File Description: go-stats: Difference between revisions
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* '''[[GO_stats-glossary#model_organism|by_model_organism]]:''' For each species, the number of annotations are shown: | * '''[[GO_stats-glossary#model_organism|by_model_organism]]:''' For each species, the number of annotations are shown: | ||
* '''[http://geneontology.org/docs/guide-go-evidence-codes/ by evidence]:''' number of annotations for each individual evidence code, detailed by [[GO_stats-glossary#aspect |aspect]]. | * '''[http://geneontology.org/docs/guide-go-evidence-codes/ by evidence]:''' number of annotations for each individual evidence code, detailed by [[GO_stats-glossary#aspect |aspect]]. | ||
* '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]''': PHYLO, IEA, OTHER, EXP, ND
, HTP | * '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]''': Number of annotations for each [[GO_stats-glossary#evidence_cluster|evidence cluster]] (PHYLO, IEA, OTHER, EXP, ND
, HTP), detailed by [[GO_stats-glossary#aspect |aspect]]. | ||
* '''by_group:''' Number of annotation for each contributing group, obtained using the 'assigned_by' field. | * '''by_group:''' Number of annotation for each contributing group, obtained using the 'assigned_by' field. | ||
Revision as of 10:46, 24 October 2019
IN PROGRESS
Usage
Primary stat file computed.
Input data
Annotation stats are obtained by querying GOlr[1]. ***IS THIS THE RIGHT LINK???***
Format(s)
json
File description
The go-stats
file contains the following information:
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 theis_obsolete
field is true in thego.obo
file) (this excludes merges). - merged_terms: Total number of merged terms (calculated by counting the
term_ids
for which the fieldis_obsolete
is true in thego.obo
file, and that also are are asalt_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, F, C.
- by_bioentity_type
- all: Number of annotations for each bioentity type.
- cluster: Number of annotations for each bioentity type cluster.
- by_taxon: Number of annotations for each of the annotated species in the database.
- by_evidence
- 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 (PHYLO, IEA, OTHER, EXP, ND , HTP), 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