File Description: go-stats: Difference between revisions
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=Usage= | =Usage= | ||
Primary | Primary stats file computed. | ||
=Input data = | =Input data = | ||
Annotation stats are obtained by querying GOlr | Annotation stats are obtained by querying the GOlr (GO Solr instance). | ||
=Format(s)= | =Format(s)= | ||
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The <code>go-stats</code> file contains the following information: | The <code>go-stats</code> file contains the following information: | ||
==release_date== | ==release_date== | ||
*'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> | *'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> or <code>snapshot/metadata/release-date.json</code>. | ||
==ontology== | ==ontology== | ||
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* '''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. | * '''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_created_terms:''' Number of created terms since the previous release. | ||
* '''changes_valid_terms:''' Number of valid terms since the previous release. | |||
* '''changes_obsolete_terms:''' Number of terms obsoleted 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. | * '''changes_merged_terms:''' Number of created merged since the previous release. | ||
* '''changes_biological_process_terms:''' Changes in the number of BP terms. | |||
* '''changes_molecular_function_terms":''' Changes in the number of MF terms. | |||
* '''changes_cellular_component_terms":'''Changes in the number of CC terms. | |||
==annotations== | ==annotations== | ||
* '''total:''' The total number of annotations. | * '''total:''' The total number of annotations. | ||
* '''by_aspect''' | * '''[[GO_stats-glossary#aspect |by_aspect]]''': P, F, C. | ||
* | * '''[[GO_stats-glossary#bioentity_type |by_bioentity_type]]:''' | ||
** | ** '''[[GO_stats-glossary#bioentity_type| all]]''': Number of annotations for each bioentity type. | ||
** | ** '''[[GO_stats-glossary#bioentity_type_cluster| cluster]]''': Number of annotations for each [[GO_stats-glossary#bioentity_type_cluster|bioentity type cluster]]. | ||
* ''' | * '''by_qualifier:''' contributes_to, colocalizes_with, NOT | ||
* | * '''by_taxon''': Number of annotations for each of the annotated species in the database. | ||
* '''by_evidence''' | * '''by_evidence''' | ||
** '''all''' | ** '''[http://geneontology.org/docs/guide-go-evidence-codes/ all]''' | ||
** ''' | ** '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]''' | ||
* '''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: | ||
* '''by evidence:''' number of annotations for each individual evidence code, detailed by 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]]. | ||
* '''by_evidence_cluster | ** '''[[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 | ** '''by_qualifier:''' contributes_to, colocalizes_with, NOT | ||
* '''by_group:''' Number of annotation for each contributing group, obtained using the <code>assigned_by</code> field of each input file. | |||
==taxa== | ==taxa== | ||
* total: | * '''total:''' Number of species with annotations. | ||
* filtered: | * '''filtered:''' Number of species with at least 1,000 annotations. | ||
==bioentities== | ==bioentities== | ||
* total: | *'''total: ''' Total number of annotated bioentities. | ||
* by_type | * '''by_type''' | ||
** all | ** '''[[GO_stats-glossary#bioentity_type |all]]:''' Number of annotated bioentities by [[GO_stats-glossary#bioentity_type_cluster |bioentity type]]. | ||
** | ** '''[[GO_stats-glossary#bioentity_type_cluster |by_type_cluster]]:''' Number of annotated bioentities grouped by [[GO_stats-glossary#bioentity_type_cluster |clusters]]. | ||
* by_filtered_taxon | * '''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]: | ||
** all: number of annotations for each species, by bioentity_type | ** '''[[GO_stats-glossary#bioentity_type |all]]''': number of annotations for each species, by [[GO_stats-glossary#bioentity_type |bioentity type]], detailed by aspect. | ||
** | ** '''[[GO_stats-glossary#bioentity_type_cluster |by_type_cluster]]''': number of annotations for each species, by [[GO_stats-glossary#bioentity_type_cluster |bioentity_type_cluster]], detailed by aspect. | ||
==references== | ==references== | ||
* all | *'''all''' | ||
** total: | **'''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 | **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Total number of annotated references by species. | ||
** | **'''by_group:''' Total number of annotated references for each contributing group, obtained using the <code>assigned_by</code> field. | ||
* | *'''pmids''' | ||
** total: | **'''total:''' Total number of annotated PMIDs. | ||
** by_filtered_taxon | **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Total number of annotated PMIDs by species. | ||
** by_group | **'''by_group:''' Total number of annotated PMIDs for each contributing group, obtained using the <code>assigned_by</code> field. | ||
=Direct access to files= | =Direct access to files= | ||
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= Review Status = | = Review Status = | ||
Last reviewed: | Last reviewed: March 5, 2020 | ||
[[Category:Release Pipeline]] | [[Category:Release Pipeline]] |
Latest revision as of 19:56, 5 March 2020
Usage
Primary stats file computed.
Input data
Annotation stats are obtained by querying the GOlr (GO Solr instance).
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_valid_terms: Number of valid 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.
- changes_biological_process_terms: Changes in the number of BP terms.
- changes_molecular_function_terms": Changes in the number of MF terms.
- changes_cellular_component_terms":Changes in the number of CC terms.
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_qualifier: contributes_to, colocalizes_with, NOT
- 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_qualifier: contributes_to, colocalizes_with, NOT
- by_group: Number of annotation for each contributing group, obtained using the
assigned_by
field of each input file.
taxa
- total: Number of species with annotations.
- filtered: Number of species with at least 1,000 annotations.
bioentities
- total: Total number of annotated bioentities.
- by_type
- all: Number of annotated bioentities by bioentity type.
- by_type_cluster: Number of annotated bioentities grouped by clusters.
- by_filtered_taxon:
- all: number of annotations for each species, by bioentity type, detailed by aspect.
- by_type_cluster: number of annotations for each species, by bioentity_type_cluster, detailed 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: Total number of annotated references by species.
- by_group: Total number of annotated references for each contributing group, obtained using the
assigned_by
field.
- pmids
- total: Total number of annotated PMIDs.
- by_filtered_taxon: Total number of annotated PMIDs by species.
- by_group: Total number of annotated PMIDs for each contributing group, obtained using the
assigned_by
field.
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: March 5, 2020