File Description: go-stats-no-pb: Difference between revisions

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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==
*'''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_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.
* '''[[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_taxon''': Number of annotations for each of the annotated species in the database.
* '''by_evidence'''
** '''[http://geneontology.org/docs/guide-go-evidence-codes/ all]'''
** '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]'''
* '''[[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]].
** '''[[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 <code>assigned_by</code> field of each input file.
 
==taxa==
* '''taxa:''' Number of species with annotations.
* '''taxa_filtered:''' Number of species with at least 1,000 annotations.
 
==bioentities==
*'''total: ''' Total number of annotated bioentities.
* '''by_bioentity'''
** '''[[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]].
* '''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:
** '''[[GO_stats-glossary#bioentity_type |all]]''': number of annotations for each species, by [[GO_stats-glossary#bioentity_type |bioentity type]].
** '''[[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]].
 
==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).
**'''[[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 number of annotated PMIDs.
**'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Total number of annotated PMIDs by species.
**'''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: October 24, 2019
Last reviewed: March 5, 2020




[[Category:Release Pipeline]]
[[Category:Release Pipeline]]

Latest revision as of 19:58, 5 March 2020

Usage

Same as the go-stats file, the primary stat file computed, but excluding direct annotations to GO:0005515 protein binding. Therefore, the total number of annotations is lower, as well as the number of annotated species (both total and filtered), and the number of annotated references.

Input data

Calculated as the go-stats, but excluding direct annotations to GO:0005515 protein binding.

Format(s)

json

File description

See documentation for go-stats file.

Direct access to files

snapshot

http://snapshot.geneontology.org/release_stats/go-stats-no-pb.json

current

http://current.geneontology.org/release_stats/go-stats-no-pb.json

Review Status

Last reviewed: March 5, 2020