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| =Usage= | | =Usage= |
| This file is used for doing QC on annotations for GO releases. | | This file is used for doing QC on annotations for GO releases. Direct annotations to <code>GO:0005515 protein binding</code> are excluded from the counts, 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. |
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| =Input data = | | =Input data = |
| Calculated from the [[File_Description:_go-annotation-changes |go-annotation-changes.json]], in which annotations to <code>GO:0005515 protein binding</code> are removed. 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. | | Calculated as the [[File_Description:_go-annotation-changes |go-annotation-changes.json]], but excluding direct annotations to <code>GO:0005515 protein binding</code>. |
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| =Format(s)= | | =Format(s)= |
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| =File description= | | =File description= |
| The <code>go-annotation-changes_no_pb</code> file contains the following information:
| | See documentation for [[File_Description:_go-annotation-changes|go-annotation-changes]] file. |
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| ==summary==
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| ===current===
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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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| * '''annotations
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| ** '''total''': Total number of annotations.
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| ** '''[[GO_stats-glossary#aspect |by_aspect]]''': P, F, C.
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| ** '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]''': PHYLO, IEA, OTHER, EXP, ND
, HTP.
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| * '''[[GO_stats-glossary#bioentity_type |bioentities]]:''' Number of bioentities annotated in the GO database.
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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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| * '''references:''' 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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| * '''pmids:''' Number of annotated PMIDs.
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| ===previous===
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| * Same information as for the [[File_Description:_go-annotation-changes#current | current release]].
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| * Note that the date of the previous release is the most recent release in <code>release.geneontology.org/</code>, using the file <code>release.geneontology.org/YYYY-MM-DD/metadata/release-date.json</code>.
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| ===changes===
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| Differences between the current and the previous release for all the fields above. In addition, for taxa, references and pmids, the number of added and removed items are counted.
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| ====annotations====
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| * '''total''': Change in the total number of annotations.
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| * '''[[GO_stats-glossary#aspect |by_aspect]]:''' Changes in the total number of annotations for each aspect: P, F, C.
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| * '''[[GO_stats-glossary#evidence_cluster|by_evidence_cluster]]''': Changes in the total number of annotations for each [[GO_stats-glossary#evidence_cluster| evidence cluster]] (PHYLO, IEA, OTHER, EXP, ND
, HTP.).
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| ====[[GO_stats-glossary#bioentity_type |bioentities]]====
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| Change in the number of annotated [[GO_stats-glossary#bioentity_type |bioentities]].
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| ====taxa====
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| * '''total:''' Changes in the total number of annotated species.
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| * '''[[GO_stats-glossary#filtered_taxa |filtered]]:''' Changes in the number of annotated species by [[GO_stats-glossary#filtered_taxa |filtered taxa]].
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| * '''added:''' Number of new species annotated.
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| * '''removed:''' Number of removed species having lost all annotations.
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| ====references====
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| * '''total''': Change in the number of annotated references .
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| * '''added ''': Number of newly annotated references (data not yet available).
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| * '''removed''': Number of references having lost all annotations (data not yet available).
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| ====pmids====
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| * '''total''': Change in the number of annotated PMIDs.
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| * '''added ''': Number of newly annotated PMIDs (data not yet available).
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| * '''removed''': Number of PMIDs having lost all annotations (data not yet available).
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| ==detailed_changes==
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| All data in this section is shown as x/y, where x is the difference in the total number of annotations, y is the total number of annotations in the current release, and the % change in shown in parentheses.
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| ===annotations===
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| *'''total: '''Change in the total number of annotations.
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| * '''[[GO_stats-glossary#aspect |by_aspect]]:''' Change in the total number of annotation for each [[GO_stats-glossary#aspect |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]] :''' Change in the number of annotations for each [[GO_stats-glossary#bioentity_type| bioentity type]].
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| **'''[[GO_stats-glossary#bioentity_type_cluster| cluster]]:''' Change in the number of annotations by [[GO_stats-glossary#bioentity_type_cluster| bioentity type cluster]].
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| *'''by_taxon''': Change in the number of annotations by species.
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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]]'''
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| **'''[http://geneontology.org/docs/guide-go-evidence-codes by_evidence]:''' For each species, the number of annotations are shown for each individual evidence code, detailed by [[GO_stats-glossary#aspect |aspect]].
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| **'''[[GO_stats-glossary#evidence_cluster|by_evidence cluster]]:''' For each species, the number of annotations are shown for each [[GO_stats-glossary#evidence_cluster|evidence cluster]], detailed by [[GO_stats-glossary#aspect |aspect]].
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| *'''by_group:''' Changes in the total number of annotations for each contributing group, obtained using the 'assigned_by' field..
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| ===taxa===
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| *'''added: '''List of added species with current number of annotations.
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| *'''removed:''' List of removed species with previous number of annotations.
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| ===bioentities===
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| *'''total:''' The difference in the total number of annotated bioentities.
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| *'''by_type: '''
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| **'''[[GO_stats-glossary#bioentity_type| all]]:''' Difference in the number of annotated bioentities.
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| **'''[[GO_stats-glossary#bioentity_type_cluster|cluster]]:''' Difference in the number of annotated bioentities, grouped by [[GO_stats-glossary#bioentity_type_cluster |bioentity type clusters]].
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| *'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Difference in the number of annotated bioentities for each [[GO_stats-glossary#filtered_taxa|filtered species]], detailed by aspect (A, P, F, C).
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| **'''[[GO_stats-glossary#bioentity_type |all]]:''' Difference in the number of annotated bioentities for each species.
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| **'''[[GO_stats-glossary#bioentity_type_cluster|cluster]]:''' Difference in the number of annotated bioentities grouped by [[GO_stats-glossary#bioentity_type_cluster|bioentity clusters]], for each species.
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| ===references===
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| *'''all'''
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| **'''total''' Change in annotated references.
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| **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Change in annotated references by species.
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| **'''by_group:''' Change in annotated references for each contributing group, obtained using the 'assigned_by' field..
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| *'''pmids'''
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| **'''total''' Change in annotated PMIDs.
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| **'''[[GO_stats-glossary#filtered_taxa |by_filtered_taxon]]:''' Change in annotated PMIDs by species.
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| **'''by_group:''' Change in annotated PMIDs for each contributing group, obtained using the 'assigned_by' 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]] |