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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 | ||
'''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'''] | ||
* 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].'' | ||
---- | ---- | ||
==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.
- BFO:0000007 process, which corresponds to GO Biological Process and Molecular Function
Range
Range describes the types of entities that can be used with the relation.
- Modified gene product, e.g. PRO identifier
- ChemicalEntity: CHEBI:24431 chemical entity
- ProteinContainingComplex: GO:0032991 protein-containing complex
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