-
- def outgoing_relationship_map(self, curie: CURIE, isa_only: bool = False) -> RELATIONSHIP_MAP:
- rmap = defaultdict(list)
- for pred, obj in self._get_outgoing_edges_by_curie(
- curie, graph=RelationGraphEnum.nonredundant
- ):
- rmap[pred].append(obj)
- return rmap
-
- def incoming_relationship_map(self, curie: CURIE, isa_only: bool = False) -> RELATIONSHIP_MAP:
- rmap = defaultdict(list)
- for pred, s in self._get_incoming_edges_by_curie(
- curie, graph=RelationGraphEnum.nonredundant
- ):
- rmap[pred].append(s)
- return rmap
-
- def relationships(
- self,
- subjects: List[CURIE] = None,
- predicates: List[PRED_CURIE] = None,
- objects: List[CURIE] = None,
- include_tbox: bool = True,
- include_abox: bool = True,
- include_entailed: bool = False,
- ) -> Iterator[RELATIONSHIP]:
- query = SparqlQuery(select=["?s", "?p", "?o"], where=["?s ?p ?o"])
- if not include_entailed:
- query.graph = RelationGraphEnum.nonredundant.value
- if subjects:
- query.where.append(_sparql_values("s", [self.curie_to_sparql(x) for x in subjects]))
- if predicates:
- query.where.append(_sparql_values("p", [self.curie_to_sparql(x) for x in predicates]))
- if objects:
- query.where.append(_sparql_values("o", [self.curie_to_sparql(x) for x in objects]))
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- sub = self.uri_to_curie(row["s"]["value"])
- pred = self.uri_to_curie(row["p"]["value"])
- obj = self.uri_to_curie(row["o"]["value"])
- yield sub, pred, obj
-
- def entailed_outgoing_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None
- ) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- return self._get_outgoing_edges_by_curie(
- curie, graph=RelationGraphEnum.redundant, predicates=predicates
- )
-
- def entailed_incoming_relationships(
- self, curie: CURIE, predicates: List[PRED_CURIE] = None
- ) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
- return self._get_incoming_edges_by_curie(
- curie, graph=RelationGraphEnum.redundant, predicates=predicates
- )
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: OboGraph
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def _values(self, var: str, in_list: Optional[List[str]]) -> str:
- if in_list is None:
- return ""
- else:
- return f'VALUES ?{var} {{ {" ".join(in_list)} }}'
-
- def _from_subjects_chunked(
- self, subjects: List[CURIE], predicates: List[PRED_CURIE] = None, **kwargs
- ):
- size = 10
- while len(subjects) > 0:
- next_subjects = subjects[0:size]
- subjects = subjects[size:]
- for r in self._from_subjects(next_subjects, predicates, **kwargs):
- yield r
-
- def _from_subjects(
- self,
- subjects: List[CURIE],
- predicates: List[PRED_CURIE] = None,
- graph: str = None,
- object_is_literal=False,
- where=None,
- ) -> Iterable[Tuple[CURIE, PRED_CURIE, CURIE]]:
- if where is None:
- where = []
- subject_uris = [self.curie_to_sparql(curie) for curie in subjects]
- if predicates:
- predicate_uris = [self.curie_to_sparql(curie) for curie in predicates]
- else:
- predicate_uris = None
- query = SparqlQuery(
- select=["?s ?p ?o"],
- distinct=True,
- graph=graph,
- where=[
- "?s ?p ?o",
- _sparql_values("s", subject_uris),
- _sparql_values("p", predicate_uris),
- ]
- + where,
- )
- # print(f'G={graph} Q={query.query_str()}')
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- v = row["o"]["value"]
- if not object_is_literal:
- v = self.uri_to_curie(v)
- yield (self.uri_to_curie(row["s"]["value"]), self.uri_to_curie(row["p"]["value"]), v)
-
- def _object_properties(self) -> List[PRED_CURIE]:
- return list(set([t[0] for t in self._triples(None, RDF.type, OWL.ObjectProperty)]))
-
- def ancestor_graph(
- self, start_curies: Union[CURIE, List[CURIE]], predicates: List[PRED_CURIE] = None
- ) -> obograph.Graph:
- ancs = list(self.ancestors(start_curies, predicates))
- logging.info(f"NUM ANCS: {len(ancs)}")
- edges = []
- nodes = {}
- for rel in self._from_subjects_chunked(
- ancs, predicates, graph=RelationGraphEnum.nonredundant.value, where=[]
- ):
- edges.append(obograph.Edge(sub=rel[0], pred=rel[1], obj=rel[2]))
- logging.info(f"NUM EDGES: {len(edges)}")
- for rel in self._from_subjects_chunked(ancs, [RDFS.label], object_is_literal=True):
- id = rel[0]
- nodes[id] = obograph.Node(id=id, lbl=rel[2])
- logging.info(f"NUM NODES: {len(nodes)}")
- return obograph.Graph(id="query", nodes=list(nodes.values()), edges=edges)
-
- def relationships_to_graph(self, relationships: Iterable[RELATIONSHIP]) -> obograph.Graph:
- relationships = list(relationships)
- edges = [obograph.Edge(sub=s, pred=p, obj=o) for s, p, o in relationships]
- node_ids = set()
- for rel in relationships:
- node_ids.update(list(rel))
- nodes = {}
- for s, _, o in self._from_subjects_chunked(
- list(node_ids), [RDFS.label], object_is_literal=True
- ):
- nodes[s] = obograph.Node(id=s, lbl=o)
- logging.info(f"NUM EDGES: {len(edges)}")
- return obograph.Graph(id="query", nodes=list(nodes.values()), edges=edges)
-
- def ancestors(
- self,
- start_curies: Union[CURIE, List[CURIE]],
- predicates: List[PRED_CURIE] = None,
- reflexive=True,
- method: Optional[GraphTraversalMethod] = None,
- ) -> Iterable[CURIE]:
- if method and method == GraphTraversalMethod.HOP:
- raise NotImplementedError("HOP not implemented for ubergraph")
- # TODO: DRY
- if not isinstance(start_curies, list):
- start_curies = [start_curies]
- query_uris = [self.curie_to_sparql(curie) for curie in start_curies]
- where = [
- "?s ?p ?o",
- "?o a owl:Class",
- # f'?p a owl:ObjectProperty',
- _sparql_values("s", query_uris),
- ]
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(_sparql_values("p", pred_uris))
- query = SparqlQuery(select=["?o"], distinct=True, where=where)
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- yield self.uri_to_curie(row["o"]["value"])
-
- def descendants(
- self,
- start_curies: Union[CURIE, List[CURIE]],
- predicates: List[PRED_CURIE] = None,
- reflexive=True,
- method: Optional[GraphTraversalMethod] = None,
- ) -> Iterable[CURIE]:
- if method and method == GraphTraversalMethod.HOP:
- raise NotImplementedError("HOP not implemented for ubergraph")
- # TODO: DRY
- query_uris = [self.curie_to_sparql(curie) for curie in start_curies]
- where = ["?s ?p ?o", "?s a owl:Class", f'VALUES ?o {{ {" ".join(query_uris)} }}']
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(f'VALUES ?p {{ {" ".join(pred_uris)} }}')
- query = SparqlQuery(select=["?s"], distinct=True, where=where)
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- yield self.uri_to_curie(row["s"]["value"])
-
- def dump(self, path: str = None, syntax: str = None):
- raise NotImplementedError("Dump not allowed on ubergraph")
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: Subsetter
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def gap_fill_relationships(
- self, seed_curies: List[CURIE], predicates: List[PRED_CURIE] = None
- ) -> Iterator[RELATIONSHIP]:
- # TODO: compare with https://api.triplydb.com/s/_mZ9q_-rg
- query_uris = [self.curie_to_sparql(curie) for curie in seed_curies]
- where = ["?s ?p ?o", _sparql_values("s", query_uris), _sparql_values("o", query_uris)]
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(_sparql_values("p", pred_uris))
- query = SparqlQuery(select=["?s ?p ?o"], where=where)
- bindings = self._sparql_query(query.query_str())
- # TODO: remove redundancy
- rels = []
- for row in bindings:
- rels.append(
- (
- self.uri_to_curie(row["s"]["value"]),
- self.uri_to_curie(row["p"]["value"]),
- self.uri_to_curie(row["o"]["value"]),
- )
- )
- for rel in transitive_reduction_by_predicate(rels):
- yield rel
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: SemSim
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def common_ancestors(
- self, subject: CURIE, object: CURIE, predicates: List[PRED_CURIE] = None
- ) -> Iterable[CURIE]:
- s_uri = self.curie_to_sparql(subject)
- o_uri = self.curie_to_sparql(object)
- where = [f"{s_uri} ?sp ?a", f"{o_uri} ?op ?a", "?a a owl:Class"]
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(_sparql_values("sp", pred_uris))
- where.append(_sparql_values("op", pred_uris))
- query = SparqlQuery(select=["?a"], distinct=True, where=where)
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- yield self.uri_to_curie(row["a"]["value"])
-
- def most_recent_common_ancestors(
- self, subject: CURIE, object: CURIE, predicates: List[PRED_CURIE] = None
- ) -> Iterable[CURIE]:
- s_uri = self.curie_to_sparql(subject)
- o_uri = self.curie_to_sparql(object)
- where = [f"{s_uri} ?sp ?a", f"{o_uri} ?op ?a", "?a a owl:Class"]
- where2 = [f"{s_uri} ?sp2 ?a2", f"{o_uri} ?op2 ?a2", "?a2 ?ap2 ?a", "FILTER( ?a != ?a2)"]
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(_sparql_values("sp", pred_uris))
- where.append(_sparql_values("op", pred_uris))
- where2.append(_sparql_values("sp2", pred_uris))
- where2.append(_sparql_values("op2", pred_uris))
- where2.append(_sparql_values("ap2", pred_uris))
- query = SparqlQuery(select=["?a"], distinct=True, where=where)
- subq = SparqlQuery(select=["?a2"], where=where2)
- query.add_not_in(subq)
- bindings = self._sparql_query(query.query_str())
- for row in bindings:
- yield self.uri_to_curie(row["a"]["value"])
-
- def get_information_content(
- self, curie: CURIE, background: CURIE = None, predicates: List[PRED_CURIE] = None
- ) -> float:
- if predicates is not None:
- raise NotImplementedError("Only predetermined predicates allowed")
- ics = self._get_anns(curie, URIRef(RelationGraphEnum.normalizedInformationContent.value))
- if len(ics) > 1:
- raise ValueError(f"Multiple ICs for {curie} = {ics}")
- return float(ics[0])
-
- def pairwise_similarity(
- self, subject: CURIE, object: CURIE = None, predicates: List[PRED_CURIE] = None
- ) -> TermPairwiseSimilarity:
- s_uri = self.curie_to_sparql(subject)
- o_uri = self.curie_to_sparql(object)
- where = [
- f"{s_uri} ?sp ?a",
- f"{o_uri} ?op ?a",
- "?a a owl:Class",
- f"?a <{RelationGraphEnum.normalizedInformationContent.value}> ?ic",
- ]
- if predicates:
- pred_uris = [self.curie_to_sparql(pred) for pred in predicates]
- where.append(_sparql_values("sp", pred_uris))
- where.append(_sparql_values("op", pred_uris))
- query = SparqlQuery(select=["?a", "?ic"], distinct=True, where=where)
- bindings = self._sparql_query(query.query_str())
- ics = {
- self.uri_to_curie(row["a"]["value"]): float(self.uri_to_curie(row["ic"]["value"]))
- for row in bindings
- }
- max_ic = max(list(ics.values()))
- best_mrcas = [a for a in ics if ics[a] == max_ic]
- mrca = best_mrcas[0]
- sim = TermPairwiseSimilarity(subject_id=subject, object_id=object, ancestor_id=mrca)
- for curie, label in self.labels([subject, object, mrca]):
- if label is None:
- continue
- # print(f'C={curie} L={label}')
- if curie == subject:
- sim.subject_label = label
- if curie == object:
- sim.object_label = label
- if curie == mrca:
- sim.ancestor_label = label
- sim.ancestor_information_content = max_ic
- sim.jaccard_similarity = setwise_jaccard_similarity(
- list(self.ancestors(subject, predicates=predicates)),
- list(self.ancestors(object, predicates=predicates)),
- )
- sim.phenodigm_score = math.sqrt(sim.jaccard_similarity * sim.ancestor_information_content)
- return sim
-
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # Implements: RdfInterface
- # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
- def extract_triples(
- self,
- seed_curies: List[CURIE],
- predicates: List[PRED_CURIE] = None,
- strategy=None,
- map_to_curies=True,
- ) -> Iterator[TRIPLE]:
- seed_uris = [self.curie_to_sparql(c) for c in seed_curies]
- # Note that some triplestores will have performance issues with this query
- traverse_preds = [
- "rdfs:subClassOf",
- "owl:onProperty",
- "owl:someValuesFrom",
- "owl:annotatedSource",
- "owl:equivalentClass",
- ]
- if predicates:
- # note that predicates are only used in the ABox - for a RelationGraph-implementing
- # triplestore this will also include TBox existentials
- traverse_preds = list(set(traverse_preds + predicates))
- query = SparqlQuery(
- select=["?s", "?p", "?o"],
- graph=[RelationGraphEnum.ontology.value],
- where=[
- "?s ?p ?o ." f'?seed ({"|".join(traverse_preds)})* ?s',
- _sparql_values("seed", seed_uris),
- ],
- )
- bindings = self._sparql_query(query)
- n = 0
- for row in bindings:
- n += 1
- triple = (row["s"], row["p"], row["o"])
- if map_to_curies:
- yield tuple([self.uri_to_curie(v["value"]) for v in list(triple)])
- else:
- yield tuple([_as_rdf_obj(v) for v in list(triple)])
- logging.info(f"Total triples: {n}")
-
-
Source code for oaklib.interfaces.class_enrichment_calculation_interface
-import logging
-from abc import ABC
-from dataclasses import dataclass
-from typing import Iterable, Iterator, List, Optional
-
-from typing_extensions import ClassVar
-
-from oaklib.datamodels.association import Association
-from oaklib.datamodels.class_enrichment import ClassEnrichmentResult
-from oaklib.datamodels.item_list import ItemList
-from oaklib.datamodels.vocabulary import EQUIVALENT_CLASS
-from oaklib.interfaces.association_provider_interface import (
- AssociationProviderInterface,
-)
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-from oaklib.types import CURIE, PRED_CURIE
-from oaklib.utilities.stats.hypergeometric import hypergeometric_p_value
-
-
-
-[docs]
-@dataclass
-class ClassEnrichmentCalculationInterface(AssociationProviderInterface, ABC):
- """
- An interface that provides services to test for over representation of class membership in a set of entities.
-
- This interface is intended to be used to test for over representation of a class in a set of entities,
-
- for example: to
- test for over representation of a disease in a set of genes.
- """
-
- requires_associations: ClassVar[bool] = True
-
-
-[docs]
- def enriched_classes(
- self,
- subjects: Optional[Iterable[CURIE]] = None,
- item_list: Optional[ItemList] = None,
- predicates: Iterable[CURIE] = None,
- object_closure_predicates: Optional[List[PRED_CURIE]] = None,
- background: Iterable[CURIE] = None,
- hypotheses: Iterable[CURIE] = None,
- cutoff=0.05,
- autolabel=False,
- filter_redundant=False,
- sort_by: str = None,
- direction="greater",
- ) -> Iterator[ClassEnrichmentResult]:
- """
- Test for over-representation of classes in a set of entities.
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("src/oaklib/conf/go-pombase-input-spec.yaml")
- >>> sample = ["PomBase:SPAC1142.02c", "PomBase:SPAC3H1.05", "PomBase:SPAC1142.06", "PomBase:SPAC4G8.02c"]
- >>> for result in adapter.enriched_classes(sample, autolabel=True):
- ... assert result.p_value < 0.05
- ... print(f"{result.class_id} {result.class_label}")
- <BLANKLINE>
- GO:0006620 post-translational protein targeting to endoplasmic reticulum membrane
- ...
-
- By default, results may include redundant terms. If we set `filter_redundant=True`,
- then redundant terms are removed, unless they are more significant than the
- descendant term
-
- :param subjects: The set of entities to test for over-representation of classes
- :param item_list: An item list objects as an alternate way to specify subjects
- :param background: The set of entities to use as a background for the test (recommended)
- :param hypotheses: The set of classes to test for over-representation (default is all)
- :param cutoff: The threshold to use for the adjusted p-value
- :param labels: Whether to include labels (names) for the classes
- :param direction: The direction of the test. One of 'greater', 'less', 'two-sided'
- :param filter_redundant: Whether to filter out redundant hypotheses
- :param sort_by: The field to sort by. One of 'p_value', 'sample_count', 'background_count', 'odds_ratio'
- :param direction: The direction of the test. One of 'greater', 'less', 'two-sided'
- :return: An iterator over ClassEnrichmentResult objects
- """
- if subjects and item_list:
- raise ValueError("Only one of subjects or item_list may be provided")
- if subjects is None:
- if not item_list:
- raise ValueError("Either subjects or item_list must be provided")
- if not item_list.itemListElements:
- raise ValueError("item_list must not be empty")
- subjects = item_list.itemListElements
- subjects = list(subjects)
- sample_size = len(subjects)
- logging.info(f"Calculating sample_counts for {sample_size} subjects")
- if not sample_size:
- raise ValueError("No subjects provided")
- sample_count = {
- k: v
- for k, v in self.association_subject_counts(
- subjects, predicates=predicates, object_closure_predicates=object_closure_predicates
- )
- }
- if all(v == 0 for v in sample_count.values()):
- raise ValueError("No associations found for subjects")
- potential_hypotheses = set(sample_count.keys())
- if hypotheses is None:
- hypotheses = potential_hypotheses
- else:
- hypotheses = potential_hypotheses.intersection(hypotheses)
- logging.info(f"Num Hypotheses: {len(hypotheses)}")
- logging.debug("Hypotheses: {}".format(hypotheses))
-
- # get background counts
- if background is None:
- logging.info(
- f"Calculating backgrounds for all associations using {object_closure_predicates}"
- )
- background = set()
- for a in self.associations(
- predicates=predicates, object_closure_predicates=object_closure_predicates
- ):
- background.add(a.subject)
- else:
- background = set(background)
- # ensure background includes all subjects
- background.update(subjects)
-
- bg_size = len(background)
-
- logging.info(f"Calculating background_counts for {bg_size} background entities")
- bg_count = {
- k: v
- for k, v in self.association_subject_counts(
- background,
- predicates=predicates,
- object_closure_predicates=object_closure_predicates,
- )
- }
-
- hypotheses = [x for x in hypotheses if bg_count[x] > 1]
- logging.info("Filtered hypotheses: {}".format(hypotheses))
- num_hypotheses = len(hypotheses)
-
- results = []
- for cls in hypotheses:
- logging.debug(f"Calculating enrichment for {cls}")
- p_val_raw, _dn = hypergeometric_p_value(
- sample_count[cls], sample_size, bg_count[cls], bg_size
- )
- p_val_adj = p_val_raw * num_hypotheses
- if p_val_adj > 1.0:
- p_val_adj = 1.0
- if p_val_adj <= cutoff:
- r = ClassEnrichmentResult(
- cls,
- p_value=p_val_raw,
- p_value_adjusted=p_val_adj,
- sample_count=sample_count[cls],
- sample_total=sample_size,
- background_count=bg_count[cls],
- background_total=bg_size,
- )
- if autolabel:
- r.class_label = self.label(cls)
- results.append(r)
- if isinstance(self, OboGraphInterface):
- anc_counts = {
- x.class_id: len(
- list(self.ancestors([x.class_id], predicates=object_closure_predicates))
- )
- for x in results
- }
- else:
- anc_counts = {}
- results.sort(key=lambda x: (x.p_value, -anc_counts.get(x.class_id, 0)))
- yielded = set()
- yielded_ancs = set()
- for r in results:
- if yielded.intersection(
- set(self.ancestors(r.class_id, predicates=object_closure_predicates))
- ):
- r.descendant_of_more_informative_result = True
- if r.class_id in yielded_ancs:
- r.ancestor_of_more_informative_result = True
- yielded.add(r.class_id)
- yielded_ancs.update(
- list(self.ancestors(r.class_id, predicates=object_closure_predicates))
- )
- if filter_redundant and (
- r.ancestor_of_more_informative_result or r.descendant_of_more_informative_result
- ):
- continue
- r.rank = len(yielded)
- yield r
-
-
-
-[docs]
- def create_self_associations(self):
- """
- Create self associations for all terms in the ontology.
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("tests/input/go-nucleus.obo")
- >>> adapter.create_self_associations()
- >>> assocs = list(adapter.associations(["GO:0005773"]))
- >>> assert len(assocs) == 1
- >>> assoc = assocs[0]
- >>> print(assoc.subject, assoc.predicate, assoc.object)
- GO:0005773 owl:equivalentClass GO:0005773
-
- This is useful for simple over-representation tests over term sets without any annotations.
-
- >>> from oaklib import get_adapter
- >>> adapter = get_adapter("tests/input/go-nucleus.obo")
- >>> adapter.create_self_associations()
- >>> terms = ["GO:0034357", "GO:0031965", "GO:0005773"]
- >>> for r in adapter.enriched_classes(terms, autolabel=True, filter_redundant=True):
- ... print(r.class_id, r.class_label, round(r.p_value_adjusted,3))
- GO:0016020 membrane 0.004
- ...
-
-
- """
- assocs = []
- for e in self.entities(filter_obsoletes=True):
- assoc = Association(subject=e, predicate=EQUIVALENT_CLASS, object=e)
- assocs.append(assoc)
- self.add_associations(assocs)
-
-
-
Source code for oaklib.interfaces.dumper_interface
-import logging
-from abc import ABC
-from typing import Any, Dict
-
-from linkml_runtime.dumpers import json_dumper
-
-from oaklib.converters.obo_graph_to_cx_converter import OboGraphToCXConverter
-from oaklib.converters.obo_graph_to_fhir_converter import OboGraphToFHIRConverter
-from oaklib.converters.obo_graph_to_obo_format_converter import (
- OboGraphToOboFormatConverter,
-)
-from oaklib.converters.obo_graph_to_rdf_owl_converter import OboGraphToRdfOwlConverter
-from oaklib.datamodels.obograph import GraphDocument
-from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface
-from oaklib.interfaces.obograph_interface import OboGraphInterface
-
-SUMMARY_STATISTICS_MAP = Dict[str, Any]
-
-OBOGRAPH_CONVERTERS = {
- "obo": OboGraphToOboFormatConverter,
- "fhirjson": OboGraphToFHIRConverter,
- "owl": OboGraphToRdfOwlConverter,
- "turtle": OboGraphToRdfOwlConverter,
- "rdf": OboGraphToRdfOwlConverter,
- "rdfxml": (OboGraphToRdfOwlConverter, {"format": "xml"}),
- "cx": OboGraphToCXConverter,
- "obojson": None,
- "json": None,
-}
-
-FORMAT_SYNONYMS = {
- "json": "obojson",
- "obographs": "obojson",
-}
-
-
-
-[docs]
-class DumperInterface(BasicOntologyInterface, ABC):
- """
- An OntologyInterface that is capable of exporting entire contents.
- """
-
-
-[docs]
- def dump(
- self, path: str = None, syntax: str = None, enforce_canonical_ordering=False, **kwargs
- ):
- """
- Exports current contents.
-
- :param path: Path to file to write to. If None, then write to stdout.
- :param syntax: Syntax to use. If None, then use the default syntax.
- :param enforce_canonical_ordering:
- :param kwargs: Additional arguments to pass to the dumper
- :return:
- """
- logging.info(f"Dumping graph to {path} in {syntax}")
- if not syntax:
- raise ValueError(f"Unknown syntax: {syntax}")
- if syntax in FORMAT_SYNONYMS:
- syntax = FORMAT_SYNONYMS[syntax]
- if syntax not in OBOGRAPH_CONVERTERS:
- raise ValueError(f"Cannot handle syntax: {syntax}")
- if not isinstance(self, OboGraphInterface):
- raise ValueError(f"Cannot handle interface: {self}")
- og = self.as_obograph()
- ogdoc = GraphDocument(graphs=[og])
- converter_class = OBOGRAPH_CONVERTERS.get(syntax, None)
- if not converter_class:
- json_str = json_dumper.dumps(ogdoc, inject_type=False)
- if path:
- with open(path, "w", encoding="utf-8") as f:
- f.write(json_str)
- else:
- print(json_str)
- else:
- if isinstance(converter_class, tuple):
- converter_class, converter_kwargs = converter_class
- kwargs.update(converter_kwargs)
- converter = converter_class()
- converter.enforce_canonical_ordering = enforce_canonical_ordering
- logging.info(f"Using {converter}, kwargs={kwargs}")
- converter.curie_converter = self.converter
- kwargs = {k: v for k, v in kwargs.items() if v is not None}
- if "format" not in kwargs:
- kwargs["format"] = syntax
- converter.dump(ogdoc, target=path, **kwargs)
-
-
-
Source code for oaklib.interfaces.obograph_interface
Source code for oaklib.interfaces.validator_interface
from abc import ABC
-from typing import Dict, Iterable
+from typing import Any, Dict, Iterable, List, Optional, Union
+from linkml_runtime.dumpers import json_dumper
+
+from oaklib.datamodels.ontology_metadata import DefinitionConstraintComponent
+from oaklib.datamodels.synonymizer_datamodel import RuleSet
from oaklib.datamodels.validation_datamodel import (
MappingValidationResult,
RepairConfiguration,
RepairOperation,
+ SeverityOptions,
ValidationConfiguration,
ValidationResult,
)
-from oaklib.interfaces import MappingProviderInterface
+from oaklib.datamodels.vocabulary import HAS_DEFINITION_CURIE
+from oaklib.interfaces import MappingProviderInterface, OboGraphInterface
from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface
from oaklib.types import CURIE
+from oaklib.utilities.iterator_utils import chunk
+from oaklib.utilities.lexical.synonymizer import apply_synonymizer
+from oaklib.utilities.publication_utils.pubmed_wrapper import PubmedWrapper
[docs]
class ValidatorInterface(BasicOntologyInterface, ABC):
"""
- Basic ontology QC
+ Multi-faceted ontology validator.
+
+ This interface defines a number of different validation processes
The overall goal is to support the following
@@ -127,7 +138,7 @@ Source code for oaklib.interfaces.validator_interface
[docs]
def term_curies_without_definitions(self) -> Iterable[CURIE]:
"""
- TODO: decide whether to write highly specific methods or use a generic validate method
+ Yields all entities that do not have a definition.
:return:
"""
@@ -164,7 +175,17 @@ Source code for oaklib.interfaces.validator_interface
"""
Validate mappings for a set of entities.
- :param entities:
+ Different adapters may implement different aspects of mapping validation.
+
+ It includes:
+
+ - checking cardinality of mappings (e.g. skos:exactMatch should be 1:1)
+ - looking up mapped entities to check they are not obsolete
+ - using AI to validate the content of mappings
+
+ :param entities: entities to validate mappings for (None=all)
+ :param adapters: adapter mapping to look up external entities
+ :param configuration: validation configuration
:return:
"""
from oaklib.utilities.mapping.mapping_validation import validate_mappings
@@ -183,6 +204,149 @@ Source code for oaklib.interfaces.validator_interface
yield result
+
+[docs]
+ def validate_synonyms(
+ self,
+ entities: Iterable[CURIE] = None,
+ adapters: Dict[str, BasicOntologyInterface] = None,
+ configuration: ValidationConfiguration = None,
+ synonymizer_rules: Optional[RuleSet] = None,
+ ) -> Iterable[ValidationResult]:
+ """
+ Validate synonyms for a set of entities.
+
+ Different adapters may implement different aspects of synonym validation.
+
+ It includes:
+
+ - checking for duplicates
+ - looking up mapped entities to check they are not obsolete
+ - ensuring that a referenced synonym is still supported
+ - using AI to validate the content of mappings
+
+ :param entities: entities to validate mappings for (None=all)
+ :param adapters: adapter mapping to look up external entities
+ :param configuration: validation configuration
+ :return:
+ """
+
+ if not isinstance(self, OboGraphInterface):
+ raise ValueError(f"Cannot validate synonyms on {self}")
+ nodes = [self.node(n, include_metadata=True) for n in entities]
+ for node in nodes:
+ if node is None:
+ continue
+ syns = node.meta.synonyms
+ for syn in syns:
+ if syn.xrefs:
+ for xref in syn.xrefs:
+ from oaklib.utilities.mapping.mapping_validation import (
+ lookup_mapping_adapter,
+ )
+
+ ext_adapter = lookup_mapping_adapter(xref, adapters)
+ if ext_adapter is None:
+ continue
+ if not isinstance(ext_adapter, OboGraphInterface):
+ raise ValueError(f"Cannot validate synonyms on {ext_adapter}")
+ ext_node = ext_adapter.node(xref, include_metadata=True)
+ ext_syns = ext_node.meta.synonyms
+ # normalize to lower case for comparison
+ # TODO: allow configurability of case rules
+ synonym_forms = {syn.val}
+ if synonymizer_rules:
+ for _, syn_form, _ in apply_synonymizer(
+ syn.val, synonymizer_rules.rules
+ ):
+ synonym_forms.add(syn_form.lower())
+ ext_syn_vals = [x.val.lower() for x in ext_syns]
+ if not synonym_forms.intersection(ext_syn_vals):
+ yield ValidationResult(
+ subject=node.id,
+ predicate=syn.pred,
+ object=xref,
+ object_str=syn.val,
+ severity=SeverityOptions(SeverityOptions.ERROR),
+ type="oio:SynonymNotFound",
+ info=f"synonym not found in {xref}",
+ )
+
+
+
+[docs]
+ def validate_definitions(
+ self,
+ entities: Iterable[CURIE] = None,
+ adapters: Dict[str, BasicOntologyInterface] = None,
+ configuration: ValidationConfiguration = None,
+ skip_text_annotation=False,
+ **kwargs,
+ ) -> Iterable[ValidationResult]:
+ """
+ Validate text definitions for a set of entities.
+
+ Different adapters may implement different aspects of mapping validation.
+
+ It includes:
+
+ - testing definitions are present
+ - validating the text definition against the SRS rubric
+ - using AI to align the definition against any references
+
+ :param entities:
+ :param configuration:
+ :param kwargs:
+ :return:
+ """
+ from oaklib.utilities.validation.definition_ontology_rule import DefinitionOntologyRule
+
+ definition_rule = DefinitionOntologyRule(skip_text_annotation=skip_text_annotation)
+ entities = list(entities) if entities else self.entities(filter_obsoletes=True)
+
+ def _contract(url):
+ return url.replace("https://w3id.org/oak/ontology-metadata/DCC.", "oaklib.om:DCC#")
+
+ for r in definition_rule.evaluate(self, entities=entities):
+ r.type = _contract(r.type)
+ yield r
+ if configuration and configuration.lookup_references:
+ for entity_it in chunk(entities):
+ for entity, defn, metadata in self.definitions(
+ entity_it,
+ include_metadata=True,
+ ):
+ if not metadata:
+ continue
+ for _k, vs in metadata.items():
+ refs = self.lookup_references(vs, adapters=adapters)
+ for ref, obj in refs.items():
+ if obj is not None and not obj:
+ yield ValidationResult(
+ subject=entity,
+ predicate=HAS_DEFINITION_CURIE,
+ object=ref,
+ object_str=defn,
+ severity=SeverityOptions(SeverityOptions.ERROR),
+ type=_contract(
+ DefinitionConstraintComponent.ReferenceNotFound.meaning
+ ),
+ info=f"publication not found: {ref}",
+ )
+ continue
+ if isinstance(obj, dict) and obj.get("retracted", False):
+ yield ValidationResult(
+ subject=entity,
+ predicate=HAS_DEFINITION_CURIE,
+ object=ref,
+ severity=SeverityOptions(SeverityOptions.ERROR),
+ type=_contract(
+ DefinitionConstraintComponent.ReferenceIsRetracted.meaning
+ ),
+ info=f"publication is retracted: {obj.get('title', obj)}",
+ )
+
+
[docs]
def repair(
@@ -224,6 +388,44 @@ Source code for oaklib.interfaces.validator_interface
:return: class curie iterator
"""
raise NotImplementedError
+
+
+
+[docs]
+ def lookup_references(
+ self, references: List[CURIE], adapters: Dict[str, BasicOntologyInterface] = None, **kwargs
+ ) -> Dict[CURIE, Union[bool, Dict[str, Any]]]:
+ """
+ Lookup references in external ontologies.
+
+ :param references: list of CURIEs to look up
+ :param adapters: adapter mapping to look up external entities
+ :param kwargs: additional arguments
+ :return: mapping between CURIEs and pub objects
+ """
+ pubmed_wrapper = PubmedWrapper()
+ pub_prefixes = ["PMID", "DOI", "PMC", "PMCID"]
+ publication_ids = [
+ x for x in references if any(x.upper().startswith(y) for y in pub_prefixes)
+ ]
+ objs = pubmed_wrapper.objects_by_ids(publication_ids)
+ # seed with Nones
+ obj_map = {pmid: False for pmid in references if pmid.startswith("PMID")}
+ for x in objs:
+ obj_map[x["id"]] = x
+ for x in references:
+ # split out the prefix
+ prefix, _ = x.split(":", 1)
+ if prefix.upper() in pub_prefixes:
+ continue
+ if adapters is not None:
+ if prefix in adapters:
+ adapter = adapters[prefix]
+ if not isinstance(adapter, OboGraphInterface):
+ continue
+ obj = adapter.node(x)
+ obj_map[x] = json_dumper.to_dict(obj)
+ return obj_map
diff --git a/_modules/oaklib/selector.html b/_modules/oaklib/selector.html
deleted file mode 100644
index d5a8d1271..000000000
--- a/_modules/oaklib/selector.html
+++ /dev/null
@@ -1,566 +0,0 @@
-
-
-
-
-
- oaklib.selector — oaklib documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Source code for oaklib.selector
-import gzip
-import io
-import logging
-import os
-from pathlib import Path
-from typing import List, Optional, Type, TypeVar, Union
-
-import requests
-from deprecation import deprecated
-from linkml_runtime.loaders import yaml_loader
-
-from oaklib import BasicOntologyInterface
-from oaklib import datamodels as datamodels_package
-from oaklib.constants import TIMEOUT_SECONDS
-from oaklib.datamodels.input_specification import InputSpecification, Normalizer
-from oaklib.implementations import GildaImplementation
-from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation
-from oaklib.interfaces import OntologyInterface
-from oaklib.interfaces.association_provider_interface import (
- AssociationProviderInterface,
- EntityNormalizer,
-)
-from oaklib.parsers.association_parser_factory import get_association_parser
-from oaklib.resource import OntologyResource
-
-RDF_SUFFIX_TO_FORMAT = {
- "ttl": "turtle",
- "nt": "ntriples",
- "rdf": "turtle",
- "jsonld": "json-ld",
- "json-ld": "json-ld",
- "xml": "xml",
- "n3": "n3",
-}
-
-
-ASSOCIATION_REGISTRY = {
- "hpoa": ([], "hpoa", "http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa", False),
- "hpoa_g2p": (
- [],
- "hpoa_g2p",
- "http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt",
- False,
- ),
- "hpoa_g2d": (
- [],
- "hpoa_g2d",
- "http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt",
- False,
- ),
- "gaf": (["group"], "gaf", "http://current.geneontology.org/annotations/{group}.gaf.gz", True),
- "gaf_archive": (
- ["date", "group"],
- "gaf",
- "http://release.geneontology.org/{date}/annotations/{group}.gaf.gz",
- True,
- ),
- "gencc": (
- [],
- "gencc",
- "https://search.thegencc.org/download/action/submissions-export-csv",
- False,
- ),
- "medgen_mim_g2d": (
- [],
- "medgen_mim_g2d",
- "http://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen",
- False,
- ),
-}
-
-T = TypeVar("T", bound=BasicOntologyInterface)
-
-
-
-[docs]
-def get_adapter(
- descriptor: Union[str, Path, InputSpecification],
- format: str = None,
- implements: Optional[Type[T]] = None,
- **kwargs,
-) -> T:
- """
- Gets an adapter (implementation) for a given descriptor.
-
- OAK allows for multiple different *adapters* (aka *implementations*);
- for example, :ref:`SQLImplementation` and :ref:`BioPortalImplementation`.
-
- This function allows you to get an adapter for a given descriptor.
- A descriptor combines a *scheme* followed by a colon symbol, and then
- optionally additional information that specifies how to access a particular
- resource or ontology within that scheme.
-
- Example:
- -------
- .. packages :: python
-
- >>> from oaklib import get_adapter
- >>>
- >>> ## Use the simpleobo adapter to read a local OBO file:
- >>> adapter = get_adapter('simpleobo:tests/input/go-nucleus.obo')
- >>> print(adapter.label("GO:0005634"))
- nucleus
- >>> ## Use the ubergraph adapter, querying within GO
- >>> adapter = get_adapter('ubergraph:go')
- >>> print(adapter.label("GO:0005634"))
- nucleus
- >>> ## Use the ubergraph adapter, querying within all
- >>> adapter = get_adapter('ubergraph:')
- >>> print(adapter.label("GO:0005634"))
- nucleus
-
- If you omit the scheme then OAK will try to guess the scheme based on the
- suffix of the descriptor
-
- .. packages :: python
-
- >>> from oaklib import get_adapter
- >>> ## Use an adapter that is able to read OBO Format:
- >>> ## (currently defaults to pronot)
- >>> adapter = get_adapter('tests/input/go-nucleus.obo')
- >>> print(adapter.label("GO:0005634"))
- nucleus
- >>> ## Use an adapter that is able to read SQLIte:
- >>> adapter = get_adapter('tests/input/go-nucleus.obo')
- >>> print(adapter.label("GO:0005634"))
- nucleus
-
- If you want to pass extra information through to the implementation
- class, you can do so with keyword arguments:
-
- .. packages :: python
-
- >>> from oaklib import get_adapter
- >>> from gilda import get_grounder
- >>> grounder = get_grounder()
- >>> adapter = get_adapter("gilda:", grounder=grounder)
- >>> annotations = adapter.annotate_text("nucleus")
-
- :param descriptor:
- The input specification, path to a YAML describing an input specification,
- or a shorthand string for instantiating an ontology interface
- :param format: file format/syntax, e.g obo, turtle
- :param kwargs: Keyword arguments to pass through to the implementation class
- :return: An instantiated interface
-
- """
- if isinstance(descriptor, InputSpecification):
- return _get_adapter_from_specification(descriptor)
- if isinstance(descriptor, Path):
- descriptor = str(descriptor)
- if descriptor.endswith(".yaml"):
- input_specification = yaml_loader.load(open(descriptor), InputSpecification)
- return get_adapter(input_specification)
- res = get_resource_from_shorthand(descriptor, format)
- return res.implementation_class(res, **kwargs)
-
-
-
-def _get_adapter_from_specification(
- input_specification: InputSpecification,
-) -> BasicOntologyInterface:
- """
- Gets an adapter (implementation) for a given input specification.
-
- :param input_specification:
- :return:
- """
- if not input_specification.ontology_resources:
- raise ValueError("No ontology resources specified")
- if len(input_specification.ontology_resources) == 1:
- r = list(input_specification.ontology_resources.values())[0]
- adapter = get_adapter(str(r.selector))
- else:
- from oaklib.implementations import AggregatorImplementation
-
- adapter = AggregatorImplementation(
- implementations=[
- get_adapter(r.selector) for r in input_specification.ontology_resources.values()
- ]
- )
- if input_specification.association_resources:
- if not isinstance(adapter, AssociationProviderInterface):
- raise ValueError(f"Adapter {adapter} does not support associations")
- for r in input_specification.association_resources.values():
- normalizers = [
- EntityNormalizer(
- adapter=get_adapter(n.selector),
- source_prefixes=n.source_prefixes,
- target_prefixes=n.target_prefixes,
- slots=n.slots,
- prefix_alias_map={str(k): str(v.alias) for k, v in n.prefix_alias_map.items()},
- )
- for n in r.normalizers
- ]
- logging.info(f"Normalizers: {normalizers}")
- add_associations(
- adapter,
- r.selector,
- r.format,
- normalizers,
- primary_knowledge_source=r.primary_knowledge_source,
- aggregator_knowledge_source=r.aggregator_knowledge_source,
- )
- return adapter
-
-
-
-[docs]
-def add_associations(
- adapter: AssociationProviderInterface,
- descriptor: str,
- format: str = None,
- normalizers: Optional[List[Normalizer]] = None,
- primary_knowledge_source: Optional[str] = None,
- aggregator_knowledge_source: Optional[str] = None,
-) -> None:
- """
- Adds associations to an adapter.
-
- :param adapter:
- :param descriptor:
- :param format:
- :param normalizers:
- :return:
- """
- logging.info(
- f"Adding associations from {descriptor} ({primary_knowledge_source}) using {format} format"
- )
- # TODO: do more robust windows check
- if ":" in descriptor and not descriptor.startswith("file:") and not descriptor[1] == ":":
- scheme, path = descriptor.split(":", 1)
- if scheme not in ASSOCIATION_REGISTRY:
- raise ValueError(f"Unknown association scheme: {scheme}")
- entry = ASSOCIATION_REGISTRY[scheme]
- params, format, url_template, compressed = entry
- if params:
- param_vals = dict(zip(params, path.split("//"), strict=False))
- else:
- param_vals = {}
- url = url_template.format(**param_vals)
- # TODO: add option to cache using pystow
- if compressed:
- file = file_from_gzip_url(url)
- else:
- file = file_from_url(url)
- association_parser = get_association_parser(format)
- logging.info(f"Adding associations from {url}")
- if primary_knowledge_source is None:
- primary_knowledge_source = f"infores:{scheme}"
- if aggregator_knowledge_source is None:
- aggregator_knowledge_source = f"infores:{scheme}"
- assocs = list(association_parser.parse(file))
- association_parser.add_metadata(
- assocs,
- primary_knowledge_source=primary_knowledge_source,
- aggregator_knowledge_source=aggregator_knowledge_source,
- )
- adapter.add_associations(assocs, normalizers=normalizers)
- return
- if not format:
- toks = descriptor.split(".")
- while toks:
- format = toks[-1]
- if format not in ("csv", "tsv", "txt"):
- break
- toks = toks[:-1]
- if not format:
- raise ValueError(f"Could not determine format from descriptor {descriptor}")
- association_parser = get_association_parser(format)
- path = descriptor
- with open(path) as file:
- logging.info(f"Adding associations from {path} ({descriptor})")
- assocs = list(association_parser.parse(file))
- logging.info(f"Read {len(assocs)} associations from {path}")
- association_parser.add_metadata(assocs, primary_knowledge_source=primary_knowledge_source)
- adapter.add_associations(assocs, normalizers=normalizers)
-
-
-
-def file_from_gzip_url(url, is_compressed=False):
- with requests.get(url, stream=True, timeout=TIMEOUT_SECONDS) as response:
- response.raise_for_status() # Raise an exception if the response contains an HTTP error status code
- # Wrap the response's raw stream in a binary file-like object
- binary_file_like_object = io.BytesIO(response.raw.read())
-
- # Uncompress the gzipped binary file-like object using gzip
- return gzip.open(binary_file_like_object, "rt")
-
-
-def file_from_url(url):
- response = requests.get(url, timeout=TIMEOUT_SECONDS)
- response.raise_for_status() # Raise an exception if the response contains an HTTP error status code
- # Create a file-like object using the response content
- file_like_object = io.StringIO(response.text)
- return file_like_object
-
-
-
-[docs]
-@deprecated("Use get_adapter instead")
-def get_implementation_from_shorthand(
- descriptor: str, format: str = None
-) -> BasicOntologyInterface:
- """
- Gets an adapter (implementation) for a given descriptor.
-
- .. warning ::
-
- this is an alias for `get_adapter` - use this instead,
- get_implementation_from_shorthand will be deprecated in future.
-
- :param descriptor:
- :param format:
- :return:
- """
- return get_adapter(descriptor, format)
-
-
-
-
-[docs]
-def get_implementation_class_from_scheme(scheme: str) -> Type[OntologyInterface]:
- """
- Given a selector schema (e.g. sqlite, ubergraph, pronto, etc.) return the adapter class.
-
- :param scheme:
- :return: adapter (implementation) class that implements the OntologyInterface
- """
- if scheme == "http" or scheme == "https":
- raise NotImplementedError("Web requests not implemented yet")
- else:
- from oaklib.implementations import get_implementation_resolver
-
- return get_implementation_resolver().lookup(scheme)
-
-
-
-def get_resource_imp_class_from_suffix_descriptor(
- suffix: str, resource: OntologyResource, descriptor: str
-):
- from oaklib.implementations import ( # SimpleOboImplementation,
- ProntoImplementation,
- SparqlImplementation,
- SqlImplementation,
- )
-
- if suffix == "db" or (resource.format and resource.format == "sqlite"):
- impl_class = SqlImplementation
- resource.slug = f"sqlite:///{Path(descriptor).absolute()}"
- elif resource.format and resource.format in RDF_SUFFIX_TO_FORMAT.values():
- impl_class = SparqlImplementation
- elif suffix in RDF_SUFFIX_TO_FORMAT:
- impl_class = SparqlImplementation
- resource.format = RDF_SUFFIX_TO_FORMAT[suffix]
- elif suffix == "owl":
- impl_class = SparqlImplementation
- resource.format = "xml"
- logging.warning("Using rdflib rdf/xml parser; this behavior may change in future")
- elif suffix == "ofn":
- impl_class = FunOwlImplementation
- # elif suffix == "obo":
- # impl_class = SimpleOboImplementation
- else:
- resource.local = True
- impl_class = ProntoImplementation
-
- return impl_class, resource
-
-
-
-[docs]
-def get_resource_from_shorthand(
- descriptor: str, format: str = None, import_depth: Optional[int] = None
-) -> OntologyResource:
- """
- Maps from a shorthand descriptor to an OntologyResource.
-
- :param descriptor:
- :param format: file format/syntax, e.g obo, turtle
- :param import_depth: maximum import depth to traverse
- :return:
- """
- from oaklib.implementations import (
- LovImplementation,
- ProntoImplementation,
- SparqlImplementation,
- )
-
- resource = OntologyResource(format=format)
- resource.import_depth = import_depth
- resource.slug = descriptor
- impl_class: Optional[Type[OntologyInterface]] = None
-
- if not descriptor:
- raise ValueError("No descriptor provided")
- # Pre-processing
- if descriptor.startswith("datamodel:"):
- # introspect the internal OAK datamodel.
- # the oak data models are intended for programmatic use, but the documentation
- # is also exposed as a pseudo-ontology by default.
- # this allows us to do things such as use the OAK CLI to find all classes
- # or fields in a data model, see their hierarchy, etc
- # this is currently an advanced/experimental feature, if useful
- # it should be exposed in user-facing sphinx docs.
- descriptor = descriptor.replace("datamodel:", "")
- dm_path = os.path.dirname(datamodels_package.__file__)
- descriptor = f"{Path(dm_path)/descriptor}.owl.ttl"
- logging.info(f"Introspecting datamodel from {descriptor}")
- resource.slug = descriptor
-
- # Prevent the driveletter from being interpreted as scheme on Windows.
- if ":" in descriptor and not os.path.exists(descriptor):
- toks = descriptor.split(":")
- scheme = toks[0]
- resource.scheme = scheme
- rest = ":".join(toks[1:])
- if not rest:
- rest = None
- resource.slug = rest
- # Get impl_class based on scheme.
- impl_class = get_implementation_class_from_scheme(scheme)
-
- if impl_class == LovImplementation:
- logging.warning("lov scheme may become plugin in future")
- elif impl_class == SparqlImplementation:
- resource.url = rest
- resource.slug = None
- elif impl_class == ProntoImplementation:
- if resource.slug and resource.slug.endswith(".obo"):
- resource.format = "obo"
- if scheme == "prontolib":
- resource.local = False
- else:
- resource.local = True
-
- resource.slug = rest
- elif impl_class == GildaImplementation:
- resource.slug = Path(rest).resolve().as_posix() if rest is not None else rest
- elif not impl_class:
- raise ValueError(f"Scheme {scheme} not known")
- else:
- logging.info(f"No schema: assuming file path {descriptor}")
- suffix = descriptor.split(".")[-1]
- impl_class, resource = get_resource_imp_class_from_suffix_descriptor(
- suffix, resource, descriptor
- )
-
- resource.implementation_class = impl_class
- return resource
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/_sources/datamodels/association/Association.md.txt b/_sources/datamodels/association/Association.md.txt
index f8565e068..9cb0e96ed 100644
--- a/_sources/datamodels/association/Association.md.txt
+++ b/_sources/datamodels/association/Association.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Association
diff --git a/_sources/datamodels/association/AssociationChange.md.txt b/_sources/datamodels/association/AssociationChange.md.txt
index f68bcb5cd..39206a0e4 100644
--- a/_sources/datamodels/association/AssociationChange.md.txt
+++ b/_sources/datamodels/association/AssociationChange.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: AssociationChange
diff --git a/_sources/datamodels/association/NegatedAssociation.md.txt b/_sources/datamodels/association/NegatedAssociation.md.txt
index bfe2c5830..1fde4aed1 100644
--- a/_sources/datamodels/association/NegatedAssociation.md.txt
+++ b/_sources/datamodels/association/NegatedAssociation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: NegatedAssociation
diff --git a/_sources/datamodels/association/PairwiseCoAssociation.md.txt b/_sources/datamodels/association/PairwiseCoAssociation.md.txt
index c7840bfd8..99743f0c3 100644
--- a/_sources/datamodels/association/PairwiseCoAssociation.md.txt
+++ b/_sources/datamodels/association/PairwiseCoAssociation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PairwiseCoAssociation
diff --git a/_sources/datamodels/association/ParserConfiguration.md.txt b/_sources/datamodels/association/ParserConfiguration.md.txt
index 56f3ae6bc..921c2fa30 100644
--- a/_sources/datamodels/association/ParserConfiguration.md.txt
+++ b/_sources/datamodels/association/ParserConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ParserConfiguration
diff --git a/_sources/datamodels/association/PositiveOrNegativeAssociation.md.txt b/_sources/datamodels/association/PositiveOrNegativeAssociation.md.txt
index 2168b0ac9..985384444 100644
--- a/_sources/datamodels/association/PositiveOrNegativeAssociation.md.txt
+++ b/_sources/datamodels/association/PositiveOrNegativeAssociation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PositiveOrNegativeAssociation
diff --git a/_sources/datamodels/association/PropertyValue.md.txt b/_sources/datamodels/association/PropertyValue.md.txt
index f6bd1115f..6f5016e57 100644
--- a/_sources/datamodels/association/PropertyValue.md.txt
+++ b/_sources/datamodels/association/PropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PropertyValue
diff --git a/_sources/datamodels/association/RollupGroup.md.txt b/_sources/datamodels/association/RollupGroup.md.txt
index 524a8b7f0..8d51c2649 100644
--- a/_sources/datamodels/association/RollupGroup.md.txt
+++ b/_sources/datamodels/association/RollupGroup.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RollupGroup
diff --git a/_sources/datamodels/association/aggregator_knowledge_source.md.txt b/_sources/datamodels/association/aggregator_knowledge_source.md.txt
index 5c5c86e80..4235ad70b 100644
--- a/_sources/datamodels/association/aggregator_knowledge_source.md.txt
+++ b/_sources/datamodels/association/aggregator_knowledge_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: aggregator_knowledge_source
@@ -14,15 +16,16 @@ URI: [biolink:aggregator_knowledge_source](https://w3id.org/biolink/vocab/aggreg
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/associations.md.txt b/_sources/datamodels/association/associations.md.txt
index 1f9f89adc..61f3d9b51 100644
--- a/_sources/datamodels/association/associations.md.txt
+++ b/_sources/datamodels/association/associations.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: associations
@@ -14,11 +16,12 @@ URI: [ontoassoc:associations](https://w3id.org/oak/association/associations)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/_sources/datamodels/association/associations_for_subjects_in_common.md.txt b/_sources/datamodels/association/associations_for_subjects_in_common.md.txt
index 20779f6d4..b13feab0d 100644
--- a/_sources/datamodels/association/associations_for_subjects_in_common.md.txt
+++ b/_sources/datamodels/association/associations_for_subjects_in_common.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: associations_for_subjects_in_common
URI: [ontoassoc:associations_for_subjects_in_common](https://w3id.org/oak/association/associations_for_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:associations_for_subjects_in_common](https://w3id.org/oak/associ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/closure_delta.md.txt b/_sources/datamodels/association/closure_delta.md.txt
index 54a469f79..8cda97305 100644
--- a/_sources/datamodels/association/closure_delta.md.txt
+++ b/_sources/datamodels/association/closure_delta.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: closure_delta
URI: [ontoassoc:closure_delta](https://w3id.org/oak/association/closure_delta)
@@ -9,11 +11,12 @@ URI: [ontoassoc:closure_delta](https://w3id.org/oak/association/closure_delta)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/closure_information_content_delta.md.txt b/_sources/datamodels/association/closure_information_content_delta.md.txt
index e178dbe3e..42a6f3ce5 100644
--- a/_sources/datamodels/association/closure_information_content_delta.md.txt
+++ b/_sources/datamodels/association/closure_information_content_delta.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: closure_information_content_delta
URI: [ontoassoc:closure_information_content_delta](https://w3id.org/oak/association/closure_information_content_delta)
@@ -12,6 +14,7 @@ URI: [ontoassoc:closure_information_content_delta](https://w3id.org/oak/associat
+
## Properties
* Range: [Float](Float.md)
diff --git a/_sources/datamodels/association/closure_predicates.md.txt b/_sources/datamodels/association/closure_predicates.md.txt
index 55a4f23ae..239136c35 100644
--- a/_sources/datamodels/association/closure_predicates.md.txt
+++ b/_sources/datamodels/association/closure_predicates.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: closure_predicates
@@ -14,11 +16,12 @@ URI: [ontoassoc:closure_predicates](https://w3id.org/oak/association/closure_pre
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/comments.md.txt b/_sources/datamodels/association/comments.md.txt
index e97541492..5338dac80 100644
--- a/_sources/datamodels/association/comments.md.txt
+++ b/_sources/datamodels/association/comments.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: comments
@@ -14,13 +16,14 @@ URI: [rdfs:comment](rdfs:comment)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/core_triple.md.txt b/_sources/datamodels/association/core_triple.md.txt
index 73c1341a3..c46f8d8f3 100644
--- a/_sources/datamodels/association/core_triple.md.txt
+++ b/_sources/datamodels/association/core_triple.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: core_triple
@@ -17,6 +19,7 @@ URI: [ontoassoc:core_triple](https://w3id.org/oak/association/core_triple)
+
## Properties
* Range: NONE
diff --git a/_sources/datamodels/association/creation_date.md.txt b/_sources/datamodels/association/creation_date.md.txt
index 8b83b861c..c17995a2e 100644
--- a/_sources/datamodels/association/creation_date.md.txt
+++ b/_sources/datamodels/association/creation_date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: creation_date
@@ -22,6 +24,7 @@ URI: [ontoassoc:creation_date](https://w3id.org/oak/association/creation_date)
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/association/date.md.txt b/_sources/datamodels/association/date.md.txt
index 8822ae1dc..89646125e 100644
--- a/_sources/datamodels/association/date.md.txt
+++ b/_sources/datamodels/association/date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: date
@@ -25,6 +27,7 @@ URI: [ontoassoc:date](https://w3id.org/oak/association/date)
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/association/denormalized_slot.md.txt b/_sources/datamodels/association/denormalized_slot.md.txt
index 664af15c0..6ea3d11d6 100644
--- a/_sources/datamodels/association/denormalized_slot.md.txt
+++ b/_sources/datamodels/association/denormalized_slot.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: denormalized_slot
@@ -16,6 +18,7 @@ URI: [ontoassoc:denormalized_slot](https://w3id.org/oak/association/denormalized
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/association/diff_slot.md.txt b/_sources/datamodels/association/diff_slot.md.txt
index da4b8a918..9674038e8 100644
--- a/_sources/datamodels/association/diff_slot.md.txt
+++ b/_sources/datamodels/association/diff_slot.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: diff_slot
@@ -16,6 +18,7 @@ URI: [ontoassoc:diff_slot](https://w3id.org/oak/association/diff_slot)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/association/evidence_type.md.txt b/_sources/datamodels/association/evidence_type.md.txt
index 56ce08bd0..b2e2255bf 100644
--- a/_sources/datamodels/association/evidence_type.md.txt
+++ b/_sources/datamodels/association/evidence_type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: evidence_type
@@ -14,13 +16,14 @@ URI: [ontoassoc:evidence_type](https://w3id.org/oak/association/evidence_type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/group_object.md.txt b/_sources/datamodels/association/group_object.md.txt
index 204e06078..8c44e92b0 100644
--- a/_sources/datamodels/association/group_object.md.txt
+++ b/_sources/datamodels/association/group_object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: group_object
@@ -16,11 +18,12 @@ URI: [rdf:object](rdf:object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/_sources/datamodels/association/include_association_attributes.md.txt b/_sources/datamodels/association/include_association_attributes.md.txt
index cd65ec7a0..4bd4e3fcb 100644
--- a/_sources/datamodels/association/include_association_attributes.md.txt
+++ b/_sources/datamodels/association/include_association_attributes.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: include_association_attributes
@@ -16,11 +18,12 @@ URI: [ontoassoc:include_association_attributes](https://w3id.org/oak/association
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
diff --git a/_sources/datamodels/association/is_creation.md.txt b/_sources/datamodels/association/is_creation.md.txt
index f42dc97a2..76cba8f14 100644
--- a/_sources/datamodels/association/is_creation.md.txt
+++ b/_sources/datamodels/association/is_creation.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_creation
URI: [ontoassoc:is_creation](https://w3id.org/oak/association/is_creation)
@@ -13,11 +15,12 @@ URI: [ontoassoc:is_creation](https://w3id.org/oak/association/is_creation)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/is_deletion.md.txt b/_sources/datamodels/association/is_deletion.md.txt
index a1dd5723a..f7c119bb1 100644
--- a/_sources/datamodels/association/is_deletion.md.txt
+++ b/_sources/datamodels/association/is_deletion.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_deletion
URI: [ontoassoc:is_deletion](https://w3id.org/oak/association/is_deletion)
@@ -13,11 +15,12 @@ URI: [ontoassoc:is_deletion](https://w3id.org/oak/association/is_deletion)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/is_generalization.md.txt b/_sources/datamodels/association/is_generalization.md.txt
index 4c42baa06..1c6dd7e59 100644
--- a/_sources/datamodels/association/is_generalization.md.txt
+++ b/_sources/datamodels/association/is_generalization.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_generalization
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_generalization](https://w3id.org/oak/association/is_generaliz
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/is_migration.md.txt b/_sources/datamodels/association/is_migration.md.txt
index e098372c6..3ce642ef8 100644
--- a/_sources/datamodels/association/is_migration.md.txt
+++ b/_sources/datamodels/association/is_migration.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_migration
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_migration](https://w3id.org/oak/association/is_migration)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/is_specialization.md.txt b/_sources/datamodels/association/is_specialization.md.txt
index 3fc50eb48..24f4200f3 100644
--- a/_sources/datamodels/association/is_specialization.md.txt
+++ b/_sources/datamodels/association/is_specialization.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_specialization
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_specialization](https://w3id.org/oak/association/is_specializ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/modification_date.md.txt b/_sources/datamodels/association/modification_date.md.txt
index a67143b71..2533dd328 100644
--- a/_sources/datamodels/association/modification_date.md.txt
+++ b/_sources/datamodels/association/modification_date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: modification_date
@@ -22,6 +24,7 @@ URI: [ontoassoc:modification_date](https://w3id.org/oak/association/modification
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/association/negated.md.txt b/_sources/datamodels/association/negated.md.txt
index 309367504..bb4ed6c2e 100644
--- a/_sources/datamodels/association/negated.md.txt
+++ b/_sources/datamodels/association/negated.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: negated
@@ -14,13 +16,14 @@ URI: [ontoassoc:negated](https://w3id.org/oak/association/negated)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | yes |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | yes |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |
diff --git a/_sources/datamodels/association/new_date.md.txt b/_sources/datamodels/association/new_date.md.txt
index 7af4466a1..2a3a652e0 100644
--- a/_sources/datamodels/association/new_date.md.txt
+++ b/_sources/datamodels/association/new_date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: new_date
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_date](https://w3id.org/oak/association/new_date)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/new_object.md.txt b/_sources/datamodels/association/new_object.md.txt
index 9057bb2cc..6e8e16647 100644
--- a/_sources/datamodels/association/new_object.md.txt
+++ b/_sources/datamodels/association/new_object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: new_object
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_object](https://w3id.org/oak/association/new_object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/new_predicate.md.txt b/_sources/datamodels/association/new_predicate.md.txt
index 2a3cb7948..f2bf07783 100644
--- a/_sources/datamodels/association/new_predicate.md.txt
+++ b/_sources/datamodels/association/new_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: new_predicate
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_predicate](https://w3id.org/oak/association/new_predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/number_subject_unique_to_entity1.md.txt b/_sources/datamodels/association/number_subject_unique_to_entity1.md.txt
index 30d376fee..50ed2c57e 100644
--- a/_sources/datamodels/association/number_subject_unique_to_entity1.md.txt
+++ b/_sources/datamodels/association/number_subject_unique_to_entity1.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: number_subject_unique_to_entity1
URI: [ontoassoc:number_subject_unique_to_entity1](https://w3id.org/oak/association/number_subject_unique_to_entity1)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subject_unique_to_entity1](https://w3id.org/oak/associati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/number_subject_unique_to_entity2.md.txt b/_sources/datamodels/association/number_subject_unique_to_entity2.md.txt
index bd05df889..a71870388 100644
--- a/_sources/datamodels/association/number_subject_unique_to_entity2.md.txt
+++ b/_sources/datamodels/association/number_subject_unique_to_entity2.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: number_subject_unique_to_entity2
URI: [ontoassoc:number_subject_unique_to_entity2](https://w3id.org/oak/association/number_subject_unique_to_entity2)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subject_unique_to_entity2](https://w3id.org/oak/associati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/number_subjects_in_common.md.txt b/_sources/datamodels/association/number_subjects_in_common.md.txt
index 23869981d..a192111ba 100644
--- a/_sources/datamodels/association/number_subjects_in_common.md.txt
+++ b/_sources/datamodels/association/number_subjects_in_common.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: number_subjects_in_common
URI: [ontoassoc:number_subjects_in_common](https://w3id.org/oak/association/number_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subjects_in_common](https://w3id.org/oak/association/numb
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/number_subjects_in_union.md.txt b/_sources/datamodels/association/number_subjects_in_union.md.txt
index dc697f45c..8ff130046 100644
--- a/_sources/datamodels/association/number_subjects_in_union.md.txt
+++ b/_sources/datamodels/association/number_subjects_in_union.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: number_subjects_in_union
URI: [ontoassoc:number_subjects_in_union](https://w3id.org/oak/association/number_subjects_in_union)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subjects_in_union](https://w3id.org/oak/association/numbe
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/object.md.txt b/_sources/datamodels/association/object.md.txt
index ff46dff60..8ecf0284e 100644
--- a/_sources/datamodels/association/object.md.txt
+++ b/_sources/datamodels/association/object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object
@@ -22,14 +24,15 @@ URI: [rdf:object](rdf:object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/object1.md.txt b/_sources/datamodels/association/object1.md.txt
index cb44fc4e8..80a7899cb 100644
--- a/_sources/datamodels/association/object1.md.txt
+++ b/_sources/datamodels/association/object1.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object1
URI: [ontoassoc:object1](https://w3id.org/oak/association/object1)
@@ -14,11 +16,12 @@ URI: [ontoassoc:object1](https://w3id.org/oak/association/object1)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/object1_label.md.txt b/_sources/datamodels/association/object1_label.md.txt
index 6126c4ebc..2c0645c0d 100644
--- a/_sources/datamodels/association/object1_label.md.txt
+++ b/_sources/datamodels/association/object1_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object1_label
URI: [ontoassoc:object1_label](https://w3id.org/oak/association/object1_label)
@@ -9,11 +11,12 @@ URI: [ontoassoc:object1_label](https://w3id.org/oak/association/object1_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/object2.md.txt b/_sources/datamodels/association/object2.md.txt
index a0765979d..b318599f2 100644
--- a/_sources/datamodels/association/object2.md.txt
+++ b/_sources/datamodels/association/object2.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object2
URI: [ontoassoc:object2](https://w3id.org/oak/association/object2)
@@ -14,11 +16,12 @@ URI: [ontoassoc:object2](https://w3id.org/oak/association/object2)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/object2_label.md.txt b/_sources/datamodels/association/object2_label.md.txt
index 1b194f012..61b80943e 100644
--- a/_sources/datamodels/association/object2_label.md.txt
+++ b/_sources/datamodels/association/object2_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object2_label
URI: [ontoassoc:object2_label](https://w3id.org/oak/association/object2_label)
@@ -9,11 +11,12 @@ URI: [ontoassoc:object2_label](https://w3id.org/oak/association/object2_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/object_closure.md.txt b/_sources/datamodels/association/object_closure.md.txt
index 971dacf41..dd17757aa 100644
--- a/_sources/datamodels/association/object_closure.md.txt
+++ b/_sources/datamodels/association/object_closure.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_closure
@@ -14,13 +16,14 @@ URI: [ontoassoc:object_closure](https://w3id.org/oak/association/object_closure)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/object_closure_label.md.txt b/_sources/datamodels/association/object_closure_label.md.txt
index fe6874215..22c81c3d9 100644
--- a/_sources/datamodels/association/object_closure_label.md.txt
+++ b/_sources/datamodels/association/object_closure_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_closure_label
@@ -14,13 +16,14 @@ URI: [ontoassoc:object_closure_label](https://w3id.org/oak/association/object_cl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/object_label.md.txt b/_sources/datamodels/association/object_label.md.txt
index 50e79ddfe..75f63c2c0 100644
--- a/_sources/datamodels/association/object_label.md.txt
+++ b/_sources/datamodels/association/object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_label
@@ -18,13 +20,14 @@ URI: [sssom:object_label](https://w3id.org/sssom/object_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/old_date.md.txt b/_sources/datamodels/association/old_date.md.txt
index 90fbd5587..aceadbfcc 100644
--- a/_sources/datamodels/association/old_date.md.txt
+++ b/_sources/datamodels/association/old_date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: old_date
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_date](https://w3id.org/oak/association/old_date)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/old_object.md.txt b/_sources/datamodels/association/old_object.md.txt
index 90e8d4fc8..388414f42 100644
--- a/_sources/datamodels/association/old_object.md.txt
+++ b/_sources/datamodels/association/old_object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: old_object
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_object](https://w3id.org/oak/association/old_object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/old_object_obsolete.md.txt b/_sources/datamodels/association/old_object_obsolete.md.txt
index 7263a8641..fb5258224 100644
--- a/_sources/datamodels/association/old_object_obsolete.md.txt
+++ b/_sources/datamodels/association/old_object_obsolete.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: old_object_obsolete
@@ -18,11 +20,12 @@ URI: [ontoassoc:old_object_obsolete](https://w3id.org/oak/association/old_object
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/old_predicate.md.txt b/_sources/datamodels/association/old_predicate.md.txt
index 808437d71..eabbabbff 100644
--- a/_sources/datamodels/association/old_predicate.md.txt
+++ b/_sources/datamodels/association/old_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: old_predicate
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_predicate](https://w3id.org/oak/association/old_predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/original_object.md.txt b/_sources/datamodels/association/original_object.md.txt
index ac624f88d..160f08131 100644
--- a/_sources/datamodels/association/original_object.md.txt
+++ b/_sources/datamodels/association/original_object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: original_object
@@ -17,6 +19,7 @@ URI: [biolink:original_object](https://w3id.org/biolink/vocab/original_object)
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/_sources/datamodels/association/original_predicate.md.txt b/_sources/datamodels/association/original_predicate.md.txt
index 075d71267..2dd79831c 100644
--- a/_sources/datamodels/association/original_predicate.md.txt
+++ b/_sources/datamodels/association/original_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: original_predicate
@@ -17,6 +19,7 @@ URI: [biolink:original_predicate](https://w3id.org/biolink/vocab/original_predic
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/_sources/datamodels/association/original_subject.md.txt b/_sources/datamodels/association/original_subject.md.txt
index 54422c76f..9699f3530 100644
--- a/_sources/datamodels/association/original_subject.md.txt
+++ b/_sources/datamodels/association/original_subject.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: original_subject
@@ -17,6 +19,7 @@ URI: [biolink:original_subject](https://w3id.org/biolink/vocab/original_subject)
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/_sources/datamodels/association/predicate.md.txt b/_sources/datamodels/association/predicate.md.txt
index 29daf4ea2..225aeff14 100644
--- a/_sources/datamodels/association/predicate.md.txt
+++ b/_sources/datamodels/association/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
@@ -20,14 +22,15 @@ URI: [rdf:predicate](rdf:predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/predicate_label.md.txt b/_sources/datamodels/association/predicate_label.md.txt
index 26a54fd8a..fb6f77f24 100644
--- a/_sources/datamodels/association/predicate_label.md.txt
+++ b/_sources/datamodels/association/predicate_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_label
@@ -18,13 +20,14 @@ URI: [sssom:predicate_label](https://w3id.org/sssom/predicate_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/preserve_negated_associations.md.txt b/_sources/datamodels/association/preserve_negated_associations.md.txt
index b346925ff..9b7a82b92 100644
--- a/_sources/datamodels/association/preserve_negated_associations.md.txt
+++ b/_sources/datamodels/association/preserve_negated_associations.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: preserve_negated_associations
@@ -16,11 +18,12 @@ URI: [ontoassoc:preserve_negated_associations](https://w3id.org/oak/association/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
diff --git a/_sources/datamodels/association/primary_knowledge_source.md.txt b/_sources/datamodels/association/primary_knowledge_source.md.txt
index df5b9574c..408f26b6b 100644
--- a/_sources/datamodels/association/primary_knowledge_source.md.txt
+++ b/_sources/datamodels/association/primary_knowledge_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: primary_knowledge_source
@@ -14,15 +16,16 @@ URI: [biolink:primary_knowledge_source](https://w3id.org/biolink/vocab/primary_k
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/property_values.md.txt b/_sources/datamodels/association/property_values.md.txt
index 3a92163fb..5b07f38cb 100644
--- a/_sources/datamodels/association/property_values.md.txt
+++ b/_sources/datamodels/association/property_values.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: property_values
@@ -14,13 +16,14 @@ URI: [ontoassoc:property_values](https://w3id.org/oak/association/property_value
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/proportion_subjects_in_common.md.txt b/_sources/datamodels/association/proportion_subjects_in_common.md.txt
index 50e95fac8..24d1c1466 100644
--- a/_sources/datamodels/association/proportion_subjects_in_common.md.txt
+++ b/_sources/datamodels/association/proportion_subjects_in_common.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: proportion_subjects_in_common
URI: [ontoassoc:proportion_subjects_in_common](https://w3id.org/oak/association/proportion_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:proportion_subjects_in_common](https://w3id.org/oak/association/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/publication_is_added.md.txt b/_sources/datamodels/association/publication_is_added.md.txt
index bcebb291e..16593417a 100644
--- a/_sources/datamodels/association/publication_is_added.md.txt
+++ b/_sources/datamodels/association/publication_is_added.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: publication_is_added
@@ -18,11 +20,12 @@ URI: [ontoassoc:publication_is_added](https://w3id.org/oak/association/publicati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/publication_is_deleted.md.txt b/_sources/datamodels/association/publication_is_deleted.md.txt
index e789f910a..e0f8d2f89 100644
--- a/_sources/datamodels/association/publication_is_deleted.md.txt
+++ b/_sources/datamodels/association/publication_is_deleted.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: publication_is_deleted
@@ -18,11 +20,12 @@ URI: [ontoassoc:publication_is_deleted](https://w3id.org/oak/association/publica
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/publications.md.txt b/_sources/datamodels/association/publications.md.txt
index 911a93bf5..d0fce79f5 100644
--- a/_sources/datamodels/association/publications.md.txt
+++ b/_sources/datamodels/association/publications.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: publications
@@ -14,14 +16,15 @@ URI: [biolink:publications](https://w3id.org/biolink/vocab/publications)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/sub_groups.md.txt b/_sources/datamodels/association/sub_groups.md.txt
index 0b0f2d761..6d720933d 100644
--- a/_sources/datamodels/association/sub_groups.md.txt
+++ b/_sources/datamodels/association/sub_groups.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sub_groups
@@ -14,11 +16,12 @@ URI: [ontoassoc:sub_groups](https://w3id.org/oak/association/sub_groups)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/_sources/datamodels/association/subject.md.txt b/_sources/datamodels/association/subject.md.txt
index 98ea8bafa..0abe5ca35 100644
--- a/_sources/datamodels/association/subject.md.txt
+++ b/_sources/datamodels/association/subject.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject
@@ -14,14 +16,15 @@ URI: [rdf:subject](rdf:subject)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/subject_closure.md.txt b/_sources/datamodels/association/subject_closure.md.txt
index fd51eda13..e6e80b77f 100644
--- a/_sources/datamodels/association/subject_closure.md.txt
+++ b/_sources/datamodels/association/subject_closure.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_closure
@@ -14,13 +16,14 @@ URI: [ontoassoc:subject_closure](https://w3id.org/oak/association/subject_closur
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/subject_closure_label.md.txt b/_sources/datamodels/association/subject_closure_label.md.txt
index 633145943..099f5454d 100644
--- a/_sources/datamodels/association/subject_closure_label.md.txt
+++ b/_sources/datamodels/association/subject_closure_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_closure_label
@@ -14,13 +16,14 @@ URI: [ontoassoc:subject_closure_label](https://w3id.org/oak/association/subject_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/subject_label.md.txt b/_sources/datamodels/association/subject_label.md.txt
index ac384ec45..a09790574 100644
--- a/_sources/datamodels/association/subject_label.md.txt
+++ b/_sources/datamodels/association/subject_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_label
@@ -18,13 +20,14 @@ URI: [sssom:subject_label](https://w3id.org/sssom/subject_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/association/subjects_in_common.md.txt b/_sources/datamodels/association/subjects_in_common.md.txt
index 88116a27c..8373ab693 100644
--- a/_sources/datamodels/association/subjects_in_common.md.txt
+++ b/_sources/datamodels/association/subjects_in_common.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subjects_in_common
URI: [ontoassoc:subjects_in_common](https://w3id.org/oak/association/subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:subjects_in_common](https://w3id.org/oak/association/subjects_in
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/_sources/datamodels/association/summary_group.md.txt b/_sources/datamodels/association/summary_group.md.txt
index c5b3f5f23..b6e524d76 100644
--- a/_sources/datamodels/association/summary_group.md.txt
+++ b/_sources/datamodels/association/summary_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: summary_group
@@ -14,11 +16,12 @@ URI: [ontoassoc:summary_group](https://w3id.org/oak/association/summary_group)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/_sources/datamodels/association/supporting_objects.md.txt b/_sources/datamodels/association/supporting_objects.md.txt
index b511bcd5e..66c2e0958 100644
--- a/_sources/datamodels/association/supporting_objects.md.txt
+++ b/_sources/datamodels/association/supporting_objects.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: supporting_objects
@@ -14,13 +16,14 @@ URI: [ontoassoc:supporting_objects](https://w3id.org/oak/association/supporting_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/_sources/datamodels/class-enrichment/ClassEnrichmentConfiguration.md.txt b/_sources/datamodels/class-enrichment/ClassEnrichmentConfiguration.md.txt
index d7b909018..233b8556d 100644
--- a/_sources/datamodels/class-enrichment/ClassEnrichmentConfiguration.md.txt
+++ b/_sources/datamodels/class-enrichment/ClassEnrichmentConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentConfiguration
diff --git a/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt b/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt
index 83b645c0d..e636d68e5 100644
--- a/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt
+++ b/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentResult
diff --git a/_sources/datamodels/class-enrichment/ClassEnrichmentResultSet.md.txt b/_sources/datamodels/class-enrichment/ClassEnrichmentResultSet.md.txt
index cb2dd0f8c..350919796 100644
--- a/_sources/datamodels/class-enrichment/ClassEnrichmentResultSet.md.txt
+++ b/_sources/datamodels/class-enrichment/ClassEnrichmentResultSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentResultSet
diff --git a/_sources/datamodels/class-enrichment/ancestor_of_more_informative_result.md.txt b/_sources/datamodels/class-enrichment/ancestor_of_more_informative_result.md.txt
index e78378f1b..86021ae36 100644
--- a/_sources/datamodels/class-enrichment/ancestor_of_more_informative_result.md.txt
+++ b/_sources/datamodels/class-enrichment/ancestor_of_more_informative_result.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_of_more_informative_result
@@ -14,11 +16,12 @@ URI: [ontoenrich:ancestor_of_more_informative_result](https://w3id.org/oak/class
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/background_count.md.txt b/_sources/datamodels/class-enrichment/background_count.md.txt
index 5239b0569..6d0f9ffe9 100644
--- a/_sources/datamodels/class-enrichment/background_count.md.txt
+++ b/_sources/datamodels/class-enrichment/background_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: background_count
@@ -14,11 +16,12 @@ URI: [ontoenrich:background_count](https://w3id.org/oak/class-enrichment/backgro
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/background_total.md.txt b/_sources/datamodels/class-enrichment/background_total.md.txt
index 4bdbe51d2..1e8e9dfce 100644
--- a/_sources/datamodels/class-enrichment/background_total.md.txt
+++ b/_sources/datamodels/class-enrichment/background_total.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: background_total
@@ -14,11 +16,12 @@ URI: [ontoenrich:background_total](https://w3id.org/oak/class-enrichment/backgro
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/class_id.md.txt b/_sources/datamodels/class-enrichment/class_id.md.txt
index e6cd668f5..752105a48 100644
--- a/_sources/datamodels/class-enrichment/class_id.md.txt
+++ b/_sources/datamodels/class-enrichment/class_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_id
@@ -14,11 +16,12 @@ URI: [ontoenrich:class_id](https://w3id.org/oak/class-enrichment/class_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/class_label.md.txt b/_sources/datamodels/class-enrichment/class_label.md.txt
index ff02e2ce5..3ac4c4c17 100644
--- a/_sources/datamodels/class-enrichment/class_label.md.txt
+++ b/_sources/datamodels/class-enrichment/class_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_label
@@ -14,11 +16,12 @@ URI: [ontoenrich:class_label](https://w3id.org/oak/class-enrichment/class_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/descendant_of_more_informative_result.md.txt b/_sources/datamodels/class-enrichment/descendant_of_more_informative_result.md.txt
index aced0a5cd..9068006a6 100644
--- a/_sources/datamodels/class-enrichment/descendant_of_more_informative_result.md.txt
+++ b/_sources/datamodels/class-enrichment/descendant_of_more_informative_result.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: descendant_of_more_informative_result
@@ -14,11 +16,12 @@ URI: [ontoenrich:descendant_of_more_informative_result](https://w3id.org/oak/cla
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/direction.md.txt b/_sources/datamodels/class-enrichment/direction.md.txt
index 1f517dcc7..ae18ce22d 100644
--- a/_sources/datamodels/class-enrichment/direction.md.txt
+++ b/_sources/datamodels/class-enrichment/direction.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: direction
@@ -14,11 +16,12 @@ URI: [ontoenrich:direction](https://w3id.org/oak/class-enrichment/direction)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/false_discovery_rate.md.txt b/_sources/datamodels/class-enrichment/false_discovery_rate.md.txt
index 5fba7b1c0..17ae3b342 100644
--- a/_sources/datamodels/class-enrichment/false_discovery_rate.md.txt
+++ b/_sources/datamodels/class-enrichment/false_discovery_rate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: false_discovery_rate
@@ -14,11 +16,12 @@ URI: [ontoenrich:false_discovery_rate](https://w3id.org/oak/class-enrichment/fal
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/fold_enrichment.md.txt b/_sources/datamodels/class-enrichment/fold_enrichment.md.txt
index fe1ac5e44..43c6330ef 100644
--- a/_sources/datamodels/class-enrichment/fold_enrichment.md.txt
+++ b/_sources/datamodels/class-enrichment/fold_enrichment.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: fold_enrichment
@@ -14,11 +16,12 @@ URI: [ontoenrich:fold_enrichment](https://w3id.org/oak/class-enrichment/fold_enr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/p_value.md.txt b/_sources/datamodels/class-enrichment/p_value.md.txt
index 61f70a30f..9ff7b0882 100644
--- a/_sources/datamodels/class-enrichment/p_value.md.txt
+++ b/_sources/datamodels/class-enrichment/p_value.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: p_value
@@ -14,11 +16,12 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/p_value_adjusted.md.txt b/_sources/datamodels/class-enrichment/p_value_adjusted.md.txt
index 0454987a8..36a088b87 100644
--- a/_sources/datamodels/class-enrichment/p_value_adjusted.md.txt
+++ b/_sources/datamodels/class-enrichment/p_value_adjusted.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: p_value_adjusted
@@ -14,11 +16,12 @@ URI: [ontoenrich:p_value_adjusted](https://w3id.org/oak/class-enrichment/p_value
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/p_value_cutoff.md.txt b/_sources/datamodels/class-enrichment/p_value_cutoff.md.txt
index 20a79e048..e3ae594ce 100644
--- a/_sources/datamodels/class-enrichment/p_value_cutoff.md.txt
+++ b/_sources/datamodels/class-enrichment/p_value_cutoff.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: p_value_cutoff
@@ -14,11 +16,12 @@ URI: [ontoenrich:p_value_cutoff](https://w3id.org/oak/class-enrichment/p_value_c
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) | configuration for search | no |
+| [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/class-enrichment/probability.md.txt b/_sources/datamodels/class-enrichment/probability.md.txt
index 14a0b7182..e48180fe3 100644
--- a/_sources/datamodels/class-enrichment/probability.md.txt
+++ b/_sources/datamodels/class-enrichment/probability.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: probability
@@ -14,11 +16,12 @@ URI: [ontoenrich:probability](https://w3id.org/oak/class-enrichment/probability)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/rank.md.txt b/_sources/datamodels/class-enrichment/rank.md.txt
index 9ce942478..0782218ed 100644
--- a/_sources/datamodels/class-enrichment/rank.md.txt
+++ b/_sources/datamodels/class-enrichment/rank.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: rank
@@ -14,11 +16,12 @@ URI: [ontoenrich:rank](https://w3id.org/oak/class-enrichment/rank)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/results.md.txt b/_sources/datamodels/class-enrichment/results.md.txt
index 46e382bdf..48d82cb43 100644
--- a/_sources/datamodels/class-enrichment/results.md.txt
+++ b/_sources/datamodels/class-enrichment/results.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: results
@@ -14,11 +16,12 @@ URI: [ontoenrich:results](https://w3id.org/oak/class-enrichment/results)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) | A collection of enrichemt results | no |
+| [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) | A collection of enrichemt results | no |
diff --git a/_sources/datamodels/class-enrichment/sample_count.md.txt b/_sources/datamodels/class-enrichment/sample_count.md.txt
index 8b70341a9..6f2885fc1 100644
--- a/_sources/datamodels/class-enrichment/sample_count.md.txt
+++ b/_sources/datamodels/class-enrichment/sample_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sample_count
@@ -14,11 +16,12 @@ URI: [ontoenrich:sample_count](https://w3id.org/oak/class-enrichment/sample_coun
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/class-enrichment/sample_total.md.txt b/_sources/datamodels/class-enrichment/sample_total.md.txt
index bb0af2f7f..3468519cf 100644
--- a/_sources/datamodels/class-enrichment/sample_total.md.txt
+++ b/_sources/datamodels/class-enrichment/sample_total.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sample_total
@@ -14,11 +16,12 @@ URI: [ontoenrich:sample_total](https://w3id.org/oak/class-enrichment/sample_tota
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/_sources/datamodels/cross-ontology-diff/RelationalDiff.md.txt b/_sources/datamodels/cross-ontology-diff/RelationalDiff.md.txt
index d8f0346ed..e523cbf73 100644
--- a/_sources/datamodels/cross-ontology-diff/RelationalDiff.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/RelationalDiff.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RelationalDiff
diff --git a/_sources/datamodels/cross-ontology-diff/StructureDiffResultSet.md.txt b/_sources/datamodels/cross-ontology-diff/StructureDiffResultSet.md.txt
index 6fb844ded..18d6ab4dc 100644
--- a/_sources/datamodels/cross-ontology-diff/StructureDiffResultSet.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/StructureDiffResultSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: StructureDiffResultSet
diff --git a/_sources/datamodels/cross-ontology-diff/category.md.txt b/_sources/datamodels/cross-ontology-diff/category.md.txt
index a7e4cc6d4..123b46bfb 100644
--- a/_sources/datamodels/cross-ontology-diff/category.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/category.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: category
@@ -14,11 +16,12 @@ URI: [xodiff:category](https://w3id.org/oak/cross-ontology-diff/category)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/is_functional.md.txt b/_sources/datamodels/cross-ontology-diff/is_functional.md.txt
index ae2d92f6b..ab55c245d 100644
--- a/_sources/datamodels/cross-ontology-diff/is_functional.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/is_functional.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_functional
@@ -16,6 +18,7 @@ URI: [xodiff:is_functional](https://w3id.org/oak/cross-ontology-diff/is_function
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/label.md.txt b/_sources/datamodels/cross-ontology-diff/label.md.txt
index 82dfbf859..a78fc6bdc 100644
--- a/_sources/datamodels/cross-ontology-diff/label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: label
@@ -16,6 +18,7 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/left_object_id.md.txt b/_sources/datamodels/cross-ontology-diff/left_object_id.md.txt
index 280ff94d6..38637d463 100644
--- a/_sources/datamodels/cross-ontology-diff/left_object_id.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_object_id
@@ -18,11 +20,12 @@ URI: [xodiff:left_object_id](https://w3id.org/oak/cross-ontology-diff/left_objec
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_object_is_functional.md.txt b/_sources/datamodels/cross-ontology-diff/left_object_is_functional.md.txt
index 29cba2a4d..2dcacc40e 100644
--- a/_sources/datamodels/cross-ontology-diff/left_object_is_functional.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_object_is_functional.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_object_is_functional
@@ -18,11 +20,12 @@ URI: [xodiff:left_object_is_functional](https://w3id.org/oak/cross-ontology-diff
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_object_label.md.txt b/_sources/datamodels/cross-ontology-diff/left_object_label.md.txt
index 6a545cedc..90149a5cf 100644
--- a/_sources/datamodels/cross-ontology-diff/left_object_label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_object_label
@@ -18,11 +20,12 @@ URI: [xodiff:left_object_label](https://w3id.org/oak/cross-ontology-diff/left_ob
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_predicate_id.md.txt b/_sources/datamodels/cross-ontology-diff/left_predicate_id.md.txt
index f7753fa2a..90781f203 100644
--- a/_sources/datamodels/cross-ontology-diff/left_predicate_id.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_predicate_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_predicate_id
@@ -18,11 +20,12 @@ URI: [xodiff:left_predicate_id](https://w3id.org/oak/cross-ontology-diff/left_pr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_predicate_label.md.txt b/_sources/datamodels/cross-ontology-diff/left_predicate_label.md.txt
index 906042c1f..d121980ab 100644
--- a/_sources/datamodels/cross-ontology-diff/left_predicate_label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_predicate_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_predicate_label
@@ -18,11 +20,12 @@ URI: [xodiff:left_predicate_label](https://w3id.org/oak/cross-ontology-diff/left
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_side.md.txt b/_sources/datamodels/cross-ontology-diff/left_side.md.txt
index 6cf39c6e7..ee4145c38 100644
--- a/_sources/datamodels/cross-ontology-diff/left_side.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_side.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_side
@@ -21,6 +23,7 @@ URI: [xodiff:left_side](https://w3id.org/oak/cross-ontology-diff/left_side)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/left_source.md.txt b/_sources/datamodels/cross-ontology-diff/left_source.md.txt
index 5cedd14a7..98eb48ee1 100644
--- a/_sources/datamodels/cross-ontology-diff/left_source.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_source
@@ -14,11 +16,12 @@ URI: [xodiff:left_source](https://w3id.org/oak/cross-ontology-diff/left_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
+| [StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_subject_id.md.txt b/_sources/datamodels/cross-ontology-diff/left_subject_id.md.txt
index 6a26eb81e..53b073027 100644
--- a/_sources/datamodels/cross-ontology-diff/left_subject_id.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_subject_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_subject_id
@@ -18,11 +20,12 @@ URI: [xodiff:left_subject_id](https://w3id.org/oak/cross-ontology-diff/left_subj
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_subject_is_functional.md.txt b/_sources/datamodels/cross-ontology-diff/left_subject_is_functional.md.txt
index 04e9cda75..73f8051e0 100644
--- a/_sources/datamodels/cross-ontology-diff/left_subject_is_functional.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_subject_is_functional.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_subject_is_functional
@@ -18,11 +20,12 @@ URI: [xodiff:left_subject_is_functional](https://w3id.org/oak/cross-ontology-dif
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/left_subject_label.md.txt b/_sources/datamodels/cross-ontology-diff/left_subject_label.md.txt
index 9ec8e09fe..4903a9e7d 100644
--- a/_sources/datamodels/cross-ontology-diff/left_subject_label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/left_subject_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: left_subject_label
@@ -18,11 +20,12 @@ URI: [xodiff:left_subject_label](https://w3id.org/oak/cross-ontology-diff/left_s
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/object.md.txt b/_sources/datamodels/cross-ontology-diff/object.md.txt
index 196591203..4e07a10c5 100644
--- a/_sources/datamodels/cross-ontology-diff/object.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object
@@ -16,6 +18,7 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/object_mapping_cardinality.md.txt b/_sources/datamodels/cross-ontology-diff/object_mapping_cardinality.md.txt
index a74372d41..8978333c9 100644
--- a/_sources/datamodels/cross-ontology-diff/object_mapping_cardinality.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/object_mapping_cardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_mapping_cardinality
@@ -14,11 +16,12 @@ URI: [xodiff:object_mapping_cardinality](https://w3id.org/oak/cross-ontology-dif
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/object_mapping_predicate.md.txt b/_sources/datamodels/cross-ontology-diff/object_mapping_predicate.md.txt
index 492f2aedc..aaee8bd91 100644
--- a/_sources/datamodels/cross-ontology-diff/object_mapping_predicate.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/object_mapping_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_mapping_predicate
@@ -18,11 +20,12 @@ URI: [xodiff:object_mapping_predicate](https://w3id.org/oak/cross-ontology-diff/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/predicate.md.txt b/_sources/datamodels/cross-ontology-diff/predicate.md.txt
index f88d635ec..59ea84748 100644
--- a/_sources/datamodels/cross-ontology-diff/predicate.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
@@ -16,6 +18,7 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/results.md.txt b/_sources/datamodels/cross-ontology-diff/results.md.txt
index b36a645b6..ff0d18f26 100644
--- a/_sources/datamodels/cross-ontology-diff/results.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/results.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: results
@@ -14,11 +16,12 @@ URI: [xodiff:results](https://w3id.org/oak/cross-ontology-diff/results)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
+| [StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_intermediate_ids.md.txt b/_sources/datamodels/cross-ontology-diff/right_intermediate_ids.md.txt
index 9ce40c50d..cf5d431f6 100644
--- a/_sources/datamodels/cross-ontology-diff/right_intermediate_ids.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_intermediate_ids.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_intermediate_ids
URI: [xodiff:right_intermediate_ids](https://w3id.org/oak/cross-ontology-diff/right_intermediate_ids)
@@ -9,11 +11,12 @@ URI: [xodiff:right_intermediate_ids](https://w3id.org/oak/cross-ontology-diff/ri
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_object_id.md.txt b/_sources/datamodels/cross-ontology-diff/right_object_id.md.txt
index 236831abf..20ee78276 100644
--- a/_sources/datamodels/cross-ontology-diff/right_object_id.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_object_id
@@ -18,11 +20,12 @@ URI: [xodiff:right_object_id](https://w3id.org/oak/cross-ontology-diff/right_obj
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_object_label.md.txt b/_sources/datamodels/cross-ontology-diff/right_object_label.md.txt
index 583cca31a..484dec348 100644
--- a/_sources/datamodels/cross-ontology-diff/right_object_label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_object_label
@@ -18,11 +20,12 @@ URI: [xodiff:right_object_label](https://w3id.org/oak/cross-ontology-diff/right_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_predicate_ids.md.txt b/_sources/datamodels/cross-ontology-diff/right_predicate_ids.md.txt
index fc5d0f176..cae04116e 100644
--- a/_sources/datamodels/cross-ontology-diff/right_predicate_ids.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_predicate_ids.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_predicate_ids
@@ -22,11 +24,12 @@ URI: [xodiff:right_predicate_ids](https://w3id.org/oak/cross-ontology-diff/right
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_predicate_labels.md.txt b/_sources/datamodels/cross-ontology-diff/right_predicate_labels.md.txt
index 4c6c25382..413a429f7 100644
--- a/_sources/datamodels/cross-ontology-diff/right_predicate_labels.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_predicate_labels.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_predicate_labels
@@ -18,11 +20,12 @@ URI: [xodiff:right_predicate_labels](https://w3id.org/oak/cross-ontology-diff/ri
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_side.md.txt b/_sources/datamodels/cross-ontology-diff/right_side.md.txt
index ebd52c59a..4caad8d77 100644
--- a/_sources/datamodels/cross-ontology-diff/right_side.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_side.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_side
@@ -21,6 +23,7 @@ URI: [xodiff:right_side](https://w3id.org/oak/cross-ontology-diff/right_side)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/right_source.md.txt b/_sources/datamodels/cross-ontology-diff/right_source.md.txt
index dd25b528c..2c007fc5b 100644
--- a/_sources/datamodels/cross-ontology-diff/right_source.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_source
@@ -14,11 +16,12 @@ URI: [xodiff:right_source](https://w3id.org/oak/cross-ontology-diff/right_source
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
+| [StructureDiffResultSet](StructureDiffResultSet.md) | A collection of relational diff results | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_subject_id.md.txt b/_sources/datamodels/cross-ontology-diff/right_subject_id.md.txt
index 29a4d2128..0063bd0c1 100644
--- a/_sources/datamodels/cross-ontology-diff/right_subject_id.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_subject_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_subject_id
@@ -18,11 +20,12 @@ URI: [xodiff:right_subject_id](https://w3id.org/oak/cross-ontology-diff/right_su
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/right_subject_label.md.txt b/_sources/datamodels/cross-ontology-diff/right_subject_label.md.txt
index 532ae5e47..3cc2d8e94 100644
--- a/_sources/datamodels/cross-ontology-diff/right_subject_label.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/right_subject_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: right_subject_label
@@ -18,11 +20,12 @@ URI: [xodiff:right_subject_label](https://w3id.org/oak/cross-ontology-diff/right
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/side.md.txt b/_sources/datamodels/cross-ontology-diff/side.md.txt
index 70d275d6a..400248f02 100644
--- a/_sources/datamodels/cross-ontology-diff/side.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/side.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: side
@@ -22,6 +24,7 @@ URI: [xodiff:side](https://w3id.org/oak/cross-ontology-diff/side)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/subject.md.txt b/_sources/datamodels/cross-ontology-diff/subject.md.txt
index ad64031cb..02f074596 100644
--- a/_sources/datamodels/cross-ontology-diff/subject.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/subject.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject
@@ -16,6 +18,7 @@ URI: [rdf:subject](http://www.w3.org/1999/02/22-rdf-syntax-ns#subject)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/_sources/datamodels/cross-ontology-diff/subject_mapping_cardinality.md.txt b/_sources/datamodels/cross-ontology-diff/subject_mapping_cardinality.md.txt
index 248d21be0..51b275a02 100644
--- a/_sources/datamodels/cross-ontology-diff/subject_mapping_cardinality.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/subject_mapping_cardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_mapping_cardinality
@@ -14,11 +16,12 @@ URI: [xodiff:subject_mapping_cardinality](https://w3id.org/oak/cross-ontology-di
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/cross-ontology-diff/subject_mapping_predicate.md.txt b/_sources/datamodels/cross-ontology-diff/subject_mapping_predicate.md.txt
index 2df1a16ed..f3592fb1b 100644
--- a/_sources/datamodels/cross-ontology-diff/subject_mapping_predicate.md.txt
+++ b/_sources/datamodels/cross-ontology-diff/subject_mapping_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_mapping_predicate
@@ -18,11 +20,12 @@ URI: [xodiff:subject_mapping_predicate](https://w3id.org/oak/cross-ontology-diff
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
+| [RelationalDiff](RelationalDiff.md) | A relational diff expresses the difference between an edge in one ontology, a... | no |
diff --git a/_sources/datamodels/item-list/ItemList.md.txt b/_sources/datamodels/item-list/ItemList.md.txt
index dfcadab76..82320a423 100644
--- a/_sources/datamodels/item-list/ItemList.md.txt
+++ b/_sources/datamodels/item-list/ItemList.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ItemList
diff --git a/_sources/datamodels/item-list/ItemListCollection.md.txt b/_sources/datamodels/item-list/ItemListCollection.md.txt
index 7ce0a4256..36f621879 100644
--- a/_sources/datamodels/item-list/ItemListCollection.md.txt
+++ b/_sources/datamodels/item-list/ItemListCollection.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ItemListCollection
diff --git a/_sources/datamodels/item-list/ListItem.md.txt b/_sources/datamodels/item-list/ListItem.md.txt
index e59140902..41f2e2ce8 100644
--- a/_sources/datamodels/item-list/ListItem.md.txt
+++ b/_sources/datamodels/item-list/ListItem.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ListItem
diff --git a/_sources/datamodels/item-list/Thing.md.txt b/_sources/datamodels/item-list/Thing.md.txt
index ca449953f..f2b9a7920 100644
--- a/_sources/datamodels/item-list/Thing.md.txt
+++ b/_sources/datamodels/item-list/Thing.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Thing
diff --git a/_sources/datamodels/item-list/additionalType.md.txt b/_sources/datamodels/item-list/additionalType.md.txt
index a8511c343..668f6d548 100644
--- a/_sources/datamodels/item-list/additionalType.md.txt
+++ b/_sources/datamodels/item-list/additionalType.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: additionalType
@@ -14,11 +16,12 @@ URI: [schema:additionalType](http://schema.org/additionalType)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/categories.md.txt b/_sources/datamodels/item-list/categories.md.txt
index c544607b2..a700018cf 100644
--- a/_sources/datamodels/item-list/categories.md.txt
+++ b/_sources/datamodels/item-list/categories.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: categories
@@ -14,11 +16,12 @@ URI: [dcterms:subject](http://purl.org/dc/terms/subject)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/description.md.txt b/_sources/datamodels/item-list/description.md.txt
index a23213d7a..c02518245 100644
--- a/_sources/datamodels/item-list/description.md.txt
+++ b/_sources/datamodels/item-list/description.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: description
URI: [itemList:description](https://w3id.org/linkml/item-list/description)
@@ -9,12 +11,13 @@ URI: [itemList:description](https://w3id.org/linkml/item-list/description)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/elementId.md.txt b/_sources/datamodels/item-list/elementId.md.txt
index edb43eca1..3c2644b4a 100644
--- a/_sources/datamodels/item-list/elementId.md.txt
+++ b/_sources/datamodels/item-list/elementId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: elementId
@@ -16,11 +18,12 @@ URI: [itemList:elementId](https://w3id.org/linkml/item-list/elementId)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ListItem](ListItem.md) | an item in an item list | no |
+| [ListItem](ListItem.md) | an item in an item list | no |
diff --git a/_sources/datamodels/item-list/id.md.txt b/_sources/datamodels/item-list/id.md.txt
index a38576ec5..5d63d422f 100644
--- a/_sources/datamodels/item-list/id.md.txt
+++ b/_sources/datamodels/item-list/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
URI: [itemList:id](https://w3id.org/linkml/item-list/id)
@@ -9,12 +11,13 @@ URI: [itemList:id](https://w3id.org/linkml/item-list/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/idType.md.txt b/_sources/datamodels/item-list/idType.md.txt
index 9b9ec1948..936130f9f 100644
--- a/_sources/datamodels/item-list/idType.md.txt
+++ b/_sources/datamodels/item-list/idType.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: idType
@@ -14,11 +16,12 @@ URI: [itemList:idType](https://w3id.org/linkml/item-list/idType)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ListItem](ListItem.md) | an item in an item list | no |
+| [ListItem](ListItem.md) | an item in an item list | no |
diff --git a/_sources/datamodels/item-list/identifiers.md.txt b/_sources/datamodels/item-list/identifiers.md.txt
index 379ac0d53..9da37c55d 100644
--- a/_sources/datamodels/item-list/identifiers.md.txt
+++ b/_sources/datamodels/item-list/identifiers.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: identifiers
@@ -14,11 +16,12 @@ URI: [itemList:identifiers](https://w3id.org/linkml/item-list/identifiers)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
diff --git a/_sources/datamodels/item-list/item.md.txt b/_sources/datamodels/item-list/item.md.txt
index d1cf38c13..310ae5667 100644
--- a/_sources/datamodels/item-list/item.md.txt
+++ b/_sources/datamodels/item-list/item.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: item
@@ -14,11 +16,12 @@ URI: [schema:item](http://schema.org/item)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ListItem](ListItem.md) | an item in an item list | no |
+| [ListItem](ListItem.md) | an item in an item list | no |
diff --git a/_sources/datamodels/item-list/itemListElements.md.txt b/_sources/datamodels/item-list/itemListElements.md.txt
index 8438b5993..68aea01b2 100644
--- a/_sources/datamodels/item-list/itemListElements.md.txt
+++ b/_sources/datamodels/item-list/itemListElements.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: itemListElements
@@ -14,11 +16,12 @@ URI: [schema:itemListElement](http://schema.org/itemListElement)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/itemLists.md.txt b/_sources/datamodels/item-list/itemLists.md.txt
index 9c2ede6d7..50fe0099b 100644
--- a/_sources/datamodels/item-list/itemLists.md.txt
+++ b/_sources/datamodels/item-list/itemLists.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: itemLists
URI: [itemList:itemLists](https://w3id.org/linkml/item-list/itemLists)
@@ -9,11 +11,12 @@ URI: [itemList:itemLists](https://w3id.org/linkml/item-list/itemLists)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemListCollection](ItemListCollection.md) | a set of item lists | no |
+| [ItemListCollection](ItemListCollection.md) | a set of item lists | no |
diff --git a/_sources/datamodels/item-list/itemMetadataMap.md.txt b/_sources/datamodels/item-list/itemMetadataMap.md.txt
index 8babd47cb..a94deebf6 100644
--- a/_sources/datamodels/item-list/itemMetadataMap.md.txt
+++ b/_sources/datamodels/item-list/itemMetadataMap.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: itemMetadataMap
@@ -14,11 +16,12 @@ URI: [itemList:itemMetadataMap](https://w3id.org/linkml/item-list/itemMetadataMa
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/keywords.md.txt b/_sources/datamodels/item-list/keywords.md.txt
index 1905f102b..760006398 100644
--- a/_sources/datamodels/item-list/keywords.md.txt
+++ b/_sources/datamodels/item-list/keywords.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: keywords
@@ -14,11 +16,12 @@ URI: [schema:keywords](http://schema.org/keywords)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/name.md.txt b/_sources/datamodels/item-list/name.md.txt
index d36e4cc56..ac4ddc6e6 100644
--- a/_sources/datamodels/item-list/name.md.txt
+++ b/_sources/datamodels/item-list/name.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: name
URI: [itemList:name](https://w3id.org/linkml/item-list/name)
@@ -9,12 +11,13 @@ URI: [itemList:name](https://w3id.org/linkml/item-list/name)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/numberOfItems.md.txt b/_sources/datamodels/item-list/numberOfItems.md.txt
index 1d2e3078a..72750b37c 100644
--- a/_sources/datamodels/item-list/numberOfItems.md.txt
+++ b/_sources/datamodels/item-list/numberOfItems.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: numberOfItems
@@ -14,11 +16,12 @@ URI: [schema:numberOfItems](http://schema.org/numberOfItems)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/item-list/position.md.txt b/_sources/datamodels/item-list/position.md.txt
index cbd562bb5..8897a53df 100644
--- a/_sources/datamodels/item-list/position.md.txt
+++ b/_sources/datamodels/item-list/position.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: position
@@ -14,11 +16,12 @@ URI: [schema:position](http://schema.org/position)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ListItem](ListItem.md) | an item in an item list | no |
+| [ListItem](ListItem.md) | an item in an item list | no |
diff --git a/_sources/datamodels/item-list/previousItem.md.txt b/_sources/datamodels/item-list/previousItem.md.txt
index ad29716df..3d59588e7 100644
--- a/_sources/datamodels/item-list/previousItem.md.txt
+++ b/_sources/datamodels/item-list/previousItem.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: previousItem
@@ -14,11 +16,12 @@ URI: [schema:previousItem](http://schema.org/previousItem)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ListItem](ListItem.md) | an item in an item list | no |
+| [ListItem](ListItem.md) | an item in an item list | no |
diff --git a/_sources/datamodels/item-list/type.md.txt b/_sources/datamodels/item-list/type.md.txt
index c1a326728..7af91b396 100644
--- a/_sources/datamodels/item-list/type.md.txt
+++ b/_sources/datamodels/item-list/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
@@ -14,11 +16,12 @@ URI: [itemList:type](https://w3id.org/linkml/item-list/type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
diff --git a/_sources/datamodels/item-list/url.md.txt b/_sources/datamodels/item-list/url.md.txt
index 418e46a0b..9acd26870 100644
--- a/_sources/datamodels/item-list/url.md.txt
+++ b/_sources/datamodels/item-list/url.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: url
@@ -14,11 +16,12 @@ URI: [itemList:url](https://w3id.org/linkml/item-list/url)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Thing](Thing.md) | | no |
+| [Thing](Thing.md) | | no |
diff --git a/_sources/datamodels/item-list/wasGeneratedBy.md.txt b/_sources/datamodels/item-list/wasGeneratedBy.md.txt
index 56ec8857f..df98f7503 100644
--- a/_sources/datamodels/item-list/wasGeneratedBy.md.txt
+++ b/_sources/datamodels/item-list/wasGeneratedBy.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: wasGeneratedBy
@@ -14,11 +16,12 @@ URI: [prov:wasGeneratedBy](http://www.w3.org/ns/prov#wasGeneratedBy)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ItemList](ItemList.md) | a list of entities plus metadata | no |
+| [ItemList](ItemList.md) | a list of entities plus metadata | no |
diff --git a/_sources/datamodels/lexical-index/Activity.md.txt b/_sources/datamodels/lexical-index/Activity.md.txt
index 98a09925b..abc1b1c2a 100644
--- a/_sources/datamodels/lexical-index/Activity.md.txt
+++ b/_sources/datamodels/lexical-index/Activity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Activity
diff --git a/_sources/datamodels/lexical-index/Any.md.txt b/_sources/datamodels/lexical-index/Any.md.txt
index d7564901f..4657da605 100644
--- a/_sources/datamodels/lexical-index/Any.md.txt
+++ b/_sources/datamodels/lexical-index/Any.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Any
diff --git a/_sources/datamodels/lexical-index/LexicalGrouping.md.txt b/_sources/datamodels/lexical-index/LexicalGrouping.md.txt
index ca9b8d91a..5ca94866f 100644
--- a/_sources/datamodels/lexical-index/LexicalGrouping.md.txt
+++ b/_sources/datamodels/lexical-index/LexicalGrouping.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalGrouping
diff --git a/_sources/datamodels/lexical-index/LexicalIndex.md.txt b/_sources/datamodels/lexical-index/LexicalIndex.md.txt
index eb00de2fb..791102d90 100644
--- a/_sources/datamodels/lexical-index/LexicalIndex.md.txt
+++ b/_sources/datamodels/lexical-index/LexicalIndex.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalIndex
diff --git a/_sources/datamodels/lexical-index/LexicalTransformation.md.txt b/_sources/datamodels/lexical-index/LexicalTransformation.md.txt
index f3c6ab1d3..57966574a 100644
--- a/_sources/datamodels/lexical-index/LexicalTransformation.md.txt
+++ b/_sources/datamodels/lexical-index/LexicalTransformation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalTransformation
diff --git a/_sources/datamodels/lexical-index/LexicalTransformationPipeline.md.txt b/_sources/datamodels/lexical-index/LexicalTransformationPipeline.md.txt
index 26a52d768..066804af9 100644
--- a/_sources/datamodels/lexical-index/LexicalTransformationPipeline.md.txt
+++ b/_sources/datamodels/lexical-index/LexicalTransformationPipeline.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalTransformationPipeline
diff --git a/_sources/datamodels/lexical-index/RelationshipToTerm.md.txt b/_sources/datamodels/lexical-index/RelationshipToTerm.md.txt
index e02d2b9c5..1bac5935d 100644
--- a/_sources/datamodels/lexical-index/RelationshipToTerm.md.txt
+++ b/_sources/datamodels/lexical-index/RelationshipToTerm.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RelationshipToTerm
diff --git a/_sources/datamodels/lexical-index/element.md.txt b/_sources/datamodels/lexical-index/element.md.txt
index 0453e315d..4d8a18b51 100644
--- a/_sources/datamodels/lexical-index/element.md.txt
+++ b/_sources/datamodels/lexical-index/element.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: element
URI: [ontolexindex:element](https://w3id.org/oak/lexical-index/element)
@@ -9,11 +11,12 @@ URI: [ontolexindex:element](https://w3id.org/oak/lexical-index/element)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/element_term.md.txt b/_sources/datamodels/lexical-index/element_term.md.txt
index 460bcd66f..1a0a1e2d2 100644
--- a/_sources/datamodels/lexical-index/element_term.md.txt
+++ b/_sources/datamodels/lexical-index/element_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: element_term
@@ -14,11 +16,12 @@ URI: [ontolexindex:element_term](https://w3id.org/oak/lexical-index/element_term
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/groupings.md.txt b/_sources/datamodels/lexical-index/groupings.md.txt
index 5e9e8e950..faa6ee5f1 100644
--- a/_sources/datamodels/lexical-index/groupings.md.txt
+++ b/_sources/datamodels/lexical-index/groupings.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: groupings
@@ -14,11 +16,12 @@ URI: [ontolexindex:groupings](https://w3id.org/oak/lexical-index/groupings)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
+| [LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
diff --git a/_sources/datamodels/lexical-index/name.md.txt b/_sources/datamodels/lexical-index/name.md.txt
index 0b36f5717..aea51f14a 100644
--- a/_sources/datamodels/lexical-index/name.md.txt
+++ b/_sources/datamodels/lexical-index/name.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: name
URI: [ontolexindex:name](https://w3id.org/oak/lexical-index/name)
@@ -9,11 +11,12 @@ URI: [ontolexindex:name](https://w3id.org/oak/lexical-index/name)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
+| [LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
diff --git a/_sources/datamodels/lexical-index/params.md.txt b/_sources/datamodels/lexical-index/params.md.txt
index a102ba0a7..255b3b22b 100644
--- a/_sources/datamodels/lexical-index/params.md.txt
+++ b/_sources/datamodels/lexical-index/params.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: params
@@ -14,11 +16,12 @@ URI: [ontolexindex:params](https://w3id.org/oak/lexical-index/params)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
+| [LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
diff --git a/_sources/datamodels/lexical-index/pipeline.md.txt b/_sources/datamodels/lexical-index/pipeline.md.txt
index 7a6b998dc..e7f596dc3 100644
--- a/_sources/datamodels/lexical-index/pipeline.md.txt
+++ b/_sources/datamodels/lexical-index/pipeline.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: pipeline
URI: [ontolexindex:pipeline](https://w3id.org/oak/lexical-index/pipeline)
@@ -9,11 +11,12 @@ URI: [ontolexindex:pipeline](https://w3id.org/oak/lexical-index/pipeline)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/pipelines.md.txt b/_sources/datamodels/lexical-index/pipelines.md.txt
index bad4cd8f6..603bde0de 100644
--- a/_sources/datamodels/lexical-index/pipelines.md.txt
+++ b/_sources/datamodels/lexical-index/pipelines.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: pipelines
@@ -14,11 +16,12 @@ URI: [ontolexindex:pipelines](https://w3id.org/oak/lexical-index/pipelines)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
+| [LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
diff --git a/_sources/datamodels/lexical-index/predicate.md.txt b/_sources/datamodels/lexical-index/predicate.md.txt
index 2ce1f4eff..b34c05329 100644
--- a/_sources/datamodels/lexical-index/predicate.md.txt
+++ b/_sources/datamodels/lexical-index/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
URI: [ontolexindex:predicate](https://w3id.org/oak/lexical-index/predicate)
@@ -9,11 +11,12 @@ URI: [ontolexindex:predicate](https://w3id.org/oak/lexical-index/predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/relationships.md.txt b/_sources/datamodels/lexical-index/relationships.md.txt
index cb0922c13..6adb1e7dc 100644
--- a/_sources/datamodels/lexical-index/relationships.md.txt
+++ b/_sources/datamodels/lexical-index/relationships.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: relationships
@@ -14,11 +16,12 @@ URI: [ontolexindex:relationships](https://w3id.org/oak/lexical-index/relationshi
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
+| [LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
diff --git a/_sources/datamodels/lexical-index/source.md.txt b/_sources/datamodels/lexical-index/source.md.txt
index d2fd4f136..86533cdbb 100644
--- a/_sources/datamodels/lexical-index/source.md.txt
+++ b/_sources/datamodels/lexical-index/source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: source
URI: [ontolexindex:source](https://w3id.org/oak/lexical-index/source)
@@ -9,11 +11,12 @@ URI: [ontolexindex:source](https://w3id.org/oak/lexical-index/source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/synonymized.md.txt b/_sources/datamodels/lexical-index/synonymized.md.txt
index bedcc26c8..aaf16919f 100644
--- a/_sources/datamodels/lexical-index/synonymized.md.txt
+++ b/_sources/datamodels/lexical-index/synonymized.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonymized
URI: [ontolexindex:synonymized](https://w3id.org/oak/lexical-index/synonymized)
@@ -9,11 +11,12 @@ URI: [ontolexindex:synonymized](https://w3id.org/oak/lexical-index/synonymized)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/lexical-index/term.md.txt b/_sources/datamodels/lexical-index/term.md.txt
index c5bb29aa4..12285029c 100644
--- a/_sources/datamodels/lexical-index/term.md.txt
+++ b/_sources/datamodels/lexical-index/term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: term
@@ -14,11 +16,12 @@ URI: [ontolexindex:term](https://w3id.org/oak/lexical-index/term)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
+| [LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
diff --git a/_sources/datamodels/lexical-index/transformations.md.txt b/_sources/datamodels/lexical-index/transformations.md.txt
index 4b351aa6f..d04dc3d69 100644
--- a/_sources/datamodels/lexical-index/transformations.md.txt
+++ b/_sources/datamodels/lexical-index/transformations.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: transformations
URI: [ontolexindex:transformations](https://w3id.org/oak/lexical-index/transformations)
@@ -9,11 +11,12 @@ URI: [ontolexindex:transformations](https://w3id.org/oak/lexical-index/transform
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
+| [LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
diff --git a/_sources/datamodels/lexical-index/type.md.txt b/_sources/datamodels/lexical-index/type.md.txt
index 1970a6d75..3c78a54b1 100644
--- a/_sources/datamodels/lexical-index/type.md.txt
+++ b/_sources/datamodels/lexical-index/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
@@ -14,11 +16,12 @@ URI: [ontolexindex:type](https://w3id.org/oak/lexical-index/type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
+| [LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
diff --git a/_sources/datamodels/mapping-rules/Activity.md.txt b/_sources/datamodels/mapping-rules/Activity.md.txt
index 210448b16..20e7c4ed2 100644
--- a/_sources/datamodels/mapping-rules/Activity.md.txt
+++ b/_sources/datamodels/mapping-rules/Activity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Activity
diff --git a/_sources/datamodels/mapping-rules/Any.md.txt b/_sources/datamodels/mapping-rules/Any.md.txt
index 0a427591a..fa8352e9e 100644
--- a/_sources/datamodels/mapping-rules/Any.md.txt
+++ b/_sources/datamodels/mapping-rules/Any.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Any
diff --git a/_sources/datamodels/mapping-rules/LexicalGrouping.md.txt b/_sources/datamodels/mapping-rules/LexicalGrouping.md.txt
index 58440107f..3f001ae42 100644
--- a/_sources/datamodels/mapping-rules/LexicalGrouping.md.txt
+++ b/_sources/datamodels/mapping-rules/LexicalGrouping.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalGrouping
diff --git a/_sources/datamodels/mapping-rules/LexicalIndex.md.txt b/_sources/datamodels/mapping-rules/LexicalIndex.md.txt
index 0c1e255df..55f06b52f 100644
--- a/_sources/datamodels/mapping-rules/LexicalIndex.md.txt
+++ b/_sources/datamodels/mapping-rules/LexicalIndex.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalIndex
diff --git a/_sources/datamodels/mapping-rules/LexicalTransformation.md.txt b/_sources/datamodels/mapping-rules/LexicalTransformation.md.txt
index 171368eb9..ac3cb69cd 100644
--- a/_sources/datamodels/mapping-rules/LexicalTransformation.md.txt
+++ b/_sources/datamodels/mapping-rules/LexicalTransformation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalTransformation
diff --git a/_sources/datamodels/mapping-rules/LexicalTransformationPipeline.md.txt b/_sources/datamodels/mapping-rules/LexicalTransformationPipeline.md.txt
index b75458b6a..151fe340e 100644
--- a/_sources/datamodels/mapping-rules/LexicalTransformationPipeline.md.txt
+++ b/_sources/datamodels/mapping-rules/LexicalTransformationPipeline.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LexicalTransformationPipeline
diff --git a/_sources/datamodels/mapping-rules/MappingRule.md.txt b/_sources/datamodels/mapping-rules/MappingRule.md.txt
index 98c5750ae..b45c02f24 100644
--- a/_sources/datamodels/mapping-rules/MappingRule.md.txt
+++ b/_sources/datamodels/mapping-rules/MappingRule.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: MappingRule
diff --git a/_sources/datamodels/mapping-rules/MappingRuleCollection.md.txt b/_sources/datamodels/mapping-rules/MappingRuleCollection.md.txt
index de8baa4f6..83ca2b9ab 100644
--- a/_sources/datamodels/mapping-rules/MappingRuleCollection.md.txt
+++ b/_sources/datamodels/mapping-rules/MappingRuleCollection.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: MappingRuleCollection
diff --git a/_sources/datamodels/mapping-rules/Postcondition.md.txt b/_sources/datamodels/mapping-rules/Postcondition.md.txt
index f509203ed..a04b4ea44 100644
--- a/_sources/datamodels/mapping-rules/Postcondition.md.txt
+++ b/_sources/datamodels/mapping-rules/Postcondition.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Postcondition
diff --git a/_sources/datamodels/mapping-rules/Precondition.md.txt b/_sources/datamodels/mapping-rules/Precondition.md.txt
index dcc7791f3..9fb7b29e0 100644
--- a/_sources/datamodels/mapping-rules/Precondition.md.txt
+++ b/_sources/datamodels/mapping-rules/Precondition.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Precondition
diff --git a/_sources/datamodels/mapping-rules/RelationshipToTerm.md.txt b/_sources/datamodels/mapping-rules/RelationshipToTerm.md.txt
index 27c1ed33b..d694a7b00 100644
--- a/_sources/datamodels/mapping-rules/RelationshipToTerm.md.txt
+++ b/_sources/datamodels/mapping-rules/RelationshipToTerm.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RelationshipToTerm
diff --git a/_sources/datamodels/mapping-rules/RuleSet.md.txt b/_sources/datamodels/mapping-rules/RuleSet.md.txt
index e8bdc9c5f..faed958b4 100644
--- a/_sources/datamodels/mapping-rules/RuleSet.md.txt
+++ b/_sources/datamodels/mapping-rules/RuleSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RuleSet
diff --git a/_sources/datamodels/mapping-rules/Synonymizer.md.txt b/_sources/datamodels/mapping-rules/Synonymizer.md.txt
index 7979b5787..e6b6b895a 100644
--- a/_sources/datamodels/mapping-rules/Synonymizer.md.txt
+++ b/_sources/datamodels/mapping-rules/Synonymizer.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Synonymizer
diff --git a/_sources/datamodels/mapping-rules/Test.md.txt b/_sources/datamodels/mapping-rules/Test.md.txt
index 8750f9612..fb1c34dcd 100644
--- a/_sources/datamodels/mapping-rules/Test.md.txt
+++ b/_sources/datamodels/mapping-rules/Test.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Test
diff --git a/_sources/datamodels/mapping-rules/description.md.txt b/_sources/datamodels/mapping-rules/description.md.txt
index 1b4c63976..723335fa9 100644
--- a/_sources/datamodels/mapping-rules/description.md.txt
+++ b/_sources/datamodels/mapping-rules/description.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: description
URI: [mappingrules:description](https://w3id.org/oak/mapping-rules-datamodel/description)
@@ -9,12 +11,13 @@ URI: [mappingrules:description](https://w3id.org/oak/mapping-rules-datamodel/des
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
-[Synonymizer](Synonymizer.md) | | no |
+| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/element.md.txt b/_sources/datamodels/mapping-rules/element.md.txt
index 1084d7b1f..051d821fc 100644
--- a/_sources/datamodels/mapping-rules/element.md.txt
+++ b/_sources/datamodels/mapping-rules/element.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: element
URI: [mappingrules:element](https://w3id.org/oak/mapping-rules-datamodel/element)
@@ -9,11 +11,12 @@ URI: [mappingrules:element](https://w3id.org/oak/mapping-rules-datamodel/element
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/element_term.md.txt b/_sources/datamodels/mapping-rules/element_term.md.txt
index 70212ec24..6d0dd92c1 100644
--- a/_sources/datamodels/mapping-rules/element_term.md.txt
+++ b/_sources/datamodels/mapping-rules/element_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: element_term
@@ -14,11 +16,12 @@ URI: [mappingrules:element_term](https://w3id.org/oak/mapping-rules-datamodel/el
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/groupings.md.txt b/_sources/datamodels/mapping-rules/groupings.md.txt
index 710ecde45..3ab0807d2 100644
--- a/_sources/datamodels/mapping-rules/groupings.md.txt
+++ b/_sources/datamodels/mapping-rules/groupings.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: groupings
@@ -14,11 +16,12 @@ URI: [mappingrules:groupings](https://w3id.org/oak/mapping-rules-datamodel/group
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
+| [LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
diff --git a/_sources/datamodels/mapping-rules/input.md.txt b/_sources/datamodels/mapping-rules/input.md.txt
index 80bfe7cc0..760f42a82 100644
--- a/_sources/datamodels/mapping-rules/input.md.txt
+++ b/_sources/datamodels/mapping-rules/input.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: input
@@ -14,11 +16,12 @@ URI: [mappingrules:input](https://w3id.org/oak/mapping-rules-datamodel/input)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Test](Test.md) | | no |
+| [Test](Test.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/mapping_source_one_of.md.txt b/_sources/datamodels/mapping-rules/mapping_source_one_of.md.txt
index b0e0f2b98..729d98b84 100644
--- a/_sources/datamodels/mapping-rules/mapping_source_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/mapping_source_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: mapping_source_one_of
URI: [mappingrules:mapping_source_one_of](https://w3id.org/oak/mapping-rules-datamodel/mapping_source_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:mapping_source_one_of](https://w3id.org/oak/mapping-rules-dat
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/match.md.txt b/_sources/datamodels/mapping-rules/match.md.txt
index 65f52bc31..27180f21b 100644
--- a/_sources/datamodels/mapping-rules/match.md.txt
+++ b/_sources/datamodels/mapping-rules/match.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match
@@ -14,11 +16,12 @@ URI: [mappingrules:match](https://w3id.org/oak/mapping-rules-datamodel/match)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/match_scope.md.txt b/_sources/datamodels/mapping-rules/match_scope.md.txt
index 8cde33012..9505c1c77 100644
--- a/_sources/datamodels/mapping-rules/match_scope.md.txt
+++ b/_sources/datamodels/mapping-rules/match_scope.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_scope
@@ -14,11 +16,12 @@ URI: [mappingrules:match_scope](https://w3id.org/oak/mapping-rules-datamodel/mat
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/minimum_confidence.md.txt b/_sources/datamodels/mapping-rules/minimum_confidence.md.txt
index eb6fd4989..b900422ca 100644
--- a/_sources/datamodels/mapping-rules/minimum_confidence.md.txt
+++ b/_sources/datamodels/mapping-rules/minimum_confidence.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: minimum_confidence
URI: [mappingrules:minimum_confidence](https://w3id.org/oak/mapping-rules-datamodel/minimum_confidence)
@@ -9,11 +11,12 @@ URI: [mappingrules:minimum_confidence](https://w3id.org/oak/mapping-rules-datamo
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no |
+| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no |
diff --git a/_sources/datamodels/mapping-rules/name.md.txt b/_sources/datamodels/mapping-rules/name.md.txt
index f1da9f2f8..5c6ca32b1 100644
--- a/_sources/datamodels/mapping-rules/name.md.txt
+++ b/_sources/datamodels/mapping-rules/name.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: name
URI: [mappingrules:name](https://w3id.org/oak/mapping-rules-datamodel/name)
@@ -9,11 +11,12 @@ URI: [mappingrules:name](https://w3id.org/oak/mapping-rules-datamodel/name)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
+| [LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
diff --git a/_sources/datamodels/mapping-rules/object_match_field_one_of.md.txt b/_sources/datamodels/mapping-rules/object_match_field_one_of.md.txt
index 0759de262..029f4d9db 100644
--- a/_sources/datamodels/mapping-rules/object_match_field_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/object_match_field_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_match_field_one_of
URI: [mappingrules:object_match_field_one_of](https://w3id.org/oak/mapping-rules-datamodel/object_match_field_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:object_match_field_one_of](https://w3id.org/oak/mapping-rules
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/object_source_one_of.md.txt b/_sources/datamodels/mapping-rules/object_source_one_of.md.txt
index d2773f24b..e66690a1e 100644
--- a/_sources/datamodels/mapping-rules/object_source_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/object_source_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_source_one_of
URI: [mappingrules:object_source_one_of](https://w3id.org/oak/mapping-rules-datamodel/object_source_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:object_source_one_of](https://w3id.org/oak/mapping-rules-data
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/oneway.md.txt b/_sources/datamodels/mapping-rules/oneway.md.txt
index 3021e23b3..9d1fe7064 100644
--- a/_sources/datamodels/mapping-rules/oneway.md.txt
+++ b/_sources/datamodels/mapping-rules/oneway.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: oneway
@@ -14,11 +16,12 @@ URI: [mappingrules:oneway](https://w3id.org/oak/mapping-rules-datamodel/oneway)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
+| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
diff --git a/_sources/datamodels/mapping-rules/output.md.txt b/_sources/datamodels/mapping-rules/output.md.txt
index 294b8b9a2..351914360 100644
--- a/_sources/datamodels/mapping-rules/output.md.txt
+++ b/_sources/datamodels/mapping-rules/output.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: output
@@ -14,11 +16,12 @@ URI: [mappingrules:output](https://w3id.org/oak/mapping-rules-datamodel/output)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Test](Test.md) | | no |
+| [Test](Test.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/params.md.txt b/_sources/datamodels/mapping-rules/params.md.txt
index 3cfbbf15d..0fd4e769c 100644
--- a/_sources/datamodels/mapping-rules/params.md.txt
+++ b/_sources/datamodels/mapping-rules/params.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: params
@@ -14,11 +16,12 @@ URI: [mappingrules:params](https://w3id.org/oak/mapping-rules-datamodel/params)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
+| [LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
diff --git a/_sources/datamodels/mapping-rules/pipeline.md.txt b/_sources/datamodels/mapping-rules/pipeline.md.txt
index 90c1c586e..781d23f9d 100644
--- a/_sources/datamodels/mapping-rules/pipeline.md.txt
+++ b/_sources/datamodels/mapping-rules/pipeline.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: pipeline
URI: [mappingrules:pipeline](https://w3id.org/oak/mapping-rules-datamodel/pipeline)
@@ -9,11 +11,12 @@ URI: [mappingrules:pipeline](https://w3id.org/oak/mapping-rules-datamodel/pipeli
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/pipelines.md.txt b/_sources/datamodels/mapping-rules/pipelines.md.txt
index a331161c5..79e6534b1 100644
--- a/_sources/datamodels/mapping-rules/pipelines.md.txt
+++ b/_sources/datamodels/mapping-rules/pipelines.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: pipelines
@@ -14,11 +16,12 @@ URI: [mappingrules:pipelines](https://w3id.org/oak/mapping-rules-datamodel/pipel
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
+| [LexicalIndex](LexicalIndex.md) | An index over an ontology keyed by lexical unit | no |
diff --git a/_sources/datamodels/mapping-rules/postconditions.md.txt b/_sources/datamodels/mapping-rules/postconditions.md.txt
index 5b56703ce..9d9a36354 100644
--- a/_sources/datamodels/mapping-rules/postconditions.md.txt
+++ b/_sources/datamodels/mapping-rules/postconditions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: postconditions
@@ -14,11 +16,12 @@ URI: [mappingrules:postconditions](https://w3id.org/oak/mapping-rules-datamodel/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
+| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
diff --git a/_sources/datamodels/mapping-rules/preconditions.md.txt b/_sources/datamodels/mapping-rules/preconditions.md.txt
index 64fa2431f..ae2426994 100644
--- a/_sources/datamodels/mapping-rules/preconditions.md.txt
+++ b/_sources/datamodels/mapping-rules/preconditions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: preconditions
@@ -14,11 +16,12 @@ URI: [sh:condition](https://w3id.org/shacl/condition)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
+| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
diff --git a/_sources/datamodels/mapping-rules/predicate.md.txt b/_sources/datamodels/mapping-rules/predicate.md.txt
index eb6082c96..adc16ac51 100644
--- a/_sources/datamodels/mapping-rules/predicate.md.txt
+++ b/_sources/datamodels/mapping-rules/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
URI: [mappingrules:predicate](https://w3id.org/oak/mapping-rules-datamodel/predicate)
@@ -9,11 +11,12 @@ URI: [mappingrules:predicate](https://w3id.org/oak/mapping-rules-datamodel/predi
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/predicate_id.md.txt b/_sources/datamodels/mapping-rules/predicate_id.md.txt
index 898f3d9cd..e9b3316bc 100644
--- a/_sources/datamodels/mapping-rules/predicate_id.md.txt
+++ b/_sources/datamodels/mapping-rules/predicate_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_id
URI: [mappingrules:predicate_id](https://w3id.org/oak/mapping-rules-datamodel/predicate_id)
@@ -9,11 +11,12 @@ URI: [mappingrules:predicate_id](https://w3id.org/oak/mapping-rules-datamodel/pr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Postcondition](Postcondition.md) | | no |
+| [Postcondition](Postcondition.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/predicate_id_one_of.md.txt b/_sources/datamodels/mapping-rules/predicate_id_one_of.md.txt
index 4618f806f..03c008f9c 100644
--- a/_sources/datamodels/mapping-rules/predicate_id_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/predicate_id_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_id_one_of
URI: [mappingrules:predicate_id_one_of](https://w3id.org/oak/mapping-rules-datamodel/predicate_id_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:predicate_id_one_of](https://w3id.org/oak/mapping-rules-datam
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/prefix.md.txt b/_sources/datamodels/mapping-rules/prefix.md.txt
index 344ab5063..fd22ca403 100644
--- a/_sources/datamodels/mapping-rules/prefix.md.txt
+++ b/_sources/datamodels/mapping-rules/prefix.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: prefix
URI: [mappingrules:prefix](https://w3id.org/oak/mapping-rules-datamodel/prefix)
@@ -9,13 +11,14 @@ URI: [mappingrules:prefix](https://w3id.org/oak/mapping-rules-datamodel/prefix)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
-[Test](Test.md) | | no |
-[RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
+| [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
+| [Synonymizer](Synonymizer.md) | | no |
+| [Test](Test.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/qualifier.md.txt b/_sources/datamodels/mapping-rules/qualifier.md.txt
index 1aee7c920..8cd914ebe 100644
--- a/_sources/datamodels/mapping-rules/qualifier.md.txt
+++ b/_sources/datamodels/mapping-rules/qualifier.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: qualifier
@@ -14,11 +16,12 @@ URI: [mappingrules:qualifier](https://w3id.org/oak/mapping-rules-datamodel/quali
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/relationships.md.txt b/_sources/datamodels/mapping-rules/relationships.md.txt
index 23727437c..627228bc9 100644
--- a/_sources/datamodels/mapping-rules/relationships.md.txt
+++ b/_sources/datamodels/mapping-rules/relationships.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: relationships
@@ -14,11 +16,12 @@ URI: [mappingrules:relationships](https://w3id.org/oak/mapping-rules-datamodel/r
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
+| [LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/replacement.md.txt b/_sources/datamodels/mapping-rules/replacement.md.txt
index 4eb85be30..83bb08e2a 100644
--- a/_sources/datamodels/mapping-rules/replacement.md.txt
+++ b/_sources/datamodels/mapping-rules/replacement.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: replacement
@@ -14,11 +16,12 @@ URI: [mappingrules:replacement](https://w3id.org/oak/mapping-rules-datamodel/rep
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/rules.md.txt b/_sources/datamodels/mapping-rules/rules.md.txt
index eb0671fa7..1b068045d 100644
--- a/_sources/datamodels/mapping-rules/rules.md.txt
+++ b/_sources/datamodels/mapping-rules/rules.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: rules
URI: [mappingrules:rules](https://w3id.org/oak/mapping-rules-datamodel/rules)
@@ -9,12 +11,13 @@ URI: [mappingrules:rules](https://w3id.org/oak/mapping-rules-datamodel/rules)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no |
-[RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
+| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no |
+| [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
diff --git a/_sources/datamodels/mapping-rules/source.md.txt b/_sources/datamodels/mapping-rules/source.md.txt
index d4d49e12c..cf6fb5c01 100644
--- a/_sources/datamodels/mapping-rules/source.md.txt
+++ b/_sources/datamodels/mapping-rules/source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: source
URI: [mappingrules:source](https://w3id.org/oak/mapping-rules-datamodel/source)
@@ -9,11 +11,12 @@ URI: [mappingrules:source](https://w3id.org/oak/mapping-rules-datamodel/source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/subject_match_field_one_of.md.txt b/_sources/datamodels/mapping-rules/subject_match_field_one_of.md.txt
index 25bd395cb..e69b3068e 100644
--- a/_sources/datamodels/mapping-rules/subject_match_field_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/subject_match_field_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_match_field_one_of
URI: [mappingrules:subject_match_field_one_of](https://w3id.org/oak/mapping-rules-datamodel/subject_match_field_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:subject_match_field_one_of](https://w3id.org/oak/mapping-rule
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/subject_source_one_of.md.txt b/_sources/datamodels/mapping-rules/subject_source_one_of.md.txt
index d642bec0f..4620aa585 100644
--- a/_sources/datamodels/mapping-rules/subject_source_one_of.md.txt
+++ b/_sources/datamodels/mapping-rules/subject_source_one_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_source_one_of
URI: [mappingrules:subject_source_one_of](https://w3id.org/oak/mapping-rules-datamodel/subject_source_one_of)
@@ -9,11 +11,12 @@ URI: [mappingrules:subject_source_one_of](https://w3id.org/oak/mapping-rules-dat
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/synonymized.md.txt b/_sources/datamodels/mapping-rules/synonymized.md.txt
index 5088f02d6..2011bc39e 100644
--- a/_sources/datamodels/mapping-rules/synonymized.md.txt
+++ b/_sources/datamodels/mapping-rules/synonymized.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonymized
URI: [mappingrules:synonymized](https://w3id.org/oak/mapping-rules-datamodel/synonymized)
@@ -9,11 +11,12 @@ URI: [mappingrules:synonymized](https://w3id.org/oak/mapping-rules-datamodel/syn
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
+| [RelationshipToTerm](RelationshipToTerm.md) | A relationship of an ontology element to a lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/synonymizer.md.txt b/_sources/datamodels/mapping-rules/synonymizer.md.txt
index 22be7bee3..b52f59872 100644
--- a/_sources/datamodels/mapping-rules/synonymizer.md.txt
+++ b/_sources/datamodels/mapping-rules/synonymizer.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonymizer
@@ -14,11 +16,12 @@ URI: [mappingrules:synonymizer](https://w3id.org/oak/mapping-rules-datamodel/syn
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
+| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |
diff --git a/_sources/datamodels/mapping-rules/term.md.txt b/_sources/datamodels/mapping-rules/term.md.txt
index 7ca32804d..96719782d 100644
--- a/_sources/datamodels/mapping-rules/term.md.txt
+++ b/_sources/datamodels/mapping-rules/term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: term
@@ -14,11 +16,12 @@ URI: [mappingrules:term](https://w3id.org/oak/mapping-rules-datamodel/term)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
+| [LexicalGrouping](LexicalGrouping.md) | A grouping of ontology elements by a shared lexical term | no |
diff --git a/_sources/datamodels/mapping-rules/tests.md.txt b/_sources/datamodels/mapping-rules/tests.md.txt
index cd5a0275d..b8bc14518 100644
--- a/_sources/datamodels/mapping-rules/tests.md.txt
+++ b/_sources/datamodels/mapping-rules/tests.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: tests
@@ -14,11 +16,12 @@ URI: [mappingrules:tests](https://w3id.org/oak/mapping-rules-datamodel/tests)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Synonymizer](Synonymizer.md) | | no |
+| [Synonymizer](Synonymizer.md) | | no |
diff --git a/_sources/datamodels/mapping-rules/transformations.md.txt b/_sources/datamodels/mapping-rules/transformations.md.txt
index f987fc1f9..88e20830e 100644
--- a/_sources/datamodels/mapping-rules/transformations.md.txt
+++ b/_sources/datamodels/mapping-rules/transformations.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: transformations
URI: [mappingrules:transformations](https://w3id.org/oak/mapping-rules-datamodel/transformations)
@@ -9,11 +11,12 @@ URI: [mappingrules:transformations](https://w3id.org/oak/mapping-rules-datamodel
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
+| [LexicalTransformationPipeline](LexicalTransformationPipeline.md) | A collection of atomic lexical transformations that are applied in serial fas... | no |
diff --git a/_sources/datamodels/mapping-rules/transformations_included_in.md.txt b/_sources/datamodels/mapping-rules/transformations_included_in.md.txt
index 0db01c75b..a535006b9 100644
--- a/_sources/datamodels/mapping-rules/transformations_included_in.md.txt
+++ b/_sources/datamodels/mapping-rules/transformations_included_in.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: transformations_included_in
URI: [mappingrules:transformations_included_in](https://w3id.org/oak/mapping-rules-datamodel/transformations_included_in)
@@ -9,11 +11,12 @@ URI: [mappingrules:transformations_included_in](https://w3id.org/oak/mapping-rul
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
+| [Precondition](Precondition.md) | A pattern to be matched against an individual SSSOM mapping | no |
diff --git a/_sources/datamodels/mapping-rules/type.md.txt b/_sources/datamodels/mapping-rules/type.md.txt
index a822f8425..9def218bc 100644
--- a/_sources/datamodels/mapping-rules/type.md.txt
+++ b/_sources/datamodels/mapping-rules/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
@@ -14,11 +16,12 @@ URI: [mappingrules:type](https://w3id.org/oak/mapping-rules-datamodel/type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
+| [LexicalTransformation](LexicalTransformation.md) | An atomic lexical transformation applied on a term (string) yielding a transf... | no |
diff --git a/_sources/datamodels/mapping-rules/weight.md.txt b/_sources/datamodels/mapping-rules/weight.md.txt
index 42ff83b04..08508454b 100644
--- a/_sources/datamodels/mapping-rules/weight.md.txt
+++ b/_sources/datamodels/mapping-rules/weight.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: weight
@@ -14,11 +16,12 @@ URI: [mappingrules:weight](https://w3id.org/oak/mapping-rules-datamodel/weight)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Postcondition](Postcondition.md) | | no |
+| [Postcondition](Postcondition.md) | | no |
diff --git a/_sources/datamodels/obograph/Axiom.md.txt b/_sources/datamodels/obograph/Axiom.md.txt
index e07b4a62b..743287897 100644
--- a/_sources/datamodels/obograph/Axiom.md.txt
+++ b/_sources/datamodels/obograph/Axiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Axiom
diff --git a/_sources/datamodels/obograph/BasicPropertyValue.md.txt b/_sources/datamodels/obograph/BasicPropertyValue.md.txt
index 35c602c1c..d0283d62b 100644
--- a/_sources/datamodels/obograph/BasicPropertyValue.md.txt
+++ b/_sources/datamodels/obograph/BasicPropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: BasicPropertyValue
diff --git a/_sources/datamodels/obograph/DefinitionPropertyValue.md.txt b/_sources/datamodels/obograph/DefinitionPropertyValue.md.txt
index f1a9cb372..5b5a82a1c 100644
--- a/_sources/datamodels/obograph/DefinitionPropertyValue.md.txt
+++ b/_sources/datamodels/obograph/DefinitionPropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: DefinitionPropertyValue
diff --git a/_sources/datamodels/obograph/DisjointClassExpressionsAxiom.md.txt b/_sources/datamodels/obograph/DisjointClassExpressionsAxiom.md.txt
index 6e39771b4..5a63c5901 100644
--- a/_sources/datamodels/obograph/DisjointClassExpressionsAxiom.md.txt
+++ b/_sources/datamodels/obograph/DisjointClassExpressionsAxiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: DisjointClassExpressionsAxiom
diff --git a/_sources/datamodels/obograph/DomainRangeAxiom.md.txt b/_sources/datamodels/obograph/DomainRangeAxiom.md.txt
index 9d02dd59b..58c6e0b5e 100644
--- a/_sources/datamodels/obograph/DomainRangeAxiom.md.txt
+++ b/_sources/datamodels/obograph/DomainRangeAxiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: DomainRangeAxiom
diff --git a/_sources/datamodels/obograph/Edge.md.txt b/_sources/datamodels/obograph/Edge.md.txt
index 03358718b..0ae8d5fc4 100644
--- a/_sources/datamodels/obograph/Edge.md.txt
+++ b/_sources/datamodels/obograph/Edge.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Edge
diff --git a/_sources/datamodels/obograph/EquivalentNodesSet.md.txt b/_sources/datamodels/obograph/EquivalentNodesSet.md.txt
index 4af475203..6b3b621a4 100644
--- a/_sources/datamodels/obograph/EquivalentNodesSet.md.txt
+++ b/_sources/datamodels/obograph/EquivalentNodesSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: EquivalentNodesSet
diff --git a/_sources/datamodels/obograph/ExistentialRestrictionExpression.md.txt b/_sources/datamodels/obograph/ExistentialRestrictionExpression.md.txt
index 0e05d9dd1..388483a5d 100644
--- a/_sources/datamodels/obograph/ExistentialRestrictionExpression.md.txt
+++ b/_sources/datamodels/obograph/ExistentialRestrictionExpression.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ExistentialRestrictionExpression
diff --git a/_sources/datamodels/obograph/Graph.md.txt b/_sources/datamodels/obograph/Graph.md.txt
index bf2ddd5ca..c553767bf 100644
--- a/_sources/datamodels/obograph/Graph.md.txt
+++ b/_sources/datamodels/obograph/Graph.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Graph
diff --git a/_sources/datamodels/obograph/GraphDocument.md.txt b/_sources/datamodels/obograph/GraphDocument.md.txt
index fe24a4cea..7cf16f8ec 100644
--- a/_sources/datamodels/obograph/GraphDocument.md.txt
+++ b/_sources/datamodels/obograph/GraphDocument.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: GraphDocument
diff --git a/_sources/datamodels/obograph/LogicalDefinitionAxiom.md.txt b/_sources/datamodels/obograph/LogicalDefinitionAxiom.md.txt
index 94f56f20e..7ce0e80fb 100644
--- a/_sources/datamodels/obograph/LogicalDefinitionAxiom.md.txt
+++ b/_sources/datamodels/obograph/LogicalDefinitionAxiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: LogicalDefinitionAxiom
diff --git a/_sources/datamodels/obograph/Meta.md.txt b/_sources/datamodels/obograph/Meta.md.txt
index dc585ec26..702b83b16 100644
--- a/_sources/datamodels/obograph/Meta.md.txt
+++ b/_sources/datamodels/obograph/Meta.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Meta
diff --git a/_sources/datamodels/obograph/Node.md.txt b/_sources/datamodels/obograph/Node.md.txt
index 5a51ef8a9..6e6432c70 100644
--- a/_sources/datamodels/obograph/Node.md.txt
+++ b/_sources/datamodels/obograph/Node.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Node
diff --git a/_sources/datamodels/obograph/PrefixDeclaration.md.txt b/_sources/datamodels/obograph/PrefixDeclaration.md.txt
index f95fe53e8..5750de14d 100644
--- a/_sources/datamodels/obograph/PrefixDeclaration.md.txt
+++ b/_sources/datamodels/obograph/PrefixDeclaration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PrefixDeclaration
diff --git a/_sources/datamodels/obograph/PropertyChainAxiom.md.txt b/_sources/datamodels/obograph/PropertyChainAxiom.md.txt
index 1ecb150ef..835fed095 100644
--- a/_sources/datamodels/obograph/PropertyChainAxiom.md.txt
+++ b/_sources/datamodels/obograph/PropertyChainAxiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PropertyChainAxiom
diff --git a/_sources/datamodels/obograph/PropertyValue.md.txt b/_sources/datamodels/obograph/PropertyValue.md.txt
index cab3687be..babf25053 100644
--- a/_sources/datamodels/obograph/PropertyValue.md.txt
+++ b/_sources/datamodels/obograph/PropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PropertyValue
diff --git a/_sources/datamodels/obograph/SubsetDefinition.md.txt b/_sources/datamodels/obograph/SubsetDefinition.md.txt
index 3df8bd57e..1a690eeb9 100644
--- a/_sources/datamodels/obograph/SubsetDefinition.md.txt
+++ b/_sources/datamodels/obograph/SubsetDefinition.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SubsetDefinition
diff --git a/_sources/datamodels/obograph/SynonymPropertyValue.md.txt b/_sources/datamodels/obograph/SynonymPropertyValue.md.txt
index d807f8649..67cfd01fc 100644
--- a/_sources/datamodels/obograph/SynonymPropertyValue.md.txt
+++ b/_sources/datamodels/obograph/SynonymPropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SynonymPropertyValue
diff --git a/_sources/datamodels/obograph/SynonymTypeDefinition.md.txt b/_sources/datamodels/obograph/SynonymTypeDefinition.md.txt
index 63db2b09e..8c602253d 100644
--- a/_sources/datamodels/obograph/SynonymTypeDefinition.md.txt
+++ b/_sources/datamodels/obograph/SynonymTypeDefinition.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SynonymTypeDefinition
diff --git a/_sources/datamodels/obograph/XrefPropertyValue.md.txt b/_sources/datamodels/obograph/XrefPropertyValue.md.txt
index 3d2d41e00..2a38920c0 100644
--- a/_sources/datamodels/obograph/XrefPropertyValue.md.txt
+++ b/_sources/datamodels/obograph/XrefPropertyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: XrefPropertyValue
diff --git a/_sources/datamodels/obograph/allValuesFromEdges.md.txt b/_sources/datamodels/obograph/allValuesFromEdges.md.txt
index 415f1b95f..03c91bfb8 100644
--- a/_sources/datamodels/obograph/allValuesFromEdges.md.txt
+++ b/_sources/datamodels/obograph/allValuesFromEdges.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: allValuesFromEdges
@@ -14,12 +16,13 @@ URI: [obographs:allValuesFromEdges](https://github.com/geneontology/obographs/al
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
-[DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
diff --git a/_sources/datamodels/obograph/basicPropertyValues.md.txt b/_sources/datamodels/obograph/basicPropertyValues.md.txt
index 3b14d9b50..abca717ed 100644
--- a/_sources/datamodels/obograph/basicPropertyValues.md.txt
+++ b/_sources/datamodels/obograph/basicPropertyValues.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: basicPropertyValues
@@ -14,11 +16,12 @@ URI: [obographs:basicPropertyValues](https://github.com/geneontology/obographs/b
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/chainPredicateIds.md.txt b/_sources/datamodels/obograph/chainPredicateIds.md.txt
index 005fb826b..57e7f82f0 100644
--- a/_sources/datamodels/obograph/chainPredicateIds.md.txt
+++ b/_sources/datamodels/obograph/chainPredicateIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: chainPredicateIds
@@ -14,11 +16,12 @@ URI: [obographs:chainPredicateIds](https://github.com/geneontology/obographs/cha
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
+| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
diff --git a/_sources/datamodels/obograph/classExpressions.md.txt b/_sources/datamodels/obograph/classExpressions.md.txt
index 36d4d18ea..a99456445 100644
--- a/_sources/datamodels/obograph/classExpressions.md.txt
+++ b/_sources/datamodels/obograph/classExpressions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: classExpressions
@@ -14,11 +16,12 @@ URI: [obographs:classExpressions](https://github.com/geneontology/obographs/clas
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
+| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
diff --git a/_sources/datamodels/obograph/classIds.md.txt b/_sources/datamodels/obograph/classIds.md.txt
index 55275bc49..b0783e1f4 100644
--- a/_sources/datamodels/obograph/classIds.md.txt
+++ b/_sources/datamodels/obograph/classIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: classIds
@@ -14,11 +16,12 @@ URI: [obographs:classIds](https://github.com/geneontology/obographs/classIds)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
+| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
diff --git a/_sources/datamodels/obograph/comments.md.txt b/_sources/datamodels/obograph/comments.md.txt
index 2affc9d01..d604bedc8 100644
--- a/_sources/datamodels/obograph/comments.md.txt
+++ b/_sources/datamodels/obograph/comments.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: comments
@@ -14,11 +16,12 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/definedClassId.md.txt b/_sources/datamodels/obograph/definedClassId.md.txt
index 2e708be3b..416370095 100644
--- a/_sources/datamodels/obograph/definedClassId.md.txt
+++ b/_sources/datamodels/obograph/definedClassId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: definedClassId
@@ -14,11 +16,12 @@ URI: [obographs:definedClassId](https://github.com/geneontology/obographs/define
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
+| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
diff --git a/_sources/datamodels/obograph/definition.md.txt b/_sources/datamodels/obograph/definition.md.txt
index a23c57227..b94304627 100644
--- a/_sources/datamodels/obograph/definition.md.txt
+++ b/_sources/datamodels/obograph/definition.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: definition
@@ -14,11 +16,12 @@ URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/deprecated.md.txt b/_sources/datamodels/obograph/deprecated.md.txt
index 5decd3422..8d757b1b2 100644
--- a/_sources/datamodels/obograph/deprecated.md.txt
+++ b/_sources/datamodels/obograph/deprecated.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: deprecated
URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated)
@@ -9,11 +11,12 @@ URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/disjointClassExpressionsAxioms.md.txt b/_sources/datamodels/obograph/disjointClassExpressionsAxioms.md.txt
index e8fbc8ed6..7dfa3879e 100644
--- a/_sources/datamodels/obograph/disjointClassExpressionsAxioms.md.txt
+++ b/_sources/datamodels/obograph/disjointClassExpressionsAxioms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: disjointClassExpressionsAxioms
@@ -17,6 +19,7 @@ URI: [obographs:disjointClassExpressionsAxioms](https://github.com/geneontology/
+
## Properties
* Range: [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md)
diff --git a/_sources/datamodels/obograph/domainClassIds.md.txt b/_sources/datamodels/obograph/domainClassIds.md.txt
index 68aad413c..109c7bb55 100644
--- a/_sources/datamodels/obograph/domainClassIds.md.txt
+++ b/_sources/datamodels/obograph/domainClassIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: domainClassIds
URI: [obographs:domainClassIds](https://github.com/geneontology/obographs/domainClassIds)
@@ -9,11 +11,12 @@ URI: [obographs:domainClassIds](https://github.com/geneontology/obographs/domain
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
+| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
diff --git a/_sources/datamodels/obograph/domainRangeAxioms.md.txt b/_sources/datamodels/obograph/domainRangeAxioms.md.txt
index be3ea6402..a55708f57 100644
--- a/_sources/datamodels/obograph/domainRangeAxioms.md.txt
+++ b/_sources/datamodels/obograph/domainRangeAxioms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: domainRangeAxioms
@@ -14,11 +16,12 @@ URI: [obographs:domainRangeAxioms](https://github.com/geneontology/obographs/dom
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/edges.md.txt b/_sources/datamodels/obograph/edges.md.txt
index 687e4ccc5..902d307e6 100644
--- a/_sources/datamodels/obograph/edges.md.txt
+++ b/_sources/datamodels/obograph/edges.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: edges
@@ -14,11 +16,12 @@ URI: [obographs:edges](https://github.com/geneontology/obographs/edges)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/equivalentNodesSets.md.txt b/_sources/datamodels/obograph/equivalentNodesSets.md.txt
index dbf8bf429..0509c959d 100644
--- a/_sources/datamodels/obograph/equivalentNodesSets.md.txt
+++ b/_sources/datamodels/obograph/equivalentNodesSets.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: equivalentNodesSets
@@ -14,11 +16,12 @@ URI: [obographs:equivalentNodesSets](https://github.com/geneontology/obographs/e
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/fillerId.md.txt b/_sources/datamodels/obograph/fillerId.md.txt
index 61a2f8b3a..01f3bab32 100644
--- a/_sources/datamodels/obograph/fillerId.md.txt
+++ b/_sources/datamodels/obograph/fillerId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: fillerId
@@ -14,11 +16,12 @@ URI: [obographs:fillerId](https://github.com/geneontology/obographs/fillerId)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExistentialRestrictionExpression](ExistentialRestrictionExpression.md) | An existential restriction (OWL some values from) expression | no |
+| [ExistentialRestrictionExpression](ExistentialRestrictionExpression.md) | An existential restriction (OWL some values from) expression | no |
diff --git a/_sources/datamodels/obograph/genusIds.md.txt b/_sources/datamodels/obograph/genusIds.md.txt
index 2f16e7a4d..e853c6b4b 100644
--- a/_sources/datamodels/obograph/genusIds.md.txt
+++ b/_sources/datamodels/obograph/genusIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: genusIds
@@ -14,11 +16,12 @@ URI: [obographs:genusIds](https://github.com/geneontology/obographs/genusIds)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
+| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
diff --git a/_sources/datamodels/obograph/graphs.md.txt b/_sources/datamodels/obograph/graphs.md.txt
index 5b6d17466..732b09035 100644
--- a/_sources/datamodels/obograph/graphs.md.txt
+++ b/_sources/datamodels/obograph/graphs.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: graphs
@@ -14,11 +16,12 @@ URI: [obographs:graphs](https://github.com/geneontology/obographs/graphs)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
+| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
diff --git a/_sources/datamodels/obograph/id.md.txt b/_sources/datamodels/obograph/id.md.txt
index 8dbf95e65..200928bab 100644
--- a/_sources/datamodels/obograph/id.md.txt
+++ b/_sources/datamodels/obograph/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
@@ -14,14 +16,15 @@ URI: [obographs:id](https://github.com/geneontology/obographs/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
-[Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
-[SubsetDefinition](SubsetDefinition.md) | | no |
-[SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
+| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
+| [SubsetDefinition](SubsetDefinition.md) | | no |
diff --git a/_sources/datamodels/obograph/isExact.md.txt b/_sources/datamodels/obograph/isExact.md.txt
index 66e3b22bb..0b77412d8 100644
--- a/_sources/datamodels/obograph/isExact.md.txt
+++ b/_sources/datamodels/obograph/isExact.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: isExact
URI: [obographs:isExact](https://github.com/geneontology/obographs/isExact)
@@ -9,11 +11,12 @@ URI: [obographs:isExact](https://github.com/geneontology/obographs/isExact)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
diff --git a/_sources/datamodels/obograph/lang.md.txt b/_sources/datamodels/obograph/lang.md.txt
index 3d05bebf6..81779d483 100644
--- a/_sources/datamodels/obograph/lang.md.txt
+++ b/_sources/datamodels/obograph/lang.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: lang
@@ -14,15 +16,16 @@ URI: [obographs:lang](https://github.com/geneontology/obographs/lang)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
diff --git a/_sources/datamodels/obograph/lbl.md.txt b/_sources/datamodels/obograph/lbl.md.txt
index d4e38b923..d147d0085 100644
--- a/_sources/datamodels/obograph/lbl.md.txt
+++ b/_sources/datamodels/obograph/lbl.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: lbl
@@ -14,14 +16,15 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
-[Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
-[SubsetDefinition](SubsetDefinition.md) | | no |
-[SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
+| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
+| [SubsetDefinition](SubsetDefinition.md) | | no |
diff --git a/_sources/datamodels/obograph/logicalDefinitionAxioms.md.txt b/_sources/datamodels/obograph/logicalDefinitionAxioms.md.txt
index ee275f0ba..981a3370e 100644
--- a/_sources/datamodels/obograph/logicalDefinitionAxioms.md.txt
+++ b/_sources/datamodels/obograph/logicalDefinitionAxioms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: logicalDefinitionAxioms
@@ -14,11 +16,12 @@ URI: [obographs:logicalDefinitionAxioms](https://github.com/geneontology/obograp
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/meta.md.txt b/_sources/datamodels/obograph/meta.md.txt
index abad85faa..fc05456b9 100644
--- a/_sources/datamodels/obograph/meta.md.txt
+++ b/_sources/datamodels/obograph/meta.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: meta
@@ -14,25 +16,26 @@ URI: [obographs:meta](https://github.com/geneontology/obographs/meta)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
-[Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
-[Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[Axiom](Axiom.md) | A generic grouping for any OWL axiom or group of axioms that is not captured ... | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
-[DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
-[EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
-[LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
-[DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
-[PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
+| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
+| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
+| [Axiom](Axiom.md) | A generic grouping for any OWL axiom or group of axioms that is not captured ... | no |
+| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
+| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
+| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
diff --git a/_sources/datamodels/obograph/namespace.md.txt b/_sources/datamodels/obograph/namespace.md.txt
index fe3342fd9..e5a1d92dc 100644
--- a/_sources/datamodels/obograph/namespace.md.txt
+++ b/_sources/datamodels/obograph/namespace.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: namespace
@@ -14,11 +16,12 @@ URI: [sh:namespace](https://w3id.org/shacl/namespace)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PrefixDeclaration](PrefixDeclaration.md) | A mapping between an individual prefix (e | no |
+| [PrefixDeclaration](PrefixDeclaration.md) | A mapping between an individual prefix (e | no |
diff --git a/_sources/datamodels/obograph/nodeIds.md.txt b/_sources/datamodels/obograph/nodeIds.md.txt
index a12ecc7aa..752c9adc2 100644
--- a/_sources/datamodels/obograph/nodeIds.md.txt
+++ b/_sources/datamodels/obograph/nodeIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: nodeIds
URI: [obographs:nodeIds](https://github.com/geneontology/obographs/nodeIds)
@@ -9,11 +11,12 @@ URI: [obographs:nodeIds](https://github.com/geneontology/obographs/nodeIds)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
+| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
diff --git a/_sources/datamodels/obograph/nodes.md.txt b/_sources/datamodels/obograph/nodes.md.txt
index 54fb5d473..b95328510 100644
--- a/_sources/datamodels/obograph/nodes.md.txt
+++ b/_sources/datamodels/obograph/nodes.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: nodes
@@ -14,11 +16,12 @@ URI: [obographs:nodes](https://github.com/geneontology/obographs/nodes)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/obj.md.txt b/_sources/datamodels/obograph/obj.md.txt
index 09ac0e42f..b0f568dad 100644
--- a/_sources/datamodels/obograph/obj.md.txt
+++ b/_sources/datamodels/obograph/obj.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: obj
@@ -14,11 +16,12 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
+| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
diff --git a/_sources/datamodels/obograph/pred.md.txt b/_sources/datamodels/obograph/pred.md.txt
index a10d2c1cb..5a8c8303a 100644
--- a/_sources/datamodels/obograph/pred.md.txt
+++ b/_sources/datamodels/obograph/pred.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: pred
@@ -14,17 +16,18 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
+| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
+| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
diff --git a/_sources/datamodels/obograph/predicateId.md.txt b/_sources/datamodels/obograph/predicateId.md.txt
index 26968317e..f7e56b5ce 100644
--- a/_sources/datamodels/obograph/predicateId.md.txt
+++ b/_sources/datamodels/obograph/predicateId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicateId
URI: [obographs:predicateId](https://github.com/geneontology/obographs/predicateId)
@@ -9,12 +11,13 @@ URI: [obographs:predicateId](https://github.com/geneontology/obographs/predicate
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
-[PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
+| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no |
+| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
diff --git a/_sources/datamodels/obograph/prefix.md.txt b/_sources/datamodels/obograph/prefix.md.txt
index 537b090e7..01e0dbc05 100644
--- a/_sources/datamodels/obograph/prefix.md.txt
+++ b/_sources/datamodels/obograph/prefix.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: prefix
@@ -14,11 +16,12 @@ URI: [sh:prefix](https://w3id.org/shacl/prefix)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PrefixDeclaration](PrefixDeclaration.md) | A mapping between an individual prefix (e | no |
+| [PrefixDeclaration](PrefixDeclaration.md) | A mapping between an individual prefix (e | no |
diff --git a/_sources/datamodels/obograph/prefixes.md.txt b/_sources/datamodels/obograph/prefixes.md.txt
index 83704113b..09d8fdf1d 100644
--- a/_sources/datamodels/obograph/prefixes.md.txt
+++ b/_sources/datamodels/obograph/prefixes.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: prefixes
@@ -14,12 +16,13 @@ URI: [sh:declare](https://w3id.org/shacl/declare)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no |
diff --git a/_sources/datamodels/obograph/propertyChainAxioms.md.txt b/_sources/datamodels/obograph/propertyChainAxioms.md.txt
index 70c539100..5815c1ea3 100644
--- a/_sources/datamodels/obograph/propertyChainAxioms.md.txt
+++ b/_sources/datamodels/obograph/propertyChainAxioms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: propertyChainAxioms
@@ -14,11 +16,12 @@ URI: [obographs:propertyChainAxioms](https://github.com/geneontology/obographs/p
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/propertyId.md.txt b/_sources/datamodels/obograph/propertyId.md.txt
index e79ebcc49..d9ed9899e 100644
--- a/_sources/datamodels/obograph/propertyId.md.txt
+++ b/_sources/datamodels/obograph/propertyId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: propertyId
@@ -14,11 +16,12 @@ URI: [obographs:propertyId](https://github.com/geneontology/obographs/propertyId
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExistentialRestrictionExpression](ExistentialRestrictionExpression.md) | An existential restriction (OWL some values from) expression | no |
+| [ExistentialRestrictionExpression](ExistentialRestrictionExpression.md) | An existential restriction (OWL some values from) expression | no |
diff --git a/_sources/datamodels/obograph/propertyType.md.txt b/_sources/datamodels/obograph/propertyType.md.txt
index 2d164ceae..5020911c3 100644
--- a/_sources/datamodels/obograph/propertyType.md.txt
+++ b/_sources/datamodels/obograph/propertyType.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: propertyType
URI: [obographs:propertyType](https://github.com/geneontology/obographs/propertyType)
@@ -9,11 +11,12 @@ URI: [obographs:propertyType](https://github.com/geneontology/obographs/property
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
+| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
diff --git a/_sources/datamodels/obograph/rangeClassIds.md.txt b/_sources/datamodels/obograph/rangeClassIds.md.txt
index 3be0004fc..6d2111e3c 100644
--- a/_sources/datamodels/obograph/rangeClassIds.md.txt
+++ b/_sources/datamodels/obograph/rangeClassIds.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: rangeClassIds
URI: [obographs:rangeClassIds](https://github.com/geneontology/obographs/rangeClassIds)
@@ -9,11 +11,12 @@ URI: [obographs:rangeClassIds](https://github.com/geneontology/obographs/rangeCl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
+| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
diff --git a/_sources/datamodels/obograph/representativeNodeId.md.txt b/_sources/datamodels/obograph/representativeNodeId.md.txt
index 5359ec878..66149658e 100644
--- a/_sources/datamodels/obograph/representativeNodeId.md.txt
+++ b/_sources/datamodels/obograph/representativeNodeId.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: representativeNodeId
@@ -14,11 +16,12 @@ URI: [obographs:representativeNodeId](https://github.com/geneontology/obographs/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
+| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
diff --git a/_sources/datamodels/obograph/restrictions.md.txt b/_sources/datamodels/obograph/restrictions.md.txt
index c1a1f3dae..9fb429602 100644
--- a/_sources/datamodels/obograph/restrictions.md.txt
+++ b/_sources/datamodels/obograph/restrictions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: restrictions
@@ -14,11 +16,12 @@ URI: [owl:someValuesFrom](http://www.w3.org/2002/07/owl#someValuesFrom)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
+| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no |
diff --git a/_sources/datamodels/obograph/sub.md.txt b/_sources/datamodels/obograph/sub.md.txt
index 2e0cb9421..cd74ebb28 100644
--- a/_sources/datamodels/obograph/sub.md.txt
+++ b/_sources/datamodels/obograph/sub.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sub
@@ -14,11 +16,12 @@ URI: [rdf:subject](http://www.w3.org/1999/02/22-rdf-syntax-ns#subject)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
+| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
diff --git a/_sources/datamodels/obograph/subsetDefinitions.md.txt b/_sources/datamodels/obograph/subsetDefinitions.md.txt
index 56e7271d5..31c9dd979 100644
--- a/_sources/datamodels/obograph/subsetDefinitions.md.txt
+++ b/_sources/datamodels/obograph/subsetDefinitions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subsetDefinitions
URI: [obographs:subsetDefinitions](https://github.com/geneontology/obographs/subsetDefinitions)
@@ -9,11 +11,12 @@ URI: [obographs:subsetDefinitions](https://github.com/geneontology/obographs/sub
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/subsets.md.txt b/_sources/datamodels/obograph/subsets.md.txt
index 76449d05d..a05bdd85d 100644
--- a/_sources/datamodels/obograph/subsets.md.txt
+++ b/_sources/datamodels/obograph/subsets.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subsets
@@ -14,11 +16,12 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/synonymType.md.txt b/_sources/datamodels/obograph/synonymType.md.txt
index fd725e5fa..4970ade10 100644
--- a/_sources/datamodels/obograph/synonymType.md.txt
+++ b/_sources/datamodels/obograph/synonymType.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonymType
@@ -14,11 +16,12 @@ URI: [obographs:synonymType](https://github.com/geneontology/obographs/synonymTy
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
diff --git a/_sources/datamodels/obograph/synonymTypeDefinitions.md.txt b/_sources/datamodels/obograph/synonymTypeDefinitions.md.txt
index b3b91edb4..164d59cc2 100644
--- a/_sources/datamodels/obograph/synonymTypeDefinitions.md.txt
+++ b/_sources/datamodels/obograph/synonymTypeDefinitions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonymTypeDefinitions
URI: [obographs:synonymTypeDefinitions](https://github.com/geneontology/obographs/synonymTypeDefinitions)
@@ -9,11 +11,12 @@ URI: [obographs:synonymTypeDefinitions](https://github.com/geneontology/obograph
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
+| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
diff --git a/_sources/datamodels/obograph/synonyms.md.txt b/_sources/datamodels/obograph/synonyms.md.txt
index 983f811fc..e7dcedc4c 100644
--- a/_sources/datamodels/obograph/synonyms.md.txt
+++ b/_sources/datamodels/obograph/synonyms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonyms
@@ -14,11 +16,12 @@ URI: [obographs:synonyms](https://github.com/geneontology/obographs/synonyms)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/type.md.txt b/_sources/datamodels/obograph/type.md.txt
index 08858afc4..63c56d372 100644
--- a/_sources/datamodels/obograph/type.md.txt
+++ b/_sources/datamodels/obograph/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
URI: [obographs:type](https://github.com/geneontology/obographs/type)
@@ -9,11 +11,12 @@ URI: [obographs:type](https://github.com/geneontology/obographs/type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
+| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
diff --git a/_sources/datamodels/obograph/unionEquivalentTo.md.txt b/_sources/datamodels/obograph/unionEquivalentTo.md.txt
index d763dbf69..543d9bc06 100644
--- a/_sources/datamodels/obograph/unionEquivalentTo.md.txt
+++ b/_sources/datamodels/obograph/unionEquivalentTo.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: unionEquivalentTo
@@ -14,11 +16,12 @@ URI: [obographs:unionEquivalentTo](https://github.com/geneontology/obographs/uni
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
+| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
diff --git a/_sources/datamodels/obograph/unionEquivalentToExpression.md.txt b/_sources/datamodels/obograph/unionEquivalentToExpression.md.txt
index 8ade8833e..a35967ad9 100644
--- a/_sources/datamodels/obograph/unionEquivalentToExpression.md.txt
+++ b/_sources/datamodels/obograph/unionEquivalentToExpression.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: unionEquivalentToExpression
@@ -14,11 +16,12 @@ URI: [obographs:unionEquivalentToExpression](https://github.com/geneontology/obo
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
+| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
diff --git a/_sources/datamodels/obograph/val.md.txt b/_sources/datamodels/obograph/val.md.txt
index 1f8a64705..2fafc362f 100644
--- a/_sources/datamodels/obograph/val.md.txt
+++ b/_sources/datamodels/obograph/val.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: val
@@ -14,15 +16,16 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes |
diff --git a/_sources/datamodels/obograph/valType.md.txt b/_sources/datamodels/obograph/valType.md.txt
index 001639b2c..dcc8e56e7 100644
--- a/_sources/datamodels/obograph/valType.md.txt
+++ b/_sources/datamodels/obograph/valType.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: valType
@@ -14,15 +16,16 @@ URI: [obographs:valType](https://github.com/geneontology/obographs/valType)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
diff --git a/_sources/datamodels/obograph/version.md.txt b/_sources/datamodels/obograph/version.md.txt
index 59a30cc01..860b3526c 100644
--- a/_sources/datamodels/obograph/version.md.txt
+++ b/_sources/datamodels/obograph/version.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: version
URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
@@ -9,11 +11,12 @@ URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | no |
diff --git a/_sources/datamodels/obograph/xrefs.md.txt b/_sources/datamodels/obograph/xrefs.md.txt
index 24275093b..1733c652f 100644
--- a/_sources/datamodels/obograph/xrefs.md.txt
+++ b/_sources/datamodels/obograph/xrefs.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: xrefs
@@ -14,16 +16,17 @@ URI: [obographs:xrefs](https://github.com/geneontology/obographs/xrefs)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | yes |
-[PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
-[DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes |
-[BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
-[XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
-[SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
+| [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | yes |
+| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
+| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes |
+| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no |
+| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
diff --git a/_sources/datamodels/ontology-metadata/Agent.md.txt b/_sources/datamodels/ontology-metadata/Agent.md.txt
index b0c0ea773..318b3bf4d 100644
--- a/_sources/datamodels/ontology-metadata/Agent.md.txt
+++ b/_sources/datamodels/ontology-metadata/Agent.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Agent
@@ -283,7 +285,7 @@ Instances of this class *should* have identifiers with one of the following pref
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -311,7 +313,7 @@ Instances of this class *should* have identifiers with one of the following pref
name: Agent
id_prefixes:
- orcid
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
slot_usage:
id:
@@ -331,7 +333,7 @@ class_uri: prov:Agent
name: Agent
id_prefixes:
- orcid
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
slot_usage:
id:
@@ -342,7 +344,7 @@ slot_usage:
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -357,7 +359,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -369,7 +371,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -381,7 +383,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -394,7 +396,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -407,7 +409,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -419,7 +421,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -433,7 +435,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -447,7 +449,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -463,7 +465,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -481,7 +483,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -499,7 +501,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -517,7 +519,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -537,7 +539,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -552,7 +554,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -562,7 +564,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -573,7 +575,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -586,7 +588,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -597,7 +599,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -613,7 +615,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -626,7 +628,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -644,7 +646,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -664,7 +666,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -680,7 +682,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -694,7 +696,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -707,7 +709,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -719,7 +721,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -735,7 +737,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -747,7 +749,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -758,7 +760,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -772,7 +774,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -784,7 +786,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -796,7 +798,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -808,7 +810,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -820,7 +822,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -832,7 +834,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -845,7 +847,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -856,7 +858,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -868,7 +870,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -879,7 +881,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -893,7 +895,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -909,7 +911,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -921,7 +923,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -934,7 +936,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -948,7 +950,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -960,7 +962,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -971,7 +973,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -983,7 +985,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1003,7 +1005,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -1024,7 +1026,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
@@ -1039,7 +1041,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1052,7 +1054,7 @@ attributes:
pattern: ^orcid:.*
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/AllotropePermittedProfile.md.txt b/_sources/datamodels/ontology-metadata/AllotropePermittedProfile.md.txt
index 95d456c07..9be1b29e6 100644
--- a/_sources/datamodels/ontology-metadata/AllotropePermittedProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/AllotropePermittedProfile.md.txt
@@ -20,7 +20,7 @@ URI: [AllotropePermittedProfile](AllotropePermittedProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/AllotropeRequiredProfile.md.txt b/_sources/datamodels/ontology-metadata/AllotropeRequiredProfile.md.txt
index f06eee8d9..36c6fc159 100644
--- a/_sources/datamodels/ontology-metadata/AllotropeRequiredProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/AllotropeRequiredProfile.md.txt
@@ -20,7 +20,7 @@ URI: [AllotropeRequiredProfile](AllotropeRequiredProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Annotation.md.txt b/_sources/datamodels/ontology-metadata/Annotation.md.txt
index fba485d97..d5c4b81d7 100644
--- a/_sources/datamodels/ontology-metadata/Annotation.md.txt
+++ b/_sources/datamodels/ontology-metadata/Annotation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Annotation
@@ -7,7 +9,7 @@ _A reified property-object pair_
-URI: [omoschema:Annotation](http://purl.obolibrary.org/obo/omo/schema/Annotation)
+URI: [omoschema:Annotation](https://w3id.org/oak/ontology-metadata/Annotation)
@@ -61,7 +63,7 @@ URI: [omoschema:Annotation](http://purl.obolibrary.org/obo/omo/schema/Annotation
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -88,17 +90,17 @@ URI: [omoschema:Annotation](http://purl.obolibrary.org/obo/omo/schema/Annotation
```yaml
name: Annotation
description: A reified property-object pair
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
attributes:
predicate:
name: predicate
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
domain_of:
- Annotation
relational_role: PREDICATE
object:
name: object
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
domain_of:
- Annotation
relational_role: OBJECT
@@ -113,11 +115,11 @@ represents_relationship: true
```yaml
name: Annotation
description: A reified property-object pair
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
attributes:
predicate:
name: predicate
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
alias: predicate
owner: Annotation
domain_of:
@@ -126,7 +128,7 @@ attributes:
range: string
object:
name: object
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
alias: object
owner: Annotation
domain_of:
diff --git a/_sources/datamodels/ontology-metadata/AnnotationProperty.md.txt b/_sources/datamodels/ontology-metadata/AnnotationProperty.md.txt
index 6578cfb45..746151950 100644
--- a/_sources/datamodels/ontology-metadata/AnnotationProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/AnnotationProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: AnnotationProperty
@@ -277,7 +279,7 @@ URI: [owl:AnnotationProperty](http://www.w3.org/2002/07/owl#AnnotationProperty)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -304,7 +306,7 @@ URI: [owl:AnnotationProperty](http://www.w3.org/2002/07/owl#AnnotationProperty)
```yaml
name: AnnotationProperty
description: A property used in non-logical axioms
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Property
slots:
- shorthand
@@ -319,13 +321,13 @@ class_uri: owl:AnnotationProperty
```yaml
name: AnnotationProperty
description: A property used in non-logical axioms
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Property
attributes:
shorthand:
name: shorthand
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:shorthand
multivalued: true
@@ -339,7 +341,7 @@ attributes:
name: domain
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
@@ -353,7 +355,7 @@ attributes:
name: range
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
@@ -366,7 +368,7 @@ attributes:
is_class_level:
name: is_class_level
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
@@ -377,7 +379,7 @@ attributes:
is_metadata_tag:
name: is_metadata_tag
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
@@ -387,7 +389,7 @@ attributes:
range: boolean
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -402,7 +404,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -414,7 +416,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -426,7 +428,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -439,7 +441,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -452,7 +454,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -464,7 +466,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -478,7 +480,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -492,7 +494,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -508,7 +510,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -526,7 +528,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -544,7 +546,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -562,7 +564,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -582,7 +584,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -597,7 +599,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -607,7 +609,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -618,7 +620,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -631,7 +633,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -642,7 +644,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -658,7 +660,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -671,7 +673,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -689,7 +691,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -709,7 +711,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -725,7 +727,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -739,7 +741,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -752,7 +754,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -764,7 +766,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -780,7 +782,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -792,7 +794,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -803,7 +805,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -817,7 +819,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -829,7 +831,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -841,7 +843,7 @@ attributes:
range: Property
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -853,7 +855,7 @@ attributes:
range: Property
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -865,7 +867,7 @@ attributes:
range: Property
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -877,7 +879,7 @@ attributes:
range: Property
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -890,7 +892,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -901,7 +903,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -913,7 +915,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -924,7 +926,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -938,7 +940,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -954,7 +956,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -966,7 +968,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -979,7 +981,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -993,7 +995,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1005,7 +1007,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1016,7 +1018,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1028,7 +1030,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1040,7 +1042,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1054,7 +1056,7 @@ attributes:
recommended: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1068,7 +1070,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1080,7 +1082,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/AnnotationPropertyMixin.md.txt b/_sources/datamodels/ontology-metadata/AnnotationPropertyMixin.md.txt
index d7cbd6cda..db1ae1788 100644
--- a/_sources/datamodels/ontology-metadata/AnnotationPropertyMixin.md.txt
+++ b/_sources/datamodels/ontology-metadata/AnnotationPropertyMixin.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: AnnotationPropertyMixin
@@ -7,7 +9,7 @@ _Groups all annotation property bundles_
-URI: [omoschema:AnnotationPropertyMixin](http://purl.obolibrary.org/obo/omo/schema/AnnotationPropertyMixin)
+URI: [omoschema:AnnotationPropertyMixin](https://w3id.org/oak/ontology-metadata/AnnotationPropertyMixin)
@@ -72,7 +74,7 @@ URI: [omoschema:AnnotationPropertyMixin](http://purl.obolibrary.org/obo/omo/sche
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -99,7 +101,7 @@ URI: [omoschema:AnnotationPropertyMixin](http://purl.obolibrary.org/obo/omo/sche
```yaml
name: AnnotationPropertyMixin
description: Groups all annotation property bundles
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
```
@@ -111,7 +113,7 @@ mixin: true
```yaml
name: AnnotationPropertyMixin
description: Groups all annotation property bundles
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
```
diff --git a/_sources/datamodels/ontology-metadata/Anonymous.md.txt b/_sources/datamodels/ontology-metadata/Anonymous.md.txt
index 30d118458..1dca517f8 100644
--- a/_sources/datamodels/ontology-metadata/Anonymous.md.txt
+++ b/_sources/datamodels/ontology-metadata/Anonymous.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Anonymous
@@ -9,7 +11,7 @@ _Abstract root class for all anonymous (non-named; lacking an identifier) expres
* __NOTE__: this is an abstract class and should not be instantiated directly
-URI: [omoschema:Anonymous](http://purl.obolibrary.org/obo/omo/schema/Anonymous)
+URI: [omoschema:Anonymous](https://w3id.org/oak/ontology-metadata/Anonymous)
@@ -56,7 +58,7 @@ URI: [omoschema:Anonymous](http://purl.obolibrary.org/obo/omo/schema/Anonymous)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -84,7 +86,7 @@ URI: [omoschema:Anonymous](http://purl.obolibrary.org/obo/omo/schema/Anonymous)
name: Anonymous
description: Abstract root class for all anonymous (non-named; lacking an identifier)
expressions
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
abstract: true
```
@@ -97,7 +99,7 @@ abstract: true
name: Anonymous
description: Abstract root class for all anonymous (non-named; lacking an identifier)
expressions
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
abstract: true
```
diff --git a/_sources/datamodels/ontology-metadata/AnonymousClassExpression.md.txt b/_sources/datamodels/ontology-metadata/AnonymousClassExpression.md.txt
index ec32af2dc..f1794b4b4 100644
--- a/_sources/datamodels/ontology-metadata/AnonymousClassExpression.md.txt
+++ b/_sources/datamodels/ontology-metadata/AnonymousClassExpression.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: AnonymousClassExpression
-URI: [omoschema:AnonymousClassExpression](http://purl.obolibrary.org/obo/omo/schema/AnonymousClassExpression)
+URI: [omoschema:AnonymousClassExpression](https://w3id.org/oak/ontology-metadata/AnonymousClassExpression)
@@ -54,7 +56,7 @@ URI: [omoschema:AnonymousClassExpression](http://purl.obolibrary.org/obo/omo/sch
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -80,7 +82,7 @@ URI: [omoschema:AnonymousClassExpression](http://purl.obolibrary.org/obo/omo/sch
```yaml
name: AnonymousClassExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Anonymous
```
@@ -91,7 +93,7 @@ is_a: Anonymous
```yaml
name: AnonymousClassExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Anonymous
```
diff --git a/_sources/datamodels/ontology-metadata/Any.md.txt b/_sources/datamodels/ontology-metadata/Any.md.txt
index 074452219..b06660bb4 100644
--- a/_sources/datamodels/ontology-metadata/Any.md.txt
+++ b/_sources/datamodels/ontology-metadata/Any.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Any
@@ -74,7 +76,7 @@ URI: [linkml:Any](https://w3id.org/linkml/Any)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -100,7 +102,7 @@ URI: [linkml:Any](https://w3id.org/linkml/Any)
```yaml
name: Any
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
class_uri: linkml:Any
```
@@ -111,7 +113,7 @@ class_uri: linkml:Any
```yaml
name: Any
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
class_uri: linkml:Any
```
diff --git a/_sources/datamodels/ontology-metadata/Axiom.md.txt b/_sources/datamodels/ontology-metadata/Axiom.md.txt
index 272aeb77c..5de3839be 100644
--- a/_sources/datamodels/ontology-metadata/Axiom.md.txt
+++ b/_sources/datamodels/ontology-metadata/Axiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Axiom
@@ -125,7 +127,7 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -153,7 +155,7 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
```yaml
name: Axiom
description: A logical or non-logical statement
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:Statement
slots:
@@ -201,7 +203,7 @@ represents_relationship: true
```yaml
name: Axiom
description: A logical or non-logical statement
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:Statement
slot_usage:
@@ -218,7 +220,7 @@ slot_usage:
attributes:
annotatedProperty:
name: annotatedProperty
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:predicate
rank: 1000
@@ -234,7 +236,7 @@ attributes:
name: annotatedSource
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:subject
rank: 1000
@@ -250,7 +252,7 @@ attributes:
name: annotatedTarget
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:object
rank: 1000
@@ -264,7 +266,7 @@ attributes:
range: Any
annotations:
name: annotations
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
multivalued: true
alias: annotations
@@ -274,7 +276,7 @@ attributes:
range: Annotation
source:
name: source
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- http://purl.org/dc/terms/source
- oio:source
@@ -291,7 +293,7 @@ attributes:
is_inferred:
name: is_inferred
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_inferred
alias: is_inferred
@@ -302,7 +304,7 @@ attributes:
notes:
name: notes
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:notes
multivalued: true
@@ -314,7 +316,7 @@ attributes:
url:
name: url
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:url
alias: url
@@ -324,7 +326,7 @@ attributes:
range: string
has_axiom_label:
name: has_axiom_label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0010000
@@ -335,7 +337,7 @@ attributes:
range: Thing
is_a_defining_property_chain_axiom:
name: is_a_defining_property_chain_axiom
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002581
alias: is_a_defining_property_chain_axiom
@@ -345,7 +347,7 @@ attributes:
range: string
is_a_defining_property_chain_axiom_where_second_argument_is_reflexive:
name: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002582
alias: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive
@@ -356,7 +358,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -369,7 +371,7 @@ attributes:
range: string
date_retrieved:
name: date_retrieved
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: oio:date_retrieved
@@ -381,7 +383,7 @@ attributes:
evidence:
name: evidence
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:evidence
alias: evidence
@@ -392,7 +394,7 @@ attributes:
external_ontology:
name: external_ontology
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:external_ontology
multivalued: true
@@ -406,7 +408,7 @@ attributes:
description: Uses to indicate the source of an axiom
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:source
rank: 1000
@@ -421,7 +423,7 @@ attributes:
range: CURIELiteral
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -436,7 +438,7 @@ attributes:
range: label type
has_synonym_type:
name: has_synonym_type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasSynonymType
multivalued: true
@@ -449,7 +451,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -471,7 +473,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -488,7 +490,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/Boolean.md.txt b/_sources/datamodels/ontology-metadata/Boolean.md.txt
index 6c3ce3b70..4ffccc24b 100644
--- a/_sources/datamodels/ontology-metadata/Boolean.md.txt
+++ b/_sources/datamodels/ontology-metadata/Boolean.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/CURIELiteral.md.txt b/_sources/datamodels/ontology-metadata/CURIELiteral.md.txt
index 3e516078b..d4d93bf3a 100644
--- a/_sources/datamodels/ontology-metadata/CURIELiteral.md.txt
+++ b/_sources/datamodels/ontology-metadata/CURIELiteral.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Class.md.txt b/_sources/datamodels/ontology-metadata/Class.md.txt
index edd15dc16..4e1640350 100644
--- a/_sources/datamodels/ontology-metadata/Class.md.txt
+++ b/_sources/datamodels/ontology-metadata/Class.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Class
@@ -323,7 +325,7 @@ URI: [owl:Class](http://www.w3.org/2002/07/owl#Class)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -350,7 +352,7 @@ URI: [owl:Class](http://www.w3.org/2002/07/owl#Class)
```yaml
name: Class
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- term
- concept
@@ -410,7 +412,7 @@ class_uri: owl:Class
```yaml
name: Class
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- term
- concept
@@ -459,7 +461,7 @@ slot_usage:
attributes:
never_in_taxon:
name: never_in_taxon
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002161
multivalued: true
@@ -470,7 +472,7 @@ attributes:
range: Class
disconnected_from:
name: disconnected_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: shortcut_annotation_property
alias: disconnected_from
@@ -480,7 +482,7 @@ attributes:
range: Class
has_rank:
name: has_rank
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- obo:ncbitaxon/subsets/taxslim#has_rank
rank: 1000
@@ -493,7 +495,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
@@ -508,7 +510,7 @@ attributes:
name: equivalentClass
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
@@ -524,7 +526,7 @@ attributes:
name: intersectionOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:intersectionOf
@@ -535,7 +537,7 @@ attributes:
range: ClassExpression
subClassOf:
name: subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:subClassOf
@@ -547,7 +549,7 @@ attributes:
range: Class
cardinality:
name: cardinality
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:cardinality
@@ -560,7 +562,7 @@ attributes:
name: complementOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:complementOf
@@ -571,7 +573,7 @@ attributes:
range: string
oneOf:
name: oneOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:oneOf
@@ -582,7 +584,7 @@ attributes:
range: ClassExpression
unionOf:
name: unionOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:unionOf
@@ -593,7 +595,7 @@ attributes:
range: string
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -608,7 +610,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -620,7 +622,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -632,7 +634,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -645,7 +647,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -658,7 +660,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -670,7 +672,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -684,7 +686,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -698,7 +700,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -714,7 +716,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -732,7 +734,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -750,7 +752,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -768,7 +770,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -788,7 +790,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -803,7 +805,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -813,7 +815,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -824,7 +826,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -837,7 +839,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -848,7 +850,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -864,7 +866,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -877,7 +879,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -895,7 +897,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -915,7 +917,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -931,7 +933,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -945,7 +947,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -958,7 +960,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -970,7 +972,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -986,7 +988,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -998,7 +1000,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -1009,7 +1011,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -1023,7 +1025,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -1035,7 +1037,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -1047,7 +1049,7 @@ attributes:
range: Class
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -1059,7 +1061,7 @@ attributes:
range: Class
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -1071,7 +1073,7 @@ attributes:
range: Class
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -1083,7 +1085,7 @@ attributes:
range: Class
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -1096,7 +1098,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -1107,7 +1109,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -1119,7 +1121,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -1130,7 +1132,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -1144,7 +1146,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -1160,7 +1162,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -1172,7 +1174,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -1185,7 +1187,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -1199,7 +1201,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1211,7 +1213,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1222,7 +1224,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1234,7 +1236,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1246,7 +1248,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1260,7 +1262,7 @@ attributes:
required: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1274,7 +1276,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1286,7 +1288,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/ClassExpression.md.txt b/_sources/datamodels/ontology-metadata/ClassExpression.md.txt
index 5d6a42cce..0fcb8b9ff 100644
--- a/_sources/datamodels/ontology-metadata/ClassExpression.md.txt
+++ b/_sources/datamodels/ontology-metadata/ClassExpression.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: ClassExpression
-URI: [omoschema:ClassExpression](http://purl.obolibrary.org/obo/omo/schema/ClassExpression)
+URI: [omoschema:ClassExpression](https://w3id.org/oak/ontology-metadata/ClassExpression)
@@ -111,7 +113,7 @@ URI: [omoschema:ClassExpression](http://purl.obolibrary.org/obo/omo/schema/Class
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -137,7 +139,7 @@ URI: [omoschema:ClassExpression](http://purl.obolibrary.org/obo/omo/schema/Class
```yaml
name: ClassExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Expression
mixin: true
slots:
@@ -158,7 +160,7 @@ slots:
```yaml
name: ClassExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Expression
mixin: true
attributes:
@@ -166,7 +168,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
@@ -181,7 +183,7 @@ attributes:
name: equivalentClass
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
@@ -197,7 +199,7 @@ attributes:
name: intersectionOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:intersectionOf
@@ -208,7 +210,7 @@ attributes:
range: ClassExpression
subClassOf:
name: subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:subClassOf
@@ -220,7 +222,7 @@ attributes:
range: ClassExpression
cardinality:
name: cardinality
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:cardinality
@@ -233,7 +235,7 @@ attributes:
name: complementOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:complementOf
@@ -244,7 +246,7 @@ attributes:
range: string
oneOf:
name: oneOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:oneOf
@@ -255,7 +257,7 @@ attributes:
range: ClassExpression
unionOf:
name: unionOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:unionOf
diff --git a/_sources/datamodels/ontology-metadata/Curie.md.txt b/_sources/datamodels/ontology-metadata/Curie.md.txt
index 4aafde3b5..5af9848d1 100644
--- a/_sources/datamodels/ontology-metadata/Curie.md.txt
+++ b/_sources/datamodels/ontology-metadata/Curie.md.txt
@@ -38,7 +38,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Date.md.txt b/_sources/datamodels/ontology-metadata/Date.md.txt
index 6aae8c453..b95f89f2a 100644
--- a/_sources/datamodels/ontology-metadata/Date.md.txt
+++ b/_sources/datamodels/ontology-metadata/Date.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:date](http://www.w3.org/2001/XMLSchema#date)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/DateOrDatetime.md.txt b/_sources/datamodels/ontology-metadata/DateOrDatetime.md.txt
index 6e0063fa8..fa4cc73dc 100644
--- a/_sources/datamodels/ontology-metadata/DateOrDatetime.md.txt
+++ b/_sources/datamodels/ontology-metadata/DateOrDatetime.md.txt
@@ -33,7 +33,7 @@ URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Datetime.md.txt b/_sources/datamodels/ontology-metadata/Datetime.md.txt
index a092ab45d..f13b9daa8 100644
--- a/_sources/datamodels/ontology-metadata/Datetime.md.txt
+++ b/_sources/datamodels/ontology-metadata/Datetime.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:dateTime](http://www.w3.org/2001/XMLSchema#dateTime)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Decimal.md.txt b/_sources/datamodels/ontology-metadata/Decimal.md.txt
index b7a72c8bb..e77d225ec 100644
--- a/_sources/datamodels/ontology-metadata/Decimal.md.txt
+++ b/_sources/datamodels/ontology-metadata/Decimal.md.txt
@@ -32,7 +32,7 @@ URI: [xsd:decimal](http://www.w3.org/2001/XMLSchema#decimal)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/DefinitionConstraintComponent.md.txt b/_sources/datamodels/ontology-metadata/DefinitionConstraintComponent.md.txt
index 4ea345ec7..22d7ae266 100644
--- a/_sources/datamodels/ontology-metadata/DefinitionConstraintComponent.md.txt
+++ b/_sources/datamodels/ontology-metadata/DefinitionConstraintComponent.md.txt
@@ -21,6 +21,11 @@ URI: [DefinitionConstraintComponent](DefinitionConstraintComponent.md)
| SingleGenus | omoschema:DCC.S3.1 | An entity must have a single genus |
| Circularity | omoschema:DCC.S7 | A definition must not be circular |
| MatchTextAndLogical | omoschema:DCC.S11 | Text definitions and logical forms should match |
+| MatchTextAndLogicalGenusNotInText | omoschema:DCC.S11.1 | The genus in the logical definition should be in the text definition |
+| MatchTextAndLogicalDifferentiaNotInText | omoschema:DCC.S11.2 | The differentia in the logical definition should be in the text definition |
+| MatchTextAndReference | omoschema:DCC.S20 | Text definitions and cited references and provenance for the text definition ... |
+| ReferenceNotFound | omoschema:DCC.S20.1 | The citation for the reference cannot be found |
+| ReferenceIsRetracted | omoschema:DCC.S20.2 | The citation for the reference is retracted |
@@ -45,7 +50,7 @@ URI: [DefinitionConstraintComponent](DefinitionConstraintComponent.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -56,7 +61,7 @@ URI: [DefinitionConstraintComponent](DefinitionConstraintComponent.md)
```yaml
name: DefinitionConstraintComponent
description: An extension of SHACL constraint component for constraining definitions
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
source: https://philpapers.org/archive/SEPGFW.pdf
see_also:
- https://github.com/INCATools/ontology-access-kit/issues/305
@@ -101,6 +106,32 @@ permissible_values:
description: Text definitions and logical forms should match
meaning: omoschema:DCC.S11
is_a: DefinitionConstraint
+ MatchTextAndLogicalGenusNotInText:
+ text: MatchTextAndLogicalGenusNotInText
+ description: The genus in the logical definition should be in the text definition
+ meaning: omoschema:DCC.S11.1
+ is_a: DefinitionConstraint
+ MatchTextAndLogicalDifferentiaNotInText:
+ text: MatchTextAndLogicalDifferentiaNotInText
+ description: The differentia in the logical definition should be in the text definition
+ meaning: omoschema:DCC.S11.2
+ is_a: DefinitionConstraint
+ MatchTextAndReference:
+ text: MatchTextAndReference
+ description: Text definitions and cited references and provenance for the text
+ definition should match
+ meaning: omoschema:DCC.S20
+ is_a: DefinitionConstraint
+ ReferenceNotFound:
+ text: ReferenceNotFound
+ description: The citation for the reference cannot be found
+ meaning: omoschema:DCC.S20.1
+ is_a: MatchTextAndReference
+ ReferenceIsRetracted:
+ text: ReferenceIsRetracted
+ description: The citation for the reference is retracted
+ meaning: omoschema:DCC.S20.2
+ is_a: MatchTextAndReference
```
diff --git a/_sources/datamodels/ontology-metadata/Double.md.txt b/_sources/datamodels/ontology-metadata/Double.md.txt
index f33c41df5..0347417de 100644
--- a/_sources/datamodels/ontology-metadata/Double.md.txt
+++ b/_sources/datamodels/ontology-metadata/Double.md.txt
@@ -32,7 +32,7 @@ URI: [xsd:double](http://www.w3.org/2001/XMLSchema#double)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Expression.md.txt b/_sources/datamodels/ontology-metadata/Expression.md.txt
index 3f8544b51..bab561635 100644
--- a/_sources/datamodels/ontology-metadata/Expression.md.txt
+++ b/_sources/datamodels/ontology-metadata/Expression.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: Expression
-URI: [omoschema:Expression](http://purl.obolibrary.org/obo/omo/schema/Expression)
+URI: [omoschema:Expression](https://w3id.org/oak/ontology-metadata/Expression)
@@ -57,7 +59,7 @@ URI: [omoschema:Expression](http://purl.obolibrary.org/obo/omo/schema/Expression
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -83,7 +85,7 @@ URI: [omoschema:Expression](http://purl.obolibrary.org/obo/omo/schema/Expression
```yaml
name: Expression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
```
@@ -94,7 +96,7 @@ mixin: true
```yaml
name: Expression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
```
diff --git a/_sources/datamodels/ontology-metadata/Float.md.txt b/_sources/datamodels/ontology-metadata/Float.md.txt
index 69b59e31e..1032ba78b 100644
--- a/_sources/datamodels/ontology-metadata/Float.md.txt
+++ b/_sources/datamodels/ontology-metadata/Float.md.txt
@@ -32,7 +32,7 @@ URI: [xsd:float](http://www.w3.org/2001/XMLSchema#float)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/GoPermittedProfile.md.txt b/_sources/datamodels/ontology-metadata/GoPermittedProfile.md.txt
index 32da9fe87..304d20caa 100644
--- a/_sources/datamodels/ontology-metadata/GoPermittedProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/GoPermittedProfile.md.txt
@@ -16,7 +16,7 @@ URI: [GoPermittedProfile](GoPermittedProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/GoRecommendedProfile.md.txt b/_sources/datamodels/ontology-metadata/GoRecommendedProfile.md.txt
index 3402a7805..9cd37cb8d 100644
--- a/_sources/datamodels/ontology-metadata/GoRecommendedProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/GoRecommendedProfile.md.txt
@@ -16,7 +16,7 @@ URI: [GoRecommendedProfile](GoRecommendedProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/GoRequiredProfile.md.txt b/_sources/datamodels/ontology-metadata/GoRequiredProfile.md.txt
index a11740839..4df625b41 100644
--- a/_sources/datamodels/ontology-metadata/GoRequiredProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/GoRequiredProfile.md.txt
@@ -16,7 +16,7 @@ URI: [GoRequiredProfile](GoRequiredProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/HasCategory.md.txt b/_sources/datamodels/ontology-metadata/HasCategory.md.txt
index b36e00479..1e939dd85 100644
--- a/_sources/datamodels/ontology-metadata/HasCategory.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasCategory.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: HasCategory
-URI: [omoschema:HasCategory](http://purl.obolibrary.org/obo/omo/schema/HasCategory)
+URI: [omoschema:HasCategory](https://w3id.org/oak/ontology-metadata/HasCategory)
@@ -76,7 +78,7 @@ URI: [omoschema:HasCategory](http://purl.obolibrary.org/obo/omo/schema/HasCatego
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -102,7 +104,7 @@ URI: [omoschema:HasCategory](http://purl.obolibrary.org/obo/omo/schema/HasCatego
```yaml
name: HasCategory
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -119,13 +121,13 @@ slots:
```yaml
name: HasCategory
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -136,7 +138,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -148,7 +150,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -159,7 +161,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
diff --git a/_sources/datamodels/ontology-metadata/HasLifeCycle.md.txt b/_sources/datamodels/ontology-metadata/HasLifeCycle.md.txt
index 6b80e46d4..9bea82919 100644
--- a/_sources/datamodels/ontology-metadata/HasLifeCycle.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasLifeCycle.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: HasLifeCycle
-URI: [omoschema:HasLifeCycle](http://purl.obolibrary.org/obo/omo/schema/HasLifeCycle)
+URI: [omoschema:HasLifeCycle](https://w3id.org/oak/ontology-metadata/HasLifeCycle)
@@ -97,7 +99,7 @@ URI: [omoschema:HasLifeCycle](http://purl.obolibrary.org/obo/omo/schema/HasLifeC
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -123,7 +125,7 @@ URI: [omoschema:HasLifeCycle](http://purl.obolibrary.org/obo/omo/schema/HasLifeC
```yaml
name: HasLifeCycle
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -192,7 +194,7 @@ rules:
```yaml
name: HasLifeCycle
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
@@ -202,7 +204,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -220,7 +222,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -238,7 +240,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -256,7 +258,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -276,7 +278,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -291,7 +293,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -301,7 +303,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -312,7 +314,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -325,7 +327,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
diff --git a/_sources/datamodels/ontology-metadata/HasMappings.md.txt b/_sources/datamodels/ontology-metadata/HasMappings.md.txt
index eee191402..f8a74ef99 100644
--- a/_sources/datamodels/ontology-metadata/HasMappings.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasMappings.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: HasMappings
-URI: [omoschema:HasMappings](http://purl.obolibrary.org/obo/omo/schema/HasMappings)
+URI: [omoschema:HasMappings](https://w3id.org/oak/ontology-metadata/HasMappings)
@@ -83,7 +85,7 @@ URI: [omoschema:HasMappings](http://purl.obolibrary.org/obo/omo/schema/HasMappin
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -109,7 +111,7 @@ URI: [omoschema:HasMappings](http://purl.obolibrary.org/obo/omo/schema/HasMappin
```yaml
name: HasMappings
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -127,13 +129,13 @@ slots:
```yaml
name: HasMappings
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -145,7 +147,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -157,7 +159,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -169,7 +171,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -181,7 +183,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
diff --git a/_sources/datamodels/ontology-metadata/HasMinimalMetadata.md.txt b/_sources/datamodels/ontology-metadata/HasMinimalMetadata.md.txt
index 74ef5ffbf..8d2657025 100644
--- a/_sources/datamodels/ontology-metadata/HasMinimalMetadata.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasMinimalMetadata.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: HasMinimalMetadata
@@ -7,7 +9,7 @@ _Absolute minimum metadata model_
-URI: [omoschema:HasMinimalMetadata](http://purl.obolibrary.org/obo/omo/schema/HasMinimalMetadata)
+URI: [omoschema:HasMinimalMetadata](https://w3id.org/oak/ontology-metadata/HasMinimalMetadata)
@@ -71,7 +73,7 @@ URI: [omoschema:HasMinimalMetadata](http://purl.obolibrary.org/obo/omo/schema/Ha
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -98,7 +100,7 @@ URI: [omoschema:HasMinimalMetadata](http://purl.obolibrary.org/obo/omo/schema/Ha
```yaml
name: HasMinimalMetadata
description: Absolute minimum metadata model
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -114,7 +116,7 @@ slots:
```yaml
name: HasMinimalMetadata
description: Absolute minimum metadata model
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
@@ -128,7 +130,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -149,7 +151,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/HasProvenance.md.txt b/_sources/datamodels/ontology-metadata/HasProvenance.md.txt
index ed4046fb7..9bc27f3a1 100644
--- a/_sources/datamodels/ontology-metadata/HasProvenance.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasProvenance.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: HasProvenance
-URI: [omoschema:HasProvenance](http://purl.obolibrary.org/obo/omo/schema/HasProvenance)
+URI: [omoschema:HasProvenance](https://w3id.org/oak/ontology-metadata/HasProvenance)
@@ -107,7 +109,7 @@ URI: [omoschema:HasProvenance](http://purl.obolibrary.org/obo/omo/schema/HasProv
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -133,7 +135,7 @@ URI: [omoschema:HasProvenance](http://purl.obolibrary.org/obo/omo/schema/HasProv
```yaml
name: HasProvenance
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -159,14 +161,14 @@ slots:
```yaml
name: HasProvenance
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -182,7 +184,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -195,7 +197,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -213,7 +215,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -233,7 +235,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -249,7 +251,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -263,7 +265,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -276,7 +278,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -288,7 +290,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -304,7 +306,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -316,7 +318,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -327,7 +329,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -341,7 +343,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
diff --git a/_sources/datamodels/ontology-metadata/HasSynonyms.md.txt b/_sources/datamodels/ontology-metadata/HasSynonyms.md.txt
index 4213feca2..aedfd2857 100644
--- a/_sources/datamodels/ontology-metadata/HasSynonyms.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasSynonyms.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: HasSynonyms
@@ -7,7 +9,7 @@ _a mixin for a class whose members can have synonyms_
-URI: [omoschema:HasSynonyms](http://purl.obolibrary.org/obo/omo/schema/HasSynonyms)
+URI: [omoschema:HasSynonyms](https://w3id.org/oak/ontology-metadata/HasSynonyms)
@@ -97,7 +99,7 @@ URI: [omoschema:HasSynonyms](http://purl.obolibrary.org/obo/omo/schema/HasSynony
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -128,7 +130,7 @@ comments:
- the GO-style synonym model has four distinct scopes, with additional types as annotation
axioms
- the OBI synonym model is to use alternative_term, or potentially a subproperty
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -155,13 +157,13 @@ comments:
- the GO-style synonym model has four distinct scopes, with additional types as annotation
axioms
- the OBI synonym model is to use alternative_term, or potentially a subproperty
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -176,7 +178,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -188,7 +190,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -200,7 +202,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -213,7 +215,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -226,7 +228,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -238,7 +240,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -252,7 +254,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -266,7 +268,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
diff --git a/_sources/datamodels/ontology-metadata/HasUserInformation.md.txt b/_sources/datamodels/ontology-metadata/HasUserInformation.md.txt
index ecf77d8fd..df3cdd996 100644
--- a/_sources/datamodels/ontology-metadata/HasUserInformation.md.txt
+++ b/_sources/datamodels/ontology-metadata/HasUserInformation.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: HasUserInformation
-URI: [omoschema:HasUserInformation](http://purl.obolibrary.org/obo/omo/schema/HasUserInformation)
+URI: [omoschema:HasUserInformation](https://w3id.org/oak/ontology-metadata/HasUserInformation)
@@ -90,7 +92,7 @@ URI: [omoschema:HasUserInformation](http://purl.obolibrary.org/obo/omo/schema/Ha
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -116,7 +118,7 @@ URI: [omoschema:HasUserInformation](http://purl.obolibrary.org/obo/omo/schema/Ha
```yaml
name: HasUserInformation
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
slots:
@@ -137,7 +139,7 @@ slots:
```yaml
name: HasUserInformation
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationPropertyMixin
mixin: true
attributes:
@@ -145,7 +147,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -161,7 +163,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -173,7 +175,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -186,7 +188,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -200,7 +202,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -212,7 +214,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -223,7 +225,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -235,7 +237,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
diff --git a/_sources/datamodels/ontology-metadata/HomoSapiens.md.txt b/_sources/datamodels/ontology-metadata/HomoSapiens.md.txt
index f6f71f48b..2976a1021 100644
--- a/_sources/datamodels/ontology-metadata/HomoSapiens.md.txt
+++ b/_sources/datamodels/ontology-metadata/HomoSapiens.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: HomoSapiens
@@ -257,7 +259,7 @@ Instances of this class *should* have identifiers with one of the following pref
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -286,7 +288,7 @@ name: HomoSapiens
id_prefixes:
- orcid
description: An individual human being
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
slot_usage:
id:
@@ -307,7 +309,7 @@ name: HomoSapiens
id_prefixes:
- orcid
description: An individual human being
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
slot_usage:
id:
@@ -318,7 +320,7 @@ slot_usage:
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -333,7 +335,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -345,7 +347,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -357,7 +359,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -370,7 +372,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -383,7 +385,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -395,7 +397,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -409,7 +411,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -423,7 +425,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -439,7 +441,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -457,7 +459,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -475,7 +477,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -493,7 +495,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -513,7 +515,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -528,7 +530,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -538,7 +540,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -549,7 +551,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -562,7 +564,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -573,7 +575,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -589,7 +591,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -602,7 +604,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -620,7 +622,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -640,7 +642,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -656,7 +658,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -670,7 +672,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -683,7 +685,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -695,7 +697,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -711,7 +713,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -723,7 +725,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -734,7 +736,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -748,7 +750,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -760,7 +762,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -772,7 +774,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -784,7 +786,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -796,7 +798,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -808,7 +810,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -821,7 +823,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -832,7 +834,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -844,7 +846,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -855,7 +857,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -869,7 +871,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -885,7 +887,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -897,7 +899,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -910,7 +912,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -924,7 +926,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -936,7 +938,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -947,7 +949,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -959,7 +961,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -979,7 +981,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -1000,7 +1002,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
@@ -1015,7 +1017,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1028,7 +1030,7 @@ attributes:
pattern: ^orcid:.*
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt b/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt
index f0c811cf8..a649b8abd 100644
--- a/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt
+++ b/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: IEDB_alternative_term
URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118)
@@ -14,22 +16,23 @@ URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -58,7 +61,7 @@ URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118)
```yaml
name: IEDB_alternative_term
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
diff --git a/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt b/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt
index b3b94d6c8..427bdbcab 100644
--- a/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt
+++ b/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ISA_alternative_term
URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847)
@@ -14,22 +16,23 @@ URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -58,7 +61,7 @@ URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847)
```yaml
name: ISA_alternative_term
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
diff --git a/_sources/datamodels/ontology-metadata/Image.md.txt b/_sources/datamodels/ontology-metadata/Image.md.txt
index fa003cf7c..c7a6d58c4 100644
--- a/_sources/datamodels/ontology-metadata/Image.md.txt
+++ b/_sources/datamodels/ontology-metadata/Image.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Image
@@ -262,7 +264,7 @@ URI: [IAO:0000101](http://purl.obolibrary.org/obo/IAO_0000101)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -288,7 +290,7 @@ URI: [IAO:0000101](http://purl.obolibrary.org/obo/IAO_0000101)
```yaml
name: Image
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
class_uri: IAO:0000101
@@ -300,12 +302,12 @@ class_uri: IAO:0000101
```yaml
name: Image
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedIndividual
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -320,7 +322,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -332,7 +334,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -344,7 +346,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -357,7 +359,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -370,7 +372,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -382,7 +384,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -396,7 +398,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -410,7 +412,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -426,7 +428,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -444,7 +446,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -462,7 +464,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -480,7 +482,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -500,7 +502,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -515,7 +517,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -525,7 +527,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -536,7 +538,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -549,7 +551,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -560,7 +562,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -576,7 +578,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -589,7 +591,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -607,7 +609,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -627,7 +629,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -643,7 +645,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -657,7 +659,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -670,7 +672,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -682,7 +684,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -698,7 +700,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -710,7 +712,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -721,7 +723,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -735,7 +737,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -747,7 +749,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -759,7 +761,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -771,7 +773,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -783,7 +785,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -795,7 +797,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -808,7 +810,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -819,7 +821,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -831,7 +833,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -842,7 +844,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -856,7 +858,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -872,7 +874,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -884,7 +886,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -897,7 +899,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -911,7 +913,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -923,7 +925,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -934,7 +936,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -946,7 +948,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -966,7 +968,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -987,7 +989,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
@@ -1002,7 +1004,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1014,7 +1016,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/Integer.md.txt b/_sources/datamodels/ontology-metadata/Integer.md.txt
index 31bcf054e..4639a7a6e 100644
--- a/_sources/datamodels/ontology-metadata/Integer.md.txt
+++ b/_sources/datamodels/ontology-metadata/Integer.md.txt
@@ -32,7 +32,7 @@ URI: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/IriType.md.txt b/_sources/datamodels/ontology-metadata/IriType.md.txt
index 2f923f509..5cd5c3d9a 100644
--- a/_sources/datamodels/ontology-metadata/IriType.md.txt
+++ b/_sources/datamodels/ontology-metadata/IriType.md.txt
@@ -34,7 +34,7 @@ URI: [xsd:anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Jsonpath.md.txt b/_sources/datamodels/ontology-metadata/Jsonpath.md.txt
index d5db58e9d..c8fee215b 100644
--- a/_sources/datamodels/ontology-metadata/Jsonpath.md.txt
+++ b/_sources/datamodels/ontology-metadata/Jsonpath.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Jsonpointer.md.txt b/_sources/datamodels/ontology-metadata/Jsonpointer.md.txt
index 6ee8d88b6..ad642b36f 100644
--- a/_sources/datamodels/ontology-metadata/Jsonpointer.md.txt
+++ b/_sources/datamodels/ontology-metadata/Jsonpointer.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/LabelType.md.txt b/_sources/datamodels/ontology-metadata/LabelType.md.txt
index e069c2ea5..a2507c2ad 100644
--- a/_sources/datamodels/ontology-metadata/LabelType.md.txt
+++ b/_sources/datamodels/ontology-metadata/LabelType.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/NCIT_definition_source.md.txt b/_sources/datamodels/ontology-metadata/NCIT_definition_source.md.txt
index 2de2eb651..34fe55c36 100644
--- a/_sources/datamodels/ontology-metadata/NCIT_definition_source.md.txt
+++ b/_sources/datamodels/ontology-metadata/NCIT_definition_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: NCIT_definition_source
URI: [NCIT:P378](http://purl.obolibrary.org/obo/NCIT_P378)
@@ -12,6 +14,7 @@ URI: [NCIT:P378](http://purl.obolibrary.org/obo/NCIT_P378)
+
## Properties
* Range: [String](String.md)
@@ -31,7 +34,7 @@ URI: [NCIT:P378](http://purl.obolibrary.org/obo/NCIT_P378)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -42,7 +45,7 @@ URI: [NCIT:P378](http://purl.obolibrary.org/obo/NCIT_P378)
```yaml
name: NCIT_definition_source
deprecated: use OMO over NCIT
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: definition_source
rank: 1000
slot_uri: NCIT:P378
diff --git a/_sources/datamodels/ontology-metadata/NCIT_term_source.md.txt b/_sources/datamodels/ontology-metadata/NCIT_term_source.md.txt
index 3d3598541..190f58567 100644
--- a/_sources/datamodels/ontology-metadata/NCIT_term_source.md.txt
+++ b/_sources/datamodels/ontology-metadata/NCIT_term_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: NCIT_term_source
URI: [NCIT:P384](http://purl.obolibrary.org/obo/NCIT_P384)
@@ -12,6 +14,7 @@ URI: [NCIT:P384](http://purl.obolibrary.org/obo/NCIT_P384)
+
## Properties
* Range: [String](String.md)
@@ -31,7 +34,7 @@ URI: [NCIT:P384](http://purl.obolibrary.org/obo/NCIT_P384)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -42,7 +45,7 @@ URI: [NCIT:P384](http://purl.obolibrary.org/obo/NCIT_P384)
```yaml
name: NCIT_term_source
deprecated: use OMO over NCIT
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: isDefinedBy
rank: 1000
slot_uri: NCIT:P384
diff --git a/_sources/datamodels/ontology-metadata/NCIT_term_type.md.txt b/_sources/datamodels/ontology-metadata/NCIT_term_type.md.txt
index 4be6d177f..67de6afba 100644
--- a/_sources/datamodels/ontology-metadata/NCIT_term_type.md.txt
+++ b/_sources/datamodels/ontology-metadata/NCIT_term_type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: NCIT_term_type
URI: [NCIT:P383](http://purl.obolibrary.org/obo/NCIT_P383)
@@ -12,6 +14,7 @@ URI: [NCIT:P383](http://purl.obolibrary.org/obo/NCIT_P383)
+
## Properties
* Range: [String](String.md)
@@ -31,7 +34,7 @@ URI: [NCIT:P383](http://purl.obolibrary.org/obo/NCIT_P383)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -42,7 +45,7 @@ URI: [NCIT:P383](http://purl.obolibrary.org/obo/NCIT_P383)
```yaml
name: NCIT_term_type
deprecated: use OMO over NCIT
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: category
rank: 1000
slot_uri: NCIT:P383
diff --git a/_sources/datamodels/ontology-metadata/NamedIndividual.md.txt b/_sources/datamodels/ontology-metadata/NamedIndividual.md.txt
index 5838748fa..f523f4745 100644
--- a/_sources/datamodels/ontology-metadata/NamedIndividual.md.txt
+++ b/_sources/datamodels/ontology-metadata/NamedIndividual.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: NamedIndividual
@@ -277,7 +279,7 @@ URI: [owl:NamedIndividual](http://www.w3.org/2002/07/owl#NamedIndividual)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -304,7 +306,7 @@ URI: [owl:NamedIndividual](http://www.w3.org/2002/07/owl#NamedIndividual)
```yaml
name: NamedIndividual
description: An instance that has a IRI
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Term
class_uri: owl:NamedIndividual
@@ -317,12 +319,12 @@ class_uri: owl:NamedIndividual
```yaml
name: NamedIndividual
description: An instance that has a IRI
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Term
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -337,7 +339,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -349,7 +351,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -361,7 +363,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -374,7 +376,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -387,7 +389,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -399,7 +401,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -413,7 +415,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -427,7 +429,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -443,7 +445,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -461,7 +463,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -479,7 +481,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -497,7 +499,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -517,7 +519,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -532,7 +534,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -542,7 +544,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -553,7 +555,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -566,7 +568,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -577,7 +579,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -593,7 +595,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -606,7 +608,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -624,7 +626,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -644,7 +646,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -660,7 +662,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -674,7 +676,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -687,7 +689,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -699,7 +701,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -715,7 +717,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -727,7 +729,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -738,7 +740,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -752,7 +754,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -764,7 +766,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -776,7 +778,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -788,7 +790,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -800,7 +802,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -812,7 +814,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -825,7 +827,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -836,7 +838,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -848,7 +850,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -859,7 +861,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -873,7 +875,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -889,7 +891,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -901,7 +903,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -914,7 +916,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -928,7 +930,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -940,7 +942,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -951,7 +953,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -963,7 +965,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -983,7 +985,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -1004,7 +1006,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
@@ -1019,7 +1021,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1031,7 +1033,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/NamedObject.md.txt b/_sources/datamodels/ontology-metadata/NamedObject.md.txt
index 42a3f1d28..bd2de6285 100644
--- a/_sources/datamodels/ontology-metadata/NamedObject.md.txt
+++ b/_sources/datamodels/ontology-metadata/NamedObject.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: NamedObject
@@ -7,7 +9,7 @@ _Anything with an IRI_
-URI: [omoschema:NamedObject](http://purl.obolibrary.org/obo/omo/schema/NamedObject)
+URI: [omoschema:NamedObject](https://w3id.org/oak/ontology-metadata/NamedObject)
@@ -81,7 +83,7 @@ URI: [omoschema:NamedObject](http://purl.obolibrary.org/obo/omo/schema/NamedObje
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -108,7 +110,7 @@ URI: [omoschema:NamedObject](http://purl.obolibrary.org/obo/omo/schema/NamedObje
```yaml
name: NamedObject
description: Anything with an IRI
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- named entity
- identified object
@@ -126,7 +128,7 @@ slots:
```yaml
name: NamedObject
description: Anything with an IRI
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- named entity
- identified object
@@ -136,7 +138,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -148,7 +150,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/NarrativeText.md.txt b/_sources/datamodels/ontology-metadata/NarrativeText.md.txt
index 42f65fc47..f44bce927 100644
--- a/_sources/datamodels/ontology-metadata/NarrativeText.md.txt
+++ b/_sources/datamodels/ontology-metadata/NarrativeText.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Ncname.md.txt b/_sources/datamodels/ontology-metadata/Ncname.md.txt
index 00be2a92c..bdd138a04 100644
--- a/_sources/datamodels/ontology-metadata/Ncname.md.txt
+++ b/_sources/datamodels/ontology-metadata/Ncname.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Nodeidentifier.md.txt b/_sources/datamodels/ontology-metadata/Nodeidentifier.md.txt
index c72d9240b..b9c914c39 100644
--- a/_sources/datamodels/ontology-metadata/Nodeidentifier.md.txt
+++ b/_sources/datamodels/ontology-metadata/Nodeidentifier.md.txt
@@ -33,7 +33,7 @@ URI: [shex:nonLiteral](http://www.w3.org/ns/shex#nonLiteral)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/NotObsoleteAspect.md.txt b/_sources/datamodels/ontology-metadata/NotObsoleteAspect.md.txt
index f6f544f36..956a0bc68 100644
--- a/_sources/datamodels/ontology-metadata/NotObsoleteAspect.md.txt
+++ b/_sources/datamodels/ontology-metadata/NotObsoleteAspect.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: NotObsoleteAspect
@@ -7,7 +9,7 @@ _Auto-classifies anything that is not obsolete_
-URI: [omoschema:NotObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/NotObsoleteAspect)
+URI: [omoschema:NotObsoleteAspect](https://w3id.org/oak/ontology-metadata/NotObsoleteAspect)
@@ -72,7 +74,7 @@ URI: [omoschema:NotObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/Not
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -99,7 +101,7 @@ URI: [omoschema:NotObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/Not
```yaml
name: NotObsoleteAspect
description: Auto-classifies anything that is not obsolete
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
rules:
- postconditions:
@@ -123,7 +125,7 @@ classification_rules:
```yaml
name: NotObsoleteAspect
description: Auto-classifies anything that is not obsolete
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
rules:
- postconditions:
diff --git a/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt b/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt
index c82cea395..45c8e6914 100644
--- a/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt
+++ b/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: OBO_foundry_unique_label
URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589)
@@ -14,22 +16,23 @@ URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -62,7 +65,7 @@ URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -74,7 +77,7 @@ URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589)
name: OBO_foundry_unique_label
todos:
- add uniquekey
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
diff --git a/_sources/datamodels/ontology-metadata/ObiPermittedProfile.md.txt b/_sources/datamodels/ontology-metadata/ObiPermittedProfile.md.txt
index 70d48bd43..77095304e 100644
--- a/_sources/datamodels/ontology-metadata/ObiPermittedProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/ObiPermittedProfile.md.txt
@@ -16,7 +16,7 @@ URI: [ObiPermittedProfile](ObiPermittedProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/ObiRequiredProfile.md.txt b/_sources/datamodels/ontology-metadata/ObiRequiredProfile.md.txt
index 006bc3791..802d34bb4 100644
--- a/_sources/datamodels/ontology-metadata/ObiRequiredProfile.md.txt
+++ b/_sources/datamodels/ontology-metadata/ObiRequiredProfile.md.txt
@@ -16,7 +16,7 @@ URI: [ObiRequiredProfile](ObiRequiredProfile.md)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/ObjectProperty.md.txt b/_sources/datamodels/ontology-metadata/ObjectProperty.md.txt
index 01692b4a4..6274aefdd 100644
--- a/_sources/datamodels/ontology-metadata/ObjectProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/ObjectProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ObjectProperty
@@ -297,7 +299,7 @@ URI: [owl:ObjectProperty](http://www.w3.org/2002/07/owl#ObjectProperty)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -324,7 +326,7 @@ URI: [owl:ObjectProperty](http://www.w3.org/2002/07/owl#ObjectProperty)
```yaml
name: ObjectProperty
description: A property that connects two objects in logical axioms
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Property
mixins:
- PropertyExpression
@@ -347,14 +349,14 @@ class_uri: owl:ObjectProperty
```yaml
name: ObjectProperty
description: A property that connects two objects in logical axioms
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Property
mixins:
- PropertyExpression
attributes:
temporal_interpretation:
name: temporal_interpretation
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0001900
alias: temporal_interpretation
@@ -365,7 +367,7 @@ attributes:
is_cyclic:
name: is_cyclic
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_cyclic
alias: is_cyclic
@@ -376,7 +378,7 @@ attributes:
is_transitive:
name: is_transitive
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: TransitiveProperty
rank: 1000
slot_uri: oio:is_transitive
@@ -388,7 +390,7 @@ attributes:
shorthand:
name: shorthand
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:shorthand
multivalued: true
@@ -400,7 +402,7 @@ attributes:
range: string
equivalentProperty:
name: equivalentProperty
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
@@ -416,7 +418,7 @@ attributes:
name: inverseOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:inverseOf
@@ -429,7 +431,7 @@ attributes:
name: propertyChainAxiom
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:propertyChainAxiom
@@ -443,7 +445,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
@@ -458,7 +460,7 @@ attributes:
name: domain
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
@@ -472,7 +474,7 @@ attributes:
name: range
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
@@ -485,7 +487,7 @@ attributes:
is_class_level:
name: is_class_level
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
@@ -496,7 +498,7 @@ attributes:
is_metadata_tag:
name: is_metadata_tag
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
@@ -506,7 +508,7 @@ attributes:
range: boolean
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -521,7 +523,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -533,7 +535,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -545,7 +547,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -558,7 +560,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -571,7 +573,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -583,7 +585,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -597,7 +599,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -611,7 +613,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -627,7 +629,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -645,7 +647,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -663,7 +665,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -681,7 +683,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -701,7 +703,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -716,7 +718,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -726,7 +728,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -737,7 +739,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -750,7 +752,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -761,7 +763,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -777,7 +779,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -790,7 +792,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -808,7 +810,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -828,7 +830,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -844,7 +846,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -858,7 +860,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -871,7 +873,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -883,7 +885,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -899,7 +901,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -911,7 +913,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -922,7 +924,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -936,7 +938,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -948,7 +950,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -960,7 +962,7 @@ attributes:
range: Property
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -972,7 +974,7 @@ attributes:
range: Property
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -984,7 +986,7 @@ attributes:
range: Property
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -996,7 +998,7 @@ attributes:
range: Property
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -1009,7 +1011,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -1020,7 +1022,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -1032,7 +1034,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -1043,7 +1045,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -1057,7 +1059,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -1073,7 +1075,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -1085,7 +1087,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -1098,7 +1100,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -1112,7 +1114,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1124,7 +1126,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1135,7 +1137,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1147,7 +1149,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1159,7 +1161,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1173,7 +1175,7 @@ attributes:
recommended: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1187,7 +1189,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1199,7 +1201,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/Objectidentifier.md.txt b/_sources/datamodels/ontology-metadata/Objectidentifier.md.txt
index dedb364a3..cb9bc4cb8 100644
--- a/_sources/datamodels/ontology-metadata/Objectidentifier.md.txt
+++ b/_sources/datamodels/ontology-metadata/Objectidentifier.md.txt
@@ -37,7 +37,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/ObsoleteAspect.md.txt b/_sources/datamodels/ontology-metadata/ObsoleteAspect.md.txt
index a8e42c9b8..b5b740eaf 100644
--- a/_sources/datamodels/ontology-metadata/ObsoleteAspect.md.txt
+++ b/_sources/datamodels/ontology-metadata/ObsoleteAspect.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ObsoleteAspect
@@ -7,7 +9,7 @@ _Auto-classifies anything that is obsolete_
-URI: [omoschema:ObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/ObsoleteAspect)
+URI: [omoschema:ObsoleteAspect](https://w3id.org/oak/ontology-metadata/ObsoleteAspect)
@@ -108,7 +110,7 @@ URI: [omoschema:ObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/Obsole
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -135,7 +137,7 @@ URI: [omoschema:ObsoleteAspect](http://purl.obolibrary.org/obo/omo/schema/Obsole
```yaml
name: ObsoleteAspect
description: Auto-classifies anything that is obsolete
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
slot_usage:
label:
@@ -156,7 +158,7 @@ classification_rules:
```yaml
name: ObsoleteAspect
description: Auto-classifies anything that is obsolete
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
mixin: true
slot_usage:
label:
diff --git a/_sources/datamodels/ontology-metadata/Ontology-Metadata.md.txt b/_sources/datamodels/ontology-metadata/Ontology-Metadata.md.txt
index e67fa2aa4..e104717be 100644
--- a/_sources/datamodels/ontology-metadata/Ontology-Metadata.md.txt
+++ b/_sources/datamodels/ontology-metadata/Ontology-Metadata.md.txt
@@ -2,5 +2,5 @@
Schema for ontology metadata
-URI: http://purl.obolibrary.org/obo/omo/schema
+URI: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Ontology.md.txt b/_sources/datamodels/ontology-metadata/Ontology.md.txt
index d70426733..6829e5dd7 100644
--- a/_sources/datamodels/ontology-metadata/Ontology.md.txt
+++ b/_sources/datamodels/ontology-metadata/Ontology.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Ontology
@@ -115,7 +117,7 @@ URI: [owl:Ontology](http://www.w3.org/2002/07/owl#Ontology)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -142,7 +144,7 @@ URI: [owl:Ontology](http://www.w3.org/2002/07/owl#Ontology)
```yaml
name: Ontology
description: An OWL ontology
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedObject
slots:
- title
@@ -187,7 +189,7 @@ class_uri: owl:Ontology
```yaml
name: Ontology
description: An OWL ontology
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: NamedObject
slot_usage:
title:
@@ -213,7 +215,7 @@ slot_usage:
attributes:
title:
name: title
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: dcterms:title
alias: title
@@ -224,7 +226,7 @@ attributes:
required: true
has_ontology_root_term:
name: has_ontology_root_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000700
@@ -236,7 +238,7 @@ attributes:
range: Class
license:
name: license
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:license
@@ -248,7 +250,7 @@ attributes:
required: true
source:
name: source
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- http://purl.org/dc/terms/source
- oio:source
@@ -264,7 +266,7 @@ attributes:
range: string
versionIRI:
name: versionIRI
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: version_property
slot_uri: owl:versionIRI
@@ -276,7 +278,7 @@ attributes:
required: true
versionInfo:
name: versionInfo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: version_property
slot_uri: owl:versionInfo
@@ -290,7 +292,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -304,7 +306,7 @@ attributes:
range: string
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -324,7 +326,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -339,7 +341,7 @@ attributes:
range: string
imports:
name: imports
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: owl:imports
alias: imports
@@ -350,7 +352,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -362,7 +364,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/Property.md.txt b/_sources/datamodels/ontology-metadata/Property.md.txt
index e7ecb24a5..89d81a3ee 100644
--- a/_sources/datamodels/ontology-metadata/Property.md.txt
+++ b/_sources/datamodels/ontology-metadata/Property.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Property
@@ -294,7 +296,7 @@ URI: [rdf:Property](http://www.w3.org/1999/02/22-rdf-syntax-ns#Property)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -320,7 +322,7 @@ URI: [rdf:Property](http://www.w3.org/1999/02/22-rdf-syntax-ns#Property)
```yaml
name: Property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Term
abstract: true
slots:
@@ -373,7 +375,7 @@ class_uri: rdf:Property
```yaml
name: Property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Term
abstract: true
slot_usage:
@@ -416,7 +418,7 @@ attributes:
name: domain
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
@@ -430,7 +432,7 @@ attributes:
name: range
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
@@ -443,7 +445,7 @@ attributes:
is_class_level:
name: is_class_level
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
@@ -454,7 +456,7 @@ attributes:
is_metadata_tag:
name: is_metadata_tag
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
@@ -464,7 +466,7 @@ attributes:
range: boolean
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -479,7 +481,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -491,7 +493,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -503,7 +505,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -516,7 +518,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -529,7 +531,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -541,7 +543,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -555,7 +557,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -569,7 +571,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -585,7 +587,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -603,7 +605,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -621,7 +623,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -639,7 +641,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -659,7 +661,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -674,7 +676,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -684,7 +686,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -695,7 +697,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -708,7 +710,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -719,7 +721,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -735,7 +737,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -748,7 +750,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -766,7 +768,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -786,7 +788,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -802,7 +804,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -816,7 +818,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -829,7 +831,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -841,7 +843,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -857,7 +859,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -869,7 +871,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -880,7 +882,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -894,7 +896,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -906,7 +908,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -918,7 +920,7 @@ attributes:
range: Property
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -930,7 +932,7 @@ attributes:
range: Property
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -942,7 +944,7 @@ attributes:
range: Property
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -954,7 +956,7 @@ attributes:
range: Property
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -967,7 +969,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -978,7 +980,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -990,7 +992,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -1001,7 +1003,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -1015,7 +1017,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -1031,7 +1033,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -1043,7 +1045,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -1056,7 +1058,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -1070,7 +1072,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1082,7 +1084,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1093,7 +1095,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1105,7 +1107,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1117,7 +1119,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1131,7 +1133,7 @@ attributes:
recommended: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1145,7 +1147,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1157,7 +1159,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/PropertyExpression.md.txt b/_sources/datamodels/ontology-metadata/PropertyExpression.md.txt
index 54211e8e3..526dae4f4 100644
--- a/_sources/datamodels/ontology-metadata/PropertyExpression.md.txt
+++ b/_sources/datamodels/ontology-metadata/PropertyExpression.md.txt
@@ -1,8 +1,10 @@
+
+
# Class: PropertyExpression
-URI: [omoschema:PropertyExpression](http://purl.obolibrary.org/obo/omo/schema/PropertyExpression)
+URI: [omoschema:PropertyExpression](https://w3id.org/oak/ontology-metadata/PropertyExpression)
@@ -70,7 +72,7 @@ URI: [omoschema:PropertyExpression](http://purl.obolibrary.org/obo/omo/schema/Pr
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -96,7 +98,7 @@ URI: [omoschema:PropertyExpression](http://purl.obolibrary.org/obo/omo/schema/Pr
```yaml
name: PropertyExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Expression
mixin: true
slots:
@@ -110,7 +112,7 @@ slots:
```yaml
name: PropertyExpression
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: Expression
mixin: true
attributes:
@@ -118,7 +120,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
diff --git a/_sources/datamodels/ontology-metadata/Restriction.md.txt b/_sources/datamodels/ontology-metadata/Restriction.md.txt
index 7d414f385..c4c66df36 100644
--- a/_sources/datamodels/ontology-metadata/Restriction.md.txt
+++ b/_sources/datamodels/ontology-metadata/Restriction.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Restriction
@@ -100,7 +102,7 @@ URI: [owl:Restriction](http://www.w3.org/2002/07/owl#Restriction)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -126,7 +128,7 @@ URI: [owl:Restriction](http://www.w3.org/2002/07/owl#Restriction)
```yaml
name: Restriction
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnonymousClassExpression
mixin: true
mixins:
@@ -145,7 +147,7 @@ class_uri: owl:Restriction
```yaml
name: Restriction
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnonymousClassExpression
mixin: true
mixins:
@@ -153,7 +155,7 @@ mixins:
attributes:
onProperty:
name: onProperty
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:onProperty
@@ -167,7 +169,7 @@ attributes:
name: someValuesFrom
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:someValuesFrom
@@ -181,7 +183,7 @@ attributes:
name: allValuesFrom
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:allValuesFrom
@@ -194,7 +196,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
@@ -209,7 +211,7 @@ attributes:
name: equivalentClass
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
@@ -225,7 +227,7 @@ attributes:
name: intersectionOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:intersectionOf
@@ -236,7 +238,7 @@ attributes:
range: ClassExpression
subClassOf:
name: subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:subClassOf
@@ -248,7 +250,7 @@ attributes:
range: ClassExpression
cardinality:
name: cardinality
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:cardinality
@@ -261,7 +263,7 @@ attributes:
name: complementOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:complementOf
@@ -272,7 +274,7 @@ attributes:
range: string
oneOf:
name: oneOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:oneOf
@@ -283,7 +285,7 @@ attributes:
range: ClassExpression
unionOf:
name: unionOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:unionOf
diff --git a/_sources/datamodels/ontology-metadata/Sparqlpath.md.txt b/_sources/datamodels/ontology-metadata/Sparqlpath.md.txt
index 703d171be..a65960e09 100644
--- a/_sources/datamodels/ontology-metadata/Sparqlpath.md.txt
+++ b/_sources/datamodels/ontology-metadata/Sparqlpath.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/String.md.txt b/_sources/datamodels/ontology-metadata/String.md.txt
index 7de04d1bf..de4a0ebfb 100644
--- a/_sources/datamodels/ontology-metadata/String.md.txt
+++ b/_sources/datamodels/ontology-metadata/String.md.txt
@@ -32,7 +32,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Subset.md.txt b/_sources/datamodels/ontology-metadata/Subset.md.txt
index af659f9b1..9ae97c85d 100644
--- a/_sources/datamodels/ontology-metadata/Subset.md.txt
+++ b/_sources/datamodels/ontology-metadata/Subset.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Subset
@@ -283,7 +285,7 @@ URI: [oio:Subset](http://www.geneontology.org/formats/oboInOwl#Subset)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -310,7 +312,7 @@ URI: [oio:Subset](http://www.geneontology.org/formats/oboInOwl#Subset)
```yaml
name: Subset
description: A collection of terms grouped for some purpose
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationProperty
class_uri: oio:Subset
@@ -323,13 +325,13 @@ class_uri: oio:Subset
```yaml
name: Subset
description: A collection of terms grouped for some purpose
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: AnnotationProperty
attributes:
shorthand:
name: shorthand
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:shorthand
multivalued: true
@@ -343,7 +345,7 @@ attributes:
name: domain
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
@@ -357,7 +359,7 @@ attributes:
name: range
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
@@ -370,7 +372,7 @@ attributes:
is_class_level:
name: is_class_level
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
@@ -381,7 +383,7 @@ attributes:
is_metadata_tag:
name: is_metadata_tag
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
@@ -391,7 +393,7 @@ attributes:
range: boolean
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -406,7 +408,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -418,7 +420,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -430,7 +432,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -443,7 +445,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -456,7 +458,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -468,7 +470,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -482,7 +484,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -496,7 +498,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -512,7 +514,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -530,7 +532,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -548,7 +550,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -566,7 +568,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -586,7 +588,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -601,7 +603,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -611,7 +613,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -622,7 +624,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -635,7 +637,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -646,7 +648,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -662,7 +664,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -675,7 +677,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -693,7 +695,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -713,7 +715,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -729,7 +731,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -743,7 +745,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -756,7 +758,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -768,7 +770,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -784,7 +786,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -796,7 +798,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -807,7 +809,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -821,7 +823,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -833,7 +835,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -845,7 +847,7 @@ attributes:
range: Property
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -857,7 +859,7 @@ attributes:
range: Property
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -869,7 +871,7 @@ attributes:
range: Property
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -881,7 +883,7 @@ attributes:
range: Property
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -894,7 +896,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -905,7 +907,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -917,7 +919,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -928,7 +930,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -942,7 +944,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -958,7 +960,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -970,7 +972,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -983,7 +985,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -997,7 +999,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1009,7 +1011,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1020,7 +1022,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1032,7 +1034,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1044,7 +1046,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1058,7 +1060,7 @@ attributes:
recommended: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1072,7 +1074,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1084,7 +1086,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/Term.md.txt b/_sources/datamodels/ontology-metadata/Term.md.txt
index 780e56974..6549e36f2 100644
--- a/_sources/datamodels/ontology-metadata/Term.md.txt
+++ b/_sources/datamodels/ontology-metadata/Term.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Term
@@ -9,7 +11,7 @@ _A NamedThing that includes classes, properties, but not ontologies_
* __NOTE__: this is an abstract class and should not be instantiated directly
-URI: [omoschema:Term](http://purl.obolibrary.org/obo/omo/schema/Term)
+URI: [omoschema:Term](https://w3id.org/oak/ontology-metadata/Term)
@@ -270,7 +272,7 @@ URI: [omoschema:Term](http://purl.obolibrary.org/obo/omo/schema/Term)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -297,7 +299,7 @@ URI: [omoschema:Term](http://purl.obolibrary.org/obo/omo/schema/Term)
```yaml
name: Term
description: A NamedThing that includes classes, properties, but not ontologies
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- term
is_a: NamedObject
@@ -320,7 +322,7 @@ mixins:
```yaml
name: Term
description: A NamedThing that includes classes, properties, but not ontologies
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- term
is_a: NamedObject
@@ -336,7 +338,7 @@ mixins:
attributes:
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -351,7 +353,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -363,7 +365,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -375,7 +377,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -388,7 +390,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -401,7 +403,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -413,7 +415,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -427,7 +429,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -441,7 +443,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -457,7 +459,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -475,7 +477,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -493,7 +495,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -511,7 +513,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -531,7 +533,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -546,7 +548,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -556,7 +558,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -567,7 +569,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -580,7 +582,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -591,7 +593,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -607,7 +609,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -620,7 +622,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -638,7 +640,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -658,7 +660,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -674,7 +676,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -688,7 +690,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -701,7 +703,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -713,7 +715,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -729,7 +731,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -741,7 +743,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -752,7 +754,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -766,7 +768,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -778,7 +780,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -790,7 +792,7 @@ attributes:
range: Thing
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -802,7 +804,7 @@ attributes:
range: Thing
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -814,7 +816,7 @@ attributes:
range: Thing
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -826,7 +828,7 @@ attributes:
range: Thing
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -839,7 +841,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -850,7 +852,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -862,7 +864,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -873,7 +875,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -887,7 +889,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -903,7 +905,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -915,7 +917,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -928,7 +930,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -942,7 +944,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -954,7 +956,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -965,7 +967,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -977,7 +979,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -997,7 +999,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
@@ -1018,7 +1020,7 @@ attributes:
- allotrope required profile
- go required profile
- obi required profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
@@ -1033,7 +1035,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1045,7 +1047,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/Thing.md.txt b/_sources/datamodels/ontology-metadata/Thing.md.txt
index 933af8d3a..93e65a024 100644
--- a/_sources/datamodels/ontology-metadata/Thing.md.txt
+++ b/_sources/datamodels/ontology-metadata/Thing.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Thing
@@ -148,7 +150,7 @@ URI: [owl:Thing](http://www.w3.org/2002/07/owl#Thing)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -174,7 +176,7 @@ URI: [owl:Thing](http://www.w3.org/2002/07/owl#Thing)
```yaml
name: Thing
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
abstract: true
slots:
- type
@@ -188,12 +190,12 @@ class_uri: owl:Thing
```yaml
name: Thing
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
abstract: true
attributes:
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/TidyString.md.txt b/_sources/datamodels/ontology-metadata/TidyString.md.txt
index 642be69e9..0583a35d3 100644
--- a/_sources/datamodels/ontology-metadata/TidyString.md.txt
+++ b/_sources/datamodels/ontology-metadata/TidyString.md.txt
@@ -29,7 +29,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Time.md.txt b/_sources/datamodels/ontology-metadata/Time.md.txt
index ad6852e5d..ba672aa7c 100644
--- a/_sources/datamodels/ontology-metadata/Time.md.txt
+++ b/_sources/datamodels/ontology-metadata/Time.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:time](http://www.w3.org/2001/XMLSchema#time)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/TransitiveProperty.md.txt b/_sources/datamodels/ontology-metadata/TransitiveProperty.md.txt
index 88461feb4..04a72eca2 100644
--- a/_sources/datamodels/ontology-metadata/TransitiveProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/TransitiveProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TransitiveProperty
@@ -7,7 +9,7 @@ _An ObjectProperty with the property of transitivity_
-URI: [omoschema:TransitiveProperty](http://purl.obolibrary.org/obo/omo/schema/TransitiveProperty)
+URI: [omoschema:TransitiveProperty](https://w3id.org/oak/ontology-metadata/TransitiveProperty)
@@ -292,7 +294,7 @@ URI: [omoschema:TransitiveProperty](http://purl.obolibrary.org/obo/omo/schema/Tr
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -319,7 +321,7 @@ URI: [omoschema:TransitiveProperty](http://purl.obolibrary.org/obo/omo/schema/Tr
```yaml
name: TransitiveProperty
description: An ObjectProperty with the property of transitivity
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: ObjectProperty
```
@@ -331,12 +333,12 @@ is_a: ObjectProperty
```yaml
name: TransitiveProperty
description: An ObjectProperty with the property of transitivity
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
is_a: ObjectProperty
attributes:
temporal_interpretation:
name: temporal_interpretation
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0001900
alias: temporal_interpretation
@@ -347,7 +349,7 @@ attributes:
is_cyclic:
name: is_cyclic
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_cyclic
alias: is_cyclic
@@ -358,7 +360,7 @@ attributes:
is_transitive:
name: is_transitive
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: TransitiveProperty
rank: 1000
slot_uri: oio:is_transitive
@@ -370,7 +372,7 @@ attributes:
shorthand:
name: shorthand
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:shorthand
multivalued: true
@@ -382,7 +384,7 @@ attributes:
range: string
equivalentProperty:
name: equivalentProperty
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
@@ -398,7 +400,7 @@ attributes:
name: inverseOf
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:inverseOf
@@ -411,7 +413,7 @@ attributes:
name: propertyChainAxiom
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:propertyChainAxiom
@@ -425,7 +427,7 @@ attributes:
name: disjointWith
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
@@ -440,7 +442,7 @@ attributes:
name: domain
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
@@ -454,7 +456,7 @@ attributes:
name: range
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
@@ -467,7 +469,7 @@ attributes:
is_class_level:
name: is_class_level
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
@@ -478,7 +480,7 @@ attributes:
is_metadata_tag:
name: is_metadata_tag
deprecated: deprecated oboInOwl property
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
@@ -488,7 +490,7 @@ attributes:
range: boolean
has_exact_synonym:
name: has_exact_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
@@ -503,7 +505,7 @@ attributes:
range: label type
has_narrow_synonym:
name: has_narrow_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
@@ -515,7 +517,7 @@ attributes:
range: label type
has_broad_synonym:
name: has_broad_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
@@ -527,7 +529,7 @@ attributes:
range: label type
has_related_synonym:
name: has_related_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
@@ -540,7 +542,7 @@ attributes:
name: alternative_term
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
@@ -553,7 +555,7 @@ attributes:
range: string
ISA_alternative_term:
name: ISA_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:0001847
@@ -565,7 +567,7 @@ attributes:
range: string
IEDB_alternative_term:
name: IEDB_alternative_term
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: OBI:9991118
@@ -579,7 +581,7 @@ attributes:
name: editor_preferred_term
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
@@ -593,7 +595,7 @@ attributes:
name: OBO_foundry_unique_label
todos:
- add uniquekey
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000589
@@ -609,7 +611,7 @@ attributes:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
@@ -627,7 +629,7 @@ attributes:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -645,7 +647,7 @@ attributes:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
@@ -663,7 +665,7 @@ attributes:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
@@ -683,7 +685,7 @@ attributes:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
@@ -698,7 +700,7 @@ attributes:
range: uriorcurie
excluded_from_QC_check:
name: excluded_from_QC_check
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
@@ -708,7 +710,7 @@ attributes:
range: Thing
excluded_subClassOf:
name: excluded_subClassOf
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
@@ -719,7 +721,7 @@ attributes:
range: Class
excluded_synonym:
name: excluded_synonym
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
@@ -732,7 +734,7 @@ attributes:
range: string
should_conform_to:
name: should_conform_to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
@@ -743,7 +745,7 @@ attributes:
created_by:
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
@@ -759,7 +761,7 @@ attributes:
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
@@ -772,7 +774,7 @@ attributes:
range: string
contributor:
name: contributor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -790,7 +792,7 @@ attributes:
partial_match: false
creator:
name: creator
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
@@ -810,7 +812,7 @@ attributes:
created:
name: created
description: when the term came into being
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
@@ -826,7 +828,7 @@ attributes:
date:
name: date
description: when the term was updated
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
@@ -840,7 +842,7 @@ attributes:
range: string
isDefinedBy:
name: isDefinedBy
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
@@ -853,7 +855,7 @@ attributes:
range: Ontology
editor_note:
name: editor_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
@@ -865,7 +867,7 @@ attributes:
range: narrative text
term_editor:
name: term_editor
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
@@ -881,7 +883,7 @@ attributes:
- restrict range
in_subset:
- obi permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
@@ -893,7 +895,7 @@ attributes:
range: string
ontology_term_requester:
name: ontology_term_requester
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
@@ -904,7 +906,7 @@ attributes:
range: string
imported_from:
name: imported_from
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
@@ -918,7 +920,7 @@ attributes:
name: term_tracker_item
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
@@ -930,7 +932,7 @@ attributes:
range: string
broadMatch:
name: broadMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
@@ -942,7 +944,7 @@ attributes:
range: Property
closeMatch:
name: closeMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
@@ -954,7 +956,7 @@ attributes:
range: Property
exactMatch:
name: exactMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
@@ -966,7 +968,7 @@ attributes:
range: Property
narrowMatch:
name: narrowMatch
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
@@ -978,7 +980,7 @@ attributes:
range: Property
database_cross_reference:
name: database_cross_reference
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
@@ -991,7 +993,7 @@ attributes:
range: CURIELiteral
has_obo_namespace:
name: has_obo_namespace
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
@@ -1002,7 +1004,7 @@ attributes:
range: string
category:
name: category
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
@@ -1014,7 +1016,7 @@ attributes:
in_subset:
name: in_subset
description: Maps an ontology element to a subset it belongs to
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
@@ -1025,7 +1027,7 @@ attributes:
range: Subset
conformsTo:
name: conformsTo
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
@@ -1039,7 +1041,7 @@ attributes:
name: comment
comments:
- in obo format, a term cannot have more than one comment
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
@@ -1055,7 +1057,7 @@ attributes:
name: seeAlso
todos:
- restrict range
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
@@ -1067,7 +1069,7 @@ attributes:
range: Thing
image:
name: image
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
@@ -1080,7 +1082,7 @@ attributes:
name: example_of_usage
in_subset:
- allotrope permitted profile
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
@@ -1094,7 +1096,7 @@ attributes:
range: string
curator_note:
name: curator_note
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
@@ -1106,7 +1108,7 @@ attributes:
range: string
has_curation_status:
name: has_curation_status
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
@@ -1117,7 +1119,7 @@ attributes:
range: string
depicted_by:
name: depicted_by
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
@@ -1129,7 +1131,7 @@ attributes:
range: Image
page:
name: page
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
@@ -1141,7 +1143,7 @@ attributes:
range: string
label:
name: label
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: rdfs:label
@@ -1155,7 +1157,7 @@ attributes:
recommended: true
definition:
name: definition
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
slot_uri: IAO:0000115
@@ -1169,7 +1171,7 @@ attributes:
id:
name: id
description: this maps to the URI in RDF
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
@@ -1181,7 +1183,7 @@ attributes:
required: true
type:
name: type
- from_schema: http://purl.obolibrary.org/obo/omo/schema
+ from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/URLLiteral.md.txt b/_sources/datamodels/ontology-metadata/URLLiteral.md.txt
index b8282187b..9676287e8 100644
--- a/_sources/datamodels/ontology-metadata/URLLiteral.md.txt
+++ b/_sources/datamodels/ontology-metadata/URLLiteral.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Uri.md.txt b/_sources/datamodels/ontology-metadata/Uri.md.txt
index a1db932a2..b052ea6e4 100644
--- a/_sources/datamodels/ontology-metadata/Uri.md.txt
+++ b/_sources/datamodels/ontology-metadata/Uri.md.txt
@@ -37,7 +37,7 @@ URI: [xsd:anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/Uriorcurie.md.txt b/_sources/datamodels/ontology-metadata/Uriorcurie.md.txt
index f22fe9117..1f65f549f 100644
--- a/_sources/datamodels/ontology-metadata/Uriorcurie.md.txt
+++ b/_sources/datamodels/ontology-metadata/Uriorcurie.md.txt
@@ -33,7 +33,7 @@ URI: [xsd:anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
diff --git a/_sources/datamodels/ontology-metadata/allValuesFrom.md.txt b/_sources/datamodels/ontology-metadata/allValuesFrom.md.txt
index 30e6dad74..05f593e5d 100644
--- a/_sources/datamodels/ontology-metadata/allValuesFrom.md.txt
+++ b/_sources/datamodels/ontology-metadata/allValuesFrom.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: allValuesFrom
URI: [owl:allValuesFrom](http://www.w3.org/2002/07/owl#allValuesFrom)
@@ -14,11 +16,12 @@ URI: [owl:allValuesFrom](http://www.w3.org/2002/07/owl#allValuesFrom)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
@@ -49,7 +52,7 @@ URI: [owl:allValuesFrom](http://www.w3.org/2002/07/owl#allValuesFrom)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -61,7 +64,7 @@ URI: [owl:allValuesFrom](http://www.w3.org/2002/07/owl#allValuesFrom)
name: allValuesFrom
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:allValuesFrom
diff --git a/_sources/datamodels/ontology-metadata/alternative_term.md.txt b/_sources/datamodels/ontology-metadata/alternative_term.md.txt
index b1d2372b9..983da5933 100644
--- a/_sources/datamodels/ontology-metadata/alternative_term.md.txt
+++ b/_sources/datamodels/ontology-metadata/alternative_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: alternative_term
URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118)
@@ -18,22 +20,23 @@ URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -62,7 +65,7 @@ URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -74,7 +77,7 @@ URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118)
name: alternative_term
in_subset:
- allotrope permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:altLabel
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/annotatedProperty.md.txt b/_sources/datamodels/ontology-metadata/annotatedProperty.md.txt
index 7f4c4b367..13452c5a7 100644
--- a/_sources/datamodels/ontology-metadata/annotatedProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/annotatedProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: annotatedProperty
URI: [owl:annotatedProperty](http://www.w3.org/2002/07/owl#annotatedProperty)
@@ -14,11 +16,12 @@ URI: [owl:annotatedProperty](http://www.w3.org/2002/07/owl#annotatedProperty)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -45,7 +48,7 @@ URI: [owl:annotatedProperty](http://www.w3.org/2002/07/owl#annotatedProperty)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [owl:annotatedProperty](http://www.w3.org/2002/07/owl#annotatedProperty)
```yaml
name: annotatedProperty
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:predicate
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/annotatedSource.md.txt b/_sources/datamodels/ontology-metadata/annotatedSource.md.txt
index 0436472ca..edb771966 100644
--- a/_sources/datamodels/ontology-metadata/annotatedSource.md.txt
+++ b/_sources/datamodels/ontology-metadata/annotatedSource.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: annotatedSource
URI: [owl:annotatedSource](http://www.w3.org/2002/07/owl#annotatedSource)
@@ -14,11 +16,12 @@ URI: [owl:annotatedSource](http://www.w3.org/2002/07/owl#annotatedSource)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -49,7 +52,7 @@ URI: [owl:annotatedSource](http://www.w3.org/2002/07/owl#annotatedSource)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -61,7 +64,7 @@ URI: [owl:annotatedSource](http://www.w3.org/2002/07/owl#annotatedSource)
name: annotatedSource
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:subject
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/annotatedTarget.md.txt b/_sources/datamodels/ontology-metadata/annotatedTarget.md.txt
index 78e14ab75..2d120d1dd 100644
--- a/_sources/datamodels/ontology-metadata/annotatedTarget.md.txt
+++ b/_sources/datamodels/ontology-metadata/annotatedTarget.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: annotatedTarget
URI: [owl:annotatedTarget](http://www.w3.org/2002/07/owl#annotatedTarget)
@@ -14,11 +16,12 @@ URI: [owl:annotatedTarget](http://www.w3.org/2002/07/owl#annotatedTarget)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -49,7 +52,7 @@ URI: [owl:annotatedTarget](http://www.w3.org/2002/07/owl#annotatedTarget)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -61,7 +64,7 @@ URI: [owl:annotatedTarget](http://www.w3.org/2002/07/owl#annotatedTarget)
name: annotatedTarget
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- rdf:object
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/annotations.md.txt b/_sources/datamodels/ontology-metadata/annotations.md.txt
index afe6b44b2..a18b466bf 100644
--- a/_sources/datamodels/ontology-metadata/annotations.md.txt
+++ b/_sources/datamodels/ontology-metadata/annotations.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: annotations
-URI: [omoschema:annotations](http://purl.obolibrary.org/obo/omo/schema/annotations)
+URI: [omoschema:annotations](https://w3id.org/oak/ontology-metadata/annotations)
@@ -9,11 +11,12 @@ URI: [omoschema:annotations](http://purl.obolibrary.org/obo/omo/schema/annotatio
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -42,7 +45,7 @@ URI: [omoschema:annotations](http://purl.obolibrary.org/obo/omo/schema/annotatio
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [omoschema:annotations](http://purl.obolibrary.org/obo/omo/schema/annotatio
```yaml
name: annotations
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
multivalued: true
alias: annotations
diff --git a/_sources/datamodels/ontology-metadata/broadMatch.md.txt b/_sources/datamodels/ontology-metadata/broadMatch.md.txt
index 6069a32b1..9391224cf 100644
--- a/_sources/datamodels/ontology-metadata/broadMatch.md.txt
+++ b/_sources/datamodels/ontology-metadata/broadMatch.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: broadMatch
URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch)
@@ -14,22 +16,23 @@ URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMappings](HasMappings.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | yes |
+| [Image](Image.md) | | no |
+| [HasMappings](HasMappings.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch)
```yaml
name: broadMatch
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:broadMatch
diff --git a/_sources/datamodels/ontology-metadata/cardinality.md.txt b/_sources/datamodels/ontology-metadata/cardinality.md.txt
index 54fcb1812..2fca336db 100644
--- a/_sources/datamodels/ontology-metadata/cardinality.md.txt
+++ b/_sources/datamodels/ontology-metadata/cardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: cardinality
URI: [owl:cardinality](http://www.w3.org/2002/07/owl#cardinality)
@@ -14,13 +16,14 @@ URI: [owl:cardinality](http://www.w3.org/2002/07/owl#cardinality)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -47,7 +50,7 @@ URI: [owl:cardinality](http://www.w3.org/2002/07/owl#cardinality)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -57,7 +60,7 @@ URI: [owl:cardinality](http://www.w3.org/2002/07/owl#cardinality)
```yaml
name: cardinality
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:cardinality
diff --git a/_sources/datamodels/ontology-metadata/category.md.txt b/_sources/datamodels/ontology-metadata/category.md.txt
index 521c50e7d..c49532961 100644
--- a/_sources/datamodels/ontology-metadata/category.md.txt
+++ b/_sources/datamodels/ontology-metadata/category.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: category
URI: [biolink:category](https://w3id.org/biolink/vocab/category)
@@ -14,22 +16,23 @@ URI: [biolink:category](https://w3id.org/biolink/vocab/category)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasCategory](HasCategory.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasCategory](HasCategory.md) | | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [biolink:category](https://w3id.org/biolink/vocab/category)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [biolink:category](https://w3id.org/biolink/vocab/category)
```yaml
name: category
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: biolink:category
diff --git a/_sources/datamodels/ontology-metadata/changeNote.md.txt b/_sources/datamodels/ontology-metadata/changeNote.md.txt
index fbd3395f2..8ad5fadcc 100644
--- a/_sources/datamodels/ontology-metadata/changeNote.md.txt
+++ b/_sources/datamodels/ontology-metadata/changeNote.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: changeNote
URI: [skos:changeNote](http://www.w3.org/2004/02/skos/core#changeNote)
@@ -17,6 +19,7 @@ URI: [skos:changeNote](http://www.w3.org/2004/02/skos/core#changeNote)
+
## Properties
* Range: [String](String.md)
@@ -38,7 +41,7 @@ URI: [skos:changeNote](http://www.w3.org/2004/02/skos/core#changeNote)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [skos:changeNote](http://www.w3.org/2004/02/skos/core#changeNote)
name: changeNote
in_subset:
- allotrope permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: skos:changeNote
diff --git a/_sources/datamodels/ontology-metadata/closeMatch.md.txt b/_sources/datamodels/ontology-metadata/closeMatch.md.txt
index 802ea9f1e..8b673e1b4 100644
--- a/_sources/datamodels/ontology-metadata/closeMatch.md.txt
+++ b/_sources/datamodels/ontology-metadata/closeMatch.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: closeMatch
URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch)
@@ -14,22 +16,23 @@ URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMappings](HasMappings.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | yes |
+| [Image](Image.md) | | no |
+| [HasMappings](HasMappings.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch)
```yaml
name: closeMatch
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:closeMatch
diff --git a/_sources/datamodels/ontology-metadata/comment.md.txt b/_sources/datamodels/ontology-metadata/comment.md.txt
index 51b3c978d..1d8540c4f 100644
--- a/_sources/datamodels/ontology-metadata/comment.md.txt
+++ b/_sources/datamodels/ontology-metadata/comment.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: comment
URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment)
@@ -14,24 +16,25 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -64,7 +67,7 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -76,7 +79,7 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment)
name: comment
comments:
- in obo format, a term cannot have more than one comment
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: rdfs:comment
diff --git a/_sources/datamodels/ontology-metadata/complementOf.md.txt b/_sources/datamodels/ontology-metadata/complementOf.md.txt
index 68fdc4444..fea2fa4dc 100644
--- a/_sources/datamodels/ontology-metadata/complementOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/complementOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: complementOf
URI: [owl:complementOf](http://www.w3.org/2002/07/owl#complementOf)
@@ -14,13 +16,14 @@ URI: [owl:complementOf](http://www.w3.org/2002/07/owl#complementOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -51,7 +54,7 @@ URI: [owl:complementOf](http://www.w3.org/2002/07/owl#complementOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -63,7 +66,7 @@ URI: [owl:complementOf](http://www.w3.org/2002/07/owl#complementOf)
name: complementOf
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:complementOf
diff --git a/_sources/datamodels/ontology-metadata/conformsTo.md.txt b/_sources/datamodels/ontology-metadata/conformsTo.md.txt
index a6c00e511..f8228ace7 100644
--- a/_sources/datamodels/ontology-metadata/conformsTo.md.txt
+++ b/_sources/datamodels/ontology-metadata/conformsTo.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: conformsTo
URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo)
@@ -14,22 +16,23 @@ URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasCategory](HasCategory.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasCategory](HasCategory.md) | | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo)
```yaml
name: conformsTo
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:conformsTo
diff --git a/_sources/datamodels/ontology-metadata/consider.md.txt b/_sources/datamodels/ontology-metadata/consider.md.txt
index ff2d85944..1ee9ac959 100644
--- a/_sources/datamodels/ontology-metadata/consider.md.txt
+++ b/_sources/datamodels/ontology-metadata/consider.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: consider
URI: [oio:consider](http://www.geneontology.org/formats/oboInOwl#consider)
@@ -14,22 +16,23 @@ URI: [oio:consider](http://www.geneontology.org/formats/oboInOwl#consider)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [oio:consider](http://www.geneontology.org/formats/oboInOwl#consider)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -76,7 +79,7 @@ comments:
- '{''RULE'': ''subject must be deprecated''}'
in_subset:
- go permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
diff --git a/_sources/datamodels/ontology-metadata/contributor.md.txt b/_sources/datamodels/ontology-metadata/contributor.md.txt
index c3bb3fdfa..7d1997b36 100644
--- a/_sources/datamodels/ontology-metadata/contributor.md.txt
+++ b/_sources/datamodels/ontology-metadata/contributor.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: contributor
URI: [dcterms:contributor](http://purl.org/dc/terms/contributor)
@@ -14,22 +16,23 @@ URI: [dcterms:contributor](http://purl.org/dc/terms/contributor)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [dcterms:contributor](http://purl.org/dc/terms/contributor)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [dcterms:contributor](http://purl.org/dc/terms/contributor)
```yaml
name: contributor
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/core_property.md.txt b/_sources/datamodels/ontology-metadata/core_property.md.txt
index 33fca9199..e79ef9f9e 100644
--- a/_sources/datamodels/ontology-metadata/core_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/core_property.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: core_property
@@ -5,7 +7,7 @@ _abstract grouping of core properties_
-URI: [omoschema:core_property](http://purl.obolibrary.org/obo/omo/schema/core_property)
+URI: [omoschema:core_property](https://w3id.org/oak/ontology-metadata/core_property)
@@ -24,6 +26,7 @@ URI: [omoschema:core_property](http://purl.obolibrary.org/obo/omo/schema/core_pr
+
## Properties
* Range: [String](String.md)
@@ -43,7 +46,7 @@ URI: [omoschema:core_property](http://purl.obolibrary.org/obo/omo/schema/core_pr
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -54,7 +57,7 @@ URI: [omoschema:core_property](http://purl.obolibrary.org/obo/omo/schema/core_pr
```yaml
name: core_property
description: abstract grouping of core properties
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: core_property
diff --git a/_sources/datamodels/ontology-metadata/created.md.txt b/_sources/datamodels/ontology-metadata/created.md.txt
index 21ca3654c..a4237c158 100644
--- a/_sources/datamodels/ontology-metadata/created.md.txt
+++ b/_sources/datamodels/ontology-metadata/created.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: created
@@ -19,23 +21,24 @@ URI: [dcterms:created](http://purl.org/dc/terms/created)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [dcterms:created](http://purl.org/dc/terms/created)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -73,7 +76,7 @@ URI: [dcterms:created](http://purl.org/dc/terms/created)
```yaml
name: created
description: when the term came into being
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:createdOn
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/created_by.md.txt b/_sources/datamodels/ontology-metadata/created_by.md.txt
index e7d8b4511..474c6d05f 100644
--- a/_sources/datamodels/ontology-metadata/created_by.md.txt
+++ b/_sources/datamodels/ontology-metadata/created_by.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: created_by
URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by)
@@ -14,23 +16,24 @@ URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -57,7 +60,7 @@ URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by)
```yaml
name: created_by
deprecated: proposed obsoleted by OMO group 2022-04-12
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: creator
rank: 1000
is_a: provenance_property
diff --git a/_sources/datamodels/ontology-metadata/creation_date.md.txt b/_sources/datamodels/ontology-metadata/creation_date.md.txt
index 9aba70d21..9742bea24 100644
--- a/_sources/datamodels/ontology-metadata/creation_date.md.txt
+++ b/_sources/datamodels/ontology-metadata/creation_date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: creation_date
URI: [oio:creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date)
@@ -14,22 +16,23 @@ URI: [oio:creation_date](http://www.geneontology.org/formats/oboInOwl#creation_d
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [oio:creation_date](http://www.geneontology.org/formats/oboInOwl#creation_d
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -75,7 +78,7 @@ name: creation_date
deprecated: proposed obsoleted by OMO group 2022-04-12
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: created
rank: 1000
is_a: provenance_property
diff --git a/_sources/datamodels/ontology-metadata/creator.md.txt b/_sources/datamodels/ontology-metadata/creator.md.txt
index 04af9bad7..4edc08504 100644
--- a/_sources/datamodels/ontology-metadata/creator.md.txt
+++ b/_sources/datamodels/ontology-metadata/creator.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: creator
URI: [dcterms:creator](http://purl.org/dc/terms/creator)
@@ -14,23 +16,24 @@ URI: [dcterms:creator](http://purl.org/dc/terms/creator)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -59,7 +62,7 @@ URI: [dcterms:creator](http://purl.org/dc/terms/creator)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -69,7 +72,7 @@ URI: [dcterms:creator](http://purl.org/dc/terms/creator)
```yaml
name: creator
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- prov:wasAttributedTo
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/curator_note.md.txt b/_sources/datamodels/ontology-metadata/curator_note.md.txt
index 54471edf1..3b27b2794 100644
--- a/_sources/datamodels/ontology-metadata/curator_note.md.txt
+++ b/_sources/datamodels/ontology-metadata/curator_note.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: curator_note
URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232)
@@ -14,22 +16,23 @@ URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232)
```yaml
name: curator_note
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000232
diff --git a/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt b/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt
index d50158ec6..0488b0bff 100644
--- a/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt
+++ b/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: database_cross_reference
URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref)
@@ -14,23 +16,24 @@ URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMappings](HasMappings.md) | | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | yes |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | yes |
+| [HasMappings](HasMappings.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -59,7 +62,7 @@ URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -69,7 +72,7 @@ URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref)
```yaml
name: database_cross_reference
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: oio:hasDbXref
diff --git a/_sources/datamodels/ontology-metadata/date.md.txt b/_sources/datamodels/ontology-metadata/date.md.txt
index 8edfe9506..a24688d90 100644
--- a/_sources/datamodels/ontology-metadata/date.md.txt
+++ b/_sources/datamodels/ontology-metadata/date.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: date
@@ -19,22 +21,23 @@ URI: [dcterms:date](http://purl.org/dc/terms/date)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -63,7 +66,7 @@ URI: [dcterms:date](http://purl.org/dc/terms/date)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -74,7 +77,7 @@ URI: [dcterms:date](http://purl.org/dc/terms/date)
```yaml
name: date
description: when the term was updated
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:authoredOn
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/date_retrieved.md.txt b/_sources/datamodels/ontology-metadata/date_retrieved.md.txt
index 1fbeaf376..ff47b5b0f 100644
--- a/_sources/datamodels/ontology-metadata/date_retrieved.md.txt
+++ b/_sources/datamodels/ontology-metadata/date_retrieved.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: date_retrieved
URI: [oio:date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved)
@@ -14,11 +16,12 @@ URI: [oio:date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -45,7 +48,7 @@ URI: [oio:date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retr
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [oio:date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retr
```yaml
name: date_retrieved
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: oio:date_retrieved
diff --git a/_sources/datamodels/ontology-metadata/defaultLanguage.md.txt b/_sources/datamodels/ontology-metadata/defaultLanguage.md.txt
index ab3d92284..4ccb6e27a 100644
--- a/_sources/datamodels/ontology-metadata/defaultLanguage.md.txt
+++ b/_sources/datamodels/ontology-metadata/defaultLanguage.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: defaultLanguage
URI: [protege:defaultLanguage](protege:defaultLanguage)
@@ -17,6 +19,7 @@ URI: [protege:defaultLanguage](protege:defaultLanguage)
+
## Properties
* Range: [String](String.md)
@@ -36,7 +39,7 @@ URI: [protege:defaultLanguage](protege:defaultLanguage)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [protege:defaultLanguage](protege:defaultLanguage)
```yaml
name: defaultLanguage
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: protege:defaultLanguage
diff --git a/_sources/datamodels/ontology-metadata/definition.md.txt b/_sources/datamodels/ontology-metadata/definition.md.txt
index 23da72b27..e170ee73c 100644
--- a/_sources/datamodels/ontology-metadata/definition.md.txt
+++ b/_sources/datamodels/ontology-metadata/definition.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: definition
URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115)
@@ -14,22 +16,23 @@ URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | yes |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -78,7 +81,7 @@ in_subset:
- allotrope required profile
- go required profile
- obi required profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:definition
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/definition_source.md.txt b/_sources/datamodels/ontology-metadata/definition_source.md.txt
index f430312cb..a8857b922 100644
--- a/_sources/datamodels/ontology-metadata/definition_source.md.txt
+++ b/_sources/datamodels/ontology-metadata/definition_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: definition_source
URI: [IAO:0000119](http://purl.obolibrary.org/obo/IAO_0000119)
@@ -14,22 +16,23 @@ URI: [IAO:0000119](http://purl.obolibrary.org/obo/IAO_0000119)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [IAO:0000119](http://purl.obolibrary.org/obo/IAO_0000119)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -76,7 +79,7 @@ todos:
- restrict range
in_subset:
- obi permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000119
diff --git a/_sources/datamodels/ontology-metadata/depicted_by.md.txt b/_sources/datamodels/ontology-metadata/depicted_by.md.txt
index 62b6d8bb7..40afaefd1 100644
--- a/_sources/datamodels/ontology-metadata/depicted_by.md.txt
+++ b/_sources/datamodels/ontology-metadata/depicted_by.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: depicted_by
URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by)
@@ -14,22 +16,23 @@ URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by)
```yaml
name: depicted_by
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:depicted_by
diff --git a/_sources/datamodels/ontology-metadata/deprecated.md.txt b/_sources/datamodels/ontology-metadata/deprecated.md.txt
index 9829185d0..97b51e9b7 100644
--- a/_sources/datamodels/ontology-metadata/deprecated.md.txt
+++ b/_sources/datamodels/ontology-metadata/deprecated.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: deprecated
URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated)
@@ -14,22 +16,23 @@ URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -61,7 +64,7 @@ URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -75,7 +78,7 @@ in_subset:
- allotrope permitted profile
- go permitted profile
- obi permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
aliases:
- is obsolete
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/disconnected_from.md.txt b/_sources/datamodels/ontology-metadata/disconnected_from.md.txt
index 2dfa95947..ffe2e1080 100644
--- a/_sources/datamodels/ontology-metadata/disconnected_from.md.txt
+++ b/_sources/datamodels/ontology-metadata/disconnected_from.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: disconnected_from
-URI: [omoschema:disconnected_from](http://purl.obolibrary.org/obo/omo/schema/disconnected_from)
+URI: [omoschema:disconnected_from](https://w3id.org/oak/ontology-metadata/disconnected_from)
@@ -14,11 +16,12 @@ URI: [omoschema:disconnected_from](http://purl.obolibrary.org/obo/omo/schema/dis
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Class](Class.md) | | no |
+| [Class](Class.md) | | no |
@@ -45,7 +48,7 @@ URI: [omoschema:disconnected_from](http://purl.obolibrary.org/obo/omo/schema/dis
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [omoschema:disconnected_from](http://purl.obolibrary.org/obo/omo/schema/dis
```yaml
name: disconnected_from
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: shortcut_annotation_property
alias: disconnected_from
diff --git a/_sources/datamodels/ontology-metadata/disjointWith.md.txt b/_sources/datamodels/ontology-metadata/disjointWith.md.txt
index 19eea1555..a170785fc 100644
--- a/_sources/datamodels/ontology-metadata/disjointWith.md.txt
+++ b/_sources/datamodels/ontology-metadata/disjointWith.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: disjointWith
URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith)
@@ -14,16 +16,17 @@ URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[PropertyExpression](PropertyExpression.md) | | no |
-[Class](Class.md) | | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [PropertyExpression](PropertyExpression.md) | | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Restriction](Restriction.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith)
name: disjointWith
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:disjointWith
diff --git a/_sources/datamodels/ontology-metadata/distinctMembers.md.txt b/_sources/datamodels/ontology-metadata/distinctMembers.md.txt
index 41e4f58cc..8efea47d3 100644
--- a/_sources/datamodels/ontology-metadata/distinctMembers.md.txt
+++ b/_sources/datamodels/ontology-metadata/distinctMembers.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: distinctMembers
URI: [owl:distinctMembers](http://www.w3.org/2002/07/owl#distinctMembers)
@@ -17,6 +19,7 @@ URI: [owl:distinctMembers](http://www.w3.org/2002/07/owl#distinctMembers)
+
## Properties
* Range: [Thing](Thing.md)
@@ -36,7 +39,7 @@ URI: [owl:distinctMembers](http://www.w3.org/2002/07/owl#distinctMembers)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:distinctMembers](http://www.w3.org/2002/07/owl#distinctMembers)
```yaml
name: distinctMembers
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:distinctMembers
diff --git a/_sources/datamodels/ontology-metadata/domain.md.txt b/_sources/datamodels/ontology-metadata/domain.md.txt
index bdd58f383..0432737ab 100644
--- a/_sources/datamodels/ontology-metadata/domain.md.txt
+++ b/_sources/datamodels/ontology-metadata/domain.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: domain
URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain)
@@ -14,15 +16,16 @@ URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -55,7 +58,7 @@ URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -67,7 +70,7 @@ URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain)
name: domain
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:domain
diff --git a/_sources/datamodels/ontology-metadata/editor_note.md.txt b/_sources/datamodels/ontology-metadata/editor_note.md.txt
index bedddd075..d2bca2336 100644
--- a/_sources/datamodels/ontology-metadata/editor_note.md.txt
+++ b/_sources/datamodels/ontology-metadata/editor_note.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: editor_note
URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116)
@@ -14,22 +16,23 @@ URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116)
```yaml
name: editor_note
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000116
diff --git a/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt b/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt
index 6b7297a64..f5c67172d 100644
--- a/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt
+++ b/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: editor_preferred_term
URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111)
@@ -14,22 +16,23 @@ URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -70,7 +73,7 @@ URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111)
name: editor_preferred_term
in_subset:
- obi permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
slot_uri: IAO:0000111
diff --git a/_sources/datamodels/ontology-metadata/equivalentClass.md.txt b/_sources/datamodels/ontology-metadata/equivalentClass.md.txt
index 20e682645..12f6ea581 100644
--- a/_sources/datamodels/ontology-metadata/equivalentClass.md.txt
+++ b/_sources/datamodels/ontology-metadata/equivalentClass.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: equivalentClass
URI: [owl:equivalentClass](http://www.w3.org/2002/07/owl#equivalentClass)
@@ -14,13 +16,14 @@ URI: [owl:equivalentClass](http://www.w3.org/2002/07/owl#equivalentClass)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -53,7 +56,7 @@ URI: [owl:equivalentClass](http://www.w3.org/2002/07/owl#equivalentClass)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -65,7 +68,7 @@ URI: [owl:equivalentClass](http://www.w3.org/2002/07/owl#equivalentClass)
name: equivalentClass
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
diff --git a/_sources/datamodels/ontology-metadata/equivalentProperty.md.txt b/_sources/datamodels/ontology-metadata/equivalentProperty.md.txt
index e22a7ecee..d51f69cbb 100644
--- a/_sources/datamodels/ontology-metadata/equivalentProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/equivalentProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: equivalentProperty
URI: [owl:equivalentProperty](http://www.w3.org/2002/07/owl#equivalentProperty)
@@ -14,12 +16,13 @@ URI: [owl:equivalentProperty](http://www.w3.org/2002/07/owl#equivalentProperty)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -48,7 +51,7 @@ URI: [owl:equivalentProperty](http://www.w3.org/2002/07/owl#equivalentProperty)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -58,7 +61,7 @@ URI: [owl:equivalentProperty](http://www.w3.org/2002/07/owl#equivalentProperty)
```yaml
name: equivalentProperty
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
diff --git a/_sources/datamodels/ontology-metadata/evidence.md.txt b/_sources/datamodels/ontology-metadata/evidence.md.txt
index 8502f760f..4fd17be46 100644
--- a/_sources/datamodels/ontology-metadata/evidence.md.txt
+++ b/_sources/datamodels/ontology-metadata/evidence.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: evidence
URI: [oio:evidence](http://www.geneontology.org/formats/oboInOwl#evidence)
@@ -9,11 +11,12 @@ URI: [oio:evidence](http://www.geneontology.org/formats/oboInOwl#evidence)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -40,7 +43,7 @@ URI: [oio:evidence](http://www.geneontology.org/formats/oboInOwl#evidence)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -51,7 +54,7 @@ URI: [oio:evidence](http://www.geneontology.org/formats/oboInOwl#evidence)
```yaml
name: evidence
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:evidence
alias: evidence
diff --git a/_sources/datamodels/ontology-metadata/exactMatch.md.txt b/_sources/datamodels/ontology-metadata/exactMatch.md.txt
index 4e6be9fbe..472216fa2 100644
--- a/_sources/datamodels/ontology-metadata/exactMatch.md.txt
+++ b/_sources/datamodels/ontology-metadata/exactMatch.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: exactMatch
URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch)
@@ -14,22 +16,23 @@ URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMappings](HasMappings.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | yes |
+| [Image](Image.md) | | no |
+| [HasMappings](HasMappings.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch)
```yaml
name: exactMatch
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:exactMatch
diff --git a/_sources/datamodels/ontology-metadata/example_of_usage.md.txt b/_sources/datamodels/ontology-metadata/example_of_usage.md.txt
index 2ce0c71a4..fce3d0efa 100644
--- a/_sources/datamodels/ontology-metadata/example_of_usage.md.txt
+++ b/_sources/datamodels/ontology-metadata/example_of_usage.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: example_of_usage
URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112)
@@ -14,22 +16,23 @@ URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -70,7 +73,7 @@ URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112)
name: example_of_usage
in_subset:
- allotrope permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:example
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/excluded_axiom.md.txt b/_sources/datamodels/ontology-metadata/excluded_axiom.md.txt
index 3bbfde9c0..329206bb4 100644
--- a/_sources/datamodels/ontology-metadata/excluded_axiom.md.txt
+++ b/_sources/datamodels/ontology-metadata/excluded_axiom.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: excluded_axiom
-URI: [omoschema:excluded_axiom](http://purl.obolibrary.org/obo/omo/schema/excluded_axiom)
+URI: [omoschema:excluded_axiom](https://w3id.org/oak/ontology-metadata/excluded_axiom)
@@ -20,6 +22,7 @@ URI: [omoschema:excluded_axiom](http://purl.obolibrary.org/obo/omo/schema/exclud
+
## Properties
* Range: [String](String.md)
@@ -39,7 +42,7 @@ URI: [omoschema:excluded_axiom](http://purl.obolibrary.org/obo/omo/schema/exclud
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -49,7 +52,7 @@ URI: [omoschema:excluded_axiom](http://purl.obolibrary.org/obo/omo/schema/exclud
```yaml
name: excluded_axiom
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: excluded_axiom
diff --git a/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt b/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt
index 7dc8136bd..01ad9f99e 100644
--- a/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt
+++ b/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: excluded_from_QC_check
-URI: [omoschema:excluded_from_QC_check](http://purl.obolibrary.org/obo/omo/schema/excluded_from_QC_check)
+URI: [omoschema:excluded_from_QC_check](https://w3id.org/oak/ontology-metadata/excluded_from_QC_check)
@@ -14,22 +16,23 @@ URI: [omoschema:excluded_from_QC_check](http://purl.obolibrary.org/obo/omo/schem
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [omoschema:excluded_from_QC_check](http://purl.obolibrary.org/obo/omo/schem
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [omoschema:excluded_from_QC_check](http://purl.obolibrary.org/obo/omo/schem
```yaml
name: excluded_from_QC_check
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: excluded_from_QC_check
diff --git a/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt b/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt
index f6b5978d0..004d5e548 100644
--- a/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: excluded_subClassOf
-URI: [omoschema:excluded_subClassOf](http://purl.obolibrary.org/obo/omo/schema/excluded_subClassOf)
+URI: [omoschema:excluded_subClassOf](https://w3id.org/oak/ontology-metadata/excluded_subClassOf)
@@ -14,22 +16,23 @@ URI: [omoschema:excluded_subClassOf](http://purl.obolibrary.org/obo/omo/schema/e
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [omoschema:excluded_subClassOf](http://purl.obolibrary.org/obo/omo/schema/e
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [omoschema:excluded_subClassOf](http://purl.obolibrary.org/obo/omo/schema/e
```yaml
name: excluded_subClassOf
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt b/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt
index 954c32a8e..4323619f3 100644
--- a/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: excluded_synonym
-URI: [omoschema:excluded_synonym](http://purl.obolibrary.org/obo/omo/schema/excluded_synonym)
+URI: [omoschema:excluded_synonym](https://w3id.org/oak/ontology-metadata/excluded_synonym)
@@ -14,22 +16,23 @@ URI: [omoschema:excluded_synonym](http://purl.obolibrary.org/obo/omo/schema/excl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [omoschema:excluded_synonym](http://purl.obolibrary.org/obo/omo/schema/excl
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [omoschema:excluded_synonym](http://purl.obolibrary.org/obo/omo/schema/excl
```yaml
name: excluded_synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:hiddenSynonym
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/external_ontology.md.txt b/_sources/datamodels/ontology-metadata/external_ontology.md.txt
index 79872c5a8..6e1dce684 100644
--- a/_sources/datamodels/ontology-metadata/external_ontology.md.txt
+++ b/_sources/datamodels/ontology-metadata/external_ontology.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: external_ontology
URI: [oio:external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology)
@@ -9,11 +11,12 @@ URI: [oio:external_ontology](http://www.geneontology.org/formats/oboInOwl#extern
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -42,7 +45,7 @@ URI: [oio:external_ontology](http://www.geneontology.org/formats/oboInOwl#extern
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -53,7 +56,7 @@ URI: [oio:external_ontology](http://www.geneontology.org/formats/oboInOwl#extern
```yaml
name: external_ontology
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:external_ontology
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/hasValue.md.txt b/_sources/datamodels/ontology-metadata/hasValue.md.txt
index 480beadc3..dc0b76cb9 100644
--- a/_sources/datamodels/ontology-metadata/hasValue.md.txt
+++ b/_sources/datamodels/ontology-metadata/hasValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: hasValue
URI: [owl:hasValue](http://www.w3.org/2002/07/owl#hasValue)
@@ -17,6 +19,7 @@ URI: [owl:hasValue](http://www.w3.org/2002/07/owl#hasValue)
+
## Properties
* Range: [Any](Any.md)
@@ -40,7 +43,7 @@ URI: [owl:hasValue](http://www.w3.org/2002/07/owl#hasValue)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [owl:hasValue](http://www.w3.org/2002/07/owl#hasValue)
name: hasValue
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:hasValue
diff --git a/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt b/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt
index 6dd778459..860a6961c 100644
--- a/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_alternative_id
@@ -19,22 +21,23 @@ URI: [oio:hasAlternativeId](http://www.geneontology.org/formats/oboInOwl#hasAlte
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -71,7 +74,7 @@ URI: [oio:hasAlternativeId](http://www.geneontology.org/formats/oboInOwl#hasAlte
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -87,7 +90,7 @@ comments:
- '{''RULE'': ''object must NOT be deprecated''}'
in_subset:
- go permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
see_also:
- https://github.com/owlcs/owlapi/issues/317
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/has_axiom_label.md.txt b/_sources/datamodels/ontology-metadata/has_axiom_label.md.txt
index 86c3eab28..d6c3ba0d6 100644
--- a/_sources/datamodels/ontology-metadata/has_axiom_label.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_axiom_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_axiom_label
URI: [IAO:0010000](http://purl.obolibrary.org/obo/IAO_0010000)
@@ -14,11 +16,12 @@ URI: [IAO:0010000](http://purl.obolibrary.org/obo/IAO_0010000)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -45,7 +48,7 @@ URI: [IAO:0010000](http://purl.obolibrary.org/obo/IAO_0010000)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [IAO:0010000](http://purl.obolibrary.org/obo/IAO_0010000)
```yaml
name: has_axiom_label
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0010000
diff --git a/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt
index 27a7fd2bd..608d69b24 100644
--- a/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_broad_synonym
URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym)
@@ -15,22 +17,23 @@ URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroad
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -59,7 +62,7 @@ URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroad
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -69,7 +72,7 @@ URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroad
```yaml
name: has_broad_synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasBroadSynonym
diff --git a/_sources/datamodels/ontology-metadata/has_curation_status.md.txt b/_sources/datamodels/ontology-metadata/has_curation_status.md.txt
index bf1cd7742..7f6f6c48f 100644
--- a/_sources/datamodels/ontology-metadata/has_curation_status.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_curation_status.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_curation_status
URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114)
@@ -14,22 +16,23 @@ URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114)
```yaml
name: has_curation_status
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000114
diff --git a/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt
index 7d96a7997..a8048d4c0 100644
--- a/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_exact_synonym
URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym)
@@ -15,23 +17,24 @@ URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExact
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -60,7 +63,7 @@ URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExact
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -70,7 +73,7 @@ URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExact
```yaml
name: has_exact_synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasExactSynonym
diff --git a/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt
index 827749e30..f2f71c3d4 100644
--- a/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_narrow_synonym
URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym)
@@ -15,22 +17,23 @@ URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -59,7 +62,7 @@ URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarr
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -69,7 +72,7 @@ URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarr
```yaml
name: has_narrow_synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: synonym
slot_uri: oio:hasNarrowSynonym
diff --git a/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt b/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt
index d84089cc2..c505dad1b 100644
--- a/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_obo_namespace
URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace)
@@ -9,22 +11,23 @@ URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONa
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasCategory](HasCategory.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasCategory](HasCategory.md) | | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -53,7 +56,7 @@ URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONa
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -63,7 +66,7 @@ URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONa
```yaml
name: has_obo_namespace
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasOBONamespace
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt b/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt
index 4c1a731c3..38817f923 100644
--- a/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_obsolescence_reason
URI: [IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231)
@@ -14,22 +16,23 @@ URI: [IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -64,7 +67,7 @@ URI: [IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -78,7 +81,7 @@ todos:
- restrict range
comments:
- '{''RULE'': ''subject must be deprecated''}'
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: obsoletion_related_property
domain: ObsoleteAspect
diff --git a/_sources/datamodels/ontology-metadata/has_ontology_root_term.md.txt b/_sources/datamodels/ontology-metadata/has_ontology_root_term.md.txt
index 5a76d5dcb..979308695 100644
--- a/_sources/datamodels/ontology-metadata/has_ontology_root_term.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_ontology_root_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_ontology_root_term
URI: [IAO:0000700](http://purl.obolibrary.org/obo/IAO_0000700)
@@ -14,11 +16,12 @@ URI: [IAO:0000700](http://purl.obolibrary.org/obo/IAO_0000700)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
@@ -47,7 +50,7 @@ URI: [IAO:0000700](http://purl.obolibrary.org/obo/IAO_0000700)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -57,7 +60,7 @@ URI: [IAO:0000700](http://purl.obolibrary.org/obo/IAO_0000700)
```yaml
name: has_ontology_root_term
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: IAO:0000700
diff --git a/_sources/datamodels/ontology-metadata/has_rank.md.txt b/_sources/datamodels/ontology-metadata/has_rank.md.txt
index ec7422e5f..ffaeb6159 100644
--- a/_sources/datamodels/ontology-metadata/has_rank.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_rank.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: has_rank
-URI: [omoschema:has_rank](http://purl.obolibrary.org/obo/omo/schema/has_rank)
+URI: [omoschema:has_rank](https://w3id.org/oak/ontology-metadata/has_rank)
@@ -9,11 +11,12 @@ URI: [omoschema:has_rank](http://purl.obolibrary.org/obo/omo/schema/has_rank)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Class](Class.md) | | no |
+| [Class](Class.md) | | no |
@@ -40,7 +43,7 @@ URI: [omoschema:has_rank](http://purl.obolibrary.org/obo/omo/schema/has_rank)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [omoschema:has_rank](http://purl.obolibrary.org/obo/omo/schema/has_rank)
```yaml
name: has_rank
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- obo:ncbitaxon/subsets/taxslim#has_rank
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt
index 8b6ad65f9..2246c39bf 100644
--- a/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_related_synonym
URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym)
@@ -9,22 +11,23 @@ URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRel
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no |
@@ -53,7 +56,7 @@ URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRel
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -63,7 +66,7 @@ URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRel
```yaml
name: has_related_synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasRelatedSynonym
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/has_synonym_type.md.txt b/_sources/datamodels/ontology-metadata/has_synonym_type.md.txt
index e3f5c3023..5a78ebd21 100644
--- a/_sources/datamodels/ontology-metadata/has_synonym_type.md.txt
+++ b/_sources/datamodels/ontology-metadata/has_synonym_type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: has_synonym_type
URI: [oio:hasSynonymType](http://www.geneontology.org/formats/oboInOwl#hasSynonymType)
@@ -9,11 +11,12 @@ URI: [oio:hasSynonymType](http://www.geneontology.org/formats/oboInOwl#hasSynony
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -42,7 +45,7 @@ URI: [oio:hasSynonymType](http://www.geneontology.org/formats/oboInOwl#hasSynony
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [oio:hasSynonymType](http://www.geneontology.org/formats/oboInOwl#hasSynony
```yaml
name: has_synonym_type
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:hasSynonymType
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/id.md.txt b/_sources/datamodels/ontology-metadata/id.md.txt
index bc37293e9..65b37e972 100644
--- a/_sources/datamodels/ontology-metadata/id.md.txt
+++ b/_sources/datamodels/ontology-metadata/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
@@ -5,7 +7,7 @@ _this maps to the URI in RDF_
-URI: [omoschema:id](http://purl.obolibrary.org/obo/omo/schema/id)
+URI: [omoschema:id](https://w3id.org/oak/ontology-metadata/id)
@@ -19,23 +21,24 @@ URI: [omoschema:id](http://purl.obolibrary.org/obo/omo/schema/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[NamedObject](NamedObject.md) | Anything with an IRI | no |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | yes |
-[Agent](Agent.md) | | yes |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | yes |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [NamedObject](NamedObject.md) | Anything with an IRI | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [Agent](Agent.md) | | yes |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -64,7 +67,7 @@ URI: [omoschema:id](http://purl.obolibrary.org/obo/omo/schema/id)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -75,7 +78,7 @@ URI: [omoschema:id](http://purl.obolibrary.org/obo/omo/schema/id)
```yaml
name: id
description: this maps to the URI in RDF
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: core_property
identifier: true
diff --git a/_sources/datamodels/ontology-metadata/image.md.txt b/_sources/datamodels/ontology-metadata/image.md.txt
index 955e77921..f1ee154f1 100644
--- a/_sources/datamodels/ontology-metadata/image.md.txt
+++ b/_sources/datamodels/ontology-metadata/image.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: image
URI: [sdo:image](http://schema.org/image)
@@ -14,22 +16,23 @@ URI: [sdo:image](http://schema.org/image)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [sdo:image](http://schema.org/image)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [sdo:image](http://schema.org/image)
```yaml
name: image
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: sdo:image
diff --git a/_sources/datamodels/ontology-metadata/imported_from.md.txt b/_sources/datamodels/ontology-metadata/imported_from.md.txt
index 43f36eb5e..9344d64fb 100644
--- a/_sources/datamodels/ontology-metadata/imported_from.md.txt
+++ b/_sources/datamodels/ontology-metadata/imported_from.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: imported_from
URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412)
@@ -14,22 +16,23 @@ URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412)
```yaml
name: imported_from
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000412
diff --git a/_sources/datamodels/ontology-metadata/imports.md.txt b/_sources/datamodels/ontology-metadata/imports.md.txt
index acee1d7ba..2515ce6f6 100644
--- a/_sources/datamodels/ontology-metadata/imports.md.txt
+++ b/_sources/datamodels/ontology-metadata/imports.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: imports
URI: [owl:imports](http://www.w3.org/2002/07/owl#imports)
@@ -9,11 +11,12 @@ URI: [owl:imports](http://www.w3.org/2002/07/owl#imports)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
@@ -40,7 +43,7 @@ URI: [owl:imports](http://www.w3.org/2002/07/owl#imports)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [owl:imports](http://www.w3.org/2002/07/owl#imports)
```yaml
name: imports
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: owl:imports
alias: imports
diff --git a/_sources/datamodels/ontology-metadata/in_subset.md.txt b/_sources/datamodels/ontology-metadata/in_subset.md.txt
index bf813f942..042ecaef7 100644
--- a/_sources/datamodels/ontology-metadata/in_subset.md.txt
+++ b/_sources/datamodels/ontology-metadata/in_subset.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: in_subset
@@ -14,22 +16,23 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasCategory](HasCategory.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasCategory](HasCategory.md) | | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -69,7 +72,7 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset)
```yaml
name: in_subset
description: Maps an ontology element to a subset it belongs to
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:inSubset
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/index.md.txt b/_sources/datamodels/ontology-metadata/index.md.txt
index 3861a4cdf..8b831e5a2 100644
--- a/_sources/datamodels/ontology-metadata/index.md.txt
+++ b/_sources/datamodels/ontology-metadata/index.md.txt
@@ -2,7 +2,7 @@
Schema for ontology metadata
-URI: http://purl.obolibrary.org/obo/omo/schema
+URI: https://w3id.org/oak/ontology-metadata
Name: Ontology-Metadata
diff --git a/_sources/datamodels/ontology-metadata/informative_property.md.txt b/_sources/datamodels/ontology-metadata/informative_property.md.txt
index 1493ac946..d17d178b6 100644
--- a/_sources/datamodels/ontology-metadata/informative_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/informative_property.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: informative_property
-URI: [omoschema:informative_property](http://purl.obolibrary.org/obo/omo/schema/informative_property)
+URI: [omoschema:informative_property](https://w3id.org/oak/ontology-metadata/informative_property)
@@ -29,6 +31,7 @@ URI: [omoschema:informative_property](http://purl.obolibrary.org/obo/omo/schema/
+
## Properties
* Range: [String](String.md)
@@ -48,7 +51,7 @@ URI: [omoschema:informative_property](http://purl.obolibrary.org/obo/omo/schema/
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -58,7 +61,7 @@ URI: [omoschema:informative_property](http://purl.obolibrary.org/obo/omo/schema/
```yaml
name: informative_property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: informative_property
diff --git a/_sources/datamodels/ontology-metadata/intersectionOf.md.txt b/_sources/datamodels/ontology-metadata/intersectionOf.md.txt
index 479e50df2..a2c64d636 100644
--- a/_sources/datamodels/ontology-metadata/intersectionOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/intersectionOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: intersectionOf
URI: [owl:intersectionOf](http://www.w3.org/2002/07/owl#intersectionOf)
@@ -14,13 +16,14 @@ URI: [owl:intersectionOf](http://www.w3.org/2002/07/owl#intersectionOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -51,7 +54,7 @@ URI: [owl:intersectionOf](http://www.w3.org/2002/07/owl#intersectionOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -63,7 +66,7 @@ URI: [owl:intersectionOf](http://www.w3.org/2002/07/owl#intersectionOf)
name: intersectionOf
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:intersectionOf
diff --git a/_sources/datamodels/ontology-metadata/inverseOf.md.txt b/_sources/datamodels/ontology-metadata/inverseOf.md.txt
index a6fa6b12e..ad9589ed8 100644
--- a/_sources/datamodels/ontology-metadata/inverseOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/inverseOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: inverseOf
URI: [owl:inverseOf](http://www.w3.org/2002/07/owl#inverseOf)
@@ -14,12 +16,13 @@ URI: [owl:inverseOf](http://www.w3.org/2002/07/owl#inverseOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -50,7 +53,7 @@ URI: [owl:inverseOf](http://www.w3.org/2002/07/owl#inverseOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -62,7 +65,7 @@ URI: [owl:inverseOf](http://www.w3.org/2002/07/owl#inverseOf)
name: inverseOf
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:inverseOf
diff --git a/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt b/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt
index 7473aa9e5..e6002afce 100644
--- a/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt
+++ b/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: isDefinedBy
URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy)
@@ -9,22 +11,23 @@ URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -51,7 +54,7 @@ URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -61,7 +64,7 @@ URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy)
```yaml
name: isDefinedBy
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:importedFrom
- dcterms:publisher
diff --git a/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom.md.txt b/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom.md.txt
index 1bd464536..dea4c4965 100644
--- a/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_a_defining_property_chain_axiom
URI: [RO:0002581](http://purl.obolibrary.org/obo/RO_0002581)
@@ -9,11 +11,12 @@ URI: [RO:0002581](http://purl.obolibrary.org/obo/RO_0002581)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -40,7 +43,7 @@ URI: [RO:0002581](http://purl.obolibrary.org/obo/RO_0002581)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [RO:0002581](http://purl.obolibrary.org/obo/RO_0002581)
```yaml
name: is_a_defining_property_chain_axiom
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002581
alias: is_a_defining_property_chain_axiom
diff --git a/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive.md.txt b/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive.md.txt
index 8c9ec5f13..7a235b6b0 100644
--- a/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive
URI: [RO:0002582](http://purl.obolibrary.org/obo/RO_0002582)
@@ -9,11 +11,12 @@ URI: [RO:0002582](http://purl.obolibrary.org/obo/RO_0002582)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -40,7 +43,7 @@ URI: [RO:0002582](http://purl.obolibrary.org/obo/RO_0002582)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [RO:0002582](http://purl.obolibrary.org/obo/RO_0002582)
```yaml
name: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002582
alias: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive
diff --git a/_sources/datamodels/ontology-metadata/is_class_level.md.txt b/_sources/datamodels/ontology-metadata/is_class_level.md.txt
index 078c7e1e6..0be26a640 100644
--- a/_sources/datamodels/ontology-metadata/is_class_level.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_class_level.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_class_level
URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level)
@@ -9,15 +11,16 @@ URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -44,7 +47,7 @@ URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_
```yaml
name: is_class_level
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_class_level
alias: is_class_level
diff --git a/_sources/datamodels/ontology-metadata/is_cyclic.md.txt b/_sources/datamodels/ontology-metadata/is_cyclic.md.txt
index 0ba7f0483..d43d66908 100644
--- a/_sources/datamodels/ontology-metadata/is_cyclic.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_cyclic.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_cyclic
URI: [oio:is_cyclic](http://www.geneontology.org/formats/oboInOwl#is_cyclic)
@@ -9,12 +11,13 @@ URI: [oio:is_cyclic](http://www.geneontology.org/formats/oboInOwl#is_cyclic)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -41,7 +44,7 @@ URI: [oio:is_cyclic](http://www.geneontology.org/formats/oboInOwl#is_cyclic)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [oio:is_cyclic](http://www.geneontology.org/formats/oboInOwl#is_cyclic)
```yaml
name: is_cyclic
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_cyclic
alias: is_cyclic
diff --git a/_sources/datamodels/ontology-metadata/is_inferred.md.txt b/_sources/datamodels/ontology-metadata/is_inferred.md.txt
index 6f43bb274..ee87399ae 100644
--- a/_sources/datamodels/ontology-metadata/is_inferred.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_inferred.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_inferred
URI: [oio:is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred)
@@ -9,11 +11,12 @@ URI: [oio:is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -40,7 +43,7 @@ URI: [oio:is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -51,7 +54,7 @@ URI: [oio:is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred)
```yaml
name: is_inferred
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_inferred
alias: is_inferred
diff --git a/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt b/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt
index cba7153d1..6e4c6e942 100644
--- a/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_metadata_tag
URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag)
@@ -9,15 +11,16 @@ URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metad
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -44,7 +47,7 @@ URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metad
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metad
```yaml
name: is_metadata_tag
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:is_metadata_tag
alias: is_metadata_tag
diff --git a/_sources/datamodels/ontology-metadata/is_transitive.md.txt b/_sources/datamodels/ontology-metadata/is_transitive.md.txt
index bcfeeaa90..f74e25ce0 100644
--- a/_sources/datamodels/ontology-metadata/is_transitive.md.txt
+++ b/_sources/datamodels/ontology-metadata/is_transitive.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_transitive
URI: [oio:is_transitive](http://www.geneontology.org/formats/oboInOwl#is_transitive)
@@ -9,12 +11,13 @@ URI: [oio:is_transitive](http://www.geneontology.org/formats/oboInOwl#is_transit
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -41,7 +44,7 @@ URI: [oio:is_transitive](http://www.geneontology.org/formats/oboInOwl#is_transit
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [oio:is_transitive](http://www.geneontology.org/formats/oboInOwl#is_transit
```yaml
name: is_transitive
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: TransitiveProperty
rank: 1000
slot_uri: oio:is_transitive
diff --git a/_sources/datamodels/ontology-metadata/label.md.txt b/_sources/datamodels/ontology-metadata/label.md.txt
index 0b8415539..eb97d077b 100644
--- a/_sources/datamodels/ontology-metadata/label.md.txt
+++ b/_sources/datamodels/ontology-metadata/label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: label
URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
@@ -14,23 +16,24 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | yes |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -63,7 +66,7 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -81,7 +84,7 @@ in_subset:
- allotrope required profile
- go required profile
- obi required profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- skos:prefLabel
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/language.md.txt b/_sources/datamodels/ontology-metadata/language.md.txt
index 635f105ba..ade6cad84 100644
--- a/_sources/datamodels/ontology-metadata/language.md.txt
+++ b/_sources/datamodels/ontology-metadata/language.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: language
URI: [dcterms:language](http://purl.org/dc/terms/language)
@@ -17,6 +19,7 @@ URI: [dcterms:language](http://purl.org/dc/terms/language)
+
## Properties
* Range: [String](String.md)
@@ -36,7 +39,7 @@ URI: [dcterms:language](http://purl.org/dc/terms/language)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [dcterms:language](http://purl.org/dc/terms/language)
```yaml
name: language
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dce:language
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/license.md.txt b/_sources/datamodels/ontology-metadata/license.md.txt
index a55751e3e..69b4931df 100644
--- a/_sources/datamodels/ontology-metadata/license.md.txt
+++ b/_sources/datamodels/ontology-metadata/license.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: license
URI: [dcterms:license](http://purl.org/dc/terms/license)
@@ -14,11 +16,12 @@ URI: [dcterms:license](http://purl.org/dc/terms/license)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | yes |
+| [Ontology](Ontology.md) | An OWL ontology | yes |
@@ -45,7 +48,7 @@ URI: [dcterms:license](http://purl.org/dc/terms/license)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [dcterms:license](http://purl.org/dc/terms/license)
```yaml
name: license
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: dcterms:license
diff --git a/_sources/datamodels/ontology-metadata/logical_predicate.md.txt b/_sources/datamodels/ontology-metadata/logical_predicate.md.txt
index 49f65dc9b..9a79794e7 100644
--- a/_sources/datamodels/ontology-metadata/logical_predicate.md.txt
+++ b/_sources/datamodels/ontology-metadata/logical_predicate.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: logical_predicate
-URI: [omoschema:logical_predicate](http://purl.obolibrary.org/obo/omo/schema/logical_predicate)
+URI: [omoschema:logical_predicate](https://w3id.org/oak/ontology-metadata/logical_predicate)
@@ -42,6 +44,7 @@ URI: [omoschema:logical_predicate](http://purl.obolibrary.org/obo/omo/schema/log
+
## Properties
* Range: [String](String.md)
@@ -61,7 +64,7 @@ URI: [omoschema:logical_predicate](http://purl.obolibrary.org/obo/omo/schema/log
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -71,7 +74,7 @@ URI: [omoschema:logical_predicate](http://purl.obolibrary.org/obo/omo/schema/log
```yaml
name: logical_predicate
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: logical_predicate
diff --git a/_sources/datamodels/ontology-metadata/match.md.txt b/_sources/datamodels/ontology-metadata/match.md.txt
index 43b30e554..ae99cd617 100644
--- a/_sources/datamodels/ontology-metadata/match.md.txt
+++ b/_sources/datamodels/ontology-metadata/match.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: match
-URI: [omoschema:match](http://purl.obolibrary.org/obo/omo/schema/match)
+URI: [omoschema:match](https://w3id.org/oak/ontology-metadata/match)
@@ -21,6 +23,7 @@ URI: [omoschema:match](http://purl.obolibrary.org/obo/omo/schema/match)
+
## Properties
* Range: [String](String.md)
@@ -40,7 +43,7 @@ URI: [omoschema:match](http://purl.obolibrary.org/obo/omo/schema/match)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [omoschema:match](http://purl.obolibrary.org/obo/omo/schema/match)
```yaml
name: match
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
mixins:
diff --git a/_sources/datamodels/ontology-metadata/match_aspect.md.txt b/_sources/datamodels/ontology-metadata/match_aspect.md.txt
index deee7cc93..50e65cf9f 100644
--- a/_sources/datamodels/ontology-metadata/match_aspect.md.txt
+++ b/_sources/datamodels/ontology-metadata/match_aspect.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: match_aspect
-URI: [omoschema:match_aspect](http://purl.obolibrary.org/obo/omo/schema/match_aspect)
+URI: [omoschema:match_aspect](https://w3id.org/oak/ontology-metadata/match_aspect)
@@ -11,6 +13,7 @@ URI: [omoschema:match_aspect](http://purl.obolibrary.org/obo/omo/schema/match_as
+
## Mixin Usage
| mixed into | description | range | domain |
@@ -43,7 +46,7 @@ URI: [omoschema:match_aspect](http://purl.obolibrary.org/obo/omo/schema/match_as
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -53,7 +56,7 @@ URI: [omoschema:match_aspect](http://purl.obolibrary.org/obo/omo/schema/match_as
```yaml
name: match_aspect
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
mixin: true
alias: match_aspect
diff --git a/_sources/datamodels/ontology-metadata/maxQualifiedCardinality.md.txt b/_sources/datamodels/ontology-metadata/maxQualifiedCardinality.md.txt
index 27c09128f..49a6b00d1 100644
--- a/_sources/datamodels/ontology-metadata/maxQualifiedCardinality.md.txt
+++ b/_sources/datamodels/ontology-metadata/maxQualifiedCardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: maxQualifiedCardinality
URI: [owl:maxQualifiedCardinality](http://www.w3.org/2002/07/owl#maxQualifiedCardinality)
@@ -17,6 +19,7 @@ URI: [owl:maxQualifiedCardinality](http://www.w3.org/2002/07/owl#maxQualifiedCar
+
## Properties
* Range: [Integer](Integer.md)
@@ -36,7 +39,7 @@ URI: [owl:maxQualifiedCardinality](http://www.w3.org/2002/07/owl#maxQualifiedCar
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:maxQualifiedCardinality](http://www.w3.org/2002/07/owl#maxQualifiedCar
```yaml
name: maxQualifiedCardinality
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:maxQualifiedCardinality
diff --git a/_sources/datamodels/ontology-metadata/members.md.txt b/_sources/datamodels/ontology-metadata/members.md.txt
index 8fca9b598..1c2f04ced 100644
--- a/_sources/datamodels/ontology-metadata/members.md.txt
+++ b/_sources/datamodels/ontology-metadata/members.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: members
URI: [owl:members](http://www.w3.org/2002/07/owl#members)
@@ -17,6 +19,7 @@ URI: [owl:members](http://www.w3.org/2002/07/owl#members)
+
## Properties
* Range: [Thing](Thing.md)
@@ -36,7 +39,7 @@ URI: [owl:members](http://www.w3.org/2002/07/owl#members)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:members](http://www.w3.org/2002/07/owl#members)
```yaml
name: members
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:members
diff --git a/_sources/datamodels/ontology-metadata/minCardinality.md.txt b/_sources/datamodels/ontology-metadata/minCardinality.md.txt
index c4bac8cb1..c76cc7159 100644
--- a/_sources/datamodels/ontology-metadata/minCardinality.md.txt
+++ b/_sources/datamodels/ontology-metadata/minCardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: minCardinality
URI: [owl:minCardinality](http://www.w3.org/2002/07/owl#minCardinality)
@@ -17,6 +19,7 @@ URI: [owl:minCardinality](http://www.w3.org/2002/07/owl#minCardinality)
+
## Properties
* Range: [Integer](Integer.md)
@@ -36,7 +39,7 @@ URI: [owl:minCardinality](http://www.w3.org/2002/07/owl#minCardinality)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:minCardinality](http://www.w3.org/2002/07/owl#minCardinality)
```yaml
name: minCardinality
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:minCardinality
diff --git a/_sources/datamodels/ontology-metadata/minQualifiedCardinality.md.txt b/_sources/datamodels/ontology-metadata/minQualifiedCardinality.md.txt
index 756501b84..5fd7b6c89 100644
--- a/_sources/datamodels/ontology-metadata/minQualifiedCardinality.md.txt
+++ b/_sources/datamodels/ontology-metadata/minQualifiedCardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: minQualifiedCardinality
URI: [owl:minQualifiedCardinality](http://www.w3.org/2002/07/owl#minQualifiedCardinality)
@@ -17,6 +19,7 @@ URI: [owl:minQualifiedCardinality](http://www.w3.org/2002/07/owl#minQualifiedCar
+
## Properties
* Range: [Integer](Integer.md)
@@ -36,7 +39,7 @@ URI: [owl:minQualifiedCardinality](http://www.w3.org/2002/07/owl#minQualifiedCar
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:minQualifiedCardinality](http://www.w3.org/2002/07/owl#minQualifiedCar
```yaml
name: minQualifiedCardinality
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:minQualifiedCardinality
diff --git a/_sources/datamodels/ontology-metadata/narrowMatch.md.txt b/_sources/datamodels/ontology-metadata/narrowMatch.md.txt
index 2444d339f..3d83eef2f 100644
--- a/_sources/datamodels/ontology-metadata/narrowMatch.md.txt
+++ b/_sources/datamodels/ontology-metadata/narrowMatch.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: narrowMatch
URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch)
@@ -14,22 +16,23 @@ URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasMappings](HasMappings.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | yes |
-[Property](Property.md) | | yes |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | yes |
+| [Image](Image.md) | | no |
+| [HasMappings](HasMappings.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | yes |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch)
```yaml
name: narrowMatch
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: match
slot_uri: skos:narrowMatch
diff --git a/_sources/datamodels/ontology-metadata/never_in_taxon.md.txt b/_sources/datamodels/ontology-metadata/never_in_taxon.md.txt
index a23e46c1f..fc2fdedbd 100644
--- a/_sources/datamodels/ontology-metadata/never_in_taxon.md.txt
+++ b/_sources/datamodels/ontology-metadata/never_in_taxon.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: never_in_taxon
URI: [RO:0002161](http://purl.obolibrary.org/obo/RO_0002161)
@@ -9,11 +11,12 @@ URI: [RO:0002161](http://purl.obolibrary.org/obo/RO_0002161)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Class](Class.md) | | no |
+| [Class](Class.md) | | no |
@@ -42,7 +45,7 @@ URI: [RO:0002161](http://purl.obolibrary.org/obo/RO_0002161)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -52,7 +55,7 @@ URI: [RO:0002161](http://purl.obolibrary.org/obo/RO_0002161)
```yaml
name: never_in_taxon
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0002161
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/notes.md.txt b/_sources/datamodels/ontology-metadata/notes.md.txt
index e755d926a..eb9ebe885 100644
--- a/_sources/datamodels/ontology-metadata/notes.md.txt
+++ b/_sources/datamodels/ontology-metadata/notes.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: notes
URI: [oio:notes](http://www.geneontology.org/formats/oboInOwl#notes)
@@ -9,11 +11,12 @@ URI: [oio:notes](http://www.geneontology.org/formats/oboInOwl#notes)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -42,7 +45,7 @@ URI: [oio:notes](http://www.geneontology.org/formats/oboInOwl#notes)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -53,7 +56,7 @@ URI: [oio:notes](http://www.geneontology.org/formats/oboInOwl#notes)
```yaml
name: notes
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:notes
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/object.md.txt b/_sources/datamodels/ontology-metadata/object.md.txt
index c12eb540d..04713cc17 100644
--- a/_sources/datamodels/ontology-metadata/object.md.txt
+++ b/_sources/datamodels/ontology-metadata/object.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: object
-URI: [omoschema:object](http://purl.obolibrary.org/obo/omo/schema/object)
+URI: [omoschema:object](https://w3id.org/oak/ontology-metadata/object)
@@ -9,11 +11,12 @@ URI: [omoschema:object](http://purl.obolibrary.org/obo/omo/schema/object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Annotation](Annotation.md) | A reified property-object pair | no |
+| [Annotation](Annotation.md) | A reified property-object pair | no |
@@ -40,7 +43,7 @@ URI: [omoschema:object](http://purl.obolibrary.org/obo/omo/schema/object)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [omoschema:object](http://purl.obolibrary.org/obo/omo/schema/object)
```yaml
name: object
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
alias: object
domain_of:
diff --git a/_sources/datamodels/ontology-metadata/oboInOwl_id.md.txt b/_sources/datamodels/ontology-metadata/oboInOwl_id.md.txt
index 0aa47c00e..f9df580fe 100644
--- a/_sources/datamodels/ontology-metadata/oboInOwl_id.md.txt
+++ b/_sources/datamodels/ontology-metadata/oboInOwl_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: oboInOwl_id
URI: [oio:id](http://www.geneontology.org/formats/oboInOwl#id)
@@ -12,6 +14,7 @@ URI: [oio:id](http://www.geneontology.org/formats/oboInOwl#id)
+
## Properties
* Range: [String](String.md)
@@ -31,7 +34,7 @@ URI: [oio:id](http://www.geneontology.org/formats/oboInOwl#id)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -41,7 +44,7 @@ URI: [oio:id](http://www.geneontology.org/formats/oboInOwl#id)
```yaml
name: oboInOwl_id
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:id
alias: oboInOwl_id
diff --git a/_sources/datamodels/ontology-metadata/oboInOwl_ontology.md.txt b/_sources/datamodels/ontology-metadata/oboInOwl_ontology.md.txt
index 6c8bf2841..0e7b88297 100644
--- a/_sources/datamodels/ontology-metadata/oboInOwl_ontology.md.txt
+++ b/_sources/datamodels/ontology-metadata/oboInOwl_ontology.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: oboInOwl_ontology
URI: [oio:ontology](http://www.geneontology.org/formats/oboInOwl#ontology)
@@ -12,6 +14,7 @@ URI: [oio:ontology](http://www.geneontology.org/formats/oboInOwl#ontology)
+
## Properties
* Range: [String](String.md)
@@ -31,7 +34,7 @@ URI: [oio:ontology](http://www.geneontology.org/formats/oboInOwl#ontology)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -42,7 +45,7 @@ URI: [oio:ontology](http://www.geneontology.org/formats/oboInOwl#ontology)
```yaml
name: oboInOwl_ontology
deprecated: todo
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
deprecated_element_has_exact_replacement: ontology
rank: 1000
slot_uri: oio:ontology
diff --git a/_sources/datamodels/ontology-metadata/obsoletion_related_property.md.txt b/_sources/datamodels/ontology-metadata/obsoletion_related_property.md.txt
index b1de343d4..76854c36c 100644
--- a/_sources/datamodels/ontology-metadata/obsoletion_related_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/obsoletion_related_property.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: obsoletion_related_property
@@ -5,7 +7,7 @@ _Grouping class for all properties related to lifecycle_
-URI: [omoschema:obsoletion_related_property](http://purl.obolibrary.org/obo/omo/schema/obsoletion_related_property)
+URI: [omoschema:obsoletion_related_property](https://w3id.org/oak/ontology-metadata/obsoletion_related_property)
@@ -26,6 +28,7 @@ URI: [omoschema:obsoletion_related_property](http://purl.obolibrary.org/obo/omo/
+
## Properties
* Range: [String](String.md)
@@ -45,7 +48,7 @@ URI: [omoschema:obsoletion_related_property](http://purl.obolibrary.org/obo/omo/
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -56,7 +59,7 @@ URI: [omoschema:obsoletion_related_property](http://purl.obolibrary.org/obo/omo/
```yaml
name: obsoletion_related_property
description: Grouping class for all properties related to lifecycle
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: obsoletion_related_property
diff --git a/_sources/datamodels/ontology-metadata/onClass.md.txt b/_sources/datamodels/ontology-metadata/onClass.md.txt
index 001627433..b96bee23e 100644
--- a/_sources/datamodels/ontology-metadata/onClass.md.txt
+++ b/_sources/datamodels/ontology-metadata/onClass.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: onClass
URI: [owl:onClass](http://www.w3.org/2002/07/owl#onClass)
@@ -17,6 +19,7 @@ URI: [owl:onClass](http://www.w3.org/2002/07/owl#onClass)
+
## Properties
* Range: [ClassExpression](ClassExpression.md)
@@ -36,7 +39,7 @@ URI: [owl:onClass](http://www.w3.org/2002/07/owl#onClass)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:onClass](http://www.w3.org/2002/07/owl#onClass)
```yaml
name: onClass
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:onClass
diff --git a/_sources/datamodels/ontology-metadata/onProperty.md.txt b/_sources/datamodels/ontology-metadata/onProperty.md.txt
index c947188dc..49a31d210 100644
--- a/_sources/datamodels/ontology-metadata/onProperty.md.txt
+++ b/_sources/datamodels/ontology-metadata/onProperty.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: onProperty
URI: [owl:onProperty](http://www.w3.org/2002/07/owl#onProperty)
@@ -14,11 +16,12 @@ URI: [owl:onProperty](http://www.w3.org/2002/07/owl#onProperty)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
@@ -47,7 +50,7 @@ URI: [owl:onProperty](http://www.w3.org/2002/07/owl#onProperty)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -57,7 +60,7 @@ URI: [owl:onProperty](http://www.w3.org/2002/07/owl#onProperty)
```yaml
name: onProperty
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:onProperty
diff --git a/_sources/datamodels/ontology-metadata/oneOf.md.txt b/_sources/datamodels/ontology-metadata/oneOf.md.txt
index 4ecbd8478..71e52146d 100644
--- a/_sources/datamodels/ontology-metadata/oneOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/oneOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: oneOf
URI: [owl:oneOf](http://www.w3.org/2002/07/owl#oneOf)
@@ -14,13 +16,14 @@ URI: [owl:oneOf](http://www.w3.org/2002/07/owl#oneOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -47,7 +50,7 @@ URI: [owl:oneOf](http://www.w3.org/2002/07/owl#oneOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -57,7 +60,7 @@ URI: [owl:oneOf](http://www.w3.org/2002/07/owl#oneOf)
```yaml
name: oneOf
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:oneOf
diff --git a/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt b/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt
index 0b2a6b9cd..818e53731 100644
--- a/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt
+++ b/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ontology_term_requester
URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234)
@@ -14,22 +16,23 @@ URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234)
```yaml
name: ontology_term_requester
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000234
diff --git a/_sources/datamodels/ontology-metadata/page.md.txt b/_sources/datamodels/ontology-metadata/page.md.txt
index 07a71dccb..e70f39c6e 100644
--- a/_sources/datamodels/ontology-metadata/page.md.txt
+++ b/_sources/datamodels/ontology-metadata/page.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: page
URI: [foaf:page](http://xmlns.com/foaf/0.1/page)
@@ -14,22 +16,23 @@ URI: [foaf:page](http://xmlns.com/foaf/0.1/page)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [foaf:page](http://xmlns.com/foaf/0.1/page)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [foaf:page](http://xmlns.com/foaf/0.1/page)
```yaml
name: page
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: informative_property
slot_uri: foaf:page
diff --git a/_sources/datamodels/ontology-metadata/predicate.md.txt b/_sources/datamodels/ontology-metadata/predicate.md.txt
index 60684fdf1..86b3e73d6 100644
--- a/_sources/datamodels/ontology-metadata/predicate.md.txt
+++ b/_sources/datamodels/ontology-metadata/predicate.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: predicate
-URI: [omoschema:predicate](http://purl.obolibrary.org/obo/omo/schema/predicate)
+URI: [omoschema:predicate](https://w3id.org/oak/ontology-metadata/predicate)
@@ -9,11 +11,12 @@ URI: [omoschema:predicate](http://purl.obolibrary.org/obo/omo/schema/predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Annotation](Annotation.md) | A reified property-object pair | no |
+| [Annotation](Annotation.md) | A reified property-object pair | no |
@@ -40,7 +43,7 @@ URI: [omoschema:predicate](http://purl.obolibrary.org/obo/omo/schema/predicate)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [omoschema:predicate](http://purl.obolibrary.org/obo/omo/schema/predicate)
```yaml
name: predicate
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
alias: predicate
domain_of:
diff --git a/_sources/datamodels/ontology-metadata/propertyChainAxiom.md.txt b/_sources/datamodels/ontology-metadata/propertyChainAxiom.md.txt
index 42adffd6f..67424ca38 100644
--- a/_sources/datamodels/ontology-metadata/propertyChainAxiom.md.txt
+++ b/_sources/datamodels/ontology-metadata/propertyChainAxiom.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: propertyChainAxiom
URI: [owl:propertyChainAxiom](http://www.w3.org/2002/07/owl#propertyChainAxiom)
@@ -14,12 +16,13 @@ URI: [owl:propertyChainAxiom](http://www.w3.org/2002/07/owl#propertyChainAxiom)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -52,7 +55,7 @@ URI: [owl:propertyChainAxiom](http://www.w3.org/2002/07/owl#propertyChainAxiom)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -64,7 +67,7 @@ URI: [owl:propertyChainAxiom](http://www.w3.org/2002/07/owl#propertyChainAxiom)
name: propertyChainAxiom
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:propertyChainAxiom
diff --git a/_sources/datamodels/ontology-metadata/provenance_property.md.txt b/_sources/datamodels/ontology-metadata/provenance_property.md.txt
index 86099b965..fd012ab3c 100644
--- a/_sources/datamodels/ontology-metadata/provenance_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/provenance_property.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: provenance_property
-URI: [omoschema:provenance_property](http://purl.obolibrary.org/obo/omo/schema/provenance_property)
+URI: [omoschema:provenance_property](https://w3id.org/oak/ontology-metadata/provenance_property)
@@ -32,6 +34,7 @@ URI: [omoschema:provenance_property](http://purl.obolibrary.org/obo/omo/schema/p
+
## Properties
* Range: [String](String.md)
@@ -51,7 +54,7 @@ URI: [omoschema:provenance_property](http://purl.obolibrary.org/obo/omo/schema/p
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -61,7 +64,7 @@ URI: [omoschema:provenance_property](http://purl.obolibrary.org/obo/omo/schema/p
```yaml
name: provenance_property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: provenance_property
diff --git a/_sources/datamodels/ontology-metadata/qualifiedCardinality.md.txt b/_sources/datamodels/ontology-metadata/qualifiedCardinality.md.txt
index 36a806898..7f284e8b3 100644
--- a/_sources/datamodels/ontology-metadata/qualifiedCardinality.md.txt
+++ b/_sources/datamodels/ontology-metadata/qualifiedCardinality.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: qualifiedCardinality
URI: [owl:qualifiedCardinality](http://www.w3.org/2002/07/owl#qualifiedCardinality)
@@ -17,6 +19,7 @@ URI: [owl:qualifiedCardinality](http://www.w3.org/2002/07/owl#qualifiedCardinali
+
## Properties
* Range: [String](String.md)
@@ -36,7 +39,7 @@ URI: [owl:qualifiedCardinality](http://www.w3.org/2002/07/owl#qualifiedCardinali
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [owl:qualifiedCardinality](http://www.w3.org/2002/07/owl#qualifiedCardinali
```yaml
name: qualifiedCardinality
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:qualifiedCardinality
diff --git a/_sources/datamodels/ontology-metadata/range.md.txt b/_sources/datamodels/ontology-metadata/range.md.txt
index 4aef13c62..cee680158 100644
--- a/_sources/datamodels/ontology-metadata/range.md.txt
+++ b/_sources/datamodels/ontology-metadata/range.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: range
URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range)
@@ -14,15 +16,16 @@ URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -55,7 +58,7 @@ URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -67,7 +70,7 @@ URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range)
name: range
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:range
diff --git a/_sources/datamodels/ontology-metadata/reification_predicate.md.txt b/_sources/datamodels/ontology-metadata/reification_predicate.md.txt
index 7d2ed5427..2f2476ded 100644
--- a/_sources/datamodels/ontology-metadata/reification_predicate.md.txt
+++ b/_sources/datamodels/ontology-metadata/reification_predicate.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: reification_predicate
-URI: [omoschema:reification_predicate](http://purl.obolibrary.org/obo/omo/schema/reification_predicate)
+URI: [omoschema:reification_predicate](https://w3id.org/oak/ontology-metadata/reification_predicate)
@@ -19,6 +21,7 @@ URI: [omoschema:reification_predicate](http://purl.obolibrary.org/obo/omo/schema
+
## Properties
* Range: [String](String.md)
@@ -38,7 +41,7 @@ URI: [omoschema:reification_predicate](http://purl.obolibrary.org/obo/omo/schema
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -48,7 +51,7 @@ URI: [omoschema:reification_predicate](http://purl.obolibrary.org/obo/omo/schema
```yaml
name: reification_predicate
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: reification_predicate
diff --git a/_sources/datamodels/ontology-metadata/sameAs.md.txt b/_sources/datamodels/ontology-metadata/sameAs.md.txt
index c23e678dc..f3500929e 100644
--- a/_sources/datamodels/ontology-metadata/sameAs.md.txt
+++ b/_sources/datamodels/ontology-metadata/sameAs.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sameAs
URI: [owl:sameAs](http://www.w3.org/2002/07/owl#sameAs)
@@ -17,6 +19,7 @@ URI: [owl:sameAs](http://www.w3.org/2002/07/owl#sameAs)
+
## Properties
* Range: [Thing](Thing.md)
@@ -42,7 +45,7 @@ URI: [owl:sameAs](http://www.w3.org/2002/07/owl#sameAs)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -54,7 +57,7 @@ URI: [owl:sameAs](http://www.w3.org/2002/07/owl#sameAs)
name: sameAs
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
mixins:
diff --git a/_sources/datamodels/ontology-metadata/seeAlso.md.txt b/_sources/datamodels/ontology-metadata/seeAlso.md.txt
index 0b59c0cc3..4bf71a745 100644
--- a/_sources/datamodels/ontology-metadata/seeAlso.md.txt
+++ b/_sources/datamodels/ontology-metadata/seeAlso.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: seeAlso
URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)
@@ -9,23 +11,24 @@ URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasUserInformation](HasUserInformation.md) | | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasUserInformation](HasUserInformation.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -70,7 +73,7 @@ URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)
name: seeAlso
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/shortcut_annotation_property.md.txt b/_sources/datamodels/ontology-metadata/shortcut_annotation_property.md.txt
index 8be038cb5..43d43f51b 100644
--- a/_sources/datamodels/ontology-metadata/shortcut_annotation_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/shortcut_annotation_property.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: shortcut_annotation_property
-URI: [omoschema:shortcut_annotation_property](http://purl.obolibrary.org/obo/omo/schema/shortcut_annotation_property)
+URI: [omoschema:shortcut_annotation_property](https://w3id.org/oak/ontology-metadata/shortcut_annotation_property)
@@ -17,6 +19,7 @@ URI: [omoschema:shortcut_annotation_property](http://purl.obolibrary.org/obo/omo
+
## Properties
* Range: [String](String.md)
@@ -36,7 +39,7 @@ URI: [omoschema:shortcut_annotation_property](http://purl.obolibrary.org/obo/omo
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -46,7 +49,7 @@ URI: [omoschema:shortcut_annotation_property](http://purl.obolibrary.org/obo/omo
```yaml
name: shortcut_annotation_property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: shortcut_annotation_property
diff --git a/_sources/datamodels/ontology-metadata/shorthand.md.txt b/_sources/datamodels/ontology-metadata/shorthand.md.txt
index 50c358582..060c28ff3 100644
--- a/_sources/datamodels/ontology-metadata/shorthand.md.txt
+++ b/_sources/datamodels/ontology-metadata/shorthand.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: shorthand
URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand)
@@ -9,14 +11,15 @@ URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -45,7 +48,7 @@ URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -56,7 +59,7 @@ URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand)
```yaml
name: shorthand
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:shorthand
multivalued: true
diff --git a/_sources/datamodels/ontology-metadata/should_conform_to.md.txt b/_sources/datamodels/ontology-metadata/should_conform_to.md.txt
index 70b3a7b01..07f37e6b2 100644
--- a/_sources/datamodels/ontology-metadata/should_conform_to.md.txt
+++ b/_sources/datamodels/ontology-metadata/should_conform_to.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: should_conform_to
-URI: [omoschema:should_conform_to](http://purl.obolibrary.org/obo/omo/schema/should_conform_to)
+URI: [omoschema:should_conform_to](https://w3id.org/oak/ontology-metadata/should_conform_to)
@@ -14,22 +16,23 @@ URI: [omoschema:should_conform_to](http://purl.obolibrary.org/obo/omo/schema/sho
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -56,7 +59,7 @@ URI: [omoschema:should_conform_to](http://purl.obolibrary.org/obo/omo/schema/sho
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -66,7 +69,7 @@ URI: [omoschema:should_conform_to](http://purl.obolibrary.org/obo/omo/schema/sho
```yaml
name: should_conform_to
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: excluded_axiom
alias: should_conform_to
diff --git a/_sources/datamodels/ontology-metadata/someValuesFrom.md.txt b/_sources/datamodels/ontology-metadata/someValuesFrom.md.txt
index c5d7d6cfb..e1f446e21 100644
--- a/_sources/datamodels/ontology-metadata/someValuesFrom.md.txt
+++ b/_sources/datamodels/ontology-metadata/someValuesFrom.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: someValuesFrom
URI: [owl:someValuesFrom](http://www.w3.org/2002/07/owl#someValuesFrom)
@@ -14,11 +16,12 @@ URI: [owl:someValuesFrom](http://www.w3.org/2002/07/owl#someValuesFrom)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
@@ -51,7 +54,7 @@ URI: [owl:someValuesFrom](http://www.w3.org/2002/07/owl#someValuesFrom)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -63,7 +66,7 @@ URI: [owl:someValuesFrom](http://www.w3.org/2002/07/owl#someValuesFrom)
name: someValuesFrom
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:someValuesFrom
diff --git a/_sources/datamodels/ontology-metadata/source.md.txt b/_sources/datamodels/ontology-metadata/source.md.txt
index f28103c99..1ef2e85ef 100644
--- a/_sources/datamodels/ontology-metadata/source.md.txt
+++ b/_sources/datamodels/ontology-metadata/source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: source
URI: [dcterms:source](http://purl.org/dc/terms/source)
@@ -14,12 +16,13 @@ URI: [dcterms:source](http://purl.org/dc/terms/source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -48,7 +51,7 @@ URI: [dcterms:source](http://purl.org/dc/terms/source)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -58,7 +61,7 @@ URI: [dcterms:source](http://purl.org/dc/terms/source)
```yaml
name: source
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- http://purl.org/dc/terms/source
- oio:source
diff --git a/_sources/datamodels/ontology-metadata/subClassOf.md.txt b/_sources/datamodels/ontology-metadata/subClassOf.md.txt
index 109326938..70245ef2c 100644
--- a/_sources/datamodels/ontology-metadata/subClassOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/subClassOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subClassOf
URI: [rdfs:subClassOf](http://www.w3.org/2000/01/rdf-schema#subClassOf)
@@ -14,13 +16,14 @@ URI: [rdfs:subClassOf](http://www.w3.org/2000/01/rdf-schema#subClassOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | yes |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | yes |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -49,7 +52,7 @@ URI: [rdfs:subClassOf](http://www.w3.org/2000/01/rdf-schema#subClassOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -59,7 +62,7 @@ URI: [rdfs:subClassOf](http://www.w3.org/2000/01/rdf-schema#subClassOf)
```yaml
name: subClassOf
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdfs:subClassOf
diff --git a/_sources/datamodels/ontology-metadata/synonym.md.txt b/_sources/datamodels/ontology-metadata/synonym.md.txt
index c74e6585e..6e6efdbe7 100644
--- a/_sources/datamodels/ontology-metadata/synonym.md.txt
+++ b/_sources/datamodels/ontology-metadata/synonym.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonym
URI: [OIO:hasSynonym](http://www.geneontology.org/formats/oboInOwl#hasSynonym)
@@ -20,6 +22,7 @@ URI: [OIO:hasSynonym](http://www.geneontology.org/formats/oboInOwl#hasSynonym)
+
## Properties
* Range: [LabelType](LabelType.md)
@@ -41,7 +44,7 @@ URI: [OIO:hasSynonym](http://www.geneontology.org/formats/oboInOwl#hasSynonym)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -51,7 +54,7 @@ URI: [OIO:hasSynonym](http://www.geneontology.org/formats/oboInOwl#hasSynonym)
```yaml
name: synonym
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: alternative_term
abstract: true
diff --git a/_sources/datamodels/ontology-metadata/temporal_interpretation.md.txt b/_sources/datamodels/ontology-metadata/temporal_interpretation.md.txt
index d05668cf3..318299899 100644
--- a/_sources/datamodels/ontology-metadata/temporal_interpretation.md.txt
+++ b/_sources/datamodels/ontology-metadata/temporal_interpretation.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: temporal_interpretation
URI: [RO:0001900](http://purl.obolibrary.org/obo/RO_0001900)
@@ -9,12 +11,13 @@ URI: [RO:0001900](http://purl.obolibrary.org/obo/RO_0001900)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
@@ -41,7 +44,7 @@ URI: [RO:0001900](http://purl.obolibrary.org/obo/RO_0001900)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -51,7 +54,7 @@ URI: [RO:0001900](http://purl.obolibrary.org/obo/RO_0001900)
```yaml
name: temporal_interpretation
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: RO:0001900
alias: temporal_interpretation
diff --git a/_sources/datamodels/ontology-metadata/term_editor.md.txt b/_sources/datamodels/ontology-metadata/term_editor.md.txt
index a2e305c29..7224737ba 100644
--- a/_sources/datamodels/ontology-metadata/term_editor.md.txt
+++ b/_sources/datamodels/ontology-metadata/term_editor.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: term_editor
URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117)
@@ -14,22 +16,23 @@ URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -58,7 +61,7 @@ URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -68,7 +71,7 @@ URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117)
```yaml
name: term_editor
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000117
diff --git a/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt b/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt
index 7d566b871..26f56bc12 100644
--- a/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt
+++ b/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: term_replaced_by
URI: [IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001)
@@ -14,22 +16,23 @@ URI: [IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasLifeCycle](HasLifeCycle.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [HasLifeCycle](HasLifeCycle.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -60,7 +63,7 @@ URI: [IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -76,7 +79,7 @@ in_subset:
- go permitted profile
- obi permitted profile
- allotrope permitted profile
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
exact_mappings:
- dcterms:isReplacedBy
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt b/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt
index ce2dd501c..eea617d27 100644
--- a/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt
+++ b/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: term_tracker_item
URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233)
@@ -14,22 +16,23 @@ URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasProvenance](HasProvenance.md) | | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Class](Class.md) | | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [HasProvenance](HasProvenance.md) | | no |
+| [Agent](Agent.md) | | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
@@ -62,7 +65,7 @@ URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -74,7 +77,7 @@ URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233)
name: term_tracker_item
todos:
- restrict range
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: provenance_property
slot_uri: IAO:0000233
diff --git a/_sources/datamodels/ontology-metadata/title.md.txt b/_sources/datamodels/ontology-metadata/title.md.txt
index 602e0a5c6..070983307 100644
--- a/_sources/datamodels/ontology-metadata/title.md.txt
+++ b/_sources/datamodels/ontology-metadata/title.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: title
URI: [dcterms:title](http://purl.org/dc/terms/title)
@@ -9,11 +11,12 @@ URI: [dcterms:title](http://purl.org/dc/terms/title)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | yes |
+| [Ontology](Ontology.md) | An OWL ontology | yes |
@@ -40,7 +43,7 @@ URI: [dcterms:title](http://purl.org/dc/terms/title)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -50,7 +53,7 @@ URI: [dcterms:title](http://purl.org/dc/terms/title)
```yaml
name: title
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: dcterms:title
alias: title
diff --git a/_sources/datamodels/ontology-metadata/type.md.txt b/_sources/datamodels/ontology-metadata/type.md.txt
index 55e34e3ed..8849915a2 100644
--- a/_sources/datamodels/ontology-metadata/type.md.txt
+++ b/_sources/datamodels/ontology-metadata/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type)
@@ -14,24 +16,25 @@ URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Thing](Thing.md) | | no |
-[NamedObject](NamedObject.md) | Anything with an IRI | no |
-[Ontology](Ontology.md) | An OWL ontology | no |
-[Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
-[Class](Class.md) | | no |
-[Property](Property.md) | | no |
-[AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
-[ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
-[TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
-[NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
-[HomoSapiens](HomoSapiens.md) | An individual human being | no |
-[Agent](Agent.md) | | no |
-[Image](Image.md) | | no |
-[Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [Class](Class.md) | | no |
+| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no |
+| [Image](Image.md) | | no |
+| [HomoSapiens](HomoSapiens.md) | An individual human being | no |
+| [Ontology](Ontology.md) | An OWL ontology | no |
+| [Subset](Subset.md) | A collection of terms grouped for some purpose | no |
+| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no |
+| [Property](Property.md) | | no |
+| [NamedObject](NamedObject.md) | Anything with an IRI | no |
+| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no |
+| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no |
+| [Agent](Agent.md) | | no |
+| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no |
+| [Thing](Thing.md) | | no |
@@ -60,7 +63,7 @@ URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -70,7 +73,7 @@ URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type)
```yaml
name: type
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: rdf:type
diff --git a/_sources/datamodels/ontology-metadata/unionOf.md.txt b/_sources/datamodels/ontology-metadata/unionOf.md.txt
index 7c23e8706..3a510612a 100644
--- a/_sources/datamodels/ontology-metadata/unionOf.md.txt
+++ b/_sources/datamodels/ontology-metadata/unionOf.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: unionOf
URI: [owl:unionOf](http://www.w3.org/2002/07/owl#unionOf)
@@ -14,13 +16,14 @@ URI: [owl:unionOf](http://www.w3.org/2002/07/owl#unionOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassExpression](ClassExpression.md) | | no |
-[Class](Class.md) | | no |
-[Restriction](Restriction.md) | | no |
+| [Restriction](Restriction.md) | | no |
+| [Class](Class.md) | | no |
+| [ClassExpression](ClassExpression.md) | | no |
@@ -47,7 +50,7 @@ URI: [owl:unionOf](http://www.w3.org/2002/07/owl#unionOf)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -57,7 +60,7 @@ URI: [owl:unionOf](http://www.w3.org/2002/07/owl#unionOf)
```yaml
name: unionOf
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: logical_predicate
slot_uri: owl:unionOf
diff --git a/_sources/datamodels/ontology-metadata/url.md.txt b/_sources/datamodels/ontology-metadata/url.md.txt
index 2aab49f6d..53b814c71 100644
--- a/_sources/datamodels/ontology-metadata/url.md.txt
+++ b/_sources/datamodels/ontology-metadata/url.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: url
URI: [oio:url](http://www.geneontology.org/formats/oboInOwl#url)
@@ -9,11 +11,12 @@ URI: [oio:url](http://www.geneontology.org/formats/oboInOwl#url)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Axiom](Axiom.md) | A logical or non-logical statement | no |
+| [Axiom](Axiom.md) | A logical or non-logical statement | no |
@@ -40,7 +43,7 @@ URI: [oio:url](http://www.geneontology.org/formats/oboInOwl#url)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -51,7 +54,7 @@ URI: [oio:url](http://www.geneontology.org/formats/oboInOwl#url)
```yaml
name: url
deprecated: deprecated oboInOwl property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
slot_uri: oio:url
alias: url
diff --git a/_sources/datamodels/ontology-metadata/versionIRI.md.txt b/_sources/datamodels/ontology-metadata/versionIRI.md.txt
index f68c6e8d4..8e825938f 100644
--- a/_sources/datamodels/ontology-metadata/versionIRI.md.txt
+++ b/_sources/datamodels/ontology-metadata/versionIRI.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: versionIRI
URI: [owl:versionIRI](http://www.w3.org/2002/07/owl#versionIRI)
@@ -14,11 +16,12 @@ URI: [owl:versionIRI](http://www.w3.org/2002/07/owl#versionIRI)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | yes |
+| [Ontology](Ontology.md) | An OWL ontology | yes |
@@ -45,7 +48,7 @@ URI: [owl:versionIRI](http://www.w3.org/2002/07/owl#versionIRI)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [owl:versionIRI](http://www.w3.org/2002/07/owl#versionIRI)
```yaml
name: versionIRI
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
is_a: version_property
slot_uri: owl:versionIRI
diff --git a/_sources/datamodels/ontology-metadata/versionInfo.md.txt b/_sources/datamodels/ontology-metadata/versionInfo.md.txt
index 7ecb254a0..508e7fd5c 100644
--- a/_sources/datamodels/ontology-metadata/versionInfo.md.txt
+++ b/_sources/datamodels/ontology-metadata/versionInfo.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: versionInfo
URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
@@ -14,11 +16,12 @@ URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An OWL ontology | yes |
+| [Ontology](Ontology.md) | An OWL ontology | yes |
@@ -45,7 +48,7 @@ URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -55,7 +58,7 @@ URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
```yaml
name: versionInfo
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
close_mappings:
- pav:version
rank: 1000
diff --git a/_sources/datamodels/ontology-metadata/version_property.md.txt b/_sources/datamodels/ontology-metadata/version_property.md.txt
index e74faf31e..3c13b5d4c 100644
--- a/_sources/datamodels/ontology-metadata/version_property.md.txt
+++ b/_sources/datamodels/ontology-metadata/version_property.md.txt
@@ -1,6 +1,8 @@
+
+
# Slot: version_property
-URI: [omoschema:version_property](http://purl.obolibrary.org/obo/omo/schema/version_property)
+URI: [omoschema:version_property](https://w3id.org/oak/ontology-metadata/version_property)
@@ -18,6 +20,7 @@ URI: [omoschema:version_property](http://purl.obolibrary.org/obo/omo/schema/vers
+
## Properties
* Range: [String](String.md)
@@ -37,7 +40,7 @@ URI: [omoschema:version_property](http://purl.obolibrary.org/obo/omo/schema/vers
### Schema Source
-* from schema: http://purl.obolibrary.org/obo/omo/schema
+* from schema: https://w3id.org/oak/ontology-metadata
@@ -47,7 +50,7 @@ URI: [omoschema:version_property](http://purl.obolibrary.org/obo/omo/schema/vers
```yaml
name: version_property
-from_schema: http://purl.obolibrary.org/obo/omo/schema
+from_schema: https://w3id.org/oak/ontology-metadata
rank: 1000
abstract: true
alias: version_property
diff --git a/_sources/datamodels/search/ComplexQuery.md.txt b/_sources/datamodels/search/ComplexQuery.md.txt
index 561ca8378..79fcdee7c 100644
--- a/_sources/datamodels/search/ComplexQuery.md.txt
+++ b/_sources/datamodels/search/ComplexQuery.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ComplexQuery
diff --git a/_sources/datamodels/search/PathExpression.md.txt b/_sources/datamodels/search/PathExpression.md.txt
index e1a0c0480..d3f5140e8 100644
--- a/_sources/datamodels/search/PathExpression.md.txt
+++ b/_sources/datamodels/search/PathExpression.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PathExpression
diff --git a/_sources/datamodels/search/SearchBaseConfiguration.md.txt b/_sources/datamodels/search/SearchBaseConfiguration.md.txt
index 94d3d3c0f..3833eb18e 100644
--- a/_sources/datamodels/search/SearchBaseConfiguration.md.txt
+++ b/_sources/datamodels/search/SearchBaseConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SearchBaseConfiguration
diff --git a/_sources/datamodels/search/SearchResult.md.txt b/_sources/datamodels/search/SearchResult.md.txt
index 3a8256250..c32bad4a4 100644
--- a/_sources/datamodels/search/SearchResult.md.txt
+++ b/_sources/datamodels/search/SearchResult.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SearchResult
diff --git a/_sources/datamodels/search/SearchResultSet.md.txt b/_sources/datamodels/search/SearchResultSet.md.txt
index 5c717ded0..d914e22df 100644
--- a/_sources/datamodels/search/SearchResultSet.md.txt
+++ b/_sources/datamodels/search/SearchResultSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SearchResultSet
diff --git a/_sources/datamodels/search/all_of.md.txt b/_sources/datamodels/search/all_of.md.txt
index 81df39c8a..f426e1b39 100644
--- a/_sources/datamodels/search/all_of.md.txt
+++ b/_sources/datamodels/search/all_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: all_of
URI: [ontosearch:all_of](https://w3id.org/oak/search-datamodel/all_of)
@@ -9,11 +11,12 @@ URI: [ontosearch:all_of](https://w3id.org/oak/search-datamodel/all_of)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ComplexQuery](ComplexQuery.md) | | no |
+| [ComplexQuery](ComplexQuery.md) | | no |
diff --git a/_sources/datamodels/search/any_of.md.txt b/_sources/datamodels/search/any_of.md.txt
index ba2bed1f0..5d55cd8d2 100644
--- a/_sources/datamodels/search/any_of.md.txt
+++ b/_sources/datamodels/search/any_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: any_of
URI: [ontosearch:any_of](https://w3id.org/oak/search-datamodel/any_of)
@@ -9,11 +11,12 @@ URI: [ontosearch:any_of](https://w3id.org/oak/search-datamodel/any_of)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ComplexQuery](ComplexQuery.md) | | no |
+| [ComplexQuery](ComplexQuery.md) | | no |
diff --git a/_sources/datamodels/search/atom.md.txt b/_sources/datamodels/search/atom.md.txt
index 282454b0f..fcadf3dbd 100644
--- a/_sources/datamodels/search/atom.md.txt
+++ b/_sources/datamodels/search/atom.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: atom
URI: [ontosearch:atom](https://w3id.org/oak/search-datamodel/atom)
@@ -9,11 +11,12 @@ URI: [ontosearch:atom](https://w3id.org/oak/search-datamodel/atom)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ComplexQuery](ComplexQuery.md) | | no |
+| [ComplexQuery](ComplexQuery.md) | | no |
diff --git a/_sources/datamodels/search/categories.md.txt b/_sources/datamodels/search/categories.md.txt
index 16d23356d..3febc0bc8 100644
--- a/_sources/datamodels/search/categories.md.txt
+++ b/_sources/datamodels/search/categories.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: categories
@@ -14,11 +16,12 @@ URI: [ontosearch:categories](https://w3id.org/oak/search-datamodel/categories)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/configuration.md.txt b/_sources/datamodels/search/configuration.md.txt
index 463158a65..19d41f975 100644
--- a/_sources/datamodels/search/configuration.md.txt
+++ b/_sources/datamodels/search/configuration.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: configuration
URI: [ontosearch:configuration](https://w3id.org/oak/search-datamodel/configuration)
@@ -9,11 +11,12 @@ URI: [ontosearch:configuration](https://w3id.org/oak/search-datamodel/configurat
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResultSet](SearchResultSet.md) | | no |
+| [SearchResultSet](SearchResultSet.md) | | no |
diff --git a/_sources/datamodels/search/cursor.md.txt b/_sources/datamodels/search/cursor.md.txt
index 08fa73e2d..50fd66e83 100644
--- a/_sources/datamodels/search/cursor.md.txt
+++ b/_sources/datamodels/search/cursor.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: cursor
URI: [ontosearch:cursor](https://w3id.org/oak/search-datamodel/cursor)
@@ -9,12 +11,13 @@ URI: [ontosearch:cursor](https://w3id.org/oak/search-datamodel/cursor)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
-[SearchResultSet](SearchResultSet.md) | | no |
+| [SearchResultSet](SearchResultSet.md) | | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/force_case_insensitive.md.txt b/_sources/datamodels/search/force_case_insensitive.md.txt
index ebc37cfaa..191c9ee7e 100644
--- a/_sources/datamodels/search/force_case_insensitive.md.txt
+++ b/_sources/datamodels/search/force_case_insensitive.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: force_case_insensitive
@@ -14,11 +16,12 @@ URI: [ontosearch:force_case_insensitive](https://w3id.org/oak/search-datamodel/f
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/graph_predicates.md.txt b/_sources/datamodels/search/graph_predicates.md.txt
index 0fa15cb66..a50822071 100644
--- a/_sources/datamodels/search/graph_predicates.md.txt
+++ b/_sources/datamodels/search/graph_predicates.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: graph_predicates
URI: [ontosearch:graph_predicates](https://w3id.org/oak/search-datamodel/graph_predicates)
@@ -9,11 +11,12 @@ URI: [ontosearch:graph_predicates](https://w3id.org/oak/search-datamodel/graph_p
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PathExpression](PathExpression.md) | A path query | no |
+| [PathExpression](PathExpression.md) | A path query | no |
diff --git a/_sources/datamodels/search/include_obsoletes_in_results.md.txt b/_sources/datamodels/search/include_obsoletes_in_results.md.txt
index 605e5d8a7..8191d80e3 100644
--- a/_sources/datamodels/search/include_obsoletes_in_results.md.txt
+++ b/_sources/datamodels/search/include_obsoletes_in_results.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: include_obsoletes_in_results
URI: [ontosearch:include_obsoletes_in_results](https://w3id.org/oak/search-datamodel/include_obsoletes_in_results)
@@ -9,11 +11,12 @@ URI: [ontosearch:include_obsoletes_in_results](https://w3id.org/oak/search-datam
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/is_complete.md.txt b/_sources/datamodels/search/is_complete.md.txt
index b9c01d6bf..32542043b 100644
--- a/_sources/datamodels/search/is_complete.md.txt
+++ b/_sources/datamodels/search/is_complete.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_complete
URI: [ontosearch:is_complete](https://w3id.org/oak/search-datamodel/is_complete)
@@ -9,11 +11,12 @@ URI: [ontosearch:is_complete](https://w3id.org/oak/search-datamodel/is_complete)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/is_fuzzy.md.txt b/_sources/datamodels/search/is_fuzzy.md.txt
index b006409c6..b8a8cac7a 100644
--- a/_sources/datamodels/search/is_fuzzy.md.txt
+++ b/_sources/datamodels/search/is_fuzzy.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_fuzzy
URI: [ontosearch:is_fuzzy](https://w3id.org/oak/search-datamodel/is_fuzzy)
@@ -9,11 +11,12 @@ URI: [ontosearch:is_fuzzy](https://w3id.org/oak/search-datamodel/is_fuzzy)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/is_partial.md.txt b/_sources/datamodels/search/is_partial.md.txt
index 68373ee7d..c05dfe78e 100644
--- a/_sources/datamodels/search/is_partial.md.txt
+++ b/_sources/datamodels/search/is_partial.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_partial
@@ -14,11 +16,12 @@ URI: [ontosearch:is_partial](https://w3id.org/oak/search-datamodel/is_partial)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/limit.md.txt b/_sources/datamodels/search/limit.md.txt
index 45d657f9e..ebb7b9817 100644
--- a/_sources/datamodels/search/limit.md.txt
+++ b/_sources/datamodels/search/limit.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: limit
@@ -14,11 +16,12 @@ URI: [ontosearch:limit](https://w3id.org/oak/search-datamodel/limit)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/matches_full_search_term.md.txt b/_sources/datamodels/search/matches_full_search_term.md.txt
index b4e813f50..72d9271bc 100644
--- a/_sources/datamodels/search/matches_full_search_term.md.txt
+++ b/_sources/datamodels/search/matches_full_search_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: matches_full_search_term
@@ -14,11 +16,12 @@ URI: [ontosearch:matches_full_search_term](https://w3id.org/oak/search-datamodel
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/none_of.md.txt b/_sources/datamodels/search/none_of.md.txt
index 64449ef05..63d375cd3 100644
--- a/_sources/datamodels/search/none_of.md.txt
+++ b/_sources/datamodels/search/none_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: none_of
URI: [ontosearch:none_of](https://w3id.org/oak/search-datamodel/none_of)
@@ -9,11 +11,12 @@ URI: [ontosearch:none_of](https://w3id.org/oak/search-datamodel/none_of)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ComplexQuery](ComplexQuery.md) | | no |
+| [ComplexQuery](ComplexQuery.md) | | no |
diff --git a/_sources/datamodels/search/object_id.md.txt b/_sources/datamodels/search/object_id.md.txt
index 6fb347072..a6e8cb895 100644
--- a/_sources/datamodels/search/object_id.md.txt
+++ b/_sources/datamodels/search/object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_id
@@ -14,11 +16,12 @@ URI: [sssom:object_id](http://w3id.org/sssom/object_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/object_label.md.txt b/_sources/datamodels/search/object_label.md.txt
index 444868f8d..20d54bb2c 100644
--- a/_sources/datamodels/search/object_label.md.txt
+++ b/_sources/datamodels/search/object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_label
@@ -14,11 +16,12 @@ URI: [sssom:object_label](http://w3id.org/sssom/object_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/object_match_field.md.txt b/_sources/datamodels/search/object_match_field.md.txt
index c7be912ad..d6acc7dc1 100644
--- a/_sources/datamodels/search/object_match_field.md.txt
+++ b/_sources/datamodels/search/object_match_field.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_match_field
@@ -14,11 +16,12 @@ URI: [sssom:object_match_field](http://w3id.org/sssom/object_match_field)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/object_source.md.txt b/_sources/datamodels/search/object_source.md.txt
index 9172b11d7..f38aed381 100644
--- a/_sources/datamodels/search/object_source.md.txt
+++ b/_sources/datamodels/search/object_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_source
@@ -14,11 +16,12 @@ URI: [sssom:object_source](http://w3id.org/sssom/object_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/object_source_version.md.txt b/_sources/datamodels/search/object_source_version.md.txt
index 4d697f666..5c4476ec3 100644
--- a/_sources/datamodels/search/object_source_version.md.txt
+++ b/_sources/datamodels/search/object_source_version.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_source_version
@@ -14,11 +16,12 @@ URI: [sssom:object_source_version](http://w3id.org/sssom/object_source_version)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/path_to.md.txt b/_sources/datamodels/search/path_to.md.txt
index a100012e9..bdf620cc4 100644
--- a/_sources/datamodels/search/path_to.md.txt
+++ b/_sources/datamodels/search/path_to.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: path_to
URI: [ontosearch:path_to](https://w3id.org/oak/search-datamodel/path_to)
@@ -9,11 +11,12 @@ URI: [ontosearch:path_to](https://w3id.org/oak/search-datamodel/path_to)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ComplexQuery](ComplexQuery.md) | | no |
+| [ComplexQuery](ComplexQuery.md) | | no |
diff --git a/_sources/datamodels/search/properties.md.txt b/_sources/datamodels/search/properties.md.txt
index 64a6f99f5..8cf34a2b2 100644
--- a/_sources/datamodels/search/properties.md.txt
+++ b/_sources/datamodels/search/properties.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: properties
@@ -14,11 +16,12 @@ URI: [ontosearch:properties](https://w3id.org/oak/search-datamodel/properties)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/rank.md.txt b/_sources/datamodels/search/rank.md.txt
index bf613e4b8..44c6b855e 100644
--- a/_sources/datamodels/search/rank.md.txt
+++ b/_sources/datamodels/search/rank.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: rank
@@ -14,11 +16,12 @@ URI: [ontosearch:rank](https://w3id.org/oak/search-datamodel/rank)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/result_count.md.txt b/_sources/datamodels/search/result_count.md.txt
index 64aa23d5a..031deca66 100644
--- a/_sources/datamodels/search/result_count.md.txt
+++ b/_sources/datamodels/search/result_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: result_count
URI: [ontosearch:result_count](https://w3id.org/oak/search-datamodel/result_count)
@@ -9,11 +11,12 @@ URI: [ontosearch:result_count](https://w3id.org/oak/search-datamodel/result_coun
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResultSet](SearchResultSet.md) | | no |
+| [SearchResultSet](SearchResultSet.md) | | no |
diff --git a/_sources/datamodels/search/results.md.txt b/_sources/datamodels/search/results.md.txt
index 14536eba2..4f18f1797 100644
--- a/_sources/datamodels/search/results.md.txt
+++ b/_sources/datamodels/search/results.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: results
URI: [ontosearch:results](https://w3id.org/oak/search-datamodel/results)
@@ -9,11 +11,12 @@ URI: [ontosearch:results](https://w3id.org/oak/search-datamodel/results)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResultSet](SearchResultSet.md) | | no |
+| [SearchResultSet](SearchResultSet.md) | | no |
diff --git a/_sources/datamodels/search/search_term.md.txt b/_sources/datamodels/search/search_term.md.txt
index 32006bafe..b26bddf9f 100644
--- a/_sources/datamodels/search/search_term.md.txt
+++ b/_sources/datamodels/search/search_term.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: search_term
URI: [ontosearch:search_term](https://w3id.org/oak/search-datamodel/search_term)
@@ -9,11 +11,12 @@ URI: [ontosearch:search_term](https://w3id.org/oak/search-datamodel/search_term)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PathExpression](PathExpression.md) | A path query | no |
+| [PathExpression](PathExpression.md) | A path query | no |
diff --git a/_sources/datamodels/search/search_terms.md.txt b/_sources/datamodels/search/search_terms.md.txt
index 4354eefb6..36c5cf68c 100644
--- a/_sources/datamodels/search/search_terms.md.txt
+++ b/_sources/datamodels/search/search_terms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: search_terms
@@ -14,11 +16,12 @@ URI: [ontosearch:search_terms](https://w3id.org/oak/search-datamodel/search_term
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/snippet.md.txt b/_sources/datamodels/search/snippet.md.txt
index 0e6b6b3b3..06792309b 100644
--- a/_sources/datamodels/search/snippet.md.txt
+++ b/_sources/datamodels/search/snippet.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: snippet
@@ -14,11 +16,12 @@ URI: [ontosearch:snippet](https://w3id.org/oak/search-datamodel/snippet)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchResult](SearchResult.md) | An individual search result | no |
+| [SearchResult](SearchResult.md) | An individual search result | no |
diff --git a/_sources/datamodels/search/syntax.md.txt b/_sources/datamodels/search/syntax.md.txt
index 9ab776be5..aa9da2f6c 100644
--- a/_sources/datamodels/search/syntax.md.txt
+++ b/_sources/datamodels/search/syntax.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: syntax
@@ -14,11 +16,12 @@ URI: [ontosearch:syntax](https://w3id.org/oak/search-datamodel/syntax)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
+| [SearchBaseConfiguration](SearchBaseConfiguration.md) | A user-specified configuration that determines how a particular search operat... | no |
diff --git a/_sources/datamodels/search/traversal.md.txt b/_sources/datamodels/search/traversal.md.txt
index 06714e377..42a0cb4a8 100644
--- a/_sources/datamodels/search/traversal.md.txt
+++ b/_sources/datamodels/search/traversal.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: traversal
URI: [ontosearch:traversal](https://w3id.org/oak/search-datamodel/traversal)
@@ -9,11 +11,12 @@ URI: [ontosearch:traversal](https://w3id.org/oak/search-datamodel/traversal)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PathExpression](PathExpression.md) | A path query | no |
+| [PathExpression](PathExpression.md) | A path query | no |
diff --git a/_sources/datamodels/similarity/BestMatch.md.txt b/_sources/datamodels/similarity/BestMatch.md.txt
index 8e167938a..7ca3af363 100644
--- a/_sources/datamodels/similarity/BestMatch.md.txt
+++ b/_sources/datamodels/similarity/BestMatch.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: BestMatch
diff --git a/_sources/datamodels/similarity/PairwiseSimilarity.md.txt b/_sources/datamodels/similarity/PairwiseSimilarity.md.txt
index 59aee0d94..0d66adcc7 100644
--- a/_sources/datamodels/similarity/PairwiseSimilarity.md.txt
+++ b/_sources/datamodels/similarity/PairwiseSimilarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PairwiseSimilarity
diff --git a/_sources/datamodels/similarity/TermInfo.md.txt b/_sources/datamodels/similarity/TermInfo.md.txt
index dcddee556..1412f5288 100644
--- a/_sources/datamodels/similarity/TermInfo.md.txt
+++ b/_sources/datamodels/similarity/TermInfo.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TermInfo
diff --git a/_sources/datamodels/similarity/TermPairwiseSimilarity.md.txt b/_sources/datamodels/similarity/TermPairwiseSimilarity.md.txt
index 584a74fd2..d3de1f228 100644
--- a/_sources/datamodels/similarity/TermPairwiseSimilarity.md.txt
+++ b/_sources/datamodels/similarity/TermPairwiseSimilarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TermPairwiseSimilarity
diff --git a/_sources/datamodels/similarity/TermSetPairwiseSimilarity.md.txt b/_sources/datamodels/similarity/TermSetPairwiseSimilarity.md.txt
index b94648bca..b2bb8f8a1 100644
--- a/_sources/datamodels/similarity/TermSetPairwiseSimilarity.md.txt
+++ b/_sources/datamodels/similarity/TermSetPairwiseSimilarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TermSetPairwiseSimilarity
diff --git a/_sources/datamodels/similarity/ancestor_id.md.txt b/_sources/datamodels/similarity/ancestor_id.md.txt
index 93cd74762..0c3c405a0 100644
--- a/_sources/datamodels/similarity/ancestor_id.md.txt
+++ b/_sources/datamodels/similarity/ancestor_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_id
@@ -14,11 +16,12 @@ URI: [sim:ancestor_id](https://w3id.org/linkml/similarity/ancestor_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/ancestor_information_content.md.txt b/_sources/datamodels/similarity/ancestor_information_content.md.txt
index 102d5dc39..e2c6b37f3 100644
--- a/_sources/datamodels/similarity/ancestor_information_content.md.txt
+++ b/_sources/datamodels/similarity/ancestor_information_content.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_information_content
@@ -20,11 +22,12 @@ URI: [sim:ancestor_information_content](https://w3id.org/linkml/similarity/ances
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/ancestor_label.md.txt b/_sources/datamodels/similarity/ancestor_label.md.txt
index 50c367638..a32b82c9b 100644
--- a/_sources/datamodels/similarity/ancestor_label.md.txt
+++ b/_sources/datamodels/similarity/ancestor_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_label
@@ -14,11 +16,12 @@ URI: [sim:ancestor_label](https://w3id.org/linkml/similarity/ancestor_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/ancestor_source.md.txt b/_sources/datamodels/similarity/ancestor_source.md.txt
index 935047a86..d4794d408 100644
--- a/_sources/datamodels/similarity/ancestor_source.md.txt
+++ b/_sources/datamodels/similarity/ancestor_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_source
URI: [sim:ancestor_source](https://w3id.org/linkml/similarity/ancestor_source)
@@ -9,11 +11,12 @@ URI: [sim:ancestor_source](https://w3id.org/linkml/similarity/ancestor_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/average_score.md.txt b/_sources/datamodels/similarity/average_score.md.txt
index 5e6675ab9..39d9f5dfb 100644
--- a/_sources/datamodels/similarity/average_score.md.txt
+++ b/_sources/datamodels/similarity/average_score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: average_score
URI: [sim:average_score](https://w3id.org/linkml/similarity/average_score)
@@ -9,11 +11,12 @@ URI: [sim:average_score](https://w3id.org/linkml/similarity/average_score)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/best_score.md.txt b/_sources/datamodels/similarity/best_score.md.txt
index 9a9acc0df..4ec65e33e 100644
--- a/_sources/datamodels/similarity/best_score.md.txt
+++ b/_sources/datamodels/similarity/best_score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: best_score
URI: [sim:best_score](https://w3id.org/linkml/similarity/best_score)
@@ -9,11 +11,12 @@ URI: [sim:best_score](https://w3id.org/linkml/similarity/best_score)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/cosine_similarity.md.txt b/_sources/datamodels/similarity/cosine_similarity.md.txt
index c6afaef98..1d96b70d7 100644
--- a/_sources/datamodels/similarity/cosine_similarity.md.txt
+++ b/_sources/datamodels/similarity/cosine_similarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: cosine_similarity
@@ -19,11 +21,12 @@ URI: [sim:cosine_similarity](https://w3id.org/linkml/similarity/cosine_similarit
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/dice_similarity.md.txt b/_sources/datamodels/similarity/dice_similarity.md.txt
index 1d8a60372..e08d7ffe4 100644
--- a/_sources/datamodels/similarity/dice_similarity.md.txt
+++ b/_sources/datamodels/similarity/dice_similarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: dice_similarity
URI: [sim:dice_similarity](https://w3id.org/linkml/similarity/dice_similarity)
@@ -14,11 +16,12 @@ URI: [sim:dice_similarity](https://w3id.org/linkml/similarity/dice_similarity)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/id.md.txt b/_sources/datamodels/similarity/id.md.txt
index a29e15e08..7dc97abc7 100644
--- a/_sources/datamodels/similarity/id.md.txt
+++ b/_sources/datamodels/similarity/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
URI: [sim:id](https://w3id.org/linkml/similarity/id)
@@ -9,11 +11,12 @@ URI: [sim:id](https://w3id.org/linkml/similarity/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermInfo](TermInfo.md) | | no |
+| [TermInfo](TermInfo.md) | | no |
diff --git a/_sources/datamodels/similarity/information_content.md.txt b/_sources/datamodels/similarity/information_content.md.txt
index 7b1d42b8c..c37bf831d 100644
--- a/_sources/datamodels/similarity/information_content.md.txt
+++ b/_sources/datamodels/similarity/information_content.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: information_content
@@ -25,6 +27,7 @@ URI: [sim:information_content](https://w3id.org/linkml/similarity/information_co
+
## Properties
* Range: [NegativeLogValue](NegativeLogValue.md)
diff --git a/_sources/datamodels/similarity/intersection_count.md.txt b/_sources/datamodels/similarity/intersection_count.md.txt
index fd88642e6..4f5e208df 100644
--- a/_sources/datamodels/similarity/intersection_count.md.txt
+++ b/_sources/datamodels/similarity/intersection_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: intersection_count
URI: [sim:intersection_count](https://w3id.org/linkml/similarity/intersection_count)
@@ -17,6 +19,7 @@ URI: [sim:intersection_count](https://w3id.org/linkml/similarity/intersection_co
+
## Properties
* Range: [ItemCount](ItemCount.md)
diff --git a/_sources/datamodels/similarity/jaccard_similarity.md.txt b/_sources/datamodels/similarity/jaccard_similarity.md.txt
index d7ea1fc9f..eff67f0ae 100644
--- a/_sources/datamodels/similarity/jaccard_similarity.md.txt
+++ b/_sources/datamodels/similarity/jaccard_similarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: jaccard_similarity
@@ -19,11 +21,12 @@ URI: [sim:jaccard_similarity](https://w3id.org/linkml/similarity/jaccard_similar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/label.md.txt b/_sources/datamodels/similarity/label.md.txt
index 1f740bff6..af4100f34 100644
--- a/_sources/datamodels/similarity/label.md.txt
+++ b/_sources/datamodels/similarity/label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: label
URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
@@ -9,11 +11,12 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermInfo](TermInfo.md) | | no |
+| [TermInfo](TermInfo.md) | | no |
diff --git a/_sources/datamodels/similarity/match_source.md.txt b/_sources/datamodels/similarity/match_source.md.txt
index 6d4ec0387..b356de926 100644
--- a/_sources/datamodels/similarity/match_source.md.txt
+++ b/_sources/datamodels/similarity/match_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_source
URI: [sim:match_source](https://w3id.org/linkml/similarity/match_source)
@@ -9,11 +11,12 @@ URI: [sim:match_source](https://w3id.org/linkml/similarity/match_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/match_source_label.md.txt b/_sources/datamodels/similarity/match_source_label.md.txt
index a903fa8df..2b2f23250 100644
--- a/_sources/datamodels/similarity/match_source_label.md.txt
+++ b/_sources/datamodels/similarity/match_source_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_source_label
URI: [sim:match_source_label](https://w3id.org/linkml/similarity/match_source_label)
@@ -9,11 +11,12 @@ URI: [sim:match_source_label](https://w3id.org/linkml/similarity/match_source_la
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/match_subsumer.md.txt b/_sources/datamodels/similarity/match_subsumer.md.txt
index 12a289f9f..4653b4e81 100644
--- a/_sources/datamodels/similarity/match_subsumer.md.txt
+++ b/_sources/datamodels/similarity/match_subsumer.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_subsumer
URI: [sim:match_subsumer](https://w3id.org/linkml/similarity/match_subsumer)
@@ -9,11 +11,12 @@ URI: [sim:match_subsumer](https://w3id.org/linkml/similarity/match_subsumer)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/match_subsumer_label.md.txt b/_sources/datamodels/similarity/match_subsumer_label.md.txt
index 2a2a797ef..55f804700 100644
--- a/_sources/datamodels/similarity/match_subsumer_label.md.txt
+++ b/_sources/datamodels/similarity/match_subsumer_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_subsumer_label
URI: [sim:match_subsumer_label](https://w3id.org/linkml/similarity/match_subsumer_label)
@@ -9,11 +11,12 @@ URI: [sim:match_subsumer_label](https://w3id.org/linkml/similarity/match_subsume
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/match_target.md.txt b/_sources/datamodels/similarity/match_target.md.txt
index 9ddd9809a..52cb7e678 100644
--- a/_sources/datamodels/similarity/match_target.md.txt
+++ b/_sources/datamodels/similarity/match_target.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_target
@@ -14,11 +16,12 @@ URI: [sim:match_target](https://w3id.org/linkml/similarity/match_target)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/match_target_label.md.txt b/_sources/datamodels/similarity/match_target_label.md.txt
index 9ff9f4f05..824e303bb 100644
--- a/_sources/datamodels/similarity/match_target_label.md.txt
+++ b/_sources/datamodels/similarity/match_target_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_target_label
URI: [sim:match_target_label](https://w3id.org/linkml/similarity/match_target_label)
@@ -9,11 +11,12 @@ URI: [sim:match_target_label](https://w3id.org/linkml/similarity/match_target_la
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/metric.md.txt b/_sources/datamodels/similarity/metric.md.txt
index 94ef29e88..4ecfe85b4 100644
--- a/_sources/datamodels/similarity/metric.md.txt
+++ b/_sources/datamodels/similarity/metric.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: metric
URI: [sim:metric](https://w3id.org/linkml/similarity/metric)
@@ -9,11 +11,12 @@ URI: [sim:metric](https://w3id.org/linkml/similarity/metric)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_best_matches.md.txt b/_sources/datamodels/similarity/object_best_matches.md.txt
index c36bc5df5..4e6b1b0d6 100644
--- a/_sources/datamodels/similarity/object_best_matches.md.txt
+++ b/_sources/datamodels/similarity/object_best_matches.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_best_matches
URI: [sim:object_best_matches](https://w3id.org/linkml/similarity/object_best_matches)
@@ -9,11 +11,12 @@ URI: [sim:object_best_matches](https://w3id.org/linkml/similarity/object_best_ma
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_id.md.txt b/_sources/datamodels/similarity/object_id.md.txt
index 329e66c85..fb2aece3b 100644
--- a/_sources/datamodels/similarity/object_id.md.txt
+++ b/_sources/datamodels/similarity/object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_id
@@ -14,11 +16,12 @@ URI: [sssom:object_id](http://w3id.org/sssom/object_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_information_content.md.txt b/_sources/datamodels/similarity/object_information_content.md.txt
index 59d46dc87..a049177f6 100644
--- a/_sources/datamodels/similarity/object_information_content.md.txt
+++ b/_sources/datamodels/similarity/object_information_content.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_information_content
@@ -20,11 +22,12 @@ URI: [sim:object_information_content](https://w3id.org/linkml/similarity/object_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_label.md.txt b/_sources/datamodels/similarity/object_label.md.txt
index 59265a5fb..73236cd00 100644
--- a/_sources/datamodels/similarity/object_label.md.txt
+++ b/_sources/datamodels/similarity/object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_label
@@ -14,11 +16,12 @@ URI: [sssom:object_label](http://w3id.org/sssom/object_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_source.md.txt b/_sources/datamodels/similarity/object_source.md.txt
index 478599411..a4a60ba17 100644
--- a/_sources/datamodels/similarity/object_source.md.txt
+++ b/_sources/datamodels/similarity/object_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_source
@@ -14,11 +16,12 @@ URI: [sssom:object_source](http://w3id.org/sssom/object_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/object_termset.md.txt b/_sources/datamodels/similarity/object_termset.md.txt
index 8c57f4537..24d58d47a 100644
--- a/_sources/datamodels/similarity/object_termset.md.txt
+++ b/_sources/datamodels/similarity/object_termset.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_termset
URI: [sim:object_termset](https://w3id.org/linkml/similarity/object_termset)
@@ -9,11 +11,12 @@ URI: [sim:object_termset](https://w3id.org/linkml/similarity/object_termset)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/overlap_coefficient.md.txt b/_sources/datamodels/similarity/overlap_coefficient.md.txt
index a80aea6a7..b585b7f36 100644
--- a/_sources/datamodels/similarity/overlap_coefficient.md.txt
+++ b/_sources/datamodels/similarity/overlap_coefficient.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: overlap_coefficient
URI: [sim:overlap_coefficient](https://w3id.org/linkml/similarity/overlap_coefficient)
@@ -17,6 +19,7 @@ URI: [sim:overlap_coefficient](https://w3id.org/linkml/similarity/overlap_coeffi
+
## Properties
* Range: [ZeroToOne](ZeroToOne.md)
diff --git a/_sources/datamodels/similarity/phenodigm_score.md.txt b/_sources/datamodels/similarity/phenodigm_score.md.txt
index 3110fbd85..ba9facd2f 100644
--- a/_sources/datamodels/similarity/phenodigm_score.md.txt
+++ b/_sources/datamodels/similarity/phenodigm_score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: phenodigm_score
@@ -19,11 +21,12 @@ URI: [sim:phenodigm_score](https://w3id.org/linkml/similarity/phenodigm_score)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/score.md.txt b/_sources/datamodels/similarity/score.md.txt
index e5481ffb1..20c3e5981 100644
--- a/_sources/datamodels/similarity/score.md.txt
+++ b/_sources/datamodels/similarity/score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: score
@@ -28,11 +30,12 @@ URI: [sim:score](https://w3id.org/linkml/similarity/score)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/similarity.md.txt b/_sources/datamodels/similarity/similarity.md.txt
index e7521b367..019416b67 100644
--- a/_sources/datamodels/similarity/similarity.md.txt
+++ b/_sources/datamodels/similarity/similarity.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: similarity
URI: [sim:similarity](https://w3id.org/linkml/similarity/similarity)
@@ -9,11 +11,12 @@ URI: [sim:similarity](https://w3id.org/linkml/similarity/similarity)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[BestMatch](BestMatch.md) | | no |
+| [BestMatch](BestMatch.md) | | no |
diff --git a/_sources/datamodels/similarity/subject_best_matches.md.txt b/_sources/datamodels/similarity/subject_best_matches.md.txt
index c61e65cc3..dc071fb3e 100644
--- a/_sources/datamodels/similarity/subject_best_matches.md.txt
+++ b/_sources/datamodels/similarity/subject_best_matches.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_best_matches
URI: [sim:subject_best_matches](https://w3id.org/linkml/similarity/subject_best_matches)
@@ -9,11 +11,12 @@ URI: [sim:subject_best_matches](https://w3id.org/linkml/similarity/subject_best_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subject_id.md.txt b/_sources/datamodels/similarity/subject_id.md.txt
index e08188286..872233000 100644
--- a/_sources/datamodels/similarity/subject_id.md.txt
+++ b/_sources/datamodels/similarity/subject_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_id
@@ -14,11 +16,12 @@ URI: [sssom:subject_id](http://w3id.org/sssom/subject_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subject_information_content.md.txt b/_sources/datamodels/similarity/subject_information_content.md.txt
index b2ab83b14..ec0f31e96 100644
--- a/_sources/datamodels/similarity/subject_information_content.md.txt
+++ b/_sources/datamodels/similarity/subject_information_content.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_information_content
@@ -20,11 +22,12 @@ URI: [sim:subject_information_content](https://w3id.org/linkml/similarity/subjec
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subject_label.md.txt b/_sources/datamodels/similarity/subject_label.md.txt
index f3245495d..7c21e003e 100644
--- a/_sources/datamodels/similarity/subject_label.md.txt
+++ b/_sources/datamodels/similarity/subject_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_label
@@ -14,11 +16,12 @@ URI: [sssom:subject_label](http://w3id.org/sssom/subject_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subject_source.md.txt b/_sources/datamodels/similarity/subject_source.md.txt
index 6583068c4..9578677f8 100644
--- a/_sources/datamodels/similarity/subject_source.md.txt
+++ b/_sources/datamodels/similarity/subject_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_source
@@ -14,11 +16,12 @@ URI: [sssom:subject_source](http://w3id.org/sssom/subject_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
+| [TermPairwiseSimilarity](TermPairwiseSimilarity.md) | A simple pairwise similarity between two atomic concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subject_termset.md.txt b/_sources/datamodels/similarity/subject_termset.md.txt
index bbe42b54a..e1d75acfd 100644
--- a/_sources/datamodels/similarity/subject_termset.md.txt
+++ b/_sources/datamodels/similarity/subject_termset.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_termset
URI: [sim:subject_termset](https://w3id.org/linkml/similarity/subject_termset)
@@ -9,11 +11,12 @@ URI: [sim:subject_termset](https://w3id.org/linkml/similarity/subject_termset)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
+| [TermSetPairwiseSimilarity](TermSetPairwiseSimilarity.md) | A simple pairwise similarity between two sets of concepts/terms | no |
diff --git a/_sources/datamodels/similarity/subsumed_by_score.md.txt b/_sources/datamodels/similarity/subsumed_by_score.md.txt
index be047a399..3e293b17d 100644
--- a/_sources/datamodels/similarity/subsumed_by_score.md.txt
+++ b/_sources/datamodels/similarity/subsumed_by_score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subsumed_by_score
URI: [sim:subsumed_by_score](https://w3id.org/linkml/similarity/subsumed_by_score)
@@ -17,6 +19,7 @@ URI: [sim:subsumed_by_score](https://w3id.org/linkml/similarity/subsumed_by_scor
+
## Properties
* Range: [ZeroToOne](ZeroToOne.md)
diff --git a/_sources/datamodels/similarity/subsumes_score.md.txt b/_sources/datamodels/similarity/subsumes_score.md.txt
index af0cd037f..5179f63ae 100644
--- a/_sources/datamodels/similarity/subsumes_score.md.txt
+++ b/_sources/datamodels/similarity/subsumes_score.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subsumes_score
URI: [sim:subsumes_score](https://w3id.org/linkml/similarity/subsumes_score)
@@ -17,6 +19,7 @@ URI: [sim:subsumes_score](https://w3id.org/linkml/similarity/subsumes_score)
+
## Properties
* Range: [ZeroToOne](ZeroToOne.md)
diff --git a/_sources/datamodels/similarity/union_count.md.txt b/_sources/datamodels/similarity/union_count.md.txt
index e228d8dad..686c78463 100644
--- a/_sources/datamodels/similarity/union_count.md.txt
+++ b/_sources/datamodels/similarity/union_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: union_count
URI: [sim:union_count](https://w3id.org/linkml/similarity/union_count)
@@ -17,6 +19,7 @@ URI: [sim:union_count](https://w3id.org/linkml/similarity/union_count)
+
## Properties
* Range: [ItemCount](ItemCount.md)
diff --git a/_sources/datamodels/summary-statistics/Agent.md.txt b/_sources/datamodels/summary-statistics/Agent.md.txt
index c96556b6c..f9afb2f40 100644
--- a/_sources/datamodels/summary-statistics/Agent.md.txt
+++ b/_sources/datamodels/summary-statistics/Agent.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Agent
diff --git a/_sources/datamodels/summary-statistics/ChangeTypeStatistic.md.txt b/_sources/datamodels/summary-statistics/ChangeTypeStatistic.md.txt
index dbb14f199..e1203ec9b 100644
--- a/_sources/datamodels/summary-statistics/ChangeTypeStatistic.md.txt
+++ b/_sources/datamodels/summary-statistics/ChangeTypeStatistic.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ChangeTypeStatistic
diff --git a/_sources/datamodels/summary-statistics/ContributorRole.md.txt b/_sources/datamodels/summary-statistics/ContributorRole.md.txt
index aebc5c46a..c37508862 100644
--- a/_sources/datamodels/summary-statistics/ContributorRole.md.txt
+++ b/_sources/datamodels/summary-statistics/ContributorRole.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ContributorRole
diff --git a/_sources/datamodels/summary-statistics/ContributorStatistics.md.txt b/_sources/datamodels/summary-statistics/ContributorStatistics.md.txt
index 50e9f4f45..13a09b472 100644
--- a/_sources/datamodels/summary-statistics/ContributorStatistics.md.txt
+++ b/_sources/datamodels/summary-statistics/ContributorStatistics.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ContributorStatistics
diff --git a/_sources/datamodels/summary-statistics/FacetedCount.md.txt b/_sources/datamodels/summary-statistics/FacetedCount.md.txt
index 542f6d925..119dbf608 100644
--- a/_sources/datamodels/summary-statistics/FacetedCount.md.txt
+++ b/_sources/datamodels/summary-statistics/FacetedCount.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: FacetedCount
diff --git a/_sources/datamodels/summary-statistics/GroupedStatistics.md.txt b/_sources/datamodels/summary-statistics/GroupedStatistics.md.txt
index 3e57d8cd6..e44132031 100644
--- a/_sources/datamodels/summary-statistics/GroupedStatistics.md.txt
+++ b/_sources/datamodels/summary-statistics/GroupedStatistics.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: GroupedStatistics
diff --git a/_sources/datamodels/summary-statistics/Ontology.md.txt b/_sources/datamodels/summary-statistics/Ontology.md.txt
index 1dfd995d8..4a20e1e90 100644
--- a/_sources/datamodels/summary-statistics/Ontology.md.txt
+++ b/_sources/datamodels/summary-statistics/Ontology.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Ontology
diff --git a/_sources/datamodels/summary-statistics/SummaryStatisticsCalculationActivity.md.txt b/_sources/datamodels/summary-statistics/SummaryStatisticsCalculationActivity.md.txt
index fcbfecd57..c8d0ca7db 100644
--- a/_sources/datamodels/summary-statistics/SummaryStatisticsCalculationActivity.md.txt
+++ b/_sources/datamodels/summary-statistics/SummaryStatisticsCalculationActivity.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SummaryStatisticsCalculationActivity
diff --git a/_sources/datamodels/summary-statistics/SummaryStatisticsReport.md.txt b/_sources/datamodels/summary-statistics/SummaryStatisticsReport.md.txt
index e9aaf849a..ba64e2009 100644
--- a/_sources/datamodels/summary-statistics/SummaryStatisticsReport.md.txt
+++ b/_sources/datamodels/summary-statistics/SummaryStatisticsReport.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SummaryStatisticsReport
diff --git a/_sources/datamodels/summary-statistics/UngroupedStatistics.md.txt b/_sources/datamodels/summary-statistics/UngroupedStatistics.md.txt
index 40965b48a..657109f14 100644
--- a/_sources/datamodels/summary-statistics/UngroupedStatistics.md.txt
+++ b/_sources/datamodels/summary-statistics/UngroupedStatistics.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: UngroupedStatistics
diff --git a/_sources/datamodels/summary-statistics/acted_on_behalf_of.md.txt b/_sources/datamodels/summary-statistics/acted_on_behalf_of.md.txt
index cdac9c69b..61b7bfd77 100644
--- a/_sources/datamodels/summary-statistics/acted_on_behalf_of.md.txt
+++ b/_sources/datamodels/summary-statistics/acted_on_behalf_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: acted_on_behalf_of
@@ -14,11 +16,12 @@ URI: [prov:actedOnBehalfOf](http://www.w3.org/ns/prov#actedOnBehalfOf)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
+| [SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
diff --git a/_sources/datamodels/summary-statistics/agents.md.txt b/_sources/datamodels/summary-statistics/agents.md.txt
index e078484eb..aa492661a 100644
--- a/_sources/datamodels/summary-statistics/agents.md.txt
+++ b/_sources/datamodels/summary-statistics/agents.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: agents
@@ -14,13 +16,14 @@ URI: [summary_statistics:agents](https://w3id.org/oaklib/summary_statistics.agen
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/summary-statistics/annotation_property_count.md.txt b/_sources/datamodels/summary-statistics/annotation_property_count.md.txt
index d96323756..54321574d 100644
--- a/_sources/datamodels/summary-statistics/annotation_property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/annotation_property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: annotation_property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:annotation_property_count](https://w3id.org/oaklib/summ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/anonymous_class_expression_count.md.txt b/_sources/datamodels/summary-statistics/anonymous_class_expression_count.md.txt
index 1589a4dcf..0460043fc 100644
--- a/_sources/datamodels/summary-statistics/anonymous_class_expression_count.md.txt
+++ b/_sources/datamodels/summary-statistics/anonymous_class_expression_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: anonymous_class_expression_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:anonymous_class_expression_count](https://w3id.org/oakl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/anonymous_individual_count.md.txt b/_sources/datamodels/summary-statistics/anonymous_individual_count.md.txt
index 730c2bf90..20909ba1f 100644
--- a/_sources/datamodels/summary-statistics/anonymous_individual_count.md.txt
+++ b/_sources/datamodels/summary-statistics/anonymous_individual_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: anonymous_individual_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:anonymous_individual_count](https://w3id.org/oaklib/sum
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/change_summary.md.txt b/_sources/datamodels/summary-statistics/change_summary.md.txt
index f95364699..7d1fd7cfd 100644
--- a/_sources/datamodels/summary-statistics/change_summary.md.txt
+++ b/_sources/datamodels/summary-statistics/change_summary.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: change_summary
@@ -14,11 +16,12 @@ URI: [summary_statistics:change_summary](https://w3id.org/oaklib/summary_statist
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_count.md.txt b/_sources/datamodels/summary-statistics/class_count.md.txt
index a99feea79..a81711d4b 100644
--- a/_sources/datamodels/summary-statistics/class_count.md.txt
+++ b/_sources/datamodels/summary-statistics/class_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:class_count](https://w3id.org/oaklib/summary_statistics
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_count_by_category.md.txt b/_sources/datamodels/summary-statistics/class_count_by_category.md.txt
index be3856484..49d7e7563 100644
--- a/_sources/datamodels/summary-statistics/class_count_by_category.md.txt
+++ b/_sources/datamodels/summary-statistics/class_count_by_category.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_count_by_category
@@ -14,11 +16,12 @@ URI: [summary_statistics:class_count_by_category](https://w3id.org/oaklib/summar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_count_by_subset.md.txt b/_sources/datamodels/summary-statistics/class_count_by_subset.md.txt
index a304ffb0d..dbeddfbaa 100644
--- a/_sources/datamodels/summary-statistics/class_count_by_subset.md.txt
+++ b/_sources/datamodels/summary-statistics/class_count_by_subset.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_count_by_subset
@@ -14,11 +16,12 @@ URI: [summary_statistics:class_count_by_subset](https://w3id.org/oaklib/summary_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_count_with_text_definitions.md.txt b/_sources/datamodels/summary-statistics/class_count_with_text_definitions.md.txt
index da640a0d6..a37ec3392 100644
--- a/_sources/datamodels/summary-statistics/class_count_with_text_definitions.md.txt
+++ b/_sources/datamodels/summary-statistics/class_count_with_text_definitions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_count_with_text_definitions
@@ -19,11 +21,12 @@ URI: [summary_statistics:class_count_with_text_definitions](https://w3id.org/oak
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_count_without_text_definitions.md.txt b/_sources/datamodels/summary-statistics/class_count_without_text_definitions.md.txt
index 7c9fca698..3e61e9dd3 100644
--- a/_sources/datamodels/summary-statistics/class_count_without_text_definitions.md.txt
+++ b/_sources/datamodels/summary-statistics/class_count_without_text_definitions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_count_without_text_definitions
@@ -19,11 +21,12 @@ URI: [summary_statistics:class_count_without_text_definitions](https://w3id.org/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/class_statistic_group.md.txt b/_sources/datamodels/summary-statistics/class_statistic_group.md.txt
index f0d23ac0e..e6b97e33c 100644
--- a/_sources/datamodels/summary-statistics/class_statistic_group.md.txt
+++ b/_sources/datamodels/summary-statistics/class_statistic_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: class_statistic_group
URI: [summary_statistics:class_statistic_group](https://w3id.org/oaklib/summary_statistics.class_statistic_group)
@@ -12,6 +14,7 @@ URI: [summary_statistics:class_statistic_group](https://w3id.org/oaklib/summary_
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/summary-statistics/compared_with.md.txt b/_sources/datamodels/summary-statistics/compared_with.md.txt
index 173f32c25..038302f2c 100644
--- a/_sources/datamodels/summary-statistics/compared_with.md.txt
+++ b/_sources/datamodels/summary-statistics/compared_with.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: compared_with
@@ -14,13 +16,14 @@ URI: [summary_statistics:compared_with](https://w3id.org/oaklib/summary_statisti
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/summary-statistics/contributor_id.md.txt b/_sources/datamodels/summary-statistics/contributor_id.md.txt
index 6e842c6d2..8e55a3143 100644
--- a/_sources/datamodels/summary-statistics/contributor_id.md.txt
+++ b/_sources/datamodels/summary-statistics/contributor_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: contributor_id
@@ -14,11 +16,12 @@ URI: [summary_statistics:contributor_id](https://w3id.org/oaklib/summary_statist
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
+| [ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
diff --git a/_sources/datamodels/summary-statistics/contributor_name.md.txt b/_sources/datamodels/summary-statistics/contributor_name.md.txt
index ea9ed3e04..91140e207 100644
--- a/_sources/datamodels/summary-statistics/contributor_name.md.txt
+++ b/_sources/datamodels/summary-statistics/contributor_name.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: contributor_name
@@ -14,11 +16,12 @@ URI: [summary_statistics:contributor_name](https://w3id.org/oaklib/summary_stati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
+| [ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
diff --git a/_sources/datamodels/summary-statistics/contributor_summary.md.txt b/_sources/datamodels/summary-statistics/contributor_summary.md.txt
index 0a1003fba..f61d339e2 100644
--- a/_sources/datamodels/summary-statistics/contributor_summary.md.txt
+++ b/_sources/datamodels/summary-statistics/contributor_summary.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: contributor_summary
URI: [summary_statistics:contributor_summary](https://w3id.org/oaklib/summary_statistics.contributor_summary)
@@ -9,11 +11,12 @@ URI: [summary_statistics:contributor_summary](https://w3id.org/oaklib/summary_st
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/count_statistic.md.txt b/_sources/datamodels/summary-statistics/count_statistic.md.txt
index 6f21b3b1f..a2d6e3bdf 100644
--- a/_sources/datamodels/summary-statistics/count_statistic.md.txt
+++ b/_sources/datamodels/summary-statistics/count_statistic.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: count_statistic
URI: [summary_statistics:count_statistic](https://w3id.org/oaklib/summary_statistics.count_statistic)
@@ -43,6 +45,7 @@ URI: [summary_statistics:count_statistic](https://w3id.org/oaklib/summary_statis
+
## Properties
* Range: [Integer](Integer.md)
diff --git a/_sources/datamodels/summary-statistics/datatype_property_count.md.txt b/_sources/datamodels/summary-statistics/datatype_property_count.md.txt
index 151669baf..f1e7623f5 100644
--- a/_sources/datamodels/summary-statistics/datatype_property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/datatype_property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: datatype_property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:datatype_property_count](https://w3id.org/oaklib/summar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/deprecated_class_count.md.txt b/_sources/datamodels/summary-statistics/deprecated_class_count.md.txt
index 221531869..e2f3b1481 100644
--- a/_sources/datamodels/summary-statistics/deprecated_class_count.md.txt
+++ b/_sources/datamodels/summary-statistics/deprecated_class_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: deprecated_class_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:deprecated_class_count](https://w3id.org/oaklib/summary
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/deprecated_object_property_count.md.txt b/_sources/datamodels/summary-statistics/deprecated_object_property_count.md.txt
index eb1356f22..a0a3c318a 100644
--- a/_sources/datamodels/summary-statistics/deprecated_object_property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/deprecated_object_property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: deprecated_object_property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:deprecated_object_property_count](https://w3id.org/oakl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/description.md.txt b/_sources/datamodels/summary-statistics/description.md.txt
index 502a141b2..2f2fca4d9 100644
--- a/_sources/datamodels/summary-statistics/description.md.txt
+++ b/_sources/datamodels/summary-statistics/description.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: description
@@ -14,11 +16,12 @@ URI: [dcterms:description](http://purl.org/dc/terms/description)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An ontology | no |
+| [Ontology](Ontology.md) | An ontology | no |
diff --git a/_sources/datamodels/summary-statistics/description_logic_profile.md.txt b/_sources/datamodels/summary-statistics/description_logic_profile.md.txt
index 377283d57..cff7fa7df 100644
--- a/_sources/datamodels/summary-statistics/description_logic_profile.md.txt
+++ b/_sources/datamodels/summary-statistics/description_logic_profile.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: description_logic_profile
@@ -14,11 +16,12 @@ URI: [summary_statistics:description_logic_profile](https://w3id.org/oaklib/summ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/distinct_synonym_count.md.txt b/_sources/datamodels/summary-statistics/distinct_synonym_count.md.txt
index c70533d1e..1c12f335d 100644
--- a/_sources/datamodels/summary-statistics/distinct_synonym_count.md.txt
+++ b/_sources/datamodels/summary-statistics/distinct_synonym_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: distinct_synonym_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:distinct_synonym_count](https://w3id.org/oaklib/summary
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/edge_count_by_predicate.md.txt b/_sources/datamodels/summary-statistics/edge_count_by_predicate.md.txt
index 410e148f6..db6b1c466 100644
--- a/_sources/datamodels/summary-statistics/edge_count_by_predicate.md.txt
+++ b/_sources/datamodels/summary-statistics/edge_count_by_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: edge_count_by_predicate
@@ -14,11 +16,12 @@ URI: [summary_statistics:edge_count_by_predicate](https://w3id.org/oaklib/summar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/ended_at_time.md.txt b/_sources/datamodels/summary-statistics/ended_at_time.md.txt
index 443d2c47d..dd0350bee 100644
--- a/_sources/datamodels/summary-statistics/ended_at_time.md.txt
+++ b/_sources/datamodels/summary-statistics/ended_at_time.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ended_at_time
@@ -14,11 +16,12 @@ URI: [prov:endedAtTime](http://www.w3.org/ns/prov#endedAtTime)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
+| [SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
diff --git a/_sources/datamodels/summary-statistics/entailed_edge_count_by_predicate.md.txt b/_sources/datamodels/summary-statistics/entailed_edge_count_by_predicate.md.txt
index 2c481e592..d81be912d 100644
--- a/_sources/datamodels/summary-statistics/entailed_edge_count_by_predicate.md.txt
+++ b/_sources/datamodels/summary-statistics/entailed_edge_count_by_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: entailed_edge_count_by_predicate
@@ -14,11 +16,12 @@ URI: [summary_statistics:entailed_edge_count_by_predicate](https://w3id.org/oakl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/equivalent_classes_axiom_count.md.txt b/_sources/datamodels/summary-statistics/equivalent_classes_axiom_count.md.txt
index eefc63fd7..420204178 100644
--- a/_sources/datamodels/summary-statistics/equivalent_classes_axiom_count.md.txt
+++ b/_sources/datamodels/summary-statistics/equivalent_classes_axiom_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: equivalent_classes_axiom_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:equivalent_classes_axiom_count](https://w3id.org/oaklib
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/facet.md.txt b/_sources/datamodels/summary-statistics/facet.md.txt
index a73b93923..f8e97e1c3 100644
--- a/_sources/datamodels/summary-statistics/facet.md.txt
+++ b/_sources/datamodels/summary-statistics/facet.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: facet
URI: [summary_statistics:facet](https://w3id.org/oaklib/summary_statistics.facet)
@@ -9,12 +11,13 @@ URI: [summary_statistics:facet](https://w3id.org/oaklib/summary_statistics.facet
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[FacetedCount](FacetedCount.md) | Counts broken down by a facet | no |
-[ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no |
+| [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no |
+| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no |
diff --git a/_sources/datamodels/summary-statistics/filtered_count.md.txt b/_sources/datamodels/summary-statistics/filtered_count.md.txt
index b316d2ca1..db4e278e2 100644
--- a/_sources/datamodels/summary-statistics/filtered_count.md.txt
+++ b/_sources/datamodels/summary-statistics/filtered_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: filtered_count
URI: [summary_statistics:filtered_count](https://w3id.org/oaklib/summary_statistics.filtered_count)
@@ -9,12 +11,13 @@ URI: [summary_statistics:filtered_count](https://w3id.org/oaklib/summary_statist
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[FacetedCount](FacetedCount.md) | Counts broken down by a facet | no |
-[ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no |
+| [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no |
+| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no |
diff --git a/_sources/datamodels/summary-statistics/id.md.txt b/_sources/datamodels/summary-statistics/id.md.txt
index bcef49b70..7b8590136 100644
--- a/_sources/datamodels/summary-statistics/id.md.txt
+++ b/_sources/datamodels/summary-statistics/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
URI: [summary_statistics:id](https://w3id.org/oaklib/summary_statistics.id)
@@ -9,16 +11,17 @@ URI: [summary_statistics:id](https://w3id.org/oaklib/summary_statistics.id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
-[Ontology](Ontology.md) | An ontology | no |
-[Agent](Agent.md) | An agent | no |
-[ContributorRole](ContributorRole.md) | A role that a contributor can have | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [ContributorRole](ContributorRole.md) | A role that a contributor can have | no |
+| [Ontology](Ontology.md) | An ontology | no |
+| [Agent](Agent.md) | An agent | no |
+| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/summary-statistics/individual_count.md.txt b/_sources/datamodels/summary-statistics/individual_count.md.txt
index 644a362ee..de815a5da 100644
--- a/_sources/datamodels/summary-statistics/individual_count.md.txt
+++ b/_sources/datamodels/summary-statistics/individual_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: individual_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:individual_count](https://w3id.org/oaklib/summary_stati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/individual_statistic_group.md.txt b/_sources/datamodels/summary-statistics/individual_statistic_group.md.txt
index f773f2a2d..796d4e68f 100644
--- a/_sources/datamodels/summary-statistics/individual_statistic_group.md.txt
+++ b/_sources/datamodels/summary-statistics/individual_statistic_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: individual_statistic_group
URI: [summary_statistics:individual_statistic_group](https://w3id.org/oaklib/summary_statistics.individual_statistic_group)
@@ -12,6 +14,7 @@ URI: [summary_statistics:individual_statistic_group](https://w3id.org/oaklib/sum
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/summary-statistics/label.md.txt b/_sources/datamodels/summary-statistics/label.md.txt
index f6db47c89..674de34b8 100644
--- a/_sources/datamodels/summary-statistics/label.md.txt
+++ b/_sources/datamodels/summary-statistics/label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: label
@@ -14,11 +16,12 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Agent](Agent.md) | An agent | no |
+| [Agent](Agent.md) | An agent | no |
diff --git a/_sources/datamodels/summary-statistics/mapping_count.md.txt b/_sources/datamodels/summary-statistics/mapping_count.md.txt
index f305ce2e3..486e39edc 100644
--- a/_sources/datamodels/summary-statistics/mapping_count.md.txt
+++ b/_sources/datamodels/summary-statistics/mapping_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: mapping_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:mapping_count](https://w3id.org/oaklib/summary_statisti
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/mapping_statement_count_by_object_source.md.txt b/_sources/datamodels/summary-statistics/mapping_statement_count_by_object_source.md.txt
index 5c972024e..435c2164d 100644
--- a/_sources/datamodels/summary-statistics/mapping_statement_count_by_object_source.md.txt
+++ b/_sources/datamodels/summary-statistics/mapping_statement_count_by_object_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: mapping_statement_count_by_object_source
@@ -14,11 +16,12 @@ URI: [summary_statistics:mapping_statement_count_by_object_source](https://w3id.
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/mapping_statement_count_by_predicate.md.txt b/_sources/datamodels/summary-statistics/mapping_statement_count_by_predicate.md.txt
index c221c4b70..159a4aca5 100644
--- a/_sources/datamodels/summary-statistics/mapping_statement_count_by_predicate.md.txt
+++ b/_sources/datamodels/summary-statistics/mapping_statement_count_by_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: mapping_statement_count_by_predicate
@@ -14,11 +16,12 @@ URI: [summary_statistics:mapping_statement_count_by_predicate](https://w3id.org/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/mapping_statement_count_subject_by_object_source.md.txt b/_sources/datamodels/summary-statistics/mapping_statement_count_subject_by_object_source.md.txt
index 34999211c..dfee7dfd0 100644
--- a/_sources/datamodels/summary-statistics/mapping_statement_count_subject_by_object_source.md.txt
+++ b/_sources/datamodels/summary-statistics/mapping_statement_count_subject_by_object_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: mapping_statement_count_subject_by_object_source
@@ -14,11 +16,12 @@ URI: [summary_statistics:mapping_statement_count_subject_by_object_source](https
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/merged_class_count.md.txt b/_sources/datamodels/summary-statistics/merged_class_count.md.txt
index 55a5776ed..ed9a5ceb5 100644
--- a/_sources/datamodels/summary-statistics/merged_class_count.md.txt
+++ b/_sources/datamodels/summary-statistics/merged_class_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: merged_class_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:merged_class_count](https://w3id.org/oaklib/summary_sta
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/metadata_statistic_group.md.txt b/_sources/datamodels/summary-statistics/metadata_statistic_group.md.txt
index a08d7f602..14698f10a 100644
--- a/_sources/datamodels/summary-statistics/metadata_statistic_group.md.txt
+++ b/_sources/datamodels/summary-statistics/metadata_statistic_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: metadata_statistic_group
URI: [summary_statistics:metadata_statistic_group](https://w3id.org/oaklib/summary_statistics.metadata_statistic_group)
@@ -12,6 +14,7 @@ URI: [summary_statistics:metadata_statistic_group](https://w3id.org/oaklib/summa
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/summary-statistics/named_individual_count.md.txt b/_sources/datamodels/summary-statistics/named_individual_count.md.txt
index 9ed46426a..9b6426b9a 100644
--- a/_sources/datamodels/summary-statistics/named_individual_count.md.txt
+++ b/_sources/datamodels/summary-statistics/named_individual_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: named_individual_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:named_individual_count](https://w3id.org/oaklib/summary
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/non_deprecated_class_count.md.txt b/_sources/datamodels/summary-statistics/non_deprecated_class_count.md.txt
index 34cbb3265..a5e96ed90 100644
--- a/_sources/datamodels/summary-statistics/non_deprecated_class_count.md.txt
+++ b/_sources/datamodels/summary-statistics/non_deprecated_class_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: non_deprecated_class_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:non_deprecated_class_count](https://w3id.org/oaklib/sum
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/non_deprecated_object_property_count.md.txt b/_sources/datamodels/summary-statistics/non_deprecated_object_property_count.md.txt
index 6b74acc94..eea281084 100644
--- a/_sources/datamodels/summary-statistics/non_deprecated_object_property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/non_deprecated_object_property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: non_deprecated_object_property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:non_deprecated_object_property_count](https://w3id.org/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/normalization_comments.md.txt b/_sources/datamodels/summary-statistics/normalization_comments.md.txt
index 60585a873..bc71ae426 100644
--- a/_sources/datamodels/summary-statistics/normalization_comments.md.txt
+++ b/_sources/datamodels/summary-statistics/normalization_comments.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: normalization_comments
@@ -14,11 +16,12 @@ URI: [summary_statistics:normalization_comments](https://w3id.org/oaklib/summary
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
+| [ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
diff --git a/_sources/datamodels/summary-statistics/object_property_count.md.txt b/_sources/datamodels/summary-statistics/object_property_count.md.txt
index 5771920cb..bc8c75482 100644
--- a/_sources/datamodels/summary-statistics/object_property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/object_property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:object_property_count](https://w3id.org/oaklib/summary_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/ontologies.md.txt b/_sources/datamodels/summary-statistics/ontologies.md.txt
index 1c89f44c8..1a6515a33 100644
--- a/_sources/datamodels/summary-statistics/ontologies.md.txt
+++ b/_sources/datamodels/summary-statistics/ontologies.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ontologies
@@ -14,13 +16,14 @@ URI: [summary_statistics:ontologies](https://w3id.org/oaklib/summary_statistics.
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/summary-statistics/ontology_count.md.txt b/_sources/datamodels/summary-statistics/ontology_count.md.txt
index e51670b1e..f1d9117d3 100644
--- a/_sources/datamodels/summary-statistics/ontology_count.md.txt
+++ b/_sources/datamodels/summary-statistics/ontology_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: ontology_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:ontology_count](https://w3id.org/oaklib/summary_statist
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/owl_axiom_count.md.txt b/_sources/datamodels/summary-statistics/owl_axiom_count.md.txt
index 8ebccd13f..51c123981 100644
--- a/_sources/datamodels/summary-statistics/owl_axiom_count.md.txt
+++ b/_sources/datamodels/summary-statistics/owl_axiom_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: owl_axiom_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:owl_axiom_count](https://w3id.org/oaklib/summary_statis
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/owl_statistic_group.md.txt b/_sources/datamodels/summary-statistics/owl_statistic_group.md.txt
index d0ea705e6..ceaa1c58f 100644
--- a/_sources/datamodels/summary-statistics/owl_statistic_group.md.txt
+++ b/_sources/datamodels/summary-statistics/owl_statistic_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: owl_statistic_group
URI: [summary_statistics:owl_statistic_group](https://w3id.org/oaklib/summary_statistics.owl_statistic_group)
@@ -12,6 +14,7 @@ URI: [summary_statistics:owl_statistic_group](https://w3id.org/oaklib/summary_st
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/summary-statistics/partitions.md.txt b/_sources/datamodels/summary-statistics/partitions.md.txt
index f1c04c0da..8ebe79527 100644
--- a/_sources/datamodels/summary-statistics/partitions.md.txt
+++ b/_sources/datamodels/summary-statistics/partitions.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: partitions
@@ -14,11 +16,12 @@ URI: [summary_statistics:partitions](https://w3id.org/oaklib/summary_statistics.
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/summary-statistics/prefix.md.txt b/_sources/datamodels/summary-statistics/prefix.md.txt
index 4d8112531..b151945ac 100644
--- a/_sources/datamodels/summary-statistics/prefix.md.txt
+++ b/_sources/datamodels/summary-statistics/prefix.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: prefix
@@ -14,11 +16,12 @@ URI: [sh:prefix](https://w3id.org/shacl/prefix)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An ontology | no |
+| [Ontology](Ontology.md) | An ontology | no |
diff --git a/_sources/datamodels/summary-statistics/property_count.md.txt b/_sources/datamodels/summary-statistics/property_count.md.txt
index ed445f1f1..c14b439df 100644
--- a/_sources/datamodels/summary-statistics/property_count.md.txt
+++ b/_sources/datamodels/summary-statistics/property_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: property_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:property_count](https://w3id.org/oaklib/summary_statist
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/property_statistic_group.md.txt b/_sources/datamodels/summary-statistics/property_statistic_group.md.txt
index 462092652..4703e9702 100644
--- a/_sources/datamodels/summary-statistics/property_statistic_group.md.txt
+++ b/_sources/datamodels/summary-statistics/property_statistic_group.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: property_statistic_group
URI: [summary_statistics:property_statistic_group](https://w3id.org/oaklib/summary_statistics.property_statistic_group)
@@ -12,6 +14,7 @@ URI: [summary_statistics:property_statistic_group](https://w3id.org/oaklib/summa
+
## Properties
* Range: [String](String.md)
diff --git a/_sources/datamodels/summary-statistics/rdf_triple_count.md.txt b/_sources/datamodels/summary-statistics/rdf_triple_count.md.txt
index 96e2b0878..6b8eb11db 100644
--- a/_sources/datamodels/summary-statistics/rdf_triple_count.md.txt
+++ b/_sources/datamodels/summary-statistics/rdf_triple_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: rdf_triple_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:rdf_triple_count](https://w3id.org/oaklib/summary_stati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/role_counts.md.txt b/_sources/datamodels/summary-statistics/role_counts.md.txt
index 5ea5a0af3..72811c388 100644
--- a/_sources/datamodels/summary-statistics/role_counts.md.txt
+++ b/_sources/datamodels/summary-statistics/role_counts.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: role_counts
URI: [summary_statistics:role_counts](https://w3id.org/oaklib/summary_statistics.role_counts)
@@ -9,11 +11,12 @@ URI: [summary_statistics:role_counts](https://w3id.org/oaklib/summary_statistics
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
+| [ContributorStatistics](ContributorStatistics.md) | Statistics for a contributor | no |
diff --git a/_sources/datamodels/summary-statistics/started_at_time.md.txt b/_sources/datamodels/summary-statistics/started_at_time.md.txt
index 3cad43f04..5648fb809 100644
--- a/_sources/datamodels/summary-statistics/started_at_time.md.txt
+++ b/_sources/datamodels/summary-statistics/started_at_time.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: started_at_time
@@ -14,11 +16,12 @@ URI: [prov:startedAtTime](http://www.w3.org/ns/prov#startedAtTime)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
+| [SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
diff --git a/_sources/datamodels/summary-statistics/subclass_of_axiom_count.md.txt b/_sources/datamodels/summary-statistics/subclass_of_axiom_count.md.txt
index 50815eb62..4195da48e 100644
--- a/_sources/datamodels/summary-statistics/subclass_of_axiom_count.md.txt
+++ b/_sources/datamodels/summary-statistics/subclass_of_axiom_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subclass_of_axiom_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:subclass_of_axiom_count](https://w3id.org/oaklib/summar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/subset_count.md.txt b/_sources/datamodels/summary-statistics/subset_count.md.txt
index 9c15fcdbf..4ed023b7e 100644
--- a/_sources/datamodels/summary-statistics/subset_count.md.txt
+++ b/_sources/datamodels/summary-statistics/subset_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subset_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:subset_count](https://w3id.org/oaklib/summary_statistic
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/synonym_statement_count.md.txt b/_sources/datamodels/summary-statistics/synonym_statement_count.md.txt
index c41299b19..6af0e4948 100644
--- a/_sources/datamodels/summary-statistics/synonym_statement_count.md.txt
+++ b/_sources/datamodels/summary-statistics/synonym_statement_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonym_statement_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:synonym_statement_count](https://w3id.org/oaklib/summar
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/synonym_statement_count_by_predicate.md.txt b/_sources/datamodels/summary-statistics/synonym_statement_count_by_predicate.md.txt
index 97e8a77df..aa83c052f 100644
--- a/_sources/datamodels/summary-statistics/synonym_statement_count_by_predicate.md.txt
+++ b/_sources/datamodels/summary-statistics/synonym_statement_count_by_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: synonym_statement_count_by_predicate
@@ -14,11 +16,12 @@ URI: [summary_statistics:synonym_statement_count_by_predicate](https://w3id.org/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/title.md.txt b/_sources/datamodels/summary-statistics/title.md.txt
index c9b7ea44e..4df17362f 100644
--- a/_sources/datamodels/summary-statistics/title.md.txt
+++ b/_sources/datamodels/summary-statistics/title.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: title
@@ -14,11 +16,12 @@ URI: [dcterms:title](http://purl.org/dc/terms/title)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An ontology | no |
+| [Ontology](Ontology.md) | An ontology | no |
diff --git a/_sources/datamodels/summary-statistics/unsatisfiable_class_count.md.txt b/_sources/datamodels/summary-statistics/unsatisfiable_class_count.md.txt
index 098bd72c1..015e1d036 100644
--- a/_sources/datamodels/summary-statistics/unsatisfiable_class_count.md.txt
+++ b/_sources/datamodels/summary-statistics/unsatisfiable_class_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: unsatisfiable_class_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:unsatisfiable_class_count](https://w3id.org/oaklib/summ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/untyped_entity_count.md.txt b/_sources/datamodels/summary-statistics/untyped_entity_count.md.txt
index 5369f6def..46782fda4 100644
--- a/_sources/datamodels/summary-statistics/untyped_entity_count.md.txt
+++ b/_sources/datamodels/summary-statistics/untyped_entity_count.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: untyped_entity_count
@@ -19,11 +21,12 @@ URI: [summary_statistics:untyped_entity_count](https://w3id.org/oaklib/summary_s
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
diff --git a/_sources/datamodels/summary-statistics/version.md.txt b/_sources/datamodels/summary-statistics/version.md.txt
index c4a2e2eb0..8dc1db92a 100644
--- a/_sources/datamodels/summary-statistics/version.md.txt
+++ b/_sources/datamodels/summary-statistics/version.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: version
@@ -14,11 +16,12 @@ URI: [owl:versionIRI](http://www.w3.org/2002/07/owl#versionIRI)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An ontology | no |
+| [Ontology](Ontology.md) | An ontology | no |
diff --git a/_sources/datamodels/summary-statistics/version_info.md.txt b/_sources/datamodels/summary-statistics/version_info.md.txt
index 74c5e95cc..ec3f167db 100644
--- a/_sources/datamodels/summary-statistics/version_info.md.txt
+++ b/_sources/datamodels/summary-statistics/version_info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: version_info
@@ -14,11 +16,12 @@ URI: [owl:versionInfo](http://www.w3.org/2002/07/owl#versionInfo)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Ontology](Ontology.md) | An ontology | no |
+| [Ontology](Ontology.md) | An ontology | no |
diff --git a/_sources/datamodels/summary-statistics/was_associated_with.md.txt b/_sources/datamodels/summary-statistics/was_associated_with.md.txt
index c46e120de..10a2a5414 100644
--- a/_sources/datamodels/summary-statistics/was_associated_with.md.txt
+++ b/_sources/datamodels/summary-statistics/was_associated_with.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: was_associated_with
@@ -14,11 +16,12 @@ URI: [prov:wasAssociatedWith](http://www.w3.org/ns/prov#wasAssociatedWith)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
+| [SummaryStatisticsCalculationActivity](SummaryStatisticsCalculationActivity.md) | An activity that calculates summary statistics for an ontology | no |
diff --git a/_sources/datamodels/summary-statistics/was_generated_by.md.txt b/_sources/datamodels/summary-statistics/was_generated_by.md.txt
index cdd0cb64e..144936119 100644
--- a/_sources/datamodels/summary-statistics/was_generated_by.md.txt
+++ b/_sources/datamodels/summary-statistics/was_generated_by.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: was_generated_by
@@ -14,13 +16,14 @@ URI: [summary_statistics:was_generated_by](https://w3id.org/oaklib/summary_stati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
-[GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
-[UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no |
+| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no |
+| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no |
diff --git a/_sources/datamodels/taxon-constraints/PredicateTerm.md.txt b/_sources/datamodels/taxon-constraints/PredicateTerm.md.txt
index 42c629a10..a69eb8c55 100644
--- a/_sources/datamodels/taxon-constraints/PredicateTerm.md.txt
+++ b/_sources/datamodels/taxon-constraints/PredicateTerm.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: PredicateTerm
diff --git a/_sources/datamodels/taxon-constraints/SubjectTerm.md.txt b/_sources/datamodels/taxon-constraints/SubjectTerm.md.txt
index de8b4ad7f..c2defe55c 100644
--- a/_sources/datamodels/taxon-constraints/SubjectTerm.md.txt
+++ b/_sources/datamodels/taxon-constraints/SubjectTerm.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: SubjectTerm
diff --git a/_sources/datamodels/taxon-constraints/Taxon.md.txt b/_sources/datamodels/taxon-constraints/Taxon.md.txt
index 0370c22e6..b14e516a0 100644
--- a/_sources/datamodels/taxon-constraints/Taxon.md.txt
+++ b/_sources/datamodels/taxon-constraints/Taxon.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Taxon
diff --git a/_sources/datamodels/taxon-constraints/TaxonConstraint.md.txt b/_sources/datamodels/taxon-constraints/TaxonConstraint.md.txt
index bda23b9da..482cb9070 100644
--- a/_sources/datamodels/taxon-constraints/TaxonConstraint.md.txt
+++ b/_sources/datamodels/taxon-constraints/TaxonConstraint.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TaxonConstraint
diff --git a/_sources/datamodels/taxon-constraints/Term.md.txt b/_sources/datamodels/taxon-constraints/Term.md.txt
index 0d1ecb74f..796d8b6d9 100644
--- a/_sources/datamodels/taxon-constraints/Term.md.txt
+++ b/_sources/datamodels/taxon-constraints/Term.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Term
diff --git a/_sources/datamodels/taxon-constraints/asserted.md.txt b/_sources/datamodels/taxon-constraints/asserted.md.txt
index 2e4f8a6e0..4ecbae8d2 100644
--- a/_sources/datamodels/taxon-constraints/asserted.md.txt
+++ b/_sources/datamodels/taxon-constraints/asserted.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: asserted
@@ -14,11 +16,12 @@ URI: [tc:asserted](https://w3id.org/linkml/taxon_constraints/asserted)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/candidate.md.txt b/_sources/datamodels/taxon-constraints/candidate.md.txt
index c4eeea799..dd9e5956b 100644
--- a/_sources/datamodels/taxon-constraints/candidate.md.txt
+++ b/_sources/datamodels/taxon-constraints/candidate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: candidate
@@ -14,11 +16,12 @@ URI: [tc:candidate](https://w3id.org/linkml/taxon_constraints/candidate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/comments.md.txt b/_sources/datamodels/taxon-constraints/comments.md.txt
index 2b069e86b..4603f8733 100644
--- a/_sources/datamodels/taxon-constraints/comments.md.txt
+++ b/_sources/datamodels/taxon-constraints/comments.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: comments
URI: [tc:comments](https://w3id.org/linkml/taxon_constraints/comments)
@@ -9,11 +11,12 @@ URI: [tc:comments](https://w3id.org/linkml/taxon_constraints/comments)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/contradicted_by.md.txt b/_sources/datamodels/taxon-constraints/contradicted_by.md.txt
index 621296f1b..fcbe09fee 100644
--- a/_sources/datamodels/taxon-constraints/contradicted_by.md.txt
+++ b/_sources/datamodels/taxon-constraints/contradicted_by.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: contradicted_by
@@ -14,11 +16,12 @@ URI: [tc:contradicted_by](https://w3id.org/linkml/taxon_constraints/contradicted
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/description.md.txt b/_sources/datamodels/taxon-constraints/description.md.txt
index 0e434d747..9745020fb 100644
--- a/_sources/datamodels/taxon-constraints/description.md.txt
+++ b/_sources/datamodels/taxon-constraints/description.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: description
@@ -14,11 +16,12 @@ URI: [tc:description](https://w3id.org/linkml/taxon_constraints/description)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/evolutionary.md.txt b/_sources/datamodels/taxon-constraints/evolutionary.md.txt
index ecd35865c..5e32e57a5 100644
--- a/_sources/datamodels/taxon-constraints/evolutionary.md.txt
+++ b/_sources/datamodels/taxon-constraints/evolutionary.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: evolutionary
@@ -14,11 +16,12 @@ URI: [tc:evolutionary](https://w3id.org/linkml/taxon_constraints/evolutionary)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/id.md.txt b/_sources/datamodels/taxon-constraints/id.md.txt
index fdb2df6ee..e20b9efe7 100644
--- a/_sources/datamodels/taxon-constraints/id.md.txt
+++ b/_sources/datamodels/taxon-constraints/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
@@ -14,14 +16,15 @@ URI: [tc:id](https://w3id.org/linkml/taxon_constraints/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Term](Term.md) | An ontology term | no |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
-[Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no |
-[PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no |
+| [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no |
+| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no |
+| [Term](Term.md) | An ontology term | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/label.md.txt b/_sources/datamodels/taxon-constraints/label.md.txt
index 87b358fdd..916fe4b1f 100644
--- a/_sources/datamodels/taxon-constraints/label.md.txt
+++ b/_sources/datamodels/taxon-constraints/label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: label
@@ -14,14 +16,15 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Term](Term.md) | An ontology term | no |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
-[Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no |
-[PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no |
+| [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no |
+| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no |
+| [Term](Term.md) | An ontology term | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/never_in.md.txt b/_sources/datamodels/taxon-constraints/never_in.md.txt
index 6a6cf207e..1de09617c 100644
--- a/_sources/datamodels/taxon-constraints/never_in.md.txt
+++ b/_sources/datamodels/taxon-constraints/never_in.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: never_in
@@ -16,11 +18,12 @@ URI: [RO:0002161](http://purl.obolibrary.org/obo/RO_0002161)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/only_in.md.txt b/_sources/datamodels/taxon-constraints/only_in.md.txt
index 917a04748..116898f99 100644
--- a/_sources/datamodels/taxon-constraints/only_in.md.txt
+++ b/_sources/datamodels/taxon-constraints/only_in.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: only_in
@@ -16,11 +18,12 @@ URI: [RO:0002160](http://purl.obolibrary.org/obo/RO_0002160)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/predicate.md.txt b/_sources/datamodels/taxon-constraints/predicate.md.txt
index 1dd3033bf..a22d40141 100644
--- a/_sources/datamodels/taxon-constraints/predicate.md.txt
+++ b/_sources/datamodels/taxon-constraints/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
@@ -14,11 +16,12 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/predicates.md.txt b/_sources/datamodels/taxon-constraints/predicates.md.txt
index f88325d94..b48a942f4 100644
--- a/_sources/datamodels/taxon-constraints/predicates.md.txt
+++ b/_sources/datamodels/taxon-constraints/predicates.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicates
@@ -14,11 +16,12 @@ URI: [tc:predicates](https://w3id.org/linkml/taxon_constraints/predicates)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/present_in.md.txt b/_sources/datamodels/taxon-constraints/present_in.md.txt
index 9bb98bd12..21c49a862 100644
--- a/_sources/datamodels/taxon-constraints/present_in.md.txt
+++ b/_sources/datamodels/taxon-constraints/present_in.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: present_in
@@ -16,11 +18,12 @@ URI: [RO:0002175](http://purl.obolibrary.org/obo/RO_0002175)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/present_in_ancestor_of.md.txt b/_sources/datamodels/taxon-constraints/present_in_ancestor_of.md.txt
index 32e6012fd..5dbb12d35 100644
--- a/_sources/datamodels/taxon-constraints/present_in_ancestor_of.md.txt
+++ b/_sources/datamodels/taxon-constraints/present_in_ancestor_of.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: present_in_ancestor_of
URI: [tc:present_in_ancestor_of](https://w3id.org/linkml/taxon_constraints/present_in_ancestor_of)
@@ -9,11 +11,12 @@ URI: [tc:present_in_ancestor_of](https://w3id.org/linkml/taxon_constraints/prese
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/redundant.md.txt b/_sources/datamodels/taxon-constraints/redundant.md.txt
index 385a6a3a7..535ac27e1 100644
--- a/_sources/datamodels/taxon-constraints/redundant.md.txt
+++ b/_sources/datamodels/taxon-constraints/redundant.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: redundant
@@ -14,11 +16,12 @@ URI: [tc:redundant](https://w3id.org/linkml/taxon_constraints/redundant)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/redundant_with.md.txt b/_sources/datamodels/taxon-constraints/redundant_with.md.txt
index 49654e456..a548e396f 100644
--- a/_sources/datamodels/taxon-constraints/redundant_with.md.txt
+++ b/_sources/datamodels/taxon-constraints/redundant_with.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: redundant_with
@@ -14,11 +16,12 @@ URI: [tc:redundant_with](https://w3id.org/linkml/taxon_constraints/redundant_wit
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/redundant_with_only_in.md.txt b/_sources/datamodels/taxon-constraints/redundant_with_only_in.md.txt
index 104daa575..0eb065d59 100644
--- a/_sources/datamodels/taxon-constraints/redundant_with_only_in.md.txt
+++ b/_sources/datamodels/taxon-constraints/redundant_with_only_in.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: redundant_with_only_in
@@ -14,11 +16,12 @@ URI: [tc:redundant_with_only_in](https://w3id.org/linkml/taxon_constraints/redun
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/sources.md.txt b/_sources/datamodels/taxon-constraints/sources.md.txt
index fbf533107..008e74295 100644
--- a/_sources/datamodels/taxon-constraints/sources.md.txt
+++ b/_sources/datamodels/taxon-constraints/sources.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sources
URI: [tc:sources](https://w3id.org/linkml/taxon_constraints/sources)
@@ -9,11 +11,12 @@ URI: [tc:sources](https://w3id.org/linkml/taxon_constraints/sources)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/subject.md.txt b/_sources/datamodels/taxon-constraints/subject.md.txt
index bd35fa741..c559737e6 100644
--- a/_sources/datamodels/taxon-constraints/subject.md.txt
+++ b/_sources/datamodels/taxon-constraints/subject.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject
@@ -14,11 +16,12 @@ URI: [rdf:subject](http://www.w3.org/1999/02/22-rdf-syntax-ns#subject)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/taxon.md.txt b/_sources/datamodels/taxon-constraints/taxon.md.txt
index 03d1d35ac..1ff92fe53 100644
--- a/_sources/datamodels/taxon-constraints/taxon.md.txt
+++ b/_sources/datamodels/taxon-constraints/taxon.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: taxon
@@ -14,11 +16,12 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/unsatisfiable.md.txt b/_sources/datamodels/taxon-constraints/unsatisfiable.md.txt
index 9adb2c0ff..cf8f13757 100644
--- a/_sources/datamodels/taxon-constraints/unsatisfiable.md.txt
+++ b/_sources/datamodels/taxon-constraints/unsatisfiable.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: unsatisfiable
@@ -14,11 +16,12 @@ URI: [tc:unsatisfiable](https://w3id.org/linkml/taxon_constraints/unsatisfiable)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
+| [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no |
diff --git a/_sources/datamodels/taxon-constraints/via_terms.md.txt b/_sources/datamodels/taxon-constraints/via_terms.md.txt
index 3d042f8da..e8f72b3a7 100644
--- a/_sources/datamodels/taxon-constraints/via_terms.md.txt
+++ b/_sources/datamodels/taxon-constraints/via_terms.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: via_terms
@@ -14,11 +16,12 @@ URI: [tc:via_terms](https://w3id.org/linkml/taxon_constraints/via_terms)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
+| [TaxonConstraint](TaxonConstraint.md) | An individual taxon constraint | no |
diff --git a/_sources/datamodels/text-annotator/HasSpan.md.txt b/_sources/datamodels/text-annotator/HasSpan.md.txt
index 99796b152..0d6b0e5e0 100644
--- a/_sources/datamodels/text-annotator/HasSpan.md.txt
+++ b/_sources/datamodels/text-annotator/HasSpan.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: HasSpan
diff --git a/_sources/datamodels/text-annotator/TextAnnotation.md.txt b/_sources/datamodels/text-annotator/TextAnnotation.md.txt
index fc3ed0ced..ec8926a1e 100644
--- a/_sources/datamodels/text-annotator/TextAnnotation.md.txt
+++ b/_sources/datamodels/text-annotator/TextAnnotation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TextAnnotation
diff --git a/_sources/datamodels/text-annotator/TextAnnotationConfiguration.md.txt b/_sources/datamodels/text-annotator/TextAnnotationConfiguration.md.txt
index ca04835aa..fb584ccdd 100644
--- a/_sources/datamodels/text-annotator/TextAnnotationConfiguration.md.txt
+++ b/_sources/datamodels/text-annotator/TextAnnotationConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TextAnnotationConfiguration
diff --git a/_sources/datamodels/text-annotator/TextAnnotationResultSet.md.txt b/_sources/datamodels/text-annotator/TextAnnotationResultSet.md.txt
index 07376ba2b..87b673462 100644
--- a/_sources/datamodels/text-annotator/TextAnnotationResultSet.md.txt
+++ b/_sources/datamodels/text-annotator/TextAnnotationResultSet.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TextAnnotationResultSet
diff --git a/_sources/datamodels/text-annotator/TextualElement.md.txt b/_sources/datamodels/text-annotator/TextualElement.md.txt
index dc1be7277..185a95e2e 100644
--- a/_sources/datamodels/text-annotator/TextualElement.md.txt
+++ b/_sources/datamodels/text-annotator/TextualElement.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TextualElement
diff --git a/_sources/datamodels/text-annotator/annotations.md.txt b/_sources/datamodels/text-annotator/annotations.md.txt
index 72084510e..840f01733 100644
--- a/_sources/datamodels/text-annotator/annotations.md.txt
+++ b/_sources/datamodels/text-annotator/annotations.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: annotations
@@ -14,11 +16,12 @@ URI: [ann:annotations](https://w3id.org/linkml/text_annotator/annotations)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationResultSet](TextAnnotationResultSet.md) | A collection of annotation results | no |
+| [TextAnnotationResultSet](TextAnnotationResultSet.md) | A collection of annotation results | no |
diff --git a/_sources/datamodels/text-annotator/categories.md.txt b/_sources/datamodels/text-annotator/categories.md.txt
index 85857bb62..c893d1aa2 100644
--- a/_sources/datamodels/text-annotator/categories.md.txt
+++ b/_sources/datamodels/text-annotator/categories.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: categories
@@ -14,11 +16,12 @@ URI: [ann:categories](https://w3id.org/linkml/text_annotator/categories)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/confidence.md.txt b/_sources/datamodels/text-annotator/confidence.md.txt
index b401a6a2d..8dae06dcc 100644
--- a/_sources/datamodels/text-annotator/confidence.md.txt
+++ b/_sources/datamodels/text-annotator/confidence.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: confidence
URI: [sssom:confidence](http://w3id.org/sssom/confidence)
@@ -9,11 +11,12 @@ URI: [sssom:confidence](http://w3id.org/sssom/confidence)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/id.md.txt b/_sources/datamodels/text-annotator/id.md.txt
index 69103c52c..1194b2111 100644
--- a/_sources/datamodels/text-annotator/id.md.txt
+++ b/_sources/datamodels/text-annotator/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
URI: [ann:id](https://w3id.org/linkml/text_annotator/id)
@@ -9,11 +11,12 @@ URI: [ann:id](https://w3id.org/linkml/text_annotator/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextualElement](TextualElement.md) | | no |
+| [TextualElement](TextualElement.md) | | no |
diff --git a/_sources/datamodels/text-annotator/include_aliases.md.txt b/_sources/datamodels/text-annotator/include_aliases.md.txt
index 09e015a00..4f5ebfebd 100644
--- a/_sources/datamodels/text-annotator/include_aliases.md.txt
+++ b/_sources/datamodels/text-annotator/include_aliases.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: include_aliases
@@ -14,11 +16,12 @@ URI: [ann:include_aliases](https://w3id.org/linkml/text_annotator/include_aliase
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/info.md.txt b/_sources/datamodels/text-annotator/info.md.txt
index 402eeaf3f..7963f0cc3 100644
--- a/_sources/datamodels/text-annotator/info.md.txt
+++ b/_sources/datamodels/text-annotator/info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: info
URI: [ann:info](https://w3id.org/linkml/text_annotator/info)
@@ -9,11 +11,12 @@ URI: [ann:info](https://w3id.org/linkml/text_annotator/info)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/is_longest_match.md.txt b/_sources/datamodels/text-annotator/is_longest_match.md.txt
index 536503748..2e406cfb3 100644
--- a/_sources/datamodels/text-annotator/is_longest_match.md.txt
+++ b/_sources/datamodels/text-annotator/is_longest_match.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: is_longest_match
URI: [ann:is_longest_match](https://w3id.org/linkml/text_annotator/is_longest_match)
@@ -9,11 +11,12 @@ URI: [ann:is_longest_match](https://w3id.org/linkml/text_annotator/is_longest_ma
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/limit.md.txt b/_sources/datamodels/text-annotator/limit.md.txt
index 59e90ebe4..6f7773e1e 100644
--- a/_sources/datamodels/text-annotator/limit.md.txt
+++ b/_sources/datamodels/text-annotator/limit.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: limit
@@ -14,11 +16,12 @@ URI: [ann:limit](https://w3id.org/linkml/text_annotator/limit)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/match_string.md.txt b/_sources/datamodels/text-annotator/match_string.md.txt
index 2cea12af4..73c8246cd 100644
--- a/_sources/datamodels/text-annotator/match_string.md.txt
+++ b/_sources/datamodels/text-annotator/match_string.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_string
URI: [sssom:match_string](http://w3id.org/sssom/match_string)
@@ -9,11 +11,12 @@ URI: [sssom:match_string](http://w3id.org/sssom/match_string)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/match_type.md.txt b/_sources/datamodels/text-annotator/match_type.md.txt
index d5b160f37..e6cee9935 100644
--- a/_sources/datamodels/text-annotator/match_type.md.txt
+++ b/_sources/datamodels/text-annotator/match_type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: match_type
URI: [ann:match_type](https://w3id.org/linkml/text_annotator/match_type)
@@ -9,11 +11,12 @@ URI: [ann:match_type](https://w3id.org/linkml/text_annotator/match_type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/matches_whole_text.md.txt b/_sources/datamodels/text-annotator/matches_whole_text.md.txt
index 4069bf0ac..5e009d3f7 100644
--- a/_sources/datamodels/text-annotator/matches_whole_text.md.txt
+++ b/_sources/datamodels/text-annotator/matches_whole_text.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: matches_whole_text
URI: [ann:matches_whole_text](https://w3id.org/linkml/text_annotator/matches_whole_text)
@@ -9,12 +11,13 @@ URI: [ann:matches_whole_text](https://w3id.org/linkml/text_annotator/matches_who
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/model.md.txt b/_sources/datamodels/text-annotator/model.md.txt
index ac4248c07..8569367e1 100644
--- a/_sources/datamodels/text-annotator/model.md.txt
+++ b/_sources/datamodels/text-annotator/model.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: model
@@ -14,11 +16,12 @@ URI: [ann:model](https://w3id.org/linkml/text_annotator/model)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/object_aliases.md.txt b/_sources/datamodels/text-annotator/object_aliases.md.txt
index 4e26641e6..e509a0e32 100644
--- a/_sources/datamodels/text-annotator/object_aliases.md.txt
+++ b/_sources/datamodels/text-annotator/object_aliases.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_aliases
URI: [ann:object_aliases](https://w3id.org/linkml/text_annotator/object_aliases)
@@ -9,11 +11,12 @@ URI: [ann:object_aliases](https://w3id.org/linkml/text_annotator/object_aliases)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/object_categories.md.txt b/_sources/datamodels/text-annotator/object_categories.md.txt
index b210bb882..ee9884098 100644
--- a/_sources/datamodels/text-annotator/object_categories.md.txt
+++ b/_sources/datamodels/text-annotator/object_categories.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_categories
URI: [ann:object_categories](https://w3id.org/linkml/text_annotator/object_categories)
@@ -9,11 +11,12 @@ URI: [ann:object_categories](https://w3id.org/linkml/text_annotator/object_categ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/object_id.md.txt b/_sources/datamodels/text-annotator/object_id.md.txt
index 1e7ba7d61..b6ad84884 100644
--- a/_sources/datamodels/text-annotator/object_id.md.txt
+++ b/_sources/datamodels/text-annotator/object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_id
URI: [sssom:object_id](http://w3id.org/sssom/object_id)
@@ -9,11 +11,12 @@ URI: [sssom:object_id](http://w3id.org/sssom/object_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/object_label.md.txt b/_sources/datamodels/text-annotator/object_label.md.txt
index d6244ee00..2980489cb 100644
--- a/_sources/datamodels/text-annotator/object_label.md.txt
+++ b/_sources/datamodels/text-annotator/object_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_label
URI: [sssom:object_label](http://w3id.org/sssom/object_label)
@@ -9,11 +11,12 @@ URI: [sssom:object_label](http://w3id.org/sssom/object_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/object_source.md.txt b/_sources/datamodels/text-annotator/object_source.md.txt
index ce91a50df..a2efa8d06 100644
--- a/_sources/datamodels/text-annotator/object_source.md.txt
+++ b/_sources/datamodels/text-annotator/object_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_source
URI: [sssom:object_source](http://w3id.org/sssom/object_source)
@@ -9,11 +11,12 @@ URI: [sssom:object_source](http://w3id.org/sssom/object_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/parent_document.md.txt b/_sources/datamodels/text-annotator/parent_document.md.txt
index f0181d6f8..3c7790050 100644
--- a/_sources/datamodels/text-annotator/parent_document.md.txt
+++ b/_sources/datamodels/text-annotator/parent_document.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: parent_document
URI: [ann:parent_document](https://w3id.org/linkml/text_annotator/parent_document)
@@ -9,11 +11,12 @@ URI: [ann:parent_document](https://w3id.org/linkml/text_annotator/parent_documen
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextualElement](TextualElement.md) | | no |
+| [TextualElement](TextualElement.md) | | no |
diff --git a/_sources/datamodels/text-annotator/predicate_id.md.txt b/_sources/datamodels/text-annotator/predicate_id.md.txt
index 0cc10b0fe..7035383e7 100644
--- a/_sources/datamodels/text-annotator/predicate_id.md.txt
+++ b/_sources/datamodels/text-annotator/predicate_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_id
URI: [sssom:predicate_id](http://w3id.org/sssom/predicate_id)
@@ -9,11 +11,12 @@ URI: [sssom:predicate_id](http://w3id.org/sssom/predicate_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/source_text.md.txt b/_sources/datamodels/text-annotator/source_text.md.txt
index aa275b603..25d5c0db6 100644
--- a/_sources/datamodels/text-annotator/source_text.md.txt
+++ b/_sources/datamodels/text-annotator/source_text.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: source_text
URI: [ann:source_text](https://w3id.org/linkml/text_annotator/source_text)
@@ -9,11 +11,12 @@ URI: [ann:source_text](https://w3id.org/linkml/text_annotator/source_text)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextualElement](TextualElement.md) | | no |
+| [TextualElement](TextualElement.md) | | no |
diff --git a/_sources/datamodels/text-annotator/sources.md.txt b/_sources/datamodels/text-annotator/sources.md.txt
index f390e70bc..772261691 100644
--- a/_sources/datamodels/text-annotator/sources.md.txt
+++ b/_sources/datamodels/text-annotator/sources.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: sources
URI: [ann:sources](https://w3id.org/linkml/text_annotator/sources)
@@ -9,11 +11,12 @@ URI: [ann:sources](https://w3id.org/linkml/text_annotator/sources)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/text-annotator/subject_end.md.txt b/_sources/datamodels/text-annotator/subject_end.md.txt
index 54edab044..20c0707b2 100644
--- a/_sources/datamodels/text-annotator/subject_end.md.txt
+++ b/_sources/datamodels/text-annotator/subject_end.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_end
URI: [ann:subject_end](https://w3id.org/linkml/text_annotator/subject_end)
@@ -9,12 +11,13 @@ URI: [ann:subject_end](https://w3id.org/linkml/text_annotator/subject_end)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSpan](HasSpan.md) | | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [HasSpan](HasSpan.md) | | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/subject_label.md.txt b/_sources/datamodels/text-annotator/subject_label.md.txt
index 4d1fa0222..ab71b81bd 100644
--- a/_sources/datamodels/text-annotator/subject_label.md.txt
+++ b/_sources/datamodels/text-annotator/subject_label.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_label
@@ -14,12 +16,13 @@ URI: [ann:subject_label](https://w3id.org/linkml/text_annotator/subject_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSpan](HasSpan.md) | | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [HasSpan](HasSpan.md) | | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/subject_source.md.txt b/_sources/datamodels/text-annotator/subject_source.md.txt
index 10616ca03..a483bfe2d 100644
--- a/_sources/datamodels/text-annotator/subject_source.md.txt
+++ b/_sources/datamodels/text-annotator/subject_source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_source
URI: [sssom:subject_source](http://w3id.org/sssom/subject_source)
@@ -9,12 +11,13 @@ URI: [sssom:subject_source](http://w3id.org/sssom/subject_source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSpan](HasSpan.md) | | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [HasSpan](HasSpan.md) | | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/subject_start.md.txt b/_sources/datamodels/text-annotator/subject_start.md.txt
index 0096235ed..b65647c1f 100644
--- a/_sources/datamodels/text-annotator/subject_start.md.txt
+++ b/_sources/datamodels/text-annotator/subject_start.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_start
URI: [ann:subject_start](https://w3id.org/linkml/text_annotator/subject_start)
@@ -9,12 +11,13 @@ URI: [ann:subject_start](https://w3id.org/linkml/text_annotator/subject_start)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSpan](HasSpan.md) | | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [HasSpan](HasSpan.md) | | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/subject_text_id.md.txt b/_sources/datamodels/text-annotator/subject_text_id.md.txt
index 52ebf5079..6ac072152 100644
--- a/_sources/datamodels/text-annotator/subject_text_id.md.txt
+++ b/_sources/datamodels/text-annotator/subject_text_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_text_id
URI: [ann:subject_text_id](https://w3id.org/linkml/text_annotator/subject_text_id)
@@ -9,12 +11,13 @@ URI: [ann:subject_text_id](https://w3id.org/linkml/text_annotator/subject_text_i
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[HasSpan](HasSpan.md) | | no |
-[TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
+| [HasSpan](HasSpan.md) | | no |
+| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no |
diff --git a/_sources/datamodels/text-annotator/text.md.txt b/_sources/datamodels/text-annotator/text.md.txt
index 5aa9858f3..83c7dea46 100644
--- a/_sources/datamodels/text-annotator/text.md.txt
+++ b/_sources/datamodels/text-annotator/text.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: text
URI: [ann:text](https://w3id.org/linkml/text_annotator/text)
@@ -9,11 +11,12 @@ URI: [ann:text](https://w3id.org/linkml/text_annotator/text)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextualElement](TextualElement.md) | | no |
+| [TextualElement](TextualElement.md) | | no |
diff --git a/_sources/datamodels/text-annotator/token_exclusion_list.md.txt b/_sources/datamodels/text-annotator/token_exclusion_list.md.txt
index c5f802365..9ccd2ca2c 100644
--- a/_sources/datamodels/text-annotator/token_exclusion_list.md.txt
+++ b/_sources/datamodels/text-annotator/token_exclusion_list.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: token_exclusion_list
@@ -14,11 +16,12 @@ URI: [ann:token_exclusion_list](https://w3id.org/linkml/text_annotator/token_exc
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
+| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no |
diff --git a/_sources/datamodels/validation/ConstraintComponent.md.txt b/_sources/datamodels/validation/ConstraintComponent.md.txt
index 191ddbdef..d9b8be873 100644
--- a/_sources/datamodels/validation/ConstraintComponent.md.txt
+++ b/_sources/datamodels/validation/ConstraintComponent.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ConstraintComponent
@@ -42,6 +44,7 @@ URI: [vm:ConstraintComponent](https://w3id.org/linkml/validation-model/Constrain
| used by | used in | type | used |
| --- | --- | --- | --- |
| [ValidationResult](ValidationResult.md) | [type](type.md) | range | [ConstraintComponent](ConstraintComponent.md) |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | [type](type.md) | range | [ConstraintComponent](ConstraintComponent.md) |
| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | [type](type.md) | range | [ConstraintComponent](ConstraintComponent.md) |
diff --git a/_sources/datamodels/validation/DefinitionValidationResult.md.txt b/_sources/datamodels/validation/DefinitionValidationResult.md.txt
new file mode 100644
index 000000000..4a6e2156a
--- /dev/null
+++ b/_sources/datamodels/validation/DefinitionValidationResult.md.txt
@@ -0,0 +1,298 @@
+
+
+# Class: DefinitionValidationResult
+
+
+
+URI: [vm:DefinitionValidationResult](https://w3id.org/linkml/validation-model/DefinitionValidationResult)
+
+
+
+
+```{mermaid}
+ classDiagram
+ class DefinitionValidationResult
+ ValidationResult <|-- DefinitionValidationResult
+
+ DefinitionValidationResult : definition
+
+ DefinitionValidationResult : definition_source
+
+ DefinitionValidationResult : info
+
+ DefinitionValidationResult : instantiates
+
+ DefinitionValidationResult --> Node : instantiates
+
+ DefinitionValidationResult : object
+
+ DefinitionValidationResult --> Node : object
+
+ DefinitionValidationResult : object_str
+
+ DefinitionValidationResult : predicate
+
+ DefinitionValidationResult --> Node : predicate
+
+ DefinitionValidationResult : proposed_new_definition
+
+ DefinitionValidationResult : severity
+
+ DefinitionValidationResult --> severity_options : severity
+
+ DefinitionValidationResult : source
+
+ DefinitionValidationResult : subject
+
+ DefinitionValidationResult --> Node : subject
+
+ DefinitionValidationResult : type
+
+ DefinitionValidationResult --> ConstraintComponent : type
+
+
+```
+
+
+
+
+
+## Inheritance
+* [Result](Result.md)
+ * [ValidationResult](ValidationResult.md)
+ * **DefinitionValidationResult**
+
+
+
+## Slots
+
+| Name | Cardinality and Range | Description | Inheritance |
+| --- | --- | --- | --- |
+| [definition](definition.md) | 0..1
[String](String.md) | | direct |
+| [definition_source](definition_source.md) | 0..1
[String](String.md) | | direct |
+| [proposed_new_definition](proposed_new_definition.md) | 0..1
[String](String.md) | | direct |
+| [type](type.md) | 1..1
[ConstraintComponent](ConstraintComponent.md) | The type of validation result | [ValidationResult](ValidationResult.md) |
+| [severity](severity.md) | 0..1
[SeverityOptions](SeverityOptions.md) | the severity of the issue | [ValidationResult](ValidationResult.md) |
+| [subject](subject.md) | 1..1
[Node](Node.md) | The instance which the result is about | [ValidationResult](ValidationResult.md) |
+| [instantiates](instantiates.md) | 0..1
[Node](Node.md) | The type of the subject | [ValidationResult](ValidationResult.md) |
+| [predicate](predicate.md) | 0..1
[Node](Node.md) | The predicate or property of the subject which the result is about | [ValidationResult](ValidationResult.md) |
+| [object](object.md) | 0..1
[Node](Node.md) | | [ValidationResult](ValidationResult.md) |
+| [object_str](object_str.md) | 0..1
[String](String.md) | | [ValidationResult](ValidationResult.md) |
+| [source](source.md) | 0..1
[String](String.md) | | [ValidationResult](ValidationResult.md) |
+| [info](info.md) | 0..1
[String](String.md) | additional information about the issue | [ValidationResult](ValidationResult.md) |
+
+
+
+
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+
+## Mappings
+
+| Mapping Type | Mapped Value |
+| --- | --- |
+| self | vm:DefinitionValidationResult |
+| native | vm:DefinitionValidationResult |
+
+
+
+
+
+## LinkML Source
+
+
+
+### Direct
+
+
+```yaml
+name: DefinitionValidationResult
+from_schema: https://w3id.org/linkml/validation_results
+is_a: ValidationResult
+attributes:
+ definition:
+ name: definition
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+ definition_source:
+ name: definition_source
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+ proposed_new_definition:
+ name: proposed_new_definition
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+
+```
+
+
+### Induced
+
+
+```yaml
+name: DefinitionValidationResult
+from_schema: https://w3id.org/linkml/validation_results
+is_a: ValidationResult
+attributes:
+ definition:
+ name: definition
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: definition
+ owner: DefinitionValidationResult
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+ definition_source:
+ name: definition_source
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: definition_source
+ owner: DefinitionValidationResult
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+ proposed_new_definition:
+ name: proposed_new_definition
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: proposed_new_definition
+ owner: DefinitionValidationResult
+ domain_of:
+ - DefinitionValidationResult
+ range: string
+ type:
+ name: type
+ description: The type of validation result. SHACL validation vocabulary is recommended
+ for checks against a datamodel. For principle checks use the corresponding rule
+ or principle, e.g. GO RULE ID, OBO Principle ID
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ slot_uri: sh:sourceConstraintComponent
+ alias: type
+ owner: DefinitionValidationResult
+ domain_of:
+ - TypeSeverityKeyValue
+ - ValidationResult
+ range: ConstraintComponent
+ required: true
+ severity:
+ name: severity
+ description: the severity of the issue
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ slot_uri: sh:resultSeverity
+ alias: severity
+ owner: DefinitionValidationResult
+ domain_of:
+ - TypeSeverityKeyValue
+ - ValidationResult
+ range: severity_options
+ subject:
+ name: subject
+ description: The instance which the result is about
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ slot_uri: sh:focusNode
+ alias: subject
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: Node
+ required: true
+ instantiates:
+ name: instantiates
+ description: The type of the subject
+ from_schema: https://w3id.org/linkml/validation_results
+ exact_mappings:
+ - sh:sourceShape
+ rank: 1000
+ alias: instantiates
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: Node
+ predicate:
+ name: predicate
+ description: The predicate or property of the subject which the result is about
+ from_schema: https://w3id.org/linkml/validation_results
+ related_mappings:
+ - sh:resultPath
+ rank: 1000
+ alias: predicate
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: Node
+ object:
+ name: object
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ slot_uri: sh:value
+ alias: object
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: Node
+ object_str:
+ name: object_str
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: object_str
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: string
+ source:
+ name: source
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: source
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ range: string
+ info:
+ name: info
+ description: additional information about the issue
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ slot_uri: sh:resultMessage
+ alias: info
+ owner: DefinitionValidationResult
+ domain_of:
+ - ValidationResult
+ - MappingValidationResult
+ - RepairOperation
+ range: string
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/ExternalReferenceValidationResult.md.txt b/_sources/datamodels/validation/ExternalReferenceValidationResult.md.txt
index 7db878810..97a1e8fd2 100644
--- a/_sources/datamodels/validation/ExternalReferenceValidationResult.md.txt
+++ b/_sources/datamodels/validation/ExternalReferenceValidationResult.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ExternalReferenceValidationResult
diff --git a/_sources/datamodels/validation/MappingValidationResult.md.txt b/_sources/datamodels/validation/MappingValidationResult.md.txt
index 32656e3b5..2bd5578c3 100644
--- a/_sources/datamodels/validation/MappingValidationResult.md.txt
+++ b/_sources/datamodels/validation/MappingValidationResult.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: MappingValidationResult
diff --git a/_sources/datamodels/validation/NamedResource.md.txt b/_sources/datamodels/validation/NamedResource.md.txt
index 92eebb391..e4d008f76 100644
--- a/_sources/datamodels/validation/NamedResource.md.txt
+++ b/_sources/datamodels/validation/NamedResource.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: NamedResource
diff --git a/_sources/datamodels/validation/Node.md.txt b/_sources/datamodels/validation/Node.md.txt
index ebb35fbda..9079bc86e 100644
--- a/_sources/datamodels/validation/Node.md.txt
+++ b/_sources/datamodels/validation/Node.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Node
@@ -45,6 +47,10 @@ URI: [vm:Node](https://w3id.org/linkml/validation-model/Node)
| [ValidationResult](ValidationResult.md) | [instantiates](instantiates.md) | range | [Node](Node.md) |
| [ValidationResult](ValidationResult.md) | [predicate](predicate.md) | range | [Node](Node.md) |
| [ValidationResult](ValidationResult.md) | [object](object.md) | range | [Node](Node.md) |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | [subject](subject.md) | range | [Node](Node.md) |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | [instantiates](instantiates.md) | range | [Node](Node.md) |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | [predicate](predicate.md) | range | [Node](Node.md) |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | [object](object.md) | range | [Node](Node.md) |
| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | [subject](subject.md) | range | [Node](Node.md) |
| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | [instantiates](instantiates.md) | range | [Node](Node.md) |
| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | [predicate](predicate.md) | range | [Node](Node.md) |
diff --git a/_sources/datamodels/validation/RepairConfiguration.md.txt b/_sources/datamodels/validation/RepairConfiguration.md.txt
index a87fecc4e..c9e3671ba 100644
--- a/_sources/datamodels/validation/RepairConfiguration.md.txt
+++ b/_sources/datamodels/validation/RepairConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RepairConfiguration
diff --git a/_sources/datamodels/validation/RepairOperation.md.txt b/_sources/datamodels/validation/RepairOperation.md.txt
index e211d5c18..d9da2547e 100644
--- a/_sources/datamodels/validation/RepairOperation.md.txt
+++ b/_sources/datamodels/validation/RepairOperation.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RepairOperation
diff --git a/_sources/datamodels/validation/RepairReport.md.txt b/_sources/datamodels/validation/RepairReport.md.txt
index 477c009de..c8445b8a7 100644
--- a/_sources/datamodels/validation/RepairReport.md.txt
+++ b/_sources/datamodels/validation/RepairReport.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: RepairReport
diff --git a/_sources/datamodels/validation/Report.md.txt b/_sources/datamodels/validation/Report.md.txt
index 96f24a414..8df26e463 100644
--- a/_sources/datamodels/validation/Report.md.txt
+++ b/_sources/datamodels/validation/Report.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Report
diff --git a/_sources/datamodels/validation/Result.md.txt b/_sources/datamodels/validation/Result.md.txt
index 4be432894..901703791 100644
--- a/_sources/datamodels/validation/Result.md.txt
+++ b/_sources/datamodels/validation/Result.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: Result
diff --git a/_sources/datamodels/validation/TypeSeverityKeyValue.md.txt b/_sources/datamodels/validation/TypeSeverityKeyValue.md.txt
index 3dccb5af5..226e31d9c 100644
--- a/_sources/datamodels/validation/TypeSeverityKeyValue.md.txt
+++ b/_sources/datamodels/validation/TypeSeverityKeyValue.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: TypeSeverityKeyValue
diff --git a/_sources/datamodels/validation/ValidationConfiguration.md.txt b/_sources/datamodels/validation/ValidationConfiguration.md.txt
index 233291c77..038a1335e 100644
--- a/_sources/datamodels/validation/ValidationConfiguration.md.txt
+++ b/_sources/datamodels/validation/ValidationConfiguration.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ValidationConfiguration
@@ -15,6 +17,10 @@ URI: [vm:ValidationConfiguration](https://w3id.org/linkml/validation-model/Valid
```{mermaid}
classDiagram
class ValidationConfiguration
+ ValidationConfiguration : documentation_objects
+
+ ValidationConfiguration : lookup_references
+
ValidationConfiguration : max_number_results_per_type
ValidationConfiguration : prompt_info
@@ -41,7 +47,9 @@ URI: [vm:ValidationConfiguration](https://w3id.org/linkml/validation-model/Valid
| [max_number_results_per_type](max_number_results_per_type.md) | 0..1
[Integer](Integer.md) | if set then truncate results such that no more than this number of results ar... | direct |
| [type_severity_map](type_severity_map.md) | 0..*
[TypeSeverityKeyValue](TypeSeverityKeyValue.md) | Allows overriding of severity of a particular type | direct |
| [schema_path](schema_path.md) | 0..1
[String](String.md) | allows overriding the default OMO schema | direct |
+| [lookup_references](lookup_references.md) | 0..1
[Boolean](Boolean.md) | if true, then look up references used as provenance (axiom annotation) | direct |
| [prompt_info](prompt_info.md) | 0..1
[String](String.md) | for AI agents, this allows passing through of additional info to the prompt | direct |
+| [documentation_objects](documentation_objects.md) | 0..*
[String](String.md) | paths or URLs to files containing best practice documentation, SOPs, etc | direct |
@@ -125,6 +133,15 @@ attributes:
domain_of:
- ValidationConfiguration
range: string
+ lookup_references:
+ name: lookup_references
+ description: if true, then look up references used as provenance (axiom annotation).
+ This may include looking up the PMID and checking if a publication is retracted.
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ domain_of:
+ - ValidationConfiguration
+ range: boolean
prompt_info:
name: prompt_info
description: for AI agents, this allows passing through of additional info to
@@ -134,6 +151,16 @@ attributes:
domain_of:
- ValidationConfiguration
range: string
+ documentation_objects:
+ name: documentation_objects
+ description: paths or URLs to files containing best practice documentation, SOPs,
+ etc. Primarily for AI agents to read when performing validation.
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - ValidationConfiguration
+ range: string
```
@@ -179,6 +206,17 @@ attributes:
domain_of:
- ValidationConfiguration
range: string
+ lookup_references:
+ name: lookup_references
+ description: if true, then look up references used as provenance (axiom annotation).
+ This may include looking up the PMID and checking if a publication is retracted.
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ alias: lookup_references
+ owner: ValidationConfiguration
+ domain_of:
+ - ValidationConfiguration
+ range: boolean
prompt_info:
name: prompt_info
description: for AI agents, this allows passing through of additional info to
@@ -190,6 +228,18 @@ attributes:
domain_of:
- ValidationConfiguration
range: string
+ documentation_objects:
+ name: documentation_objects
+ description: paths or URLs to files containing best practice documentation, SOPs,
+ etc. Primarily for AI agents to read when performing validation.
+ from_schema: https://w3id.org/linkml/validation_results
+ rank: 1000
+ multivalued: true
+ alias: documentation_objects
+ owner: ValidationConfiguration
+ domain_of:
+ - ValidationConfiguration
+ range: string
```
\ No newline at end of file
diff --git a/_sources/datamodels/validation/ValidationReport.md.txt b/_sources/datamodels/validation/ValidationReport.md.txt
index c4079976a..b786d0e64 100644
--- a/_sources/datamodels/validation/ValidationReport.md.txt
+++ b/_sources/datamodels/validation/ValidationReport.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ValidationReport
diff --git a/_sources/datamodels/validation/ValidationResult.md.txt b/_sources/datamodels/validation/ValidationResult.md.txt
index 5bbd595d8..4797eb4ef 100644
--- a/_sources/datamodels/validation/ValidationResult.md.txt
+++ b/_sources/datamodels/validation/ValidationResult.md.txt
@@ -1,3 +1,5 @@
+
+
# Class: ValidationResult
@@ -18,6 +20,7 @@ URI: [sh:ValidationResult](http://www.w3.org/ns/shacl#ValidationResult)
Result <|-- ValidationResult
+ ValidationResult <|-- DefinitionValidationResult
ValidationResult <|-- ExternalReferenceValidationResult
@@ -61,6 +64,7 @@ URI: [sh:ValidationResult](http://www.w3.org/ns/shacl#ValidationResult)
## Inheritance
* [Result](Result.md)
* **ValidationResult**
+ * [DefinitionValidationResult](DefinitionValidationResult.md)
* [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md)
diff --git a/_sources/datamodels/validation/category.md.txt b/_sources/datamodels/validation/category.md.txt
index 24d652137..62ea50bba 100644
--- a/_sources/datamodels/validation/category.md.txt
+++ b/_sources/datamodels/validation/category.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: category
@@ -14,11 +16,12 @@ URI: [vm:category](https://w3id.org/linkml/validation-model/category)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/confidence.md.txt b/_sources/datamodels/validation/confidence.md.txt
index cbf3c71b5..44c44991c 100644
--- a/_sources/datamodels/validation/confidence.md.txt
+++ b/_sources/datamodels/validation/confidence.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: confidence
URI: [vm:confidence](https://w3id.org/linkml/validation-model/confidence)
@@ -9,11 +11,12 @@ URI: [vm:confidence](https://w3id.org/linkml/validation-model/confidence)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/definition.md.txt b/_sources/datamodels/validation/definition.md.txt
new file mode 100644
index 000000000..1d3e6c23c
--- /dev/null
+++ b/_sources/datamodels/validation/definition.md.txt
@@ -0,0 +1,65 @@
+
+
+# Slot: definition
+
+URI: [vm:definition](https://w3id.org/linkml/validation-model/definition)
+
+
+
+
+
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [String](String.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+## LinkML Source
+
+
+```yaml
+name: definition
+from_schema: https://w3id.org/linkml/validation_results
+rank: 1000
+alias: definition
+owner: DefinitionValidationResult
+domain_of:
+- DefinitionValidationResult
+range: string
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/definition_source.md.txt b/_sources/datamodels/validation/definition_source.md.txt
new file mode 100644
index 000000000..eca3c1337
--- /dev/null
+++ b/_sources/datamodels/validation/definition_source.md.txt
@@ -0,0 +1,65 @@
+
+
+# Slot: definition_source
+
+URI: [vm:definition_source](https://w3id.org/linkml/validation-model/definition_source)
+
+
+
+
+
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [String](String.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+## LinkML Source
+
+
+```yaml
+name: definition_source
+from_schema: https://w3id.org/linkml/validation_results
+rank: 1000
+alias: definition_source
+owner: DefinitionValidationResult
+domain_of:
+- DefinitionValidationResult
+range: string
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/documentation_objects.md.txt b/_sources/datamodels/validation/documentation_objects.md.txt
new file mode 100644
index 000000000..7e12c3c02
--- /dev/null
+++ b/_sources/datamodels/validation/documentation_objects.md.txt
@@ -0,0 +1,75 @@
+
+
+# Slot: documentation_objects
+
+
+_paths or URLs to files containing best practice documentation, SOPs, etc. Primarily for AI agents to read when performing validation._
+
+
+
+URI: [vm:documentation_objects](https://w3id.org/linkml/validation-model/documentation_objects)
+
+
+
+
+
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [String](String.md)
+
+* Multivalued: True
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+## LinkML Source
+
+
+```yaml
+name: documentation_objects
+description: paths or URLs to files containing best practice documentation, SOPs,
+ etc. Primarily for AI agents to read when performing validation.
+from_schema: https://w3id.org/linkml/validation_results
+rank: 1000
+multivalued: true
+alias: documentation_objects
+owner: ValidationConfiguration
+domain_of:
+- ValidationConfiguration
+range: string
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/dry_run.md.txt b/_sources/datamodels/validation/dry_run.md.txt
index 7a1beb561..a7a19068f 100644
--- a/_sources/datamodels/validation/dry_run.md.txt
+++ b/_sources/datamodels/validation/dry_run.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: dry_run
URI: [vm:dry_run](https://w3id.org/linkml/validation-model/dry_run)
@@ -9,11 +11,12 @@ URI: [vm:dry_run](https://w3id.org/linkml/validation-model/dry_run)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RepairConfiguration](RepairConfiguration.md) | Configuration parameters for execution of validation repairs | no |
+| [RepairConfiguration](RepairConfiguration.md) | Configuration parameters for execution of validation repairs | no |
diff --git a/_sources/datamodels/validation/http_response_code.md.txt b/_sources/datamodels/validation/http_response_code.md.txt
index c792a4e84..aa372cde0 100644
--- a/_sources/datamodels/validation/http_response_code.md.txt
+++ b/_sources/datamodels/validation/http_response_code.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: http_response_code
URI: [vm:http_response_code](https://w3id.org/linkml/validation-model/http_response_code)
@@ -9,11 +11,12 @@ URI: [vm:http_response_code](https://w3id.org/linkml/validation-model/http_respo
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
diff --git a/_sources/datamodels/validation/id.md.txt b/_sources/datamodels/validation/id.md.txt
index bdeaf63b2..5bc6a1ca8 100644
--- a/_sources/datamodels/validation/id.md.txt
+++ b/_sources/datamodels/validation/id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: id
URI: [vm:id](https://w3id.org/linkml/validation-model/id)
@@ -9,13 +11,14 @@ URI: [vm:id](https://w3id.org/linkml/validation-model/id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[NamedResource](NamedResource.md) | | no |
-[ConstraintComponent](ConstraintComponent.md) | | no |
-[Node](Node.md) | | no |
+| [NamedResource](NamedResource.md) | | no |
+| [ConstraintComponent](ConstraintComponent.md) | | no |
+| [Node](Node.md) | | no |
diff --git a/_sources/datamodels/validation/index.md.txt b/_sources/datamodels/validation/index.md.txt
index 0fa5abca1..03df79797 100644
--- a/_sources/datamodels/validation/index.md.txt
+++ b/_sources/datamodels/validation/index.md.txt
@@ -1,4 +1,4 @@
-# Validation Results Datamodel
+# Validation Results Data Model
A datamodel for data validation results.
@@ -23,6 +23,7 @@ Name: validaton-results
| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct |
| [RepairOperation](RepairOperation.md) | The result of performing an individual repair |
| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a particular rule |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | None |
| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external resource is still valid |
| [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for overriding default severity |
| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report |
@@ -35,11 +36,15 @@ Name: validaton-results
| --- | --- |
| [category](category.md) | The category of the validation issue |
| [confidence](confidence.md) | |
+| [definition](definition.md) | |
+| [definition_source](definition_source.md) | |
+| [documentation_objects](documentation_objects.md) | paths or URLs to files containing best practice documentation, SOPs, etc |
| [dry_run](dry_run.md) | |
| [http_response_code](http_response_code.md) | |
| [id](id.md) | |
| [info](info.md) | additional information about the issue |
| [instantiates](instantiates.md) | The type of the subject |
+| [lookup_references](lookup_references.md) | if true, then look up references used as provenance (axiom annotation) |
| [max_number_results_per_type](max_number_results_per_type.md) | if set then truncate results such that no more than this number of results ar... |
| [modified](modified.md) | |
| [number_of_attempts](number_of_attempts.md) | |
@@ -51,6 +56,7 @@ Name: validaton-results
| [predicate_id](predicate_id.md) | |
| [problem](problem.md) | |
| [prompt_info](prompt_info.md) | for AI agents, this allows passing through of additional info to the prompt |
+| [proposed_new_definition](proposed_new_definition.md) | |
| [repairs](repairs.md) | |
| [results](results.md) | collection of results |
| [schema_path](schema_path.md) | allows overriding the default OMO schema |
diff --git a/_sources/datamodels/validation/info.md.txt b/_sources/datamodels/validation/info.md.txt
index 8fda880e3..025640f12 100644
--- a/_sources/datamodels/validation/info.md.txt
+++ b/_sources/datamodels/validation/info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: info
@@ -14,14 +16,16 @@ URI: [sh:resultMessage](http://www.w3.org/ns/shacl#resultMessage)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
-[RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
+| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/instantiates.md.txt b/_sources/datamodels/validation/instantiates.md.txt
index be833e49e..3a5e8c295 100644
--- a/_sources/datamodels/validation/instantiates.md.txt
+++ b/_sources/datamodels/validation/instantiates.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: instantiates
@@ -14,12 +16,14 @@ URI: [vm:instantiates](https://w3id.org/linkml/validation-model/instantiates)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/lookup_references.md.txt b/_sources/datamodels/validation/lookup_references.md.txt
new file mode 100644
index 000000000..471660c18
--- /dev/null
+++ b/_sources/datamodels/validation/lookup_references.md.txt
@@ -0,0 +1,72 @@
+
+
+# Slot: lookup_references
+
+
+_if true, then look up references used as provenance (axiom annotation). This may include looking up the PMID and checking if a publication is retracted._
+
+
+
+URI: [vm:lookup_references](https://w3id.org/linkml/validation-model/lookup_references)
+
+
+
+
+
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [Boolean](Boolean.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+## LinkML Source
+
+
+```yaml
+name: lookup_references
+description: if true, then look up references used as provenance (axiom annotation).
+ This may include looking up the PMID and checking if a publication is retracted.
+from_schema: https://w3id.org/linkml/validation_results
+rank: 1000
+alias: lookup_references
+owner: ValidationConfiguration
+domain_of:
+- ValidationConfiguration
+range: boolean
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/max_number_results_per_type.md.txt b/_sources/datamodels/validation/max_number_results_per_type.md.txt
index fab95d5a4..35ade1cd0 100644
--- a/_sources/datamodels/validation/max_number_results_per_type.md.txt
+++ b/_sources/datamodels/validation/max_number_results_per_type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: max_number_results_per_type
@@ -14,11 +16,12 @@ URI: [vm:max_number_results_per_type](https://w3id.org/linkml/validation-model/m
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
diff --git a/_sources/datamodels/validation/modified.md.txt b/_sources/datamodels/validation/modified.md.txt
index 2b28eaedf..9ceb5456c 100644
--- a/_sources/datamodels/validation/modified.md.txt
+++ b/_sources/datamodels/validation/modified.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: modified
URI: [vm:modified](https://w3id.org/linkml/validation-model/modified)
@@ -9,11 +11,12 @@ URI: [vm:modified](https://w3id.org/linkml/validation-model/modified)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
+| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
diff --git a/_sources/datamodels/validation/number_of_attempts.md.txt b/_sources/datamodels/validation/number_of_attempts.md.txt
index a37faabed..4f325b103 100644
--- a/_sources/datamodels/validation/number_of_attempts.md.txt
+++ b/_sources/datamodels/validation/number_of_attempts.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: number_of_attempts
URI: [vm:number_of_attempts](https://w3id.org/linkml/validation-model/number_of_attempts)
@@ -9,11 +11,12 @@ URI: [vm:number_of_attempts](https://w3id.org/linkml/validation-model/number_of_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
diff --git a/_sources/datamodels/validation/object.md.txt b/_sources/datamodels/validation/object.md.txt
index 7a118b399..2e3592269 100644
--- a/_sources/datamodels/validation/object.md.txt
+++ b/_sources/datamodels/validation/object.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object
URI: [sh:value](http://www.w3.org/ns/shacl#value)
@@ -9,12 +11,14 @@ URI: [sh:value](http://www.w3.org/ns/shacl#value)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/object_id.md.txt b/_sources/datamodels/validation/object_id.md.txt
index 69e79e20e..7a03c1195 100644
--- a/_sources/datamodels/validation/object_id.md.txt
+++ b/_sources/datamodels/validation/object_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_id
URI: [vm:object_id](https://w3id.org/linkml/validation-model/object_id)
@@ -9,11 +11,12 @@ URI: [vm:object_id](https://w3id.org/linkml/validation-model/object_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/object_info.md.txt b/_sources/datamodels/validation/object_info.md.txt
index 66ec0fdf2..274b60958 100644
--- a/_sources/datamodels/validation/object_info.md.txt
+++ b/_sources/datamodels/validation/object_info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_info
URI: [vm:object_info](https://w3id.org/linkml/validation-model/object_info)
@@ -9,11 +11,12 @@ URI: [vm:object_info](https://w3id.org/linkml/validation-model/object_info)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/object_str.md.txt b/_sources/datamodels/validation/object_str.md.txt
index d0a883492..840d518ef 100644
--- a/_sources/datamodels/validation/object_str.md.txt
+++ b/_sources/datamodels/validation/object_str.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: object_str
URI: [vm:object_str](https://w3id.org/linkml/validation-model/object_str)
@@ -9,12 +11,14 @@ URI: [vm:object_str](https://w3id.org/linkml/validation-model/object_str)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/predicate.md.txt b/_sources/datamodels/validation/predicate.md.txt
index 1d28ce6f7..3f80dcdd1 100644
--- a/_sources/datamodels/validation/predicate.md.txt
+++ b/_sources/datamodels/validation/predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
@@ -14,12 +16,14 @@ URI: [vm:predicate](https://w3id.org/linkml/validation-model/predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/predicate_id.md.txt b/_sources/datamodels/validation/predicate_id.md.txt
index 2cd6a56bd..bcbd834f7 100644
--- a/_sources/datamodels/validation/predicate_id.md.txt
+++ b/_sources/datamodels/validation/predicate_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_id
URI: [vm:predicate_id](https://w3id.org/linkml/validation-model/predicate_id)
@@ -9,11 +11,12 @@ URI: [vm:predicate_id](https://w3id.org/linkml/validation-model/predicate_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/problem.md.txt b/_sources/datamodels/validation/problem.md.txt
index 8ad623321..904255090 100644
--- a/_sources/datamodels/validation/problem.md.txt
+++ b/_sources/datamodels/validation/problem.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: problem
URI: [vm:problem](https://w3id.org/linkml/validation-model/problem)
@@ -9,11 +11,12 @@ URI: [vm:problem](https://w3id.org/linkml/validation-model/problem)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/prompt_info.md.txt b/_sources/datamodels/validation/prompt_info.md.txt
index 74d1dc980..8f9a10409 100644
--- a/_sources/datamodels/validation/prompt_info.md.txt
+++ b/_sources/datamodels/validation/prompt_info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: prompt_info
@@ -14,11 +16,12 @@ URI: [vm:prompt_info](https://w3id.org/linkml/validation-model/prompt_info)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
diff --git a/_sources/datamodels/validation/proposed_new_definition.md.txt b/_sources/datamodels/validation/proposed_new_definition.md.txt
new file mode 100644
index 000000000..e8890c716
--- /dev/null
+++ b/_sources/datamodels/validation/proposed_new_definition.md.txt
@@ -0,0 +1,65 @@
+
+
+# Slot: proposed_new_definition
+
+URI: [vm:proposed_new_definition](https://w3id.org/linkml/validation-model/proposed_new_definition)
+
+
+
+
+
+
+
+
+
+## Applicable Classes
+
+| Name | Description | Modifies Slot |
+| --- | --- | --- |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+
+
+
+
+
+
+
+## Properties
+
+* Range: [String](String.md)
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: https://w3id.org/linkml/validation_results
+
+
+
+
+## LinkML Source
+
+
+```yaml
+name: proposed_new_definition
+from_schema: https://w3id.org/linkml/validation_results
+rank: 1000
+alias: proposed_new_definition
+owner: DefinitionValidationResult
+domain_of:
+- DefinitionValidationResult
+range: string
+
+```
+
\ No newline at end of file
diff --git a/_sources/datamodels/validation/repairs.md.txt b/_sources/datamodels/validation/repairs.md.txt
index b0e62bb55..2e993a0d7 100644
--- a/_sources/datamodels/validation/repairs.md.txt
+++ b/_sources/datamodels/validation/repairs.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: repairs
URI: [vm:repairs](https://w3id.org/linkml/validation-model/repairs)
@@ -9,11 +11,12 @@ URI: [vm:repairs](https://w3id.org/linkml/validation-model/repairs)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
+| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
diff --git a/_sources/datamodels/validation/results.md.txt b/_sources/datamodels/validation/results.md.txt
index d3c24eb45..80002c036 100644
--- a/_sources/datamodels/validation/results.md.txt
+++ b/_sources/datamodels/validation/results.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: results
@@ -14,13 +16,14 @@ URI: [sh:result](http://www.w3.org/ns/shacl#result)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[Report](Report.md) | A report object that is a holder to multiple report results | no |
-[ValidationReport](ValidationReport.md) | A report that consists of validation results | yes |
-[RepairReport](RepairReport.md) | A report that consists of repair operation results | yes |
+| [RepairReport](RepairReport.md) | A report that consists of repair operation results | yes |
+| [Report](Report.md) | A report object that is a holder to multiple report results | no |
+| [ValidationReport](ValidationReport.md) | A report that consists of validation results | yes |
diff --git a/_sources/datamodels/validation/schema_path.md.txt b/_sources/datamodels/validation/schema_path.md.txt
index eaed1761a..a1db105de 100644
--- a/_sources/datamodels/validation/schema_path.md.txt
+++ b/_sources/datamodels/validation/schema_path.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: schema_path
@@ -14,11 +16,12 @@ URI: [vm:schema_path](https://w3id.org/linkml/validation-model/schema_path)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
diff --git a/_sources/datamodels/validation/severity.md.txt b/_sources/datamodels/validation/severity.md.txt
index 938f36cde..6e6889306 100644
--- a/_sources/datamodels/validation/severity.md.txt
+++ b/_sources/datamodels/validation/severity.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: severity
@@ -14,13 +16,15 @@ URI: [sh:resultSeverity](http://www.w3.org/ns/shacl#resultSeverity)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/source.md.txt b/_sources/datamodels/validation/source.md.txt
index b8fcb2c84..0902c4d63 100644
--- a/_sources/datamodels/validation/source.md.txt
+++ b/_sources/datamodels/validation/source.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: source
URI: [vm:source](https://w3id.org/linkml/validation-model/source)
@@ -9,12 +11,14 @@ URI: [vm:source](https://w3id.org/linkml/validation-model/source)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/subject.md.txt b/_sources/datamodels/validation/subject.md.txt
index 0a3230ecf..cdbab69a6 100644
--- a/_sources/datamodels/validation/subject.md.txt
+++ b/_sources/datamodels/validation/subject.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject
@@ -14,12 +16,14 @@ URI: [sh:focusNode](http://www.w3.org/ns/shacl#focusNode)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/subject_id.md.txt b/_sources/datamodels/validation/subject_id.md.txt
index c6a593670..fb7372ebf 100644
--- a/_sources/datamodels/validation/subject_id.md.txt
+++ b/_sources/datamodels/validation/subject_id.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_id
URI: [vm:subject_id](https://w3id.org/linkml/validation-model/subject_id)
@@ -9,11 +11,12 @@ URI: [vm:subject_id](https://w3id.org/linkml/validation-model/subject_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/subject_info.md.txt b/_sources/datamodels/validation/subject_info.md.txt
index 0a338972e..6b9f7ba40 100644
--- a/_sources/datamodels/validation/subject_info.md.txt
+++ b/_sources/datamodels/validation/subject_info.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: subject_info
URI: [vm:subject_info](https://w3id.org/linkml/validation-model/subject_info)
@@ -9,11 +11,12 @@ URI: [vm:subject_info](https://w3id.org/linkml/validation-model/subject_info)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/successful.md.txt b/_sources/datamodels/validation/successful.md.txt
index d97695225..0e36517f3 100644
--- a/_sources/datamodels/validation/successful.md.txt
+++ b/_sources/datamodels/validation/successful.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: successful
URI: [vm:successful](https://w3id.org/linkml/validation-model/successful)
@@ -9,11 +11,12 @@ URI: [vm:successful](https://w3id.org/linkml/validation-model/successful)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
+| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no |
diff --git a/_sources/datamodels/validation/suggested_modifications.md.txt b/_sources/datamodels/validation/suggested_modifications.md.txt
index 859560df0..3b6931732 100644
--- a/_sources/datamodels/validation/suggested_modifications.md.txt
+++ b/_sources/datamodels/validation/suggested_modifications.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: suggested_modifications
URI: [vm:suggested_modifications](https://w3id.org/linkml/validation-model/suggested_modifications)
@@ -9,11 +11,12 @@ URI: [vm:suggested_modifications](https://w3id.org/linkml/validation-model/sugge
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/suggested_predicate.md.txt b/_sources/datamodels/validation/suggested_predicate.md.txt
index 6b97dbc10..91e14f672 100644
--- a/_sources/datamodels/validation/suggested_predicate.md.txt
+++ b/_sources/datamodels/validation/suggested_predicate.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: suggested_predicate
URI: [vm:suggested_predicate](https://w3id.org/linkml/validation-model/suggested_predicate)
@@ -9,11 +11,12 @@ URI: [vm:suggested_predicate](https://w3id.org/linkml/validation-model/suggested
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
+| [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no |
diff --git a/_sources/datamodels/validation/time_checked.md.txt b/_sources/datamodels/validation/time_checked.md.txt
index cbebbf5cd..776e928d4 100644
--- a/_sources/datamodels/validation/time_checked.md.txt
+++ b/_sources/datamodels/validation/time_checked.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: time_checked
URI: [vm:time_checked](https://w3id.org/linkml/validation-model/time_checked)
@@ -9,11 +11,12 @@ URI: [vm:time_checked](https://w3id.org/linkml/validation-model/time_checked)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
diff --git a/_sources/datamodels/validation/type.md.txt b/_sources/datamodels/validation/type.md.txt
index 7ceb3c10d..d1d7d06df 100644
--- a/_sources/datamodels/validation/type.md.txt
+++ b/_sources/datamodels/validation/type.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type
@@ -14,13 +16,15 @@ URI: [sh:sourceConstraintComponent](http://www.w3.org/ns/shacl#sourceConstraintC
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
-[TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [DefinitionValidationResult](DefinitionValidationResult.md) | | no |
+| [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no |
+| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |
diff --git a/_sources/datamodels/validation/type_severity_map.md.txt b/_sources/datamodels/validation/type_severity_map.md.txt
index e71ea001c..d5dc1cc97 100644
--- a/_sources/datamodels/validation/type_severity_map.md.txt
+++ b/_sources/datamodels/validation/type_severity_map.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: type_severity_map
@@ -14,11 +16,12 @@ URI: [vm:type_severity_map](https://w3id.org/linkml/validation-model/type_severi
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
+| [ValidationConfiguration](ValidationConfiguration.md) | Configuration parameters for execution of a validation report | no |
diff --git a/_sources/datamodels/validation/url.md.txt b/_sources/datamodels/validation/url.md.txt
index 378d75f08..a4dea5425 100644
--- a/_sources/datamodels/validation/url.md.txt
+++ b/_sources/datamodels/validation/url.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: url
URI: [vm:url](https://w3id.org/linkml/validation-model/url)
@@ -9,11 +11,12 @@ URI: [vm:url](https://w3id.org/linkml/validation-model/url)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
+| [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no |
diff --git a/_sources/datamodels/validation/validation_configuration.md.txt b/_sources/datamodels/validation/validation_configuration.md.txt
index 3ad6d3742..40091a117 100644
--- a/_sources/datamodels/validation/validation_configuration.md.txt
+++ b/_sources/datamodels/validation/validation_configuration.md.txt
@@ -1,3 +1,5 @@
+
+
# Slot: validation_configuration
@@ -14,11 +16,12 @@ URI: [vm:validation_configuration](https://w3id.org/linkml/validation-model/vali
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RepairConfiguration](RepairConfiguration.md) | Configuration parameters for execution of validation repairs | no |
+| [RepairConfiguration](RepairConfiguration.md) | Configuration parameters for execution of validation repairs | no |
diff --git a/_sources/howtos/use-llms.rst.txt b/_sources/howtos/use-llms.rst.txt
index c08950829..b8da74186 100644
--- a/_sources/howtos/use-llms.rst.txt
+++ b/_sources/howtos/use-llms.rst.txt
@@ -115,9 +115,51 @@ Suggesting Definitions
finger toe \
--style-hints "write definitions in formal genus-differentia form"
+Validating Definitions
+~~~~~~~~~~~~~~~~~~~~~~
+
+The LLM adapter currently interprets ``validate-definitions`` as comparing the specified definition
+against the abstracts of papers cited in the definition provenance, or by comparing the definition
+against the database objects that are cited as definition provenance.
+
+Here is an example of validating definitions for GO terms:
+
+.. code-block:: bash
+
+ runoak --stacktrace -i llm:sqlite:obo:go validate-definitions \
+ i^GO: -o out.jsonl -O jsonl
+
+The semsql version of GO has other ontologies merged in, so the ``i^GO:`` query only validates
+against actual GO terms.
+
+You can also pass in a configuration object.
+This should conform to the `Validation Data Model `_
+
+For example, this configuration yaml provides a specific prompt and also a URL for
+documentation aimed at ontology developers.
+
+.. code-block:: yaml
+
+ prompt_info: Please also use the following GO guidelines
+ documentation_objects:
+ - https://wiki.geneontology.org/Guidelines_for_GO_textual_definitions
+
+All specified URLs are downloaded and converted to text and included in the prompt.
+
+The configuration yaml is passed in as follows:
+
+.. code-block:: bash
+
+
+ runoak --stacktrace -i llm:{claude-3-opus}:sqlite:obo:go validate-definitions \
+ -C src/oaklib/conf/go-definition-validation-llm-config.yaml i^GO: -O yaml
+
Validating Mappings
~~~~~~~~~~~~~~~~~~~
+The LLM adapter validates mappings by looking up info on the mapped entity and
+comparing it with the main entity.
+
.. code-block:: bash
runoak --stacktrace -i llm:{gpt-4}:sqlite:obo:go validate-mappings \
@@ -165,8 +207,14 @@ as a developer, then you can do this:
This will install the plugin in the same environment as OAK.
-TODO: instructions for non-developers.
+If you need to update this:
+
+.. code-block:: bash
+ cd ontology-access-kit
+ poetry run llm install -U llm-gemini
+
+TODO: instructions for non-developers.
Mixtral via Ollama and LiteLLM
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/_sources/packages/interfaces/validator.rst.txt b/_sources/packages/interfaces/validator.rst.txt
index 2bacd5568..9b1ba11fc 100644
--- a/_sources/packages/interfaces/validator.rst.txt
+++ b/_sources/packages/interfaces/validator.rst.txt
@@ -3,13 +3,24 @@
Validator Interface
--------------------
-.. warning ::
+The Validator Interface provides access to a number of different validation operations over ontologies.
- Currently the main validator methods are only implemented for :ref:`SqlDatabaseImplementation`
+The notion of validation in OAK is intentionally very flexible, and may encompass:
-The validate method is configured using a *metadata schema*. The default one used is:
+ * *Schema* validation, for example, checking definitions are strings and have 0..1 cardinality.
+ * *Logical* validation, using a reasoner.
+ * *Lexical* validation, for example, ensuring there are no spelling errors
+ * *Stylistic* validation, against a style guide
+ * *Content* validation, checking the content of the ontology against domain knowledge or other ontologies.
-- `Ontology Metadata `_
+Different adapters may implement different portions of this.
+
+Schema Validation
+~~~~~~~~~~~~~~~~~
+
+The core validate method is configured using a *metadata schema*. The default one used is:
+
+- `Ontology Metadata `_
This is specified using LinkML which provides an expressive way to state constraints on metadata elements,
such as :ref:`AnnotationProperty` assertions in ontologies. For example, this schema states that definition
@@ -19,6 +30,15 @@ Different projects may wish to configure this - it is possible to pass in a diff
For more details see `this howto guide `_
+.. warning::
+
+ Currently only implemented for :ref`sql_implementation`
+
+LLM-based validation
+~~~~~~~~~~~~~~~~~~~~
+
+See :ref:`use_llms`
+
.. currentmodule:: oaklib.interfaces.validator_interface
diff --git a/_sources/packages/src/oaklib.utilities.table_filler.rst.txt b/_sources/packages/src/oaklib.utilities.table_filler.rst.txt
deleted file mode 100644
index 0a3786f19..000000000
--- a/_sources/packages/src/oaklib.utilities.table_filler.rst.txt
+++ /dev/null
@@ -1,39 +0,0 @@
-oaklib.utilities.table\_filler
-==============================
-
-.. automodule:: oaklib.utilities.table_filler
-
-
-
-
-
-
-
- .. rubric:: Functions
-
- .. autosummary::
-
- apply_dict
- parse_table
- write_table
-
-
-
-
-
- .. rubric:: Classes
-
- .. autosummary::
-
- ColumnDependency
- TableFiller
- TableMetadata
-
-
-
-
-
-
-
-
-
diff --git a/_sources/packages/src/oaklib.utilities.taxon.rst.txt b/_sources/packages/src/oaklib.utilities.taxon.rst.txt
deleted file mode 100644
index 66109dd79..000000000
--- a/_sources/packages/src/oaklib.utilities.taxon.rst.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-oaklib.utilities.taxon
-======================
-
-.. automodule:: oaklib.utilities.taxon
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/_sources/packages/src/oaklib.utilities.taxon.taxon_constraint_utils.rst.txt b/_sources/packages/src/oaklib.utilities.taxon.taxon_constraint_utils.rst.txt
new file mode 100644
index 000000000..9cf1be295
--- /dev/null
+++ b/_sources/packages/src/oaklib.utilities.taxon.taxon_constraint_utils.rst.txt
@@ -0,0 +1,29 @@
+oaklib.utilities.taxon.taxon\_constraint\_utils
+===============================================
+
+.. automodule:: oaklib.utilities.taxon.taxon_constraint_utils
+
+
+
+
+
+
+
+ .. rubric:: Functions
+
+ .. autosummary::
+
+ parse_gain_loss_file
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/_sources/packages/utilities.rst.txt b/_sources/packages/utilities.rst.txt
index dafcc23da..306ed28e4 100644
--- a/_sources/packages/utilities.rst.txt
+++ b/_sources/packages/utilities.rst.txt
@@ -17,5 +17,6 @@ being turned into :ref:`interfaces`.
lexical.lexical_indexer
subsets.slimmer_utils
apikey_manager
- taxon/taxon_constraint_utils
+ taxon.taxon_constraint_utils
table_filler
+
diff --git a/association/Association.md b/association/Association.md
index f8565e068..9cb0e96ed 100644
--- a/association/Association.md
+++ b/association/Association.md
@@ -1,3 +1,5 @@
+
+
# Class: Association
diff --git a/association/AssociationChange.md b/association/AssociationChange.md
index f68bcb5cd..39206a0e4 100644
--- a/association/AssociationChange.md
+++ b/association/AssociationChange.md
@@ -1,3 +1,5 @@
+
+
# Class: AssociationChange
diff --git a/association/NegatedAssociation.md b/association/NegatedAssociation.md
index bfe2c5830..1fde4aed1 100644
--- a/association/NegatedAssociation.md
+++ b/association/NegatedAssociation.md
@@ -1,3 +1,5 @@
+
+
# Class: NegatedAssociation
diff --git a/association/PairwiseCoAssociation.md b/association/PairwiseCoAssociation.md
index c7840bfd8..99743f0c3 100644
--- a/association/PairwiseCoAssociation.md
+++ b/association/PairwiseCoAssociation.md
@@ -1,3 +1,5 @@
+
+
# Class: PairwiseCoAssociation
diff --git a/association/ParserConfiguration.md b/association/ParserConfiguration.md
index 56f3ae6bc..921c2fa30 100644
--- a/association/ParserConfiguration.md
+++ b/association/ParserConfiguration.md
@@ -1,3 +1,5 @@
+
+
# Class: ParserConfiguration
diff --git a/association/PositiveOrNegativeAssociation.md b/association/PositiveOrNegativeAssociation.md
index 2168b0ac9..985384444 100644
--- a/association/PositiveOrNegativeAssociation.md
+++ b/association/PositiveOrNegativeAssociation.md
@@ -1,3 +1,5 @@
+
+
# Class: PositiveOrNegativeAssociation
diff --git a/association/PropertyValue.md b/association/PropertyValue.md
index f6bd1115f..6f5016e57 100644
--- a/association/PropertyValue.md
+++ b/association/PropertyValue.md
@@ -1,3 +1,5 @@
+
+
# Class: PropertyValue
diff --git a/association/RollupGroup.md b/association/RollupGroup.md
index 524a8b7f0..8d51c2649 100644
--- a/association/RollupGroup.md
+++ b/association/RollupGroup.md
@@ -1,3 +1,5 @@
+
+
# Class: RollupGroup
diff --git a/association/aggregator_knowledge_source.md b/association/aggregator_knowledge_source.md
index 5c5c86e80..4235ad70b 100644
--- a/association/aggregator_knowledge_source.md
+++ b/association/aggregator_knowledge_source.md
@@ -1,3 +1,5 @@
+
+
# Slot: aggregator_knowledge_source
@@ -14,15 +16,16 @@ URI: [biolink:aggregator_knowledge_source](https://w3id.org/biolink/vocab/aggreg
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/associations.md b/association/associations.md
index 1f9f89adc..61f3d9b51 100644
--- a/association/associations.md
+++ b/association/associations.md
@@ -1,3 +1,5 @@
+
+
# Slot: associations
@@ -14,11 +16,12 @@ URI: [ontoassoc:associations](https://w3id.org/oak/association/associations)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/association/associations_for_subjects_in_common.md b/association/associations_for_subjects_in_common.md
index 20779f6d4..b13feab0d 100644
--- a/association/associations_for_subjects_in_common.md
+++ b/association/associations_for_subjects_in_common.md
@@ -1,3 +1,5 @@
+
+
# Slot: associations_for_subjects_in_common
URI: [ontoassoc:associations_for_subjects_in_common](https://w3id.org/oak/association/associations_for_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:associations_for_subjects_in_common](https://w3id.org/oak/associ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/closure_delta.md b/association/closure_delta.md
index 54a469f79..8cda97305 100644
--- a/association/closure_delta.md
+++ b/association/closure_delta.md
@@ -1,3 +1,5 @@
+
+
# Slot: closure_delta
URI: [ontoassoc:closure_delta](https://w3id.org/oak/association/closure_delta)
@@ -9,11 +11,12 @@ URI: [ontoassoc:closure_delta](https://w3id.org/oak/association/closure_delta)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/closure_information_content_delta.md b/association/closure_information_content_delta.md
index e178dbe3e..42a6f3ce5 100644
--- a/association/closure_information_content_delta.md
+++ b/association/closure_information_content_delta.md
@@ -1,3 +1,5 @@
+
+
# Slot: closure_information_content_delta
URI: [ontoassoc:closure_information_content_delta](https://w3id.org/oak/association/closure_information_content_delta)
@@ -12,6 +14,7 @@ URI: [ontoassoc:closure_information_content_delta](https://w3id.org/oak/associat
+
## Properties
* Range: [Float](Float.md)
diff --git a/association/closure_predicates.md b/association/closure_predicates.md
index 55a4f23ae..239136c35 100644
--- a/association/closure_predicates.md
+++ b/association/closure_predicates.md
@@ -1,3 +1,5 @@
+
+
# Slot: closure_predicates
@@ -14,11 +16,12 @@ URI: [ontoassoc:closure_predicates](https://w3id.org/oak/association/closure_pre
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/comments.md b/association/comments.md
index e97541492..5338dac80 100644
--- a/association/comments.md
+++ b/association/comments.md
@@ -1,3 +1,5 @@
+
+
# Slot: comments
@@ -14,13 +16,14 @@ URI: [rdfs:comment](rdfs:comment)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/core_triple.md b/association/core_triple.md
index 73c1341a3..c46f8d8f3 100644
--- a/association/core_triple.md
+++ b/association/core_triple.md
@@ -1,3 +1,5 @@
+
+
# Slot: core_triple
@@ -17,6 +19,7 @@ URI: [ontoassoc:core_triple](https://w3id.org/oak/association/core_triple)
+
## Properties
* Range: NONE
diff --git a/association/creation_date.md b/association/creation_date.md
index 8b83b861c..c17995a2e 100644
--- a/association/creation_date.md
+++ b/association/creation_date.md
@@ -1,3 +1,5 @@
+
+
# Slot: creation_date
@@ -22,6 +24,7 @@ URI: [ontoassoc:creation_date](https://w3id.org/oak/association/creation_date)
+
## Properties
* Range: [String](String.md)
diff --git a/association/date.md b/association/date.md
index 8822ae1dc..89646125e 100644
--- a/association/date.md
+++ b/association/date.md
@@ -1,3 +1,5 @@
+
+
# Slot: date
@@ -25,6 +27,7 @@ URI: [ontoassoc:date](https://w3id.org/oak/association/date)
+
## Properties
* Range: [String](String.md)
diff --git a/association/denormalized_slot.md b/association/denormalized_slot.md
index 664af15c0..6ea3d11d6 100644
--- a/association/denormalized_slot.md
+++ b/association/denormalized_slot.md
@@ -1,3 +1,5 @@
+
+
# Slot: denormalized_slot
@@ -16,6 +18,7 @@ URI: [ontoassoc:denormalized_slot](https://w3id.org/oak/association/denormalized
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/association/diff_slot.md b/association/diff_slot.md
index da4b8a918..9674038e8 100644
--- a/association/diff_slot.md
+++ b/association/diff_slot.md
@@ -1,3 +1,5 @@
+
+
# Slot: diff_slot
@@ -16,6 +18,7 @@ URI: [ontoassoc:diff_slot](https://w3id.org/oak/association/diff_slot)
+
## Mixin Usage
| mixed into | description | range | domain |
diff --git a/association/evidence_type.md b/association/evidence_type.md
index 56ce08bd0..b2e2255bf 100644
--- a/association/evidence_type.md
+++ b/association/evidence_type.md
@@ -1,3 +1,5 @@
+
+
# Slot: evidence_type
@@ -14,13 +16,14 @@ URI: [ontoassoc:evidence_type](https://w3id.org/oak/association/evidence_type)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/group_object.md b/association/group_object.md
index 204e06078..8c44e92b0 100644
--- a/association/group_object.md
+++ b/association/group_object.md
@@ -1,3 +1,5 @@
+
+
# Slot: group_object
@@ -16,11 +18,12 @@ URI: [rdf:object](rdf:object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/association/include_association_attributes.md b/association/include_association_attributes.md
index cd65ec7a0..4bd4e3fcb 100644
--- a/association/include_association_attributes.md
+++ b/association/include_association_attributes.md
@@ -1,3 +1,5 @@
+
+
# Slot: include_association_attributes
@@ -16,11 +18,12 @@ URI: [ontoassoc:include_association_attributes](https://w3id.org/oak/association
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
diff --git a/association/is_creation.md b/association/is_creation.md
index f42dc97a2..76cba8f14 100644
--- a/association/is_creation.md
+++ b/association/is_creation.md
@@ -1,3 +1,5 @@
+
+
# Slot: is_creation
URI: [ontoassoc:is_creation](https://w3id.org/oak/association/is_creation)
@@ -13,11 +15,12 @@ URI: [ontoassoc:is_creation](https://w3id.org/oak/association/is_creation)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/is_deletion.md b/association/is_deletion.md
index a1dd5723a..f7c119bb1 100644
--- a/association/is_deletion.md
+++ b/association/is_deletion.md
@@ -1,3 +1,5 @@
+
+
# Slot: is_deletion
URI: [ontoassoc:is_deletion](https://w3id.org/oak/association/is_deletion)
@@ -13,11 +15,12 @@ URI: [ontoassoc:is_deletion](https://w3id.org/oak/association/is_deletion)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/is_generalization.md b/association/is_generalization.md
index 4c42baa06..1c6dd7e59 100644
--- a/association/is_generalization.md
+++ b/association/is_generalization.md
@@ -1,3 +1,5 @@
+
+
# Slot: is_generalization
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_generalization](https://w3id.org/oak/association/is_generaliz
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/is_migration.md b/association/is_migration.md
index e098372c6..3ce642ef8 100644
--- a/association/is_migration.md
+++ b/association/is_migration.md
@@ -1,3 +1,5 @@
+
+
# Slot: is_migration
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_migration](https://w3id.org/oak/association/is_migration)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/is_specialization.md b/association/is_specialization.md
index 3fc50eb48..24f4200f3 100644
--- a/association/is_specialization.md
+++ b/association/is_specialization.md
@@ -1,3 +1,5 @@
+
+
# Slot: is_specialization
@@ -18,11 +20,12 @@ URI: [ontoassoc:is_specialization](https://w3id.org/oak/association/is_specializ
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/modification_date.md b/association/modification_date.md
index a67143b71..2533dd328 100644
--- a/association/modification_date.md
+++ b/association/modification_date.md
@@ -1,3 +1,5 @@
+
+
# Slot: modification_date
@@ -22,6 +24,7 @@ URI: [ontoassoc:modification_date](https://w3id.org/oak/association/modification
+
## Properties
* Range: [String](String.md)
diff --git a/association/negated.md b/association/negated.md
index 309367504..bb4ed6c2e 100644
--- a/association/negated.md
+++ b/association/negated.md
@@ -1,3 +1,5 @@
+
+
# Slot: negated
@@ -14,13 +16,14 @@ URI: [ontoassoc:negated](https://w3id.org/oak/association/negated)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | yes |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | yes |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |
diff --git a/association/new_date.md b/association/new_date.md
index 7af4466a1..2a3a652e0 100644
--- a/association/new_date.md
+++ b/association/new_date.md
@@ -1,3 +1,5 @@
+
+
# Slot: new_date
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_date](https://w3id.org/oak/association/new_date)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/new_object.md b/association/new_object.md
index 9057bb2cc..6e8e16647 100644
--- a/association/new_object.md
+++ b/association/new_object.md
@@ -1,3 +1,5 @@
+
+
# Slot: new_object
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_object](https://w3id.org/oak/association/new_object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/new_predicate.md b/association/new_predicate.md
index 2a3cb7948..f2bf07783 100644
--- a/association/new_predicate.md
+++ b/association/new_predicate.md
@@ -1,3 +1,5 @@
+
+
# Slot: new_predicate
@@ -19,11 +21,12 @@ URI: [ontoassoc:new_predicate](https://w3id.org/oak/association/new_predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/number_subject_unique_to_entity1.md b/association/number_subject_unique_to_entity1.md
index 30d376fee..50ed2c57e 100644
--- a/association/number_subject_unique_to_entity1.md
+++ b/association/number_subject_unique_to_entity1.md
@@ -1,3 +1,5 @@
+
+
# Slot: number_subject_unique_to_entity1
URI: [ontoassoc:number_subject_unique_to_entity1](https://w3id.org/oak/association/number_subject_unique_to_entity1)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subject_unique_to_entity1](https://w3id.org/oak/associati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/number_subject_unique_to_entity2.md b/association/number_subject_unique_to_entity2.md
index bd05df889..a71870388 100644
--- a/association/number_subject_unique_to_entity2.md
+++ b/association/number_subject_unique_to_entity2.md
@@ -1,3 +1,5 @@
+
+
# Slot: number_subject_unique_to_entity2
URI: [ontoassoc:number_subject_unique_to_entity2](https://w3id.org/oak/association/number_subject_unique_to_entity2)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subject_unique_to_entity2](https://w3id.org/oak/associati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/number_subjects_in_common.md b/association/number_subjects_in_common.md
index 23869981d..a192111ba 100644
--- a/association/number_subjects_in_common.md
+++ b/association/number_subjects_in_common.md
@@ -1,3 +1,5 @@
+
+
# Slot: number_subjects_in_common
URI: [ontoassoc:number_subjects_in_common](https://w3id.org/oak/association/number_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subjects_in_common](https://w3id.org/oak/association/numb
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/number_subjects_in_union.md b/association/number_subjects_in_union.md
index dc697f45c..8ff130046 100644
--- a/association/number_subjects_in_union.md
+++ b/association/number_subjects_in_union.md
@@ -1,3 +1,5 @@
+
+
# Slot: number_subjects_in_union
URI: [ontoassoc:number_subjects_in_union](https://w3id.org/oak/association/number_subjects_in_union)
@@ -9,11 +11,12 @@ URI: [ontoassoc:number_subjects_in_union](https://w3id.org/oak/association/numbe
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/object.md b/association/object.md
index ff46dff60..8ecf0284e 100644
--- a/association/object.md
+++ b/association/object.md
@@ -1,3 +1,5 @@
+
+
# Slot: object
@@ -22,14 +24,15 @@ URI: [rdf:object](rdf:object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/object1.md b/association/object1.md
index cb44fc4e8..80a7899cb 100644
--- a/association/object1.md
+++ b/association/object1.md
@@ -1,3 +1,5 @@
+
+
# Slot: object1
URI: [ontoassoc:object1](https://w3id.org/oak/association/object1)
@@ -14,11 +16,12 @@ URI: [ontoassoc:object1](https://w3id.org/oak/association/object1)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/object1_label.md b/association/object1_label.md
index 6126c4ebc..2c0645c0d 100644
--- a/association/object1_label.md
+++ b/association/object1_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: object1_label
URI: [ontoassoc:object1_label](https://w3id.org/oak/association/object1_label)
@@ -9,11 +11,12 @@ URI: [ontoassoc:object1_label](https://w3id.org/oak/association/object1_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/object2.md b/association/object2.md
index a0765979d..b318599f2 100644
--- a/association/object2.md
+++ b/association/object2.md
@@ -1,3 +1,5 @@
+
+
# Slot: object2
URI: [ontoassoc:object2](https://w3id.org/oak/association/object2)
@@ -14,11 +16,12 @@ URI: [ontoassoc:object2](https://w3id.org/oak/association/object2)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/object2_label.md b/association/object2_label.md
index 1b194f012..61b80943e 100644
--- a/association/object2_label.md
+++ b/association/object2_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: object2_label
URI: [ontoassoc:object2_label](https://w3id.org/oak/association/object2_label)
@@ -9,11 +11,12 @@ URI: [ontoassoc:object2_label](https://w3id.org/oak/association/object2_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/object_closure.md b/association/object_closure.md
index 971dacf41..dd17757aa 100644
--- a/association/object_closure.md
+++ b/association/object_closure.md
@@ -1,3 +1,5 @@
+
+
# Slot: object_closure
@@ -14,13 +16,14 @@ URI: [ontoassoc:object_closure](https://w3id.org/oak/association/object_closure)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/object_closure_label.md b/association/object_closure_label.md
index fe6874215..22c81c3d9 100644
--- a/association/object_closure_label.md
+++ b/association/object_closure_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: object_closure_label
@@ -14,13 +16,14 @@ URI: [ontoassoc:object_closure_label](https://w3id.org/oak/association/object_cl
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/object_label.md b/association/object_label.md
index 50e79ddfe..75f63c2c0 100644
--- a/association/object_label.md
+++ b/association/object_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: object_label
@@ -18,13 +20,14 @@ URI: [sssom:object_label](https://w3id.org/sssom/object_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/old_date.md b/association/old_date.md
index 90fbd5587..aceadbfcc 100644
--- a/association/old_date.md
+++ b/association/old_date.md
@@ -1,3 +1,5 @@
+
+
# Slot: old_date
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_date](https://w3id.org/oak/association/old_date)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/old_object.md b/association/old_object.md
index 90e8d4fc8..388414f42 100644
--- a/association/old_object.md
+++ b/association/old_object.md
@@ -1,3 +1,5 @@
+
+
# Slot: old_object
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_object](https://w3id.org/oak/association/old_object)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/old_object_obsolete.md b/association/old_object_obsolete.md
index 7263a8641..fb5258224 100644
--- a/association/old_object_obsolete.md
+++ b/association/old_object_obsolete.md
@@ -1,3 +1,5 @@
+
+
# Slot: old_object_obsolete
@@ -18,11 +20,12 @@ URI: [ontoassoc:old_object_obsolete](https://w3id.org/oak/association/old_object
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/old_predicate.md b/association/old_predicate.md
index 808437d71..eabbabbff 100644
--- a/association/old_predicate.md
+++ b/association/old_predicate.md
@@ -1,3 +1,5 @@
+
+
# Slot: old_predicate
@@ -19,11 +21,12 @@ URI: [ontoassoc:old_predicate](https://w3id.org/oak/association/old_predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/original_object.md b/association/original_object.md
index ac624f88d..160f08131 100644
--- a/association/original_object.md
+++ b/association/original_object.md
@@ -1,3 +1,5 @@
+
+
# Slot: original_object
@@ -17,6 +19,7 @@ URI: [biolink:original_object](https://w3id.org/biolink/vocab/original_object)
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/association/original_predicate.md b/association/original_predicate.md
index 075d71267..2dd79831c 100644
--- a/association/original_predicate.md
+++ b/association/original_predicate.md
@@ -1,3 +1,5 @@
+
+
# Slot: original_predicate
@@ -17,6 +19,7 @@ URI: [biolink:original_predicate](https://w3id.org/biolink/vocab/original_predic
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/association/original_subject.md b/association/original_subject.md
index 54422c76f..9699f3530 100644
--- a/association/original_subject.md
+++ b/association/original_subject.md
@@ -1,3 +1,5 @@
+
+
# Slot: original_subject
@@ -17,6 +19,7 @@ URI: [biolink:original_subject](https://w3id.org/biolink/vocab/original_subject)
+
## Properties
* Range: [Uriorcurie](Uriorcurie.md)
diff --git a/association/predicate.md b/association/predicate.md
index 29daf4ea2..225aeff14 100644
--- a/association/predicate.md
+++ b/association/predicate.md
@@ -1,3 +1,5 @@
+
+
# Slot: predicate
@@ -20,14 +22,15 @@ URI: [rdf:predicate](rdf:predicate)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/predicate_label.md b/association/predicate_label.md
index 26a54fd8a..fb6f77f24 100644
--- a/association/predicate_label.md
+++ b/association/predicate_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: predicate_label
@@ -18,13 +20,14 @@ URI: [sssom:predicate_label](https://w3id.org/sssom/predicate_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/preserve_negated_associations.md b/association/preserve_negated_associations.md
index b346925ff..9b7a82b92 100644
--- a/association/preserve_negated_associations.md
+++ b/association/preserve_negated_associations.md
@@ -1,3 +1,5 @@
+
+
# Slot: preserve_negated_associations
@@ -16,11 +18,12 @@ URI: [ontoassoc:preserve_negated_associations](https://w3id.org/oak/association/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
diff --git a/association/primary_knowledge_source.md b/association/primary_knowledge_source.md
index df5b9574c..408f26b6b 100644
--- a/association/primary_knowledge_source.md
+++ b/association/primary_knowledge_source.md
@@ -1,3 +1,5 @@
+
+
# Slot: primary_knowledge_source
@@ -14,15 +16,16 @@ URI: [biolink:primary_knowledge_source](https://w3id.org/biolink/vocab/primary_k
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
-[ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/property_values.md b/association/property_values.md
index 3a92163fb..5b07f38cb 100644
--- a/association/property_values.md
+++ b/association/property_values.md
@@ -1,3 +1,5 @@
+
+
# Slot: property_values
@@ -14,13 +16,14 @@ URI: [ontoassoc:property_values](https://w3id.org/oak/association/property_value
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/proportion_subjects_in_common.md b/association/proportion_subjects_in_common.md
index 50e95fac8..24d1c1466 100644
--- a/association/proportion_subjects_in_common.md
+++ b/association/proportion_subjects_in_common.md
@@ -1,3 +1,5 @@
+
+
# Slot: proportion_subjects_in_common
URI: [ontoassoc:proportion_subjects_in_common](https://w3id.org/oak/association/proportion_subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:proportion_subjects_in_common](https://w3id.org/oak/association/
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/publication_is_added.md b/association/publication_is_added.md
index bcebb291e..16593417a 100644
--- a/association/publication_is_added.md
+++ b/association/publication_is_added.md
@@ -1,3 +1,5 @@
+
+
# Slot: publication_is_added
@@ -18,11 +20,12 @@ URI: [ontoassoc:publication_is_added](https://w3id.org/oak/association/publicati
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/publication_is_deleted.md b/association/publication_is_deleted.md
index e789f910a..e0f8d2f89 100644
--- a/association/publication_is_deleted.md
+++ b/association/publication_is_deleted.md
@@ -1,3 +1,5 @@
+
+
# Slot: publication_is_deleted
@@ -18,11 +20,12 @@ URI: [ontoassoc:publication_is_deleted](https://w3id.org/oak/association/publica
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/publications.md b/association/publications.md
index 911a93bf5..d0fce79f5 100644
--- a/association/publications.md
+++ b/association/publications.md
@@ -1,3 +1,5 @@
+
+
# Slot: publications
@@ -14,14 +16,15 @@ URI: [biolink:publications](https://w3id.org/biolink/vocab/publications)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/sub_groups.md b/association/sub_groups.md
index 0b0f2d761..6d720933d 100644
--- a/association/sub_groups.md
+++ b/association/sub_groups.md
@@ -1,3 +1,5 @@
+
+
# Slot: sub_groups
@@ -14,11 +16,12 @@ URI: [ontoassoc:sub_groups](https://w3id.org/oak/association/sub_groups)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[RollupGroup](RollupGroup.md) | | no |
+| [RollupGroup](RollupGroup.md) | | no |
diff --git a/association/subject.md b/association/subject.md
index 98ea8bafa..0abe5ca35 100644
--- a/association/subject.md
+++ b/association/subject.md
@@ -1,3 +1,5 @@
+
+
# Slot: subject
@@ -14,14 +16,15 @@ URI: [rdf:subject](rdf:subject)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/subject_closure.md b/association/subject_closure.md
index fd51eda13..e6e80b77f 100644
--- a/association/subject_closure.md
+++ b/association/subject_closure.md
@@ -1,3 +1,5 @@
+
+
# Slot: subject_closure
@@ -14,13 +16,14 @@ URI: [ontoassoc:subject_closure](https://w3id.org/oak/association/subject_closur
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/subject_closure_label.md b/association/subject_closure_label.md
index 633145943..099f5454d 100644
--- a/association/subject_closure_label.md
+++ b/association/subject_closure_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: subject_closure_label
@@ -14,13 +16,14 @@ URI: [ontoassoc:subject_closure_label](https://w3id.org/oak/association/subject_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/subject_label.md b/association/subject_label.md
index ac384ec45..a09790574 100644
--- a/association/subject_label.md
+++ b/association/subject_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: subject_label
@@ -18,13 +20,14 @@ URI: [sssom:subject_label](https://w3id.org/sssom/subject_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/association/subjects_in_common.md b/association/subjects_in_common.md
index 88116a27c..8373ab693 100644
--- a/association/subjects_in_common.md
+++ b/association/subjects_in_common.md
@@ -1,3 +1,5 @@
+
+
# Slot: subjects_in_common
URI: [ontoassoc:subjects_in_common](https://w3id.org/oak/association/subjects_in_common)
@@ -9,11 +11,12 @@ URI: [ontoassoc:subjects_in_common](https://w3id.org/oak/association/subjects_in
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
+| [PairwiseCoAssociation](PairwiseCoAssociation.md) | A collection of subjects co-associated with two objects | no |
diff --git a/association/summary_group.md b/association/summary_group.md
index c5b3f5f23..b6e524d76 100644
--- a/association/summary_group.md
+++ b/association/summary_group.md
@@ -1,3 +1,5 @@
+
+
# Slot: summary_group
@@ -14,11 +16,12 @@ URI: [ontoassoc:summary_group](https://w3id.org/oak/association/summary_group)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
+| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
diff --git a/association/supporting_objects.md b/association/supporting_objects.md
index b511bcd5e..66c2e0958 100644
--- a/association/supporting_objects.md
+++ b/association/supporting_objects.md
@@ -1,3 +1,5 @@
+
+
# Slot: supporting_objects
@@ -14,13 +16,14 @@ URI: [ontoassoc:supporting_objects](https://w3id.org/oak/association/supporting_
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
-[Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
-[NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no |
+| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
+| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |
diff --git a/class-enrichment/ClassEnrichmentConfiguration.md b/class-enrichment/ClassEnrichmentConfiguration.md
index d7b909018..233b8556d 100644
--- a/class-enrichment/ClassEnrichmentConfiguration.md
+++ b/class-enrichment/ClassEnrichmentConfiguration.md
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentConfiguration
diff --git a/class-enrichment/ClassEnrichmentResult.md b/class-enrichment/ClassEnrichmentResult.md
index 83b645c0d..e636d68e5 100644
--- a/class-enrichment/ClassEnrichmentResult.md
+++ b/class-enrichment/ClassEnrichmentResult.md
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentResult
diff --git a/class-enrichment/ClassEnrichmentResultSet.md b/class-enrichment/ClassEnrichmentResultSet.md
index cb2dd0f8c..350919796 100644
--- a/class-enrichment/ClassEnrichmentResultSet.md
+++ b/class-enrichment/ClassEnrichmentResultSet.md
@@ -1,3 +1,5 @@
+
+
# Class: ClassEnrichmentResultSet
diff --git a/class-enrichment/ancestor_of_more_informative_result.md b/class-enrichment/ancestor_of_more_informative_result.md
index e78378f1b..86021ae36 100644
--- a/class-enrichment/ancestor_of_more_informative_result.md
+++ b/class-enrichment/ancestor_of_more_informative_result.md
@@ -1,3 +1,5 @@
+
+
# Slot: ancestor_of_more_informative_result
@@ -14,11 +16,12 @@ URI: [ontoenrich:ancestor_of_more_informative_result](https://w3id.org/oak/class
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/background_count.md b/class-enrichment/background_count.md
index 5239b0569..6d0f9ffe9 100644
--- a/class-enrichment/background_count.md
+++ b/class-enrichment/background_count.md
@@ -1,3 +1,5 @@
+
+
# Slot: background_count
@@ -14,11 +16,12 @@ URI: [ontoenrich:background_count](https://w3id.org/oak/class-enrichment/backgro
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/background_total.md b/class-enrichment/background_total.md
index 4bdbe51d2..1e8e9dfce 100644
--- a/class-enrichment/background_total.md
+++ b/class-enrichment/background_total.md
@@ -1,3 +1,5 @@
+
+
# Slot: background_total
@@ -14,11 +16,12 @@ URI: [ontoenrich:background_total](https://w3id.org/oak/class-enrichment/backgro
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/class_id.md b/class-enrichment/class_id.md
index e6cd668f5..752105a48 100644
--- a/class-enrichment/class_id.md
+++ b/class-enrichment/class_id.md
@@ -1,3 +1,5 @@
+
+
# Slot: class_id
@@ -14,11 +16,12 @@ URI: [ontoenrich:class_id](https://w3id.org/oak/class-enrichment/class_id)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/class_label.md b/class-enrichment/class_label.md
index ff02e2ce5..3ac4c4c17 100644
--- a/class-enrichment/class_label.md
+++ b/class-enrichment/class_label.md
@@ -1,3 +1,5 @@
+
+
# Slot: class_label
@@ -14,11 +16,12 @@ URI: [ontoenrich:class_label](https://w3id.org/oak/class-enrichment/class_label)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/descendant_of_more_informative_result.md b/class-enrichment/descendant_of_more_informative_result.md
index aced0a5cd..9068006a6 100644
--- a/class-enrichment/descendant_of_more_informative_result.md
+++ b/class-enrichment/descendant_of_more_informative_result.md
@@ -1,3 +1,5 @@
+
+
# Slot: descendant_of_more_informative_result
@@ -14,11 +16,12 @@ URI: [ontoenrich:descendant_of_more_informative_result](https://w3id.org/oak/cla
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/direction.md b/class-enrichment/direction.md
index 1f517dcc7..ae18ce22d 100644
--- a/class-enrichment/direction.md
+++ b/class-enrichment/direction.md
@@ -1,3 +1,5 @@
+
+
# Slot: direction
@@ -14,11 +16,12 @@ URI: [ontoenrich:direction](https://w3id.org/oak/class-enrichment/direction)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/false_discovery_rate.md b/class-enrichment/false_discovery_rate.md
index 5fba7b1c0..17ae3b342 100644
--- a/class-enrichment/false_discovery_rate.md
+++ b/class-enrichment/false_discovery_rate.md
@@ -1,3 +1,5 @@
+
+
# Slot: false_discovery_rate
@@ -14,11 +16,12 @@ URI: [ontoenrich:false_discovery_rate](https://w3id.org/oak/class-enrichment/fal
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/fold_enrichment.md b/class-enrichment/fold_enrichment.md
index fe1ac5e44..43c6330ef 100644
--- a/class-enrichment/fold_enrichment.md
+++ b/class-enrichment/fold_enrichment.md
@@ -1,3 +1,5 @@
+
+
# Slot: fold_enrichment
@@ -14,11 +16,12 @@ URI: [ontoenrich:fold_enrichment](https://w3id.org/oak/class-enrichment/fold_enr
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/p_value.md b/class-enrichment/p_value.md
index 61f70a30f..9ff7b0882 100644
--- a/class-enrichment/p_value.md
+++ b/class-enrichment/p_value.md
@@ -1,3 +1,5 @@
+
+
# Slot: p_value
@@ -14,11 +16,12 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/p_value_adjusted.md b/class-enrichment/p_value_adjusted.md
index 0454987a8..36a088b87 100644
--- a/class-enrichment/p_value_adjusted.md
+++ b/class-enrichment/p_value_adjusted.md
@@ -1,3 +1,5 @@
+
+
# Slot: p_value_adjusted
@@ -14,11 +16,12 @@ URI: [ontoenrich:p_value_adjusted](https://w3id.org/oak/class-enrichment/p_value
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/p_value_cutoff.md b/class-enrichment/p_value_cutoff.md
index 20a79e048..e3ae594ce 100644
--- a/class-enrichment/p_value_cutoff.md
+++ b/class-enrichment/p_value_cutoff.md
@@ -1,3 +1,5 @@
+
+
# Slot: p_value_cutoff
@@ -14,11 +16,12 @@ URI: [ontoenrich:p_value_cutoff](https://w3id.org/oak/class-enrichment/p_value_c
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) | configuration for search | no |
+| [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) | configuration for search | no |
diff --git a/class-enrichment/probability.md b/class-enrichment/probability.md
index 14a0b7182..e48180fe3 100644
--- a/class-enrichment/probability.md
+++ b/class-enrichment/probability.md
@@ -1,3 +1,5 @@
+
+
# Slot: probability
@@ -14,11 +16,12 @@ URI: [ontoenrich:probability](https://w3id.org/oak/class-enrichment/probability)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/rank.md b/class-enrichment/rank.md
index 9ce942478..0782218ed 100644
--- a/class-enrichment/rank.md
+++ b/class-enrichment/rank.md
@@ -1,3 +1,5 @@
+
+
# Slot: rank
@@ -14,11 +16,12 @@ URI: [ontoenrich:rank](https://w3id.org/oak/class-enrichment/rank)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/results.md b/class-enrichment/results.md
index 46e382bdf..48d82cb43 100644
--- a/class-enrichment/results.md
+++ b/class-enrichment/results.md
@@ -1,3 +1,5 @@
+
+
# Slot: results
@@ -14,11 +16,12 @@ URI: [ontoenrich:results](https://w3id.org/oak/class-enrichment/results)
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) | A collection of enrichemt results | no |
+| [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) | A collection of enrichemt results | no |
diff --git a/class-enrichment/sample_count.md b/class-enrichment/sample_count.md
index 8b70341a9..6f2885fc1 100644
--- a/class-enrichment/sample_count.md
+++ b/class-enrichment/sample_count.md
@@ -1,3 +1,5 @@
+
+
# Slot: sample_count
@@ -14,11 +16,12 @@ URI: [ontoenrich:sample_count](https://w3id.org/oak/class-enrichment/sample_coun
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/class-enrichment/sample_total.md b/class-enrichment/sample_total.md
index bb0af2f7f..3468519cf 100644
--- a/class-enrichment/sample_total.md
+++ b/class-enrichment/sample_total.md
@@ -1,3 +1,5 @@
+
+
# Slot: sample_total
@@ -14,11 +16,12 @@ URI: [ontoenrich:sample_total](https://w3id.org/oak/class-enrichment/sample_tota
+
## Applicable Classes
| Name | Description | Modifies Slot |
| --- | --- | --- |
-[ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
+| [ClassEnrichmentResult](ClassEnrichmentResult.md) | A single enrichment result | no |
diff --git a/cli.html b/cli.html
index f5558bb64..be4101e23 100644
--- a/cli.html
+++ b/cli.html
@@ -25,7 +25,7 @@
-
+
@@ -60,84 +60,7 @@
Commands
runoak viz --help
-
-runoak
-Run the oaklib Command Line.
-A subcommand must be passed - for example: ancestors, terms, …
-Most commands require an input ontology to be specified:
-
-runoak -i <INPUT SPECIFICATION> SUBCOMMAND <SUBCOMMAND OPTIONS AND ARGUMENTS>
-
-Get help on any command, e.g:
-
-runoak viz -h
-
-runoak [OPTIONS] COMMAND [ARGS]...
-
-
-Options
-
-
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-
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-
-
-
-aliases
-List aliases for a term or set of terms.
-
-Example:
-
-runoak -i ubergraph:uberon aliases UBERON:0001988
-
-TERMS should be either an explicit list of terms or queries, or can be a selector query,
-such as ‘.all’ to fetch all terms in the ontology
-Show all aliases:
-
-runoak -i db/envo.db aliases .all
-
-Currently the core behavior of this command assumes a simple datamodel for aliases, where an aliases
-is a simple property-value tuples, with the property being from some standard vocabulary (e.g. skos:altLabel,
-oboInOwl, etc)
-If you know the synonyms follow the OBO/oboInOwl datamodel you can pass –obo-model, this will give back
-richer data if present in the ontology, including synonym categories/types, synonym provenance
-In future, this may become the default
-runoak aliases [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-ancestors
-List all ancestors of a given term or terms.
-Here ancestor means the transitive closure of the parent relationship, where
-a parent includes all relationship types, not just is-a.
-
-Example:
-
-runoak -i cl.owl ancestors CL:4023094
-
-This will show ancestry over the full relationship graph. Like any relational
-OAK command, this can be filtered by relationship type (predicate), using –predicate (-p).
-For example, constrained to is-a and part-of:
-
-runoak -i cl.owl ancestors CL:4023094 -p i,BFO:0000050
-
-Multiple backends can be used, including ubergraph:
-
-runoak -i ubergraph: ancestors CL:4023094 -p i,BFO:0000050
-
-Search terms can also be used:
-
-runoak -i cl.owl ancestors ‘goblet cell’
-
-Multiple terms can be passed:
-
-runoak -i sqlite:go.db ancestors GO:0005773 GO:0005737 -p i,p
-
-Python API:
-
-
-runoak ancestors [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-annotate
-Annotate a piece of text using a Named Entity Recognition annotation.
-Some endpoints such as BioPortal have built-in support for annotation;
-in these cases the endpoint functionality is used:
-
-Example:
-
-runoak -i bioportal: annotate “enlarged nucleus in T-cells from peripheral blood”
-
-For other endpoints, the built-in OAK annotator is used. This currently uses a basic
-algorithm based on lexical matching.
-
-
-Example:
-
-runoak -i sqlite:obo:cl annotate “enlarged nucleus in T-cells from peripheral blood”
-
-Using the builtin annotator can be slow, as the lexical index is re-built every time.
-To preserve this, use the --lexical-index-file
(-L
) option to specify a file to save.
-On subsequent iterations the file is reused.
-You can also use --text-file
to pass in a text file to be parsed one line at a time
-If gilda is installed as an extra, it can be used,
-but --matches-whole-text
(-W
) must be specified,
-as gilda only performs grounding.
-
-
-Example:
-
-runoak -i gilda: annotate -W BRCA2
-
-Aliases can be listed in the output by setting the flag
-–include-aliases to true (default: false).
-Example (using the plugin oakx-spacy):
-
-runoak -i spacy:sqlite:obo:bero annotate Myeloid derived suppressor cells. –include-aliases
-
-will yield:
-
-confidence: 0.8
-object_aliases:
-- Myeloid-Derived Suppressor Cells
-- MDSCs
-- mdscs
-- myeloid-derived suppressor cells
-object_id: obo:MESH_D000072737
-object_label: Myeloid-Derived Suppressor Cells
-subject_end: 30
-subject_start: 0
-
-Python API:
-
-
-Data model:
-
-
-runoak annotate [OPTIONS] [WORDS]...
-
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-Options
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-Arguments
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-apply
-Applies a patch to an ontology. The patch should be specified using KGCL syntax, see
-https://github.com/INCATools/kgcl
-
-Example:
-
-runoak -i cl.owl.ttl apply “rename CL:0000561 to ‘amacrine neuron’” -o cl.owl.ttl -O ttl
-
-On an obo format file:
-
-runoak -i simpleobo:go-edit.obo apply “rename GO:0005634 from ‘nucleus’ to ‘foo’” -o go-edit-new.obo
-
-With URIs:
-
-runoak -i cl.owl.ttl apply “rename <http://purl.obolibrary.org/obo/CL_0000561> from ‘amacrine cell’ to ‘amacrine neuron’” -o cl.owl.ttl -O ttl
-
-
-
-Warning:
-This command is still experimental. Some things to bear in mind:
-
-
-runoak apply [OPTIONS] [COMMANDS]...
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-apply-obsolete
-Sets an ontology element to be obsolete
-
-Example:
-
-runoak -i my.obo apply-obsolete MY:0002200 -o my-modified.obo
-
-Multiple terms can be passed, as labels, IDs, or using OAK queries:
-
-runoak -i my.obo apply-obsolete MY:1 MY:2 MY:3 … -o my-modified.obo
-
-This may be chained, for example to take all terms matching a search query and then
-obsolete them all:
-
-runoak -i my.db search ‘l/^Foo/` | runoak -i my.db –autosave apply-obsolete -
-
-This command is partially redundant with the more general “apply” command
-runoak apply-obsolete [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-apply-taxon-constraints
-Test candidate taxon constraints
-Multiple candidate constraints can be passed as arguments. these are in the form of triples
-separated by periods.
-
-Example:
-
-runoak -i db/go.db apply-taxon-constraints -p i,p GO:0005743 only NCBITaxon:2759
-never NCBITaxon:2 . GO:0005634 only NCBITaxon:2
-
-The –evolution-file (-E) option can be used to pass in a file of candidates.
-This should follow the format used in https://arxiv.org/abs/1802.06004
-E.g.
-
-GO:0000229,Gain|NCBITaxon:1(root);>Loss|NCBITaxon:2759(Eukaryota);
-
-
-
-Example:
-
-runoak -i db/go.db eval-taxon-constraints -p i,p -E tests/input/go-evo-gains-losses.csv
-
-More examples:
-
-
-runoak apply-taxon-constraints [OPTIONS] [CONSTRAINTS]...
-
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-Options
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-Arguments
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-associations
-Lookup associations from or to entities.
-
-Example:
-
-runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations
-
-The above will show all associations
-To query using an ontology term, including is-a closure, specify one or more
-terms or term queries, plus the closure predicate(s), e.g.
-
-
-Example:
-
-runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i HP:0001392
-
-This shows all annotations either to “Abnormality of the liver” (HP:0001392), or
-to is-a descendants.
-Using input specifications:
-It can be awkward to specify both input ontology and association path and format. You
-can use input specifications to bundle common combinations of inputs together.
-For example, the go-dictybase-input-spec combines go plus dictybase associations.
-
-
-Example:
-
-runoak –i src/oaklib/conf/go-dictybase-input-spec.yaml associations -p i,p GO:0008104
-
-More examples:
-
-
-runoak associations [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-associations-counts
-Count associations, grouped by subject or object
-
-Example:
-
-runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts
-
-This will default to summarzing by objects (HPO term), showing the number
-of associations for each term.
-This will be direct counts only. To include is-a closure, specify
-the closure predicate(s), e.g.
-
-
-Example:
-
-runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i
-
-You can also group by other fields
-
-
-Example:
-
-runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts –group-by subject
-
-This will show the number of associations for each disease.
-OAK also includes a number of specialized adapters that implement this method
-for particular databases.
-For example, to get the number of IEA associations for each GO term:
-
-runoak -i amigo: associations-counts –limit -1 -F evidence_type=IEA –no-autolabel
-
-This can be constrained by species:
-
-runoak -i amigo:NCBITaxon:9606 associations-counts –limit -1 -F evidence_type=IEA –no-autolabel
-
-Other options:
-This command accepts many of the same options as the associations command, see
-the docs for this command for details.
-runoak associations-counts [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-associations-matrix
-Co-annotation matrix query.
-This queries for co-annotations between pairs of terms.
-See: Wood V., Carbon S., et al, https://royalsocietypublishing.org/doi/10.1098/rsob.200149
-
-Example:
-
-runoak -i amigo:NCBITaxon:9606 associations-matrix -p i,p GO:0042416 GO:0014046
-
-As a heatmap:
-
-runoak -i amigo:NCBITaxon:9606 associations-matrix -p i,p GO:0042416 GO:0014046 -o heatmap > /tmp/heatmap.png
-
-runoak associations-matrix [OPTIONS] [TERMS]...
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-Options
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-Arguments
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-axioms
-Filters axioms
-
-Example:
-
-runoak -i cl.ofn axiom
-
-The above will write all axioms.
-You can filter by axiom type:
-
-
-Example:
-
-runoak -i cl.ofn axiom –axiom-type SubClassOf
-
-Note this currently only works with the funowl adapter, on functional syntax files
-runoak axioms [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-cache-clear
-Clear the contents of the pystow oaklib cache.
-runoak cache-clear [OPTIONS]
-
-
-Options
-
-
-
-
-
-cache-ls
-List the contents of the pystow oaklib cache.
-TODO: this currently only works on unix-based systems.
-runoak cache-ls [OPTIONS]
-
-
-
-
-definitions
-Show textual definitions for term or set of terms
-
-Example:
-
-runoak -i sqlite:obo:envo definitions ‘tropical biome’ ‘temperate biome’
-
-You can use the “.all” selector to show all definitions for all terms in the ontology:
-
-
-Example:
-
-runoak -i sqlite:obo:envo definitions .all
-
-You can also include definition metadata, such as provenance and source:
-
-runoak -i sqlite:obo:cl definitions –additional-metadata neuron
-
-Python API:
-
-
-runoak definitions [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-descendants
-List all descendants of a term
-
-Example:
-
-runoak -i sqlite:obo:obi descendants assay -p i
-
-
-
-Example:
-
-runoak -i sqlite:obo:uberon descendants heart -p i,p
-
-This is the inverse of the ‘ancestors’ command; see the documentation for
-that command. But note that ‘descendants’ commands have the potential to be more
-“explosive” than ancestors commands, especially for high level terms, and for when
-predicates are not specified
-Python API:
-
-
-runoak descendants [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-diff
-Compute difference between two ontologies.
-
-Example:
-
-runoak -i foo.obo diff -X bar.obo -o diff.yaml
-
-This will produce a list of Changes that are required to go from the main input ontology (–input)
-to the other ontology (–other-ontology, or -X).
-The output follows the KGCL data model.
-See https://incatools.github.io/ontology-access-kit/datamodels/kgcl/index.html
-You can use –output-type to control the output format.
-KGCL controlled natural language:
-
-runoak -i foo.obo diff -X bar.obo -o diff.txt –output-type kgcl
-
-KGCL JSON:
-
-runoak -i foo.obo diff -X bar.obo -o diff.json –output-type json
-
-YAML (default):
-
-runoak -i foo.obo diff -X bar.obo -o diff.yaml –output-type yaml
-
-The –statistics option can be used to generate summary statistics for the changes.
-These are grouped according to the –group-by-property option. For example,
-the GO uses the oio:hasOBONamespace property to partition classes into 3 categories.
-
-
-Example:
-
-runoak -i go.obo diff -X go-new.obo -o diff.yaml –statistics –group-by-property oio:hasOBONamespace
-
-This will produce a YAML dictionary, with outer keys being the values of the oio:hasOBONamespace property,
-and inner keys being the change types.
-If –group-by-property is not specified, or there is no value for this property, then the outer key
-will be “__RESIDUAL__”
-For summary statistics, you can also specify –output-type csv, to get a tabular out
-Limitations:
-This does not do a diff over every axiom in each ontology. For a complete OWL diff, you should
-use ROBOT.
-runoak diff [OPTIONS]
-
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-Options
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-diff-associations
-Diffs two association sources.
-
-Example:
-
-runoak -i sqlite:obo:go -G gaf diff-associations –old-date ${date1} –new-date ${date2} -g “${download_dir}/${group}-${date1}.gaf” -X “${download_dir}/${group}-${date2}.gaf” –group-by publications -p i,p -o “${group}-diff-${date1}-to-${date2}.tsv
-
-See https://w3id.org/oak/association for the diff data model.
-NOTE: This functionality may move out of core
-runoak diff-associations [OPTIONS]
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-diff-terms
-Compares a pair of terms in two ontologies
-EXPERIMENTAL
-runoak diff-terms [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
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-
-
-diff-via-mappings
-Calculates cross-ontology diff using mappings
-Given a pair of ontologies, and mappings that connect terms in both ontologies, this
-command will perform a structural comparison of all mapped pairs of terms
-
-Example:
-
-runoak -i sqlite:obo:uberon diff-via-mappings –other-input sqlite:obo:zfa –source UBERON –source ZFA -O csv
-
-Note the above command does not have any mapping file specified; the mappings that are distributed within
-each ontology is used (in this case, Uberon contains mappings to ZFA)
-If the mappings are provided externally:
-
-runoak -i ont1.obo diff-via-mappings –other-input ont2.obo –mapping-input mappings.sssom.tsv
-
-(in the above example, –source is not passed, so all mappings are tested)
-If there are no existing mappings, you can use the lexmatch command to generate them:
-
-runoak -i ont1.obo diff-via-mappings -a ont2.obo lexmatch -o mappings.sssom.tsv
-runoak -i ont1.obo diff-via-mappings –other-input ont2.obo –mapping-input mappings.sssom.tsv
-
-The output from this command follows the cross-ontology-diff data model
-(https://incatools.github.io/ontology-access-kit/datamodels/cross-ontology-diff/index.html)
-This can be serialized in YAML or TSV form
-runoak diff-via-mappings [OPTIONS] [TERMS]...
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-Arguments
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-disjoints
-Show all disjoints for a set of terms, or whole ontology.
-Leave off all arguments for defaults - all terms, YAML OboGraph model
-serialization:
-
-Example:
-
-runoak -i sqlite:obo:uberon disjoints
-
-Note that this will include pairwise disjoints, setwise disjoints,
-disjoint unions, and disjoints involving simple class expressions.
-A tabular format can be easier to browse, and includes labels by default:
-
-
-Example:
-
-runoak -i sqlite:obo:uberon disjoints –autolabel -O csv
-
-To perform this on a subset:
-
-
-Example:
-
-runoak -i sqlite:obo:cl disjoints –autolabel -O csv .desc//p=i “immune cell”
-
-Data model:
-
-
-runoak disjoints [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-dump
-Exports (dumps) the entire contents of an ontology.
-
-Example:
-
-runoak -i pato.obo dump -o pato.json -O json
-
-
-
-Example:
-
-runoak -i pato.owl dump -o pato.ttl -O turtle
-
-You can also pass in a JSON configuration file to parameterize the dump process.
-Currently this is only used for fhirjson dumps, the configuration options are specified here:
-https://incatools.github.io/ontology-access-kit/converters/obo-graph-to-fhir.html
-
-
-Example:
-
-runoak -i pato.owl dump -o pato.ttl -O fhirjson -c fhir_config.json -o pato.fhir.json
-
-Currently each implementation only supports a subset of formats.
-The dump command is also blocked for remote endpoints such as Ubergraph,
-to avoid killer queries.
-Python API:
-
-
-runoak dump [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
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-enrichment
-Run class enrichment analysis.
-Given a sample file of identifiers (e.g. gene IDs), plus a set of associations (e.g. gene to term
-associations, return the terms that are over-represented in the sample set.
-
-Example:
-
-runoak -i sqlite:obo:uberon -g gene2anat.txt -G g2t enrichment -U my-genes.txt -O csv
-
-This runs an enrichment using Uberon on my-genes.txt, using the gene2anat.txt file as the
-association file (assuming simple gene-to-term format). The output is in CSV format.
-It is recommended you always provide a background set, including all the entity identifiers
-considered in the experiment.
-You can specify –filter-redundant to filter out redundant terms. This will block reporting
-of any terms that are either subsumed by or subsume a lower p-value term that is already
-reported.
-For a full example, see:
-
-
-Note that it is possible to run “pseudo-enrichments” on term lists only by passing
-no associations and using –ontology-only. This creates a fake association set that is simply
-reflexive relations between each term and itself. This can be useful for summarizing term lists,
-but note that P-values may not be meaningful.
-runoak enrichment [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-expand-subsets
-For each subset provide a mapping of each term in the ontology to a subset
-
-Example:
-
-runoak -i db/pato.db expand-subsets attribute_slim value_slim
-
-runoak expand-subsets [OPTIONS] [SUBSETS]...
-
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-Options
-
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-
-Arguments
-
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-extract
-Extracts a sub-ontology.
-Simple example:
-
-runoak -i cl.db extract neuron
-
-This will extract a single node for “neuron”. No relationships will be included,
-as –no-dangling is the default
-To include edges even if dangling:
-
-runoak -i cl.db extract neuron –dangling
-
-A subset of relationship types (predicates):
-
-runoak -i cl.db extract neuron –dangling -p i
-
-If you wish to get a fully connected is-a graph for all is-a ancestors:
-
-runoak -i cl.db extract .anc//p=i neuron –dangling -p i
-
-If you prefer, you can split this into 2 commands:
-
-runoak -i cl.db ancestors -p i neuron > seed.txt
-
-Then:
-
-runoak -i cl.db extract .idfile seed.txt –dangling -p i
-
-You can specify different output types and output paths:
-
-runoak -i cl.db extract .idfile seed.txt -O owl -o neuron.owl.ttl
-
-Allowed formats include: obo, obographs, owl/ttl, fhirjson
-runoak extract [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-fill-table
-Fills missing values in a table of ontology elements
-See https://incatools.github.io/ontology-access-kit/src/oaklib.utilities.table_filler
-Given a TSV with a populated ID column, and unpopulated columns for definition, label, mappings, ancestors,
-this will iterate through each row filling in each missing value by performing ontology lookups.
-In some cases, this can also perform reverse lookups; i.e given a table with labels populated and blank IDs,
-then fill in the IDs
-In the most basic scenario, you have a table with two columns ‘id’ and ‘label’. These are the “conventional” column
-headers for a table of ontology elements (see later for configuration when you don’t follow conventions)
-
-Example:
-
-runoak -i cl.owl.ttl fill-table my-table.tsv
-
-(any implementation can be used)
-The same command will work for the reverse scenario - when you have labels populated, but IDs are not populated
-By default this will throw an error if a lookup is not successful; this can be relaxed
-Relaxed:
-
-runoak -i cl.owl.ttl fill-table –allow-missing my-table.tsv
-
-In this case missing values that cannot be populated will remain empty
-To explicitly populate a value:
-
-runoak -i cl.owl.ttl fill-table –missing-value-token NO_DATA my-table.tsv
-
-Currently the following columns are recognized:
-
-
-The metadata inference procedure will also work for when you have denormalized TSV files
-with columns such as “foo_id” and “foo_name”. This will be recognized as an implicit normalized
-label relation between id and name of a foo element.
-You can be more explicit in one of two ways:
-
-
-
-
-For the first method, you can pass in multiple relations using the –relation arg. For example,
-given a TSV with columns cl_identifier and cl_display_label you can say:
-
-
-Example:
-
-runoak -i cl.owl.ttl fill-table –relation “{primary_key: cl_identifier, dependent_column: cl_display_label, relation: label}”
-
-You can also specify this in a YAML file
-For the 2nd method, you need to specify a LinkML schema with a class where (1) at least one field is annotated
-as being an identifier (2) one or more slots have slot_uri elements mapping them to standard metadata elements
-such as rdfs:label.
-For example, my-schema.yaml:
-
-
-
-
-This is a powerful command with many ways of configuring it - we will add separate docs for this soon,
-for now please file an issue on github with any questions
-
-
-runoak fill-table [OPTIONS] TABLE_FILE
-
-
-Options
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-Arguments
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-generate-definitions
-Generate definitions for a term or terms.
-Currently this only works with the llm extension.
-
-Example:
-
-runoak -i llm:sqlite:obo:foodon generate-definitions FOODON:03315258
-
-The –style-hints option can be used to provide hints to the definition generator.
-
-
-Example:
-
-runoak -i llm:sqlite:obo:foodon generate-definitions FOODON:03315258 –style-hints “Write the definition in the style of a pretentious food critic”
-
-Generates:
-
-“The pancake, a humble delight in the realm of breakfast fare,
-presents itself as a delectable disc of gastronomic delight…”
-
-runoak generate-definitions [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
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-
-generate-disjoints
-Generate candidate disjointness axioms.
-
-Example:
-
-runoak -i sqlite:obo:iao generate-disjoints -O obo
-
-To generate spatial disjointness axioms:
-
-runoak -i sqlite:obo:zfa generate-disjoints -O obo p i,p
-
-runoak generate-disjoints [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-generate-lexical-replacements
-Generate lexical replacements based on a set of synonymizer rules.
-If the –apply-patch flag is set, the output will be an ontology file with the changes
-applied. Pass the –patch argument to lso get the patch file in KGCL format.
-
-Example:
-
-runoak -i foo.obo generate-lexical-replacements -R foo_rules.yaml –patch patch.kgcl –apply-patch -o foo_syn.obo
-
-If the apply-patch flag is NOT set then the main input will be KGCL commands
-
-
-Example:
-
-runoak -i foo.obo generate-lexical-replacements -R foo_rules.yaml -o changes.kgcl
-
-You can also pass the expressions directly as YAML
-
-
-Example:
-
-runoak -i foo.obo generate-lexical-replacements -Y ‘{match: “nuclear (w+)”, replacement: “1 nucleus”}’ .all
-
-see https://github.com/INCATools/kgcl.
-Note: this command is very similar to generate-synonyms, but the main use case here
-is replacing terms, and applying rules to other elements such as definitions
-runoak generate-lexical-replacements [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-generate-logical-definitions
-Generate logical definitions based on patterns file.
-runoak generate-logical-definitions [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
-
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-
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-generate-synonyms
-Generate synonyms based on a set of synonymizer rules.
-If the –apply-patch flag is set, the output will be an ontology file with the changes
-applied. Pass the –patch argument to lso get the patch file in KGCL format.
-
-Example:
-
-runoak -i foo.obo generate-synonyms -R foo_rules.yaml –patch patch.kgcl –apply-patch -o foo_syn.obo
-
-If the apply-patch flag is NOT set then the main input will be KGCL commands
-
-
-Example:
-
-runoak -i foo.obo generate-synonyms -R foo_rules.yaml -o changes.kgcl
-
-see https://github.com/INCATools/kgcl.
-runoak generate-synonyms [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
-
-
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-
-
-info
-Show information on term or set of terms
-
-Example:
-
-runoak -i sqlite:obo:cl info CL:4023094
-
-The default output is minimal, showing only ID and label
-The –output-type (-O) option can be used to specify other formats for the output.
-Currently there are only a few output types are supported. More will be provided in future.
-In OBO format:
-
-runoak -i cl.owl info CL:4023094 -O obo
-
-As CSV:
-
-runoak -i cl.obo info CL:4023094 -O csv
-
-The info output format can be parameterized with –display (-D)
-With xrefs and definitions:
-
-runoak -i cl.owl info CL:4023094 -D x,d
-
-With all information:
-
-runoak -i cl.owl info CL:4023094 -D all
-
-Like all OAK commands, input term lists can be multivalued, a mixture of IDs and labels, as well
-as queries that can be combined using boolean logic
-Info on two STATO terms:
-
-runoak -i ontobee:stato info STATO:0000286 STATO:0000287 -O obo
-
-All terms in ENVO with the string “forest” in them:
-
-runoak -i sqlite:obo:envo info l~forest
-
-Info on all subtypes of “statistical hypothesis test” in STATO:
-
-runoak -i sqlite:obo:stato info .desc//p=i ‘statistical hypothesis test’
-
-runoak info [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
-
-
-
-
-
-information-content
-Show information content for term or list of terms
-
-Example:
-
-runoak -i cl.db information-content -p i .all
-
-Like all OAK commands that operate over graphs, the graph traversal is controlled
-by the –predicates option. In the above case, the frequency of each term is equal to
-the number of reflexive is-a descendants of the term divided by total number of terms
-By default, the ontology is used as the corpus for computing term frequency.
-You can use an association file as the corpus:
-
-runoak -g hpoa.tsv -G hpoa -i hp.db information-content -p i –use-associations .all
-
-runoak information-content [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
-
-
-
-
-
-labels
-Show labels for term or list of terms
-
-Example:
-
-runoak -i cl.owl labels CL:4023093 CL:4023094
-
-You can use the “.all” selector to show all labels:
-
-
-Example:
-
-runoak -i cl.owl labels .all
-
-(this may be blocked for remote endpoints)
-You can query for terms that have either no label, or to include only ones with labels:
-Nodes with no labels:
-
-runoak -i cl.owl labels .all –if-absent exclude
-
-Multilingual support: if the adapter supports multilingual querying
-(currently only SQL) and the ontology has multilingual support, you can restrict results to
-a particular language.
-
-
-Example:
-
-runoak –preferred-language fr -i sqlite:obo:hpinternational labels .ancestors HP:0020110
-
-You can also query for all languages, and see these pivoted:
-
-
-Example:
-
-runoak -i sqlite:obo:hpinternational labels .ancestors HP:0020110 –pivot-languages
-
-Python API:
-
-
-runoak labels [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
-
-
-
-
-
-languages
-Show available languages
-
-Example:
-
-runoak languages
-
-runoak languages [OPTIONS]
-
-
-
-
-
-leafs
-List all leaf nodes in the ontology
-Like all OAK relational commands, this is parameterized by –predicates (-p).
-Note that the default is to return the roots of the relation graph over all predicates
-
-Example:
-
-runoak -i db/cob.db leafs
-
-This command is a wrapper onto the “leafs” command in the BasicOntologyInterface.
-
-
-runoak leafs [OPTIONS]
-
-
-Options
-
-
-
-
-
-
-
-
-
-
-
-
-lexmatch
-Performs lexical matching between pairs of terms in one more more ontologies.
-
-Examples
-
-runoak -i foo.obo lexmatch -o foo.sssom.tsv
-
-In this example, the input ontology file is assumed to contain all pairs of terms to be mapped.
-It is more common to map between all pairs of terms in two ontology files. In this case,
-you can merge the ontologies using a tool like ROBOT; or, to avoid a merge
-preprocessing step, use the –addl (-a) option to specify a second ontology file.
-
-runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv
-
-By default, this command will compare all terms in all ontologies. You can use the OAK
-term query syntax to pass in the set of all terms to be compared.
-For example, to compare all terms in union of FOO and BAR namespaces:
-
-runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv i^FOO: i^BAR:
-
-All members of the set are compared (including FOO to FOO matches and BAR to BAR
-matches), omitting trivial reciprocal matches.
-Use an “@” separator between two queries to feed in two explicit sets:
-
-runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv i^FOO: @ i^BAR:
-
-ALGORITHM: lexmatch implements a simple algorithm:
-
-
-The lexical index can be exported (in native YAML) using -L:
-
-runoak -i foo.obo lexmatch -L foo.index.yaml -o foo.sssom.tsv
-
-Note: if you run the above command a second time it will be faster as the index
-will be reused.
-RULES: Using custom rules:
-
-runoak -i foo.obo lexmatch -R match_rules.yaml -L foo.index.yaml -o foo.sssom.tsv
-
-Full documentation:
-
-module-oaklib.utilities.lexical.lexical_indexer
-runoak lexmatch [OPTIONS] [TERMS]...
-
-
-Options
-
-
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-
-
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-
-Arguments
-
-
-
-
-
-
-lint
-Lints an ontology, applying changes in place.
-The current implementation is highly incomplete, and only handles
-linting of syntactic patterns (chains of whitespace, trailing whitespace)
-in labels and definitions.
-The output is a list of changes, in a KCGL-compliant syntax.
-By default, changes will be applied
-
-Example:
-
-runoak -i my.obo lint
-
-This can be executed in dry-run mode, in which case changes are not applied:
-
-runoak -i my.obo lint –dry-run
-
-One common workflow is to emit the changes to a KCGL file which is manually checked,
-then applied as a separate step.
-Example workflow:
-
-runoak -i my.obo lint –dry-run -o changes.kgcl
-# examine and edit changes.kgcl
-runoak -i my.obo apply –changes-input changes.kgcl
-
-runoak lint [OPTIONS]
-
-
-Options
-
-
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-
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-
-
-
-logical-definitions
-Show all logical definitions for a term or terms.
-To show all logical definitions in an ontology, pass the “.all” query term
-Example; first create an alias:
-
-alias pato=”runoak -i obo:sqlite:pato”
-
-Then run the query:
-
-pato logical-definitions .all
-
-By default, “.all” will query all axioms for all terms including merged terms;
-to restrict to only the current terms, use an ID query:
-
-pato logical-definitions i^PATO
-
-You can also restrict to branches:
-
-pato logical-definitions .desc//p=i “physical object quality”
-
-By default, the output is a subset of OboGraph datamodel rendered as YAML, e.g.
-
-
-
-
-You can also specify CSV to generate a flattened form of this.
-
-Example:
-
-pato logical-definitions .all –output-type csv
-
-You can optionally choose to “–matrix-axes” to transform the output to a matrix form.
-This is a comma-separated pair of axes, where each element is a logical definition element
-type: “f” for filler, “p” for predicate, “g” for genus, “d” for defined class.
-
-
-Example:
-
-
-
-
-Example:
-
-pato logical-definitions .all –matrix-axes d,p –output-type csv
-
-This will generate a row for each defined class with a logical definition, with columns
-for each predicate (“genus” is treated as a predicate here).
-Limitations:
-Currently this only works for definitions that follow a basic genus-differentia pattern,
-which is what is currently represented in the OboGraph datamodel.
-Consider using the “axioms” command for inspection of complex nested OWL axioms.
-More examples:
-
-
-Python API:
-
-
-Data model:
-
-
-runoak logical-definitions [OPTIONS] [TERMS]...
-
-
-Options
-
-
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-
-
-Arguments
-
-
-
-
-
-
-mappings
-List all mappings encoded in the ontology
-
-Example:
-
-runoak -i sqlite:obo:envo mappings
-
-The default output is SSSOM YAML. To use the (canonical) csv format:
-
-runoak -i sqlite:obo:envo mappings -O sssom
-
-By default, labels are not included. Use –autolabel to include labels (but note
-that if the label is not in the source ontology, then no label will be retrieved)
-
-runoak -i sqlite:obo:envo mappings -O sssom
-
-To constrain the mapped object source:
-
-runoak -i sqlite:obo:foodon mappings -O sssom –maps-to-source SUBSET_SIREN
-
-Python API:
-
-
-Data model:
-
-
-runoak mappings [OPTIONS] [TERMS]...
-
-
-Options
-
-
-
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-
-Arguments
-
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-
-
-
-
-migrate-curies
-Rewires an ontology replacing all instances of an ID or IDs
-Note: the specified ontology is modified in place
-The input for this command is a list equals-separated pairs, specifying the
-source and the target
-
-Example:
-
-runoak -i db/uberon.db migrate-curies –replace SRC1=TGT1 SRC2=TGT2
-
-This command is a wrapper onto the “migrate_curies” command in the PatcherInterface
-
-oaklib.interfaces.patcher_interface.PatcherInterface.migrate_curies
-runoak migrate-curies [OPTIONS] [CURIE_PAIRS]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-normalize
-Normalize all input identifiers.
-
-Example:
-
-runoak -i translator: normalize HGNC:1 HGNC:2 -M NCBIGene
-
-Python API:
-
-
-Data model:
-
-
-runoak normalize [OPTIONS] [TERMS]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-obsoletes
-Shows all obsolete entities.
-
-Example:
-
-runoak -i obolibrary:go.obo obsoletes
-
-To exclude merged terms, use the --no-include-merged
flag
-
-
-Example:
-
-runoak -i obolibrary:go.obo obsoletes –no-include-merged
-
-To show migration relationships, use the --show-migration-relationships
flag
-
-
-Example:
-
-runoak -i obolibrary:go.obo obsoletes –show-migration-relationships
-
-You can also specify terms to show obsoletes for:
-
-
-Example:
-
-runoak -i obolibrary:go.obo obsoletes –show-migration-relationships GO:0000187 GO:0000188
-
-More examples:
-
-
-Python API:
-
-
-runoak obsoletes [OPTIONS] [TERMS]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-ontologies
-Shows all ontologies
-If the input is a pre-merged ontology, then the output of this command is trivially
-a single line, with the name of the input ontology
-This command is more meaningful when the input is a multi-ontology endpoint, e.g
-
-runoak -i ubergraph ontologies
-
-In future this command will be expanded to allow showing more metadata about each ontology
-Python API:
-
-
-runoak ontologies [OPTIONS]
-
-
-Options
-
-
-
-
-
-ontology-metadata
-Shows ontology metadata
-
-Example:
-
-runoak -i bioportal: ontology-metadata obi uberon foodon
-
-Use the --all
option to show all ontologies
-
-
-Example:
-
-runoak -i bioportal: ontology-metadata –all
-
-By default the output is YAML. You can get the results as TSV:
-
-
-Example:
-
-runoak -i bioportal: ontology-metadata –all -O csv
-
-
-Warning
-The output data model is not yet standardized – this may change in future
-
-Python API:
-
-
-runoak ontology-metadata [OPTIONS] [ONTOLOGIES]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-ontology-versions
-Shows ontology versions
-Currently only implemented for BioPortal
-
-Example:
-
-runoak -i bioportal: ontology-versions mp
-
-All ontologies:
-
-runoak -i bioportal ontology-versions –all
-
-Python API:
-
-
-runoak ontology-versions [OPTIONS] [ONTOLOGIES]...
-
-
-Options
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-paths
-List all paths between one or more start curies.
-
-Example:
-
-runoak -i sqlite:obo:go paths -p i,p ‘nuclear membrane’
-
-This shows all shortest paths from nuclear membrane to all ancestors
-
-
-Example:
-
-runoak -i sqlite:obo:go paths -p i,p ‘nuclear membrane’ –target cytoplasm
-
-This shows shortest paths between two nodes
-
-
-Example:
-
-runoak -i sqlite:obo:go paths -p i,p ‘nuclear membrane’ ‘thylakoid’ –target cytoplasm ‘thylakoid membrane’
-
-This shows all shortest paths between 4 combinations of starts and ends
-You can also use “@” to separate start node list and end node list. Like most OAK commands,
-you can pass either explicit terms, or term queries. For example, if you have two files of IDs,
-then you can do this:
-
-runoak -i sqlite:obo:go paths -p i,p .idfile START_NODES.txt @ .idfile END_NODES.txt
-
-You can also pass in weights for each predicate, used when calculating shortest paths.
-
-
-Example:
-
-runoak -i sqlite:obo:go paths -p i,p ‘nuclear membrane’ –target cytoplasm –predicate-weights “{i: 0.0001, p: 999}”
-
-This shows all shortest paths after weighting relations
-(Note: you can use the same shorthands as in the –predicates option)
-This command can be combined with others to visualize the paths.
-
-
-Example:
-
-alias go=”runoak -i sqlite:obo:go”
-go paths -p i,p ‘nuclear membrane’ –target cytoplasm –narrow | go viz –fill-gaps -
-
-This visualizes the path by first exporting the path as a flat list, then passing the
-results to viz, using the fill-gaps option.
-More examples:
-
-
-runoak paths [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-
-
-Arguments
-
-
-
-
-
-
-prefixes
-Shows prefix declarations.
-All standard prefixes:
-
-runoak prefixes
-
-Specific prefixes:
-
-runoak prefixes GO CL oio skos
-
-By default, prefix maps are exported as simple pairwise TSVs.
-Prefixes can also be exported in different formats, such as YAML and JSON, where they are
-simple dictionaries:
-In yaml:
-
-runoak prefixes –O yaml
-
-In turtle:
-
-runoak prefixes –O rdf
-
-For RDF exports, the prefix declaration should appear in BOTH prefix declarations, AND also as
-instances of SHACL PrefixDeclarations, e.g.
-
-@prefix CL: <http://purl.obolibrary.org/obo/CL_> .
-…
-[] a sh:PrefixDeclaration ;
-
-sh:namespace CL: ;
-sh:prefix “CL” .
-
-
-The default prefixmap is always used, unless options are passed specifying additional
-prefix maps.
-
-Example:
-
-runoak –named-prefix-map prefixcc prefixes
-
-If an ontology is loaded, then –used-only can be used to restrict to
-prefixes for entities in that ontology
-
-runoak -i sqlite:obo:cl prefixes –used-only
-
-runoak prefixes [OPTIONS] [TERMS]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-
-query
-Execute an arbitrary query.
-The syntax of the query is backend-dependent.
-runoak query [OPTIONS]
-
-
-Options
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-relationships
-Show all relationships for a term or terms
-By default, this shows all relationships where the input term(s) are the subjects
-
-Example:
-
-runoak -i cl.db relationships CL:4023094
-
-Like all OAK commands, a label can be passed instead of a CURIE
-
-
-Example:
-
-runoak -i cl.db relationships neuron
-
-To reverse the direction, and query where the search term(s) are objects, use the –direction flag:
-
-
-Example:
-
-runoak -i cl.db relationships –direction down neuron
-
-Multiple terms can be passed
-
-
-Example:
-
-runoak -i uberon.db relationships heart liver lung
-
-And like all OAK commands, a query can be passed rather than an explicit term list
-The following query lists all arteries in the limb together which what structures they supply
-Query:
-
-runoak -i uberon.db relationships -p RO:0002178 .desc//p=i “artery” .and .desc//p=i,p “limb”
-
-More examples:
-
-
-Python API:
-
-
-runoak relationships [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-rollup
-Produce an association rollup report.
-The report will list associations where the subject is one of the terms provided. The
-associations will be grouped by any provided –object-group options. This option can be
-provided multiple times. If the value is a comma separated list of object IDs, the first
-will be used as a primary grouping dimension and the remainder will be used to create
-sub-groups.
-
-Example:
-
-runoak -i sqlite:go.db -g wb.gaf -G gaf rollup –object-group GO:0032502,GO:0007568,GO:0048869,GO:0098727 –object-group GO:0008152,GO:0009056,GO:0044238,GO:1901275 –object-group GO:0050896,GO:0051716,GO:0051606,GO:0051606,GO:0014823 –object-group=GO:0023052 –output rollup.html WB:WBGene00000417 WB:WBGene00000912 WB:WBGene00000898 WB:WBGene00006752
-
-By default, is-a relationships between association objects are used to perform the rollup.
-Use the -p/–predicates option to change this behavior.
-runoak rollup [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-roots
-List all root nodes in the ontology
-Like all OAK relational commands, this is parameterized by –predicates (-p).
-Note that the default is to return the roots of the relation graph over all predicates.
-This can sometimes give unintuitive results, so we recommend always being explicit
-and parameterizing
-
-Example:
-
-runoak -i db/cob.db roots
-
-This command is a wrapper onto the “roots” command in the BasicOntologyInterface.
-
-
-runoak roots [OPTIONS]
-
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-Options
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-search
-Searches ontology for entities that have a label, alias, or other property matching a search term.
-
-Example:
-
-runoak -i uberon.obo search limb
-
-This uses the Pronto implementation to load uberon from disk, and does a basic substring
-search over the labels and synonyms - results are not ranked
-Bioportal (all ontologies):
-
-runoak -i bioportal: search limb
-
-(You need to set your API key first)
-This uses the Bioportal API to search over a broad set of ontologies, returning a ranked list
-ranked by relevance. There may be many results, the results are streamed, do ctrl^C to stop
-Ubergraph (all ontologies):
-
-runoak -i ubergraph: search limb
-
-Ubergraph (one ontology):
-
-runoak -i ubergraph:uberon search limb
-
-Python API:
-
-
-Data model:
-
-
-
-Warning
-The behavior of search is not yet fully unified across endpoints
-
-
-Warning
-The behavior of search is not yet fully unified across endpoints
-
-runoak search [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-set-apikey
-Sets an API key
-
-Example:
-
-oak set-apikey -e bioportal MY-KEY-VALUE
-
-This is stored in an OS-dependent path
-runoak set-apikey [OPTIONS] KEYVAL
-
-
-Options
-
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-
-Arguments
-
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-siblings
-List all siblings of a specified term or terms
-
-Example:
-
-runoak -i cl.owl siblings CL:4023094
-
-Note that siblings is by default over ALL relationship types, so we recommend
-always being explicit and passing a predicate using -p (–predicates)
-runoak siblings [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-similarity
-All by all similarity.
-This calculates a similarity matrix for two sets of terms.
-Input sets of a terms can be specified in different ways:
-
-
-
-Example:
-
-runoak -i hp.db similarity -p i –set1-file HPO-TERMS1 –set2-file HPO-TERMS2 -O csv
-
-This will compare every term in TERMS1 vs TERMS2
-Alternatively standard OAK term queries can be used, with “@” separating the two lists
-
-
-Example:
-
-runoak -i hp.db similarity -p i TERM_1 TERM_2 … TERM_N @ TERM_N+1 … TERM_M
-
-The .all term syntax can be used to select all terms in an ontology
-
-
-Example:
-
-runoak -i ma.db similarity -p i,p .all @ .all
-
-This can be mixed with other term selectors; for example to calculate the similarity of “neuron”
-vs all terms in CL:
-
-runoak -i cl.db similarity -p i,p .all @ neuron
-
-An example pipeline to do all by all over all phenotypes in HPO:
-Explicit:
-
-runoak -i hp.db descendants -p i HP:0000118 > HPO
-runoak -i hp.db similarity -p i –set1-file HPO –set2-file HPO -O csv -o RESULTS.tsv
-
-The same thing can be done more compactly with term queries:
-
-runoak -i hp.db similarity -p i .desc//p=i HP:0000118 @ .desc//p=i HP:0000118
-
-Python API:
-
-
-Data model:
-
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-runoak similarity [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-similarity-pair
-Determine pairwise similarity between two terms using a variety of metrics
-NOTE: this command may be deprecated, consider using similarity
-Note: We recommend always specifying explicit predicate lists
-
-Example:
-
-runoak -i ubergraph: similarity-pair -p i,p CL:0000540 CL:0000000
-
-You can omit predicates if you like but be warned this may yield
-hard to interpret results.
-E.g.
-
-runoak -i ubergraph: similarity-pair CL:0000540 GO:0001750
-
-yields “fully formed stage” (i.e these are both found in the adult) as
-the MRCA
-For phenotype ontologies, UPHENO relationship types connect phenotype terms to anatomy, etc:
-
-runoak -i ubergraph: similarity-pair MP:0010922 HP:0010616 -p i,p,UPHENO:0000001
-
-Python API:
-
-
-Data model:
-
-
-runoak similarity-pair [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-singletons
-List all singleton nodes in the ontology
-Like all OAK relational commands, this is parameterized by –predicates (-p).
-Note that the default is to return the singletons of the relation graph over all predicates
-Obsoletes are filtered by default
-
-Example:
-
-runoak -i db/cob.db singletons
-
-This command is a wrapper onto the “singletons” command in the BasicOntologyInterface.
-
-
-runoak singletons [OPTIONS]
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-Options
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-statistics
-Shows all descriptive/summary statistics
-
-Example:
-
-runoak -i sqlite:obo:pr statistics
-
-By default, this will show combined summary statistics for all terms
-You can also break down the statistics in two ways:
-
-
-
-
-Example:
-
-runoak -i sqlite:obo:pr statistics -p oio:hasOBONamespace
-
-Note: the oio:hasOBONamespace is not the same as the ID prefix, it is
-a field that is used by a subset of ontologies to partition classes into
-broad groupings, similar to subsets. Its use is non-standard, yet a lot
-of ontologies use this as the main partitioning mechanism.
-A note on bundled ontologies:
-The standard release many OBO ontologies “bundles” parts of other ontologies
-(formally, the release product includes a merged imports closure of import
-modules). This can complicate generation of statistics. A naive count of
-all classes in the main OBI release will include not only “native” OBI classes,
-but also classes from other ontologies that are bundled in the release.
-For bundled ontologies, we recommend some kind of partitioning, such as via
-defined roots, or via the CURIE prefix, using the --group-by-prefix
option.
-Output formats:
-The recommended output types for this command are yaml, json, or csv.
-The default output type is yaml, following the SummaryStatistics data model.
-This is naturally nested, as the statistics includes faceted groupings
-(e.g. edge counts are broken down by predicate). When specifying a flat
-format like csv, this is flattened into a single table, with dynamic
-column names.
-Change statistics:
-You can optionally combine the ontology statistics with a change
-summary relative to another ontology, using the --compare-with
-option.
-
-
-Example:
-
-runoak -i v2.obo statistics –group-by-obo-namespace –compare-with v1.obo
-
-This will also include change stats broken down by KGCL change types. If
-a group-by option is specified, these will be grouped accordingly.
-Python API:
-
-
-Data model:
-
-
-runoak statistics [OPTIONS] [BRANCHES]...
-
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-Options
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-Arguments
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-subsets
-Shows information on subsets
-
-Example:
-
-runoak -i obolibrary:go.obo subsets
-
-
-
-Example:
-
-runoak -i cl.owl subsets
-
-For background on subsets, see https://incatools.github.io/ontology-access-kit/concepts.html#subsets
-Note you can use subsets in selector queries for other commands; e.g. to fetch all
-terms (directly) in goslim_generic in GO:
-
-
-Example:
-
-runoak -i sqlite:obo:go info .in goslim_generic
-
-Python API:
-
-
-
-
-See Also:
-
-term-subsets command, which shows relationships of terms to subsets
-
-runoak subsets [OPTIONS]
-
-
-Options
-
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-
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-synonymize
-Deprecated: use generate-synonyms
-runoak synonymize [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-taxon-constraints
-Compute all taxon constraints for a term or terms.
-This will apply rules using the inferred ancestors of subject terms, as well as inferred
-ancestors/descendants of taxon terms.
-The input ontology MUST include both the taxon constraint relationships AND the relevant portion
-of NCBI Taxonomy
-
-Example:
-
-runoak -i db/go.db taxon-constraints GO:0034357 –include-redundant -p i,p
-
-
-
-Example:
-
-runoak -i sqlite:obo:uberon taxon-constraints UBERON:0003884 UBERON:0003941 -p i,p
-
-More examples:
-
-
-This command is a wrapper onto taxon_constraints_utils:
-
-
-runoak taxon-constraints [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
-
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-term-categories
-List categories for a term or set of terms.
-runoak term-categories [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
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-term-metadata
-Shows term metadata.
-
-Example:
-
-runoak -i sqlite:obo:uberon term-metadata lung heart
-
-You can filter the results for only selected predicates:
-
-runoak -i sqlite:obo:uberon term-metadata lung heart -p id,oio:hasDbXref
-
-The default output is YAML documents, where each YAML document is a term, with
-keys representing selected predicates. Values are always lists of atoms, even
-when there is typically one value (e.g. rdfs:label)
-Python API:
-
-
-Data model:
-
-
-runoak term-metadata [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
-
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-term-subsets
-List subsets for a term or set of terms.
-
-Example:
-
-runoak -i sqlite:obo:uberon term-subsets heart lung
-
-Python API:
-
-
-runoak term-subsets [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
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-
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-terms
-List all terms in the ontology
-
-Example:
-
-runoak -i db/cob.db terms
-
-All terms without obsoletes:
-
-runoak -i prontolib:cl.obo terms –filter-obsoletes
-
-By default “terms” is considered to be any entity type in the ontology. Use –owl-type to constrain this:
-Classes:
-
-runoak -i sqlite:obo:ro terms –owl-type owl:Class
-
-Relationship types (Object properties):
-
-runoak -i sqlite:obo:ro terms –owl-type owl:ObjectProperty
-
-Annotation properties:
-
-runoak -i sqlite:obo:omo terms –owl-type owl:AnnotationProperty
-
-runoak terms [OPTIONS]
-
-
-Options
-
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-termset-similarity
-Termset similarity.
-This calculates a similarity matrix for two sets of terms.
-
-Example:
-
-runoak -i go.db termset-similarity -p i,p nucleus membrane @ “nuclear membrane” vacuole -p i,p
-
-Python API:
-
-
-Data model:
-
-
-runoak termset-similarity [OPTIONS] [TERMS]...
-
-
-Options
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-Arguments
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-transform
-Transforms an ontology
-
-Example:
-
-runoak -i pato.obo dump -o pato.json -O json
-
-
-
-Example:
-
-runoak -i pato.owl dump -o pato.ttl -O turtle
-
-You can also pass in a JSON configuration file to parameterize the dump process.
-Currently this is only used for fhirjson dumps, the configuration options are specified here:
-https://incatools.github.io/ontology-access-kit/converters/obo-graph-to-fhir.html
-
-
-Example:
-
-runoak -i pato.owl dump -o pato.ttl -O fhirjson -c fhir_config.json -o pato.fhir.json
-
-Currently each implementation only supports a subset of formats.
-The dump command is also blocked for remote endpoints such as Ubergraph,
-to avoid killer queries.
-Python API:
-
-
-runoak transform [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-Arguments
-
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-tree
-Display an ancestor graph as an ascii/markdown tree.
-For general instructions, see the viz command, which this is analogous too.
-
-Example:
-
-runoak -i envo.db tree ENVO:00000372 -p i,p
-
-This produces output like:
-.packages:
-* [i] ENVO:00000094 ! volcanic feature
- * [i] ENVO:00000247 ! volcano
- * [i] ENVO:00000403 ! shield volcano
- * [i] **ENVO:00000372 ! pyroclastic shield volcano**
-
-
-Note: for many ontologies the tree view will explode, especially if no predicates are specified.
-You may wish to start with the is-a tree (-p i).
-You can use the –gap-fill option to create a minimal tree:
-
-
-Example:
-
-runoak -i envo.db tree –gap-fill ‘pyroclastic shield volcano’ ‘subglacial volcano’ volcano -p i
-
-This will show the tree containing only these terms, and the most direct inferred relationships between them.
-You can also give a list of leaf terms and specify –add-mrcas alongside –gap-fill to fill in
-the most informative intermediate classes:
-
-
-Example:
-
-runoak -i envo.db tree –add-mrcas –gap-fill ‘pyroclastic shield volcano’ ‘subglacial volcano’ ‘mud volcano’ -p i
-
-This will fill in the term “volcano”, as it is the most recent common ancestor of the specified terms
-The –max-hops option can control the distance
-
-runoak -i envo.db tree ‘pyroclastic shield volcano’ ‘subglacial volcano’ –max-hops 1 -p i
-
-This will generate:
-
-
-
-
-Note that ‘volcano’ is the root, even though it is 2 hops from one of the terms, it can be connected
-to at least one of the seeds (highlighted with asterisks) by a path of length 1.
-Python API:
-
-
-Data model:
-
-
-runoak tree [OPTIONS] [TERMS]...
-
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-Options
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-Arguments
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-validate
-Validate an ontology against ontology metadata
-Implementation notes: Currently only works on SQLite
-
-Example:
-
-runoak -i db/ecto.db validate -o results.tsv
-
-The default validation performed is structural (conformance to the ontology_metadata schema)
-There is experimental support for additional ontology rules, which includes heuristic methods
-such as aligning text and logical definitions. These are off by default.
-To run these, pass –no-skip-ontology-rules
-
-
-Example:
-
-runoak -i db/uberon.db validate –skip-structural-validation –no-skip-ontology-rules
-
-For more information, see the OAK how-to guide:
-
-runoak validate [OPTIONS] [TERMS]...
-
-
-Options
-
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-Arguments
-
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-
-
-validate-definitions
-Checks presence and structure of text definitions.
-To run:
-
-runoak validate-definitions -i db/uberon.db -o results.tsv
-
-By default this will apply basic text mining of text definitions to check
-against machine actionable OBO text definition guideline rules.
-This can result in an initial lag - to skip this, and ONLY perform
-checks for presence of definitions, use –skip-text-annotation:
-
-Example:
-
-runoak validate-definitions -i db/uberon.db –skip-text-annotation
-
-Like most OAK commands, this accepts lists of terms or term queries
-as arguments. You can pass in a CURIE list to selectively validate
-individual classes
-
-
-Example:
-
-runoak validate-definitions -i db/cl.db CL:0002053
-
-Only on CL identifiers:
-
-runoak validate-definitions -i db/cl.db i^CL:
-
-Only on neuron hierarchy:
-
-runoak validate-definitions -i db/cl.db .desc//p=i neuron
-
-Output format:
-This command emits objects conforming to the OAK validation datamodel.
-See https://incatools.github.io/ontology-access-kit/datamodels for more
-on OAK datamodels.
-The default serialization of the datamodel is CSV.
-
-
-Notes:
-This command is largely redundant with the validate command, but is useful for
-targeted validation focused solely on definitions
-runoak validate-definitions [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-
-Arguments
-
-
-
-
-
-
-validate-mappings
-Validates mappings in ontology using additional ontologies.
-To run:
-
-runoak validate-mappings -i db/uberon.db
-
-For sssom:
-
-runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv
-
-By default this will attempt to download and connect to
-sqlite versions of different ontologies, when attempting to resolve a foreign
-subject or object id.
-You can customize this mapping:
-
-runoak validate-mappings -i db/uberon.db –adapter-mapping uberon=db/uberon.db –adapter-mapping zfa=db/zfa.db
-
-This will use a local sqlite file for ZFA:nnnnnnn IDs.
-You can use “*” as a wildcard, in the case where you have an application ontology
-with many mapped entities merged in:
-
-runoak validate-mappings -i db/uberon.db –adapter-mapping “*”=db/merged.db”
-
-The default behavior for this command is to perform deterministic rule-based
-checks; for example, the mapped IDs should not be obsolete, and if the mapping
-is skos:exactMatch, then the cardinality is expected to be 1:1.
-Other adapters may choose to implement bespoke behaviors. In future there
-might be a boomer adapter that will perform probabilistic reasoning on the
-mappings. The experimental LLM backend will use an LLM to qualitatively
-validate mappings (see the LLM how-to guide for more details).
-runoak validate-mappings [OPTIONS] [TERMS]...
-
-
-Options
-
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-
-
-
-
-Arguments
-
-
-
-
-
-validate-multiple
-Validate multiple ontologies against ontology metadata
-See the validate command - this is the same except you can pass a list of databases
-For more information, see the OAK how-to guide:
-
-runoak validate-multiple [OPTIONS] [DBS]...
-
-
-Options
-
-
-
-
-
-
-
-
-
-Arguments
-
-
-
-
-
-viz
-Visualize an ancestor graph using obographviz
-For general background on what is meant by a graph in OAK,
-see https://incatools.github.io/ontology-access-kit/interfaces/obograph
-
-Note
-This requires that obographviz is installed.
-
-
-Example:
-
-runoak -i sqlite:cl.db viz CL:4023094
-
-Same query on ubergraph:
-
-runoak -i ubergraph: viz CL:4023094
-
-Example, showing only is-a:
-
-runoak -i sqlite:cl.db viz CL:4023094 -p i
-
-Example, showing only is-a and part-of, to include Uberon:
-
-runoak -i sqlite:cl.db viz CL:4023094 -p i,p
-
-As above, including develops-from:
-
-runoak -i sqlite:cl.db viz CL:4023094 -p i,p,RO:0002202
-
-With abbreviation:
-
-runoak -i sqlite:cl.db viz CL:4023094 -p i,p,d
-
-We can also limit the number of “hops” from the seed terms; for
-example, all is-a and develops-from ancestors of T-cell, limiting
-to a distance of 2:
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-runoak -i sqlite:cl.db viz ‘T cell’ -p i,d –max-hops 2
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-Data model:
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-runoak viz [OPTIONS] [TERMS]...
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@@ -6213,7 +189,7 @@ Example: