Has output: Difference between revisions

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* [http://purl.obolibrary.org/obo/BFO_0000015 '''BFO:0000007 process'''], which corresponds to GO Biological Process and Molecular Function
* [http://purl.obolibrary.org/obo/BFO_0000015 '''BFO:0000007 process'''], which corresponds to GO Biological Process and Molecular Function


''(remove??
[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
''


'''Range'''
'''Range'''


''Range describes the types of entities that can be used with the relation.
''Range describes the types of entities that can be used with the relation.
* Modified gene product, e.g. PRO identifier
* ChemicalEntity: [https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24431 '''CHEBI:24431 chemical entity''']
* ChemicalEntity: [https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24431 '''CHEBI:24431 chemical entity''']
* AnatomicalEntity: [http://purl.obolibrary.org/obo/CARO_0000000 '''CARO:0000000 anatomical entity''']
* ProteinContainingComplex: [http://amigo.geneontology.org/amigo/term/GO:0032991 '''GO:0032991 protein-containing complex''']
* ProteinContainingComplex: [http://amigo.geneontology.org/amigo/term/GO:0032991 '''GO:0032991 protein-containing complex''']


''Note that domain and range are defined in [https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex GO Shapes].''
''Note that domain and range are defined in [https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex GO Shapes].''
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==Annotation Extension Usage Examples==
==Annotation Extension Usage Examples==
===1. Specifying the product of a catalytic activity ===
===1. Specifying the product of a catalytic activity ===

Revision as of 04:16, 28 September 2021

Definition

  • The molecule that is produced as a result of a molecular function or a biological process.
  • Note that more than one output may be used for an annotation: this means that there are multiple products for a reaction. However if an enzyme acts 'different substrates which results in different products, this should be captured as an independent annotation (or an independent statement in Protein2GO).
  • Formal definition in Relations Ontology (RO): RO:0002234 has output definition: P has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.

Scope of use

Domain

Domain refers to the GO terms that can be further specified with the relation.


Range

Range describes the types of entities that can be used with the relation.

Note that domain and range are defined in GO Shapes.


Annotation Extension Usage Examples

1. Specifying the product of a catalytic activity

Human DGKA phosphorylates 1,2-diacyl-sn-glycerol, producing 1,2-diacyl-sn-glycerol 3-phosphate, PMID:22627129.

Annotation for DGKA
Gene product UniProtKB:P23743 DGKA
GP2term relation enables
GO term GO:0004143 diacylglycerol kinase activity, has output(CHEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate)
Evidence IDA
Reference PMID:22627129

Note that this reaction has both an input and an output:

Annotation for DGKA
Gene product UniProtKB:P23743 DGKA
GP2term relation enables
GO term GO:0004143 diacylglycerol kinase activity, has input(CHEBI:17815 1,2-diacyl-sn-glycerol), has output(CHEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate)
Evidence IDA
Reference PMID:22627129


Back to Annotation usage examples for each annotation extension relation