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
+Output file, e.g. obo file
+A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
+If set, results will automatically have labels assigned
+True
Desired output type
+Output file, e.g. obo file
+Add closure fields to the output
+False
A comma-separated list of predicates for the association relation
+How to interpret query terms.
+object
subject | object | both
+Limit the number of results
+10
Additional filters in K=V format
+Minimum count for a facet to be included
+1
Group by subject or object
+object
Arguments
+Optional argument(s)
+If true, allow labels as well as CURIEs in the input files
+Arguments
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.
-You can customize this:
+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]...
direct
1..1
Float
0..1
Float
The p-value
direct
Range: Float
Required: True
</details>
See also use_llms
Use the llm selector, wrapping an existing source
runoak -i llm:sqlite:obo:go validate-mappings .desc//p=i "molecular_function"
+See:
++++
Yield objects together with the number of distinct associations.
+subjects –
predicates –
property_filter –
subject_closure_predicates –
predicate_closure_predicates –
object_closure_predicates –
include_modified –
group_by –
limit –
kwargs –
Yield objects together with the number of distinct associated subjects.
Here objects are typically nodes from ontologies and subjects are annotated entities such as genes.
@@ -342,17 +367,19 @@This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects
+This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects. +If subjects is empty, this is calculated for all subjects in the association set.
subjects –
predicates –
property_filter –
subject_closure_predicates –
predicate_closure_predicates –
object_closure_predicates –
include_modified –
subjects – constrain to these subjects (e.g. genes in a gene association)
predicates – constrain to these predicates (e.g. involved-in for a gene to pathway association)
property_filter – generic filter
subject_closure_predicates – subjects is treated as descendant via these predicates
predicate_closure_predicates – predicates is treated as descendant via these predicates
object_closure_predicates – object is treated as descendant via these predicates
include_modified – include modified associations
kwargs – additional arguments
subjects –
predicates –
objects –
subset –
subset_entities –
property_filter –
subject_closure_predicates –
predicate_closure_predicates –
object_closure_predicates –
include_modified –
subjects – constrain to these subjects
predicates – constrain to these predicates (e.g. involved-in for a gene to pathway association)
objects – constrain to these objects (e.g. terms)
subset – subset to map to
subset_entities – subset entities to map to
property_filter – generic filter
subject_closure_predicates – subjects is treated as descendant via these predicates
predicate_closure_predicates – predicates is treated as descendant via these predicates
object_closure_predicates – object is treated as descendant via these predicates
include_modified – include modified associations
AssociationProviderInterface.associations_subject_search()AssociationProviderInterface.association_pairwise_coassociations()AssociationProviderInterface.add_associations()AssociationProviderInterface.association_counts()AssociationProviderInterface.association_subject_counts()AssociationProviderInterface.map_associations()AssociationProviderInterface.normalize_associations()