Occurs in: Difference between revisions

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===3.  
===3. Specifying the anatomical structure in which a biological process takes place ===
 
 
Specifying the cell type in which a molecular function takes place ===
Type 4 phosphodiesterase [https://www.uniprot.org/uniprot/P27815 PDE4A] is a critical regulator in TCR signaling by attenuating the negative constraint of cAMP, [https://pubmed.ncbi.nlm.nih.gov/17404263/ PMID:17404263].
 
{| class="wikitable"  border="1"
| colspan="2" align="center"| '''MF Annotation for PDE4A'''
|-
| style="width: 20%"| '''Gene product'''
| style="width: 80%"| UniProtKB:P27815 ''PDE4A''
|-
| '''GP2term relation'''
| enables
|-
| '''GO term'''
| GO:0004115 ''3',5'-cyclic-AMP phosphodiesterase activity'', '''occurs in'''(CL:0000084 ''T-cell'')
|-
| '''Evidence'''
| IDA
|-
| '''Reference'''
| PMID:17404263
|-
|}
 
{| class="wikitable"  border="1"
| colspan="2" align="center"| '''BP Annotation for PDE4A'''
|-
| style="width: 20%"| '''Gene product'''
| style="width: 80%"| UniProtKB:P27815 ''PDE4A''
|-
| '''GP2term relation'''
| involved in
|-
| '''GO term'''
| GO:0043951 ''negative regulation of cAMP-mediated signaling'', '''occurs in'''(CL:0000084 ''T-cell'')
|-
| '''Evidence'''
| IDA
|-
| '''Reference'''
| PMID:17404263
|-
|}





Revision as of 10:59, 6 October 2021

Purpose of annotation extensions: See Annotation_Extension

Usage guidelines

What to capture with the occurs_in relation

  • occurs_in is used to specify the cellular component, cell or anatomical structure in which a Molecular Function or a Biological Process take place.
  • Using occurs_in for a Biological Process is restricted to instances where all molecular functions that are part of the process occurs in the same cellular component/cell/anatomical structure. If different steps occur in different compartments/cells/anatomical structures, then one cannot assert that the Biological Process occurs in that compartments/cells/anatomical structure.

What not to capture

To be completed

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.


Usage examples for the occurs_in extension

1. Specifying the cellular location in which a molecular function takes place

Human LIG3 Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair, PMID:24674627, PMID:10207110.

Annotation for LIG3
Gene product UniProtKB:P23743 LIG3
GP2term relation enables
GO term GO:0003909 DNA ligase activity, occurs in(GO:0005739 mitochondrion)
Evidence IDA
Reference PMID:24674627

2. Specifying both the cellular location and the cell type in which a molecular function takes place

Human CASQ2 sequesters calcium ions in the sarcoplasmic reticulum of cardiac muscle cells, PMID:16908766

Annotation for CASQ2
Gene product UniProtKB:O14958 CASQ2
GP2term relation enables
GO term GO:0140314 calcium ion sequestering activity, occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)
Evidence IMP
Reference PMID:16908766

Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 enables sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.


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3. Specifying the anatomical structure in which a biological process takes place


Cross-reference to Relations Ontology (RO) term

BFO:0000066 occurs in

Review Status

Last reviewed: 2021-10-06

Back to Annotation_Extension