Difference between revisions of "File Description: go-ontology-changes"

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=File usage=
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=Usage=
 
This file contains a summary as well as the detailed changes in the ontology, comparing a new file (go.obo) with the go.obo file from the previous or latest release.  
 
This file contains a summary as well as the detailed changes in the ontology, comparing a new file (go.obo) with the go.obo file from the previous or latest release.  
  
 
=Input data =
 
=Input data =
Ontology changes are calculated from the current <code>[http://purl.obolibrary.org/obo/go.obo go.obo]</code> file file and compared to the latest released file, <code>http://release.geneontology.org</code>
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Ontology changes are calculated from the current <code>[http://purl.obolibrary.org/obo/go.obo go.obo]</code> file and compared to the latest released file, <code>http://release.geneontology.org</code>
 
* For a '''release''', the most recent <code>go.obo</code> file is found at <code>http://purl.obolibrary.org/obo/go.obo</code>
 
* For a '''release''', the most recent <code>go.obo</code> file is found at <code>http://purl.obolibrary.org/obo/go.obo</code>
 
* For a '''snapshot''', the most recent <code>go.obo</code> file is found at <code>http://snapshot.geneontology.org/ontology/go.obo</code>
 
* For a '''snapshot''', the most recent <code>go.obo</code> file is found at <code>http://snapshot.geneontology.org/ontology/go.obo</code>
  
=File format(s)=
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=Format(s)=
 
* json
 
* json
 
* tsv
 
* tsv
  
 
=File description=
 
=File description=
 +
The <code>go-ontology-changes</code> file contains the following information:
 
==summary==
 
==summary==
 
===current release===
 
===current release===
 
*'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> (or <code>snapshot/metadata/release-date.json</code>).
 
*'''release_date:''' Obtained from <code>release/metadata/release-date.json</code> (or <code>snapshot/metadata/release-date.json</code>).
 
* '''valid_terms:''' Total number of valid terms (non-obsolete) in the 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 the is_obsolete field is true in the <code>go.obo</code> file) (this excludes merges).
+
* '''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 term_ids for which the field is_obsolete is true in the <code>go.obo</code> file, and that also are are as alt_ids of a valid term).
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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).
 
* '''biological_process_terms:''' Total number of valid terms for the biological_process aspect.  
 
* '''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.
 
* '''molecular_function_terms:''' Total number of valid terms for the molecular_function aspect.
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===changes===
 
===changes===
 
*'''created_terms:''' Number of terms created since the last release.
 
*'''created_terms:''' Number of terms created since the last release.
 +
*'''valid_terms:''' Change in number of valid terms compared to the last release.
 
*'''obsolete_terms:''' Number of terms obsoleted since the last release (this excludes merges).     
 
*'''obsolete_terms:''' Number of terms obsoleted since the last release (this excludes merges).     
 
*'''merged_terms:''' Number of terms merged since the last release  
 
*'''merged_terms:''' Number of terms merged since the last release  
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*'''obsolete_terms:''' List of terms obsoleted since the last release (this excludes merges), organized by GO aspect.  
 
*'''obsolete_terms:''' List of terms obsoleted since the last release (this excludes merges), organized by GO aspect.  
 
*'''merged_terms:''' List of terms merged since the last release, organized by GO aspect.     
 
*'''merged_terms:''' List of terms merged since the last release, organized by GO aspect.     
*'''meta_statements_changes:''' List of changed meta statements, organized by GO aspect.  
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*'''meta_statements_changes:''' List of changed meta statements, organized by GO aspect. Meta statements are: id, namespace, name, comment, synonyms, definition, subsets.  
 
*'''cross_references:''' List of changed cross-references.  
 
*'''cross_references:''' List of changed cross-references.  
 
*'''relations_changes:''' List of changed relations, organized by GO aspect.
 
*'''relations_changes:''' List of changed relations, organized by GO aspect.
 +
 +
=Direct access to files=
 +
==snapshot==
 +
* http://snapshot.geneontology.org/release_stats/go-ontology-changes.json
 +
* http://snapshot.geneontology.org/release_stats/go-ontology-changes.tsv
 +
 +
==current==
 +
* http://current.geneontology.org/release_stats/go-ontology-changes.json
 +
* http://current.geneontology.org/release_stats/go-ontology-changes.tsv
 +
  
 
= Review Status =
 
= Review Status =
  
Last reviewed: October 17, 2018
+
Last reviewed: March 6, 2020
  
  
 
[[Category:Release Pipeline]]
 
[[Category:Release Pipeline]]

Latest revision as of 14:57, 6 March 2020

Usage

This file contains a summary as well as the detailed changes in the ontology, comparing a new file (go.obo) with the go.obo file from the previous or latest release.

Input data

Ontology changes are calculated from the current go.obo file and compared to the latest released file, http://release.geneontology.org

Format(s)

  • json
  • tsv

File description

The go-ontology-changes file contains the following information:

summary

current release

  • release_date: Obtained from release/metadata/release-date.json (or snapshot/metadata/release-date.json).
  • 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 the is_obsolete field is true in the go.obo file) (this excludes merges).
  • merged_terms: Total number of merged terms (calculated by counting the term_ids for which the field is_obsolete is true in the go.obo file, and that also are are as alt_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 the go.obo file.
  • terms_relations: Total number of relations; the count of all relations, using the fields is_a, intersection_of and relationship of the go.obo file.

previous

Same information as for the current release.

changes

  • created_terms: Number of terms created since the last release.
  • valid_terms: Change in number of valid terms compared to the last release.
  • obsolete_terms: Number of terms obsoleted since the last release (this excludes merges).
  • merged_terms: Number of terms merged since the last release
  • biological_process_terms: New biological_process terms.
  • molecular_function_terms: New molecular_function terms.
  • cellular_component_terms: New cellular_component terms.
  • meta_statements: Total number of changed meta statements (identifiers, alternative identifiers, namespace, term label, comments, synonyms, definitions, subsets).
  • meta_statements_by_term: Number of terms with changed meta statements.
  • cross_references: Number of changed cross-references.
  • cross_references_by_term: Number of terms with changed cross-references.
  • relations: Total number of changed relations.
  • relations_by_term: Number of terms with changed relations.

detailed_changes

  • created_terms: List of terms created since the last release, organized by GO aspect.
  • obsolete_terms: List of terms obsoleted since the last release (this excludes merges), organized by GO aspect.
  • merged_terms: List of terms merged since the last release, organized by GO aspect.
  • meta_statements_changes: List of changed meta statements, organized by GO aspect. Meta statements are: id, namespace, name, comment, synonyms, definition, subsets.
  • cross_references: List of changed cross-references.
  • relations_changes: List of changed relations, organized by GO aspect.

Direct access to files

snapshot

current


Review Status

Last reviewed: March 6, 2020