Has input: Difference between revisions

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==Usage==
==Usage==
* Use of this relation is encouraged when the target of the MF/BP is more specific than what the GO term describes.  
* Use of this relation is encouraged when the molecular target of the MF/BP is more specific than what the GO term describes. A common use case is to specify the exact protein target of an MF, e.g. the target of a protein kinase activity.
* The input should nevertheless represent the biologically meaningful input. Curators need to be careful in distinguishing the conclusion from an experiment from the assay conditions.
* The input should nevertheless represent the biologically meaningful input. Curators need to be careful in distinguishing the conclusion from an experiment from the assay conditions.


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''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.
* Gene product
* 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''']
* Organism: [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1 '''NCBITaxon:1 top level of the NCBI taxonomy database''']





Revision as of 04:11, 28 September 2021


Definition

  • The specific target of a Molecular Function. Targets correspond substrates for enzymes, interactors for binding and adaptor activities, gene for transcription factors. Can also be used the describe inputs of Biological Processes.
  • Note that more than one input may be used for an annotation: this means that there are multiple substrates for a reaction. However if an enzyme can act on different substrates, or if a transcription factor has multiple targets, this should be captured as independent annotations or independent statements in Protein2GO.
  • Formal definition in Relations Ontology (RO): RO:0002233 has input definition: P has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.

Usage

  • Use of this relation is encouraged when the molecular target of the MF/BP is more specific than what the GO term describes. A common use case is to specify the exact protein target of an MF, e.g. the target of a protein kinase activity.
  • The input should nevertheless represent the biologically meaningful input. Curators need to be careful in distinguishing the conclusion from an experiment from the assay conditions.

Domain

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

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

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 substrate (chemical) of a catalytic activity

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

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)
Evidence IDA
Reference PMID:22627129

2. Specifying the protein target of a catalytic activity

Human CDC7 phosphorylates MCM2, PMID:15668232.

Annotation for CDC7
Gene product UniProtKB:O00311 CDC7
GP2term relation enables
GO term GO:0004672 protein kinase activity, has input(UniProtKB:P49736 MCM2)
Evidence IMP
Reference PMID:15668232

3. Specifying the gene target of a DNA binding transcription factor

Human NKX6-3 regulates transcription of BAK1, PMID:26314965.

Annotation for NKX6-3
Gene product UniProtKB:A6NJ46 NKX6-3
GP2term relation enables
GO term GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific, has input(UniProtKB:Q16611, BAK1)
Evidence IDA
Reference PMID:26314965

4. Specifying an interaction partner

Human DNM1L binds RAB29, PMID:25767741.

Annotation for DNM1L
Gene product UniProtKB:O00429 DNM1L
GP2term relation enables
GO term GO:0031267 small GTPase binding, has input(UniProtKB:O14966, RAB29)
Evidence IDA
Reference PMID:25767741



5. Specifying the target(s) of a macromolecule adaptor

Human TJP2 is a molecular adaptor for tight junction proteins F11R and AFDN, PMID:23885123.

Annotation for TJP2
Gene product UniProtKB:Q9UDY2 TJP2
GP2term relation enables
GO term GO:0030674 protein-macromolecule adaptor activity, has input(UniProtKB:Q9Y624, F11R), has input(UniProtKB:P55196, AFDN)
Evidence IDA
Reference PMID:23885123


Back to Annotation usage examples for each annotation extension relation