File Description: go-stats: Difference between revisions
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==ontology== | ==ontology== | ||
* '''valid_terms:''' | * '''valid_terms:''' Total number of valid terms (non-obsolete) in the ontology. | ||
* '''obsolete_terms:''' | * '''obsolete_terms:''' Total number of terms with "obsolete" status (ie, term_ids for which the is_obsolete field is true in the <code>go.obo</code> file) (this excludes merges). | ||
* '''merged_terms:''' | * '''merged_terms:''' Total number of merged terms (calculated by counting the term_ids for which the field is_obsolete is true in the <code>go.obo</code> file, and that also are are as alt_ids of a valid term). | ||
* '''biological_process_terms:''' | * '''biological_process_terms:''' Total number of valid terms for the biological_process aspect. | ||
* '''molecular_function_terms:''' | * '''molecular_function_terms:''' Total number of valid terms for the molecular_function aspect. | ||
* '''cellular_component_terms:''' | * '''cellular_component_terms:''' Total number of valid terms for the cellular_component aspect. | ||
* '''meta_statements:''' | * '''meta_statements:''' Total number of identifiers, alternative identifiers, namespace, term label, comments, synonyms, definitions, subsets, for each valid term. | ||
* '''cross_references:''' | * '''cross_references:''' Total number of cross_references, from the <code>xref</code> field of the <code>go.obo</code> file. | ||
* '''terms_relations:''' number of relations; the count of all relations, using the fields is_a, intersection_of and relationship of the go.obo file. | * '''terms_relations:''' Total number of relations; the count of all relations, using the fields <code>is_a</code>, <code>intersection_of</code> and <code>relationship</code> of the <code>go.obo</code> file. | ||
* '''changes_created_terms:''' | * '''changes_created_terms:''' Number of created terms since the previous release. | ||
* '''changes_obsolete_terms:''' | * '''changes_obsolete_terms:''' Number of terms obsoleted since the previous release. | ||
* '''changes_merged_terms:''' | * '''changes_merged_terms:''' Number of created merged since the previous release. | ||
==annotations== | ==annotations== |
Revision as of 05:15, 18 October 2019
IN PROGRESS
File usage
Primary stat file computed.
Input data
Annotation stats are obtained by querying GOlr[1]. ***IS THIS THE RIGHT LINK???***
File format(s)
json
File description
release_date
- release_date: Obtained from
release/metadata/release-date.json
(orsnapshot/metadata/release-date.json
).
ontology
- valid_terms: Total number of valid terms (non-obsolete) in the ontology.
- obsolete_terms: Total number of terms with "obsolete" status (ie, term_ids for which the is_obsolete field is true in the
go.obo
file) (this excludes merges). - merged_terms: Total number of merged terms (calculated by counting the term_ids for which the field is_obsolete is true in the
go.obo
file, and that also are are as alt_ids of a valid term). - biological_process_terms: Total number of valid terms for the biological_process aspect.
- molecular_function_terms: Total number of valid terms for the molecular_function aspect.
- cellular_component_terms: Total number of valid terms for the cellular_component aspect.
- meta_statements: Total number of identifiers, alternative identifiers, namespace, term label, comments, synonyms, definitions, subsets, for each valid term.
- cross_references: Total number of cross_references, from the
xref
field of thego.obo
file. - terms_relations: Total number of relations; the count of all relations, using the fields
is_a
,intersection_of
andrelationship
of thego.obo
file. - changes_created_terms: Number of created terms since the previous release.
- changes_obsolete_terms: Number of terms obsoleted since the previous release.
- changes_merged_terms: Number of created merged since the previous release.
annotations
- total: The total number of annotations.
- by_aspect
- P: all annotations in the database for biological_process.
- F:all annotations in the database for molecular_function.
- C:all annotations in the database for cellular_component.
- by_bioentity_type
- all (same as bioentities > total > by_type>all)
- cluster (same as bioentities > total > by_type>by_bioentity_type_cluster)
- by_taxon: Number of annotations for each of the annotated species in the database.
- by_evidence
- all
- cluster
- by_model_organism: For each species, the number of annotations are shown:
- by evidence: number of annotations for each individual evidence code, detailed by aspect
- by_evidence_cluster: number of annotations for each evidence cluster, detailed by aspect.
- by_group: Number of annotation by each group, obtained using the 'assigned_by' field.
- taxa
- total: number of species with annotations.
- filtered: number of species with > 1,000 annotations.
- bioentities
- total: total number of annotated bioentities
- by_type
- all (see list of bioentity types)
- cluster
- by_filtered_taxon
- all: number of annotations for each species, by bioentity_type and by aspect.
- cluster: number of annotations for each species, by bioentity_type_cluster and by aspect.
- references
- all
- total: total number of distinct annotated references (includes PMIDs, GO_REFs, DOIs, internal IDs for Model Organism Databases and Reactome (note that for papers with both a PMID and an internal reference ID, the paper is counted twice).
- by_filtered_taxon
- by group
- pmid: same as above, filtered for pmids.
- total: total number of distinct pmids.
- by_filtered_taxon
- by_group
- all
Review Status
Last reviewed: October 17, 2018