View source for File Description: go-stats


   IN PROGRESS 

=Usage=
Primary stat file computed.

=Input data =
Annotation stats are obtained by querying GOlr[http://golr-aux.geneontology.io/].  ***IS THIS THE RIGHT LINK???***

=Format(s)=
json

=File description=
The <code>go-stats</code> file contains the following information: 
==release_date==
*'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> (or <code>snapshot/metadata/release-date.json</code>).

==ontology==
* '''valid_terms:''' Total number of valid terms (non-obsolete) in the ontology.
* '''obsolete_terms:''' Total number of terms with <code>obsolete</code> status (ie, <code>term_ids</code> for which the <code>is_obsolete</code> field is true in the <code>go.obo</code> file) (this excludes merges).
* '''merged_terms:''' Total number of merged terms (calculated by counting the <code>term_ids</code> for which the field <code>is_obsolete</code> is true in the <code>go.obo</code> file, and that also are are as <code>alt_ids</code> 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 <code>xref</code> field of the <code>go.obo</code> 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:''' 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 for each contributing 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

=Direct access to files=
==snapshot==
http://snapshot.geneontology.org/release_stats/go-stats.json

==current==
http://current.geneontology.org/release_stats/go-stats.json
= Review Status =

Last reviewed: October 17, 2019


[[Category:Release Pipeline]]