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| =File description= | | =File description= |
| The <code>go-stats</code> file contains the following information:
| | See documentation for [[File_Description:_go-stats|go-stats]] file. |
| ==release_date==
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| *'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> or <code>snapshot/metadata/release-date.json</code>.
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| ==ontology==
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| * '''valid_terms:''' Total number of valid terms (non-obsolete) in the ontology.
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| * '''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).
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| * '''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).
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| * '''biological_process_terms:''' Total number of valid terms for the biological_process aspect.
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| * '''molecular_function_terms:''' Total number of valid terms for the molecular_function aspect.
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| * '''cellular_component_terms:''' Total number of valid terms for the cellular_component aspect.
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| * '''meta_statements:''' Total number of identifiers, alternative identifiers, namespace, term label, comments, synonyms, definitions, subsets, for each valid term.
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| * '''cross_references:''' Total number of cross_references, from the <code>xref</code> field of the <code>go.obo</code> file.
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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.
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| * '''changes_created_terms:''' Number of created terms since the previous release.
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| * '''changes_valid_terms:''' Number of valid terms since the previous release.
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| * '''changes_obsolete_terms:''' Number of terms obsoleted since the previous release.
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| * '''changes_merged_terms:''' Number of created merged since the previous release.
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| * '''changes_biological_process_terms:''' Changes in the number of BP terms.
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| * '''changes_molecular_function_terms":''' Changes in the number of MF terms.
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| * '''changes_cellular_component_terms":'''Changes in the number of CC terms.
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| ==annotations==
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| * '''total:''' The total number of annotations.
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| * '''[[GO_stats-glossary#aspect |by_aspect]]''': P, F, C.
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| * '''[[GO_stats-glossary#bioentity_type |by_bioentity_type]]:'''
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| ** '''[[GO_stats-glossary#bioentity_type| all]]''': Number of annotations for each bioentity type.
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| ** '''[[GO_stats-glossary#bioentity_type_cluster| cluster]]''': Number of annotations for each [[GO_stats-glossary#bioentity_type_cluster|bioentity type cluster]].
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| ** '''by_taxon''': Number of annotations for each of the annotated species in the database.
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| * '''by_evidence'''
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| ** '''[http://geneontology.org/docs/guide-go-evidence-codes/ all]'''
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| ** '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]'''
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| * '''[[GO_stats-glossary#model_organism|by_model_organism]]:''' For each species, the number of annotations are shown:
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| ** '''[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]].
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| ** '''[[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]].
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| * '''by_group:''' Number of annotation for each contributing group, obtained using the <code>assigned_by</code> field of each input file.
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| ==taxa==
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| * '''taxa:''' Number of species with annotations.
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| * '''taxa_filtered:''' Number of species with at least 1,000 annotations.
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| ==bioentities==
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| *'''total: ''' Total number of annotated bioentities.
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| * '''by_bioentity'''
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| ** '''[[GO_stats-glossary#bioentity_type |all]]:''' Number of annotated bioentities by [[GO_stats-glossary#bioentity_type_cluster |bioentity type]].
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| ** '''[[GO_stats-glossary#bioentity_type_cluster |by_type_cluster]]:''' Number of annotated bioentities grouped by [[GO_stats-glossary#bioentity_type_cluster |clusters]].
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| * '''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:
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| ** '''[[GO_stats-glossary#bioentity_type |all]]''': number of annotations for each species, by [[GO_stats-glossary#bioentity_type |bioentity type]].
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| ** '''[[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]].
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| ==references==
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| *'''all'''
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| **'''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).
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| **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Total number of annotated references by species.
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| **'''by_group:''' Total number of annotated references for each contributing group, obtained using the <code>assigned_by</code> field.
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| *'''pmids'''
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| **'''total:''' Total number of annotated PMIDs.
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| **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Total number of annotated PMIDs by species.
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| **'''by_group:''' Total number of annotated PMIDs for each contributing group, obtained using the <code>assigned_by</code> field.
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| =Direct access to files= | | =Direct access to files= |
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| = Review Status = | | = Review Status = |
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| Last reviewed: October 24, 2019 | | Last reviewed: March 5, 2020 |
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| [[Category:Release Pipeline]] | | [[Category:Release Pipeline]] |