Annotation Extension: Difference between revisions

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[[Category:Annotation extension]]
==Purpose of annotation extensions==
'''Annotation Extensions''' allows GO terms in standard annotations to be further specified, using gene products, chemicals, cell types, anatomical structures. The ontology terms used to extend annotations are GO term or external ontologies. Annotation extensions allows to build a more complete model of biological systems.


==Relations valid for annotation extensions==
Relations used for GO annotation extensions are from the [https://oborel.github.io/ Relation Ontology ]
* [[Annotation_Extension_Relation:has_input|has_input]]
* [[Annotation_Extension_Relation:has_output|has_output]]
* [[Annotation_Extension_Relation:occurs_in|occurs_in]]


  Note that this documentation is being reviewed
==Dependent and independent statement in annotation extensions==
 
Protein2GO allows to make dependent (linked) and independent (separate) statements that are exported in GAF as comma and pipes, respectively. More information can be found in the [https://www.ebi.ac.uk/seqdb/confluence/display/GOAP/Protein2GO+manual#Protein2GOmanual-AnnotationExtensionfield Protein2GO documentation].


==Other pages to review==
==Other pages to review==
 
* http://wiki.geneontology.org/index.php/Annotation_Extension ''(this page)''
TO DO
* http://wiki.geneontology.org/index.php/Annotation_Extension:_Capturing_cell_and_tissue_types
Include:
* Ruth's slides
* https://github.com/geneontology/go-annotation/issues/2917#event-4918578122
* Main document: https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=1318491961
Spreadsheets 'P2GO - GP2Term relations' and 'P2GO - Extensions'
* http://wiki.geneontology.org/index.php/Annotation_Relations
* http://wiki.geneontology.org/index.php/Annotation_Relations
 
* http://wiki.geneontology.org/index.php/Relations
also need to clean up
* http://wiki.geneontology.org/index.php/Annotation_Extension ''(this page)''
* http://wiki.geneontology.org/index.php/Annotation_Extension_Relation_Documentation_Jamboree
* http://wiki.geneontology.org/index.php/Guidance_for_updating_deprecated_Annotation_Extension_Relations
* http://wiki.geneontology.org/index.php/Guidance_for_updating_deprecated_Annotation_Extension_Relations
* https://github.com/geneontology/annotation_extensions (NOTE that P2GO links to this doc - ''2021-09-29 is this still the case??'') ''archived''
* https://github.com/geneontology/annotation_extensions (NOTE that P2GO links to this doc - ''2021-09-29 is this still the case??'') ''archived''
 
* [https://docs.google.com/presentation/d/1bsQGCTt_yDVBdBFwye2c77YSw06Oe3LBN-yLLJbi2C4/edit#slide=id.gadab9d5cef_2_75 Ruth's slides]  
==Introduction==
* Spreadsheets 'P2GO - GP2Term relations' and 'P2GO - Extensions' https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=1318491961
 
Each GO annotation pairs a single gene product identifier to a single term from the ontology. This format is very powerful however it can also restrict the descriptiveness of a specific instance of a functioning or subcellular location; there must be a pre-existing term in the ontology that provides full details of the specific aspects of the function.
 
It is not always possible to create individual terms that precisely describe the context of each activity (e.g. the cellular or anatomical location, the dependency on other processes, or particular, specific protein targets). 
 
It is less restrictive if the annotator is able to combine additional terms in a single annotation to provide a more detailed functional description for an individual gene product.
 
This page describes the Annotation Extension field (column 16) in the Gene Association File [http://www.geneontology.org/GO.format.gaf-2_0.shtml#annotation_ext GAF2.0 file format], which allows GO terms to be further specified, using gene product or chemical identifiers or terms from GO or external OBO ontologies.
 
When an annotator chooses to do this, they are effectively creating "on-the-fly" cross-product term. We say "on-the-fly" because the combinatorial term is not added to the ontology (although it could be at a later stage, if the ontology editors choose to create the appropriate GO term).


[[Category:relations]]
[[Category:relations]]
[[Category:annotation extension]]
[[Category:annotation extension]]

Revision as of 13:25, 13 October 2021

Purpose of annotation extensions

Annotation Extensions allows GO terms in standard annotations to be further specified, using gene products, chemicals, cell types, anatomical structures. The ontology terms used to extend annotations are GO term or external ontologies. Annotation extensions allows to build a more complete model of biological systems.

Relations valid for annotation extensions

Relations used for GO annotation extensions are from the Relation Ontology

Dependent and independent statement in annotation extensions

Protein2GO allows to make dependent (linked) and independent (separate) statements that are exported in GAF as comma and pipes, respectively. More information can be found in the Protein2GO documentation.

Other pages to review

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