diff --git a/_modules/index.html b/_modules/index.html index dc2f8e769..bc40ecef6 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -82,30 +82,12 @@

All modules for which code is available

- -
  • Commands -
    • +
  • Commands
  • Datamodels
    • @@ -259,5953 +182,6 @@

    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

    -
    -
    --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

    -
    -
    -
    - -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -WORDS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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:

    -
      -

    • 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

      • -
    -
    runoak apply [OPTIONS] [COMMANDS]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -COMMANDS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -CONSTRAINTS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    cache-clear

    -

    Clear the contents of the pystow oaklib cache.

    -
    runoak cache-clear [OPTIONS]
-
    -
    -

    Options

    -
    -
    ---days-old <days_old>
    -

    Clear anything more than this number of days old

    -
    -
    Default:
    -

    100

    -
    -
    -
    - -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]
-
    -
    -

    Options

    -
    -
    --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

    -
    - -
    -
    -
    -

    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]
-
    -
    -

    Options

    -
    -
    --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

    -
    - -
    -
    -
    -

    diff-terms

    -

    Compares a pair of terms in two ontologies

    -

    EXPERIMENTAL

    -
    runoak diff-terms [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    ---other-ontology <other_ontology>
    -

    other ontology

    -
    - -
    -
    --o, --output <output>
    -

    Output file, e.g. obo file

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -SUBSETS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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:

    -
      -

    • 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)

      • -
    -

    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:

    -
    -
      -

    1. Pass in a YAML structure (on command line or in a YAML file) listing relations

      2. -

    2. Pass in a LinkML data definitions YAML file

      3. -
    -
    -

    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:

    -
    -
    -
    classes:
    -
    Person:
    -
    attributes:
    -
    id:

    identifier: true

    -
    -
    name:

    slot_uri: rdfs:label

    -
    -
    -
    -
    -
    -
    -
    -
    -
    -

    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

    -
      -

    • 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

      • -
    -
    runoak fill-table [OPTIONS] TABLE_FILE
-
    -
    -

    Options

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TABLE_FILE
    -

    Required argument

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    generate-logical-definitions

    -

    Generate logical definitions based on patterns file.

    -
    runoak generate-logical-definitions [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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.

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -
    -
    -
    -

    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:

    -
      -

    • create a lexical index, keyed by normalized strings of labels, synonyms

      • -

    • report all pairs of entities that have the same key

      • -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -
    -
    -
    -

    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.

    -
    -
    -
    definedClassId: PATO:0045071

    genusIds: -- PATO:0001439 -restrictions: -- fillerId: PATO:0000461

    -
    -

    propertyId: RO:0015010

    -
    -
    -
    -
    -

    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:
    -
      -

    • Each property/predicate is a column

      • -

    • For repeated properties, columns of the form prop_1, prop_2, … are generated

      • -
    -
    -
    -
    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

    -
    -
    ---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.

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -CURIE_PAIRS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --o, --output <output>
    -

    Output file, e.g. obo file

    -
    - -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -ONTOLOGIES
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -ONTOLOGIES
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    query

    -

    Execute an arbitrary query.

    -

    The syntax of the query is backend-dependent.

    -
    runoak query [OPTIONS]
-
    -
    -

    Options

    -
    -
    --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

    -
    - -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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.

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -
    -
    - -
    -

    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

    -
    -
    --e, --endpoint <endpoint>
    -

    Required Name of endpoint, e.g. bioportal

    -
    - -

    Arguments

    -
    -
    -KEYVAL
    -

    Required argument

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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:

    -
      -

    • via a file

      • -

    • via explicit lists of terms or queries

      • -
    -
    -
    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:

    -
    -
    -
    runoak similarity [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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]
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -
    -
    -
    -

    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:

    -
      -

    • by a collection of branch roots

      • -

    • by a metadata property (e.g. oio:hasOBONamespace, rdfs:isDefinedBy)

      • -

    • by prefix (e.g. GO, PR, CL, OBI)

      • -
    -
    -
    -
    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -BRANCHES
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --o, --output <output>
    -

    Output file, e.g. obo file

    -
    - -
    -
    -
    -

    synonymize

    -

    Deprecated: use generate-synonyms

    -
    runoak synonymize [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    term-categories

    -

    List categories for a term or set of terms.

    -
    runoak term-categories [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    --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, …

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    --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

    -
    -
    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --o, --output <output>
    -

    Output file, e.g. obo file

    -
    - -
    -
    --O, --output-type <output_type>
    -

    Desired output type

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -
    -
    -
    -

    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

    -
    -
    --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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    --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.

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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:

    -
    -
      -
    • -
      [] ENVO:00000247 ! volcano
        -
      • -
        [i] ENVO:00000403 ! shield volcano
          -

        • [i] ENVO:00000372 ! pyroclastic shield volcano

          • -
        -
        -
        -
        • -

      • [i] ENVO:00000407 ! subglacial volcano

        • -
      -
      -
      -
      • -
    -
    -

    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]...
-
    -
    -

    Options

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -DBS
    -

    Optional argument(s)

    -
    - -
    -
    -

    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:

    -
    -

    runoak -i sqlite:cl.db viz ‘T cell’ -p i,d –max-hops 2

    -
    -

    Python API:

    -
    -
    -

    Data model:

    -
    -
    -
    runoak viz [OPTIONS] [TERMS]...
-
    -
    -

    Options

    -
    -
    ---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

    -
    - -

    Arguments

    -
    -
    -TERMS
    -

    Optional argument(s)

    -
    - -
    -
    -
    @@ -6213,7 +189,7 @@

    Example: