Annotation Extension Relation:occurs in

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The purpose of annotation extensions is described in the main Annotation_Extension documentation page.

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.
  • More than one location may be captured for a single MF or BP using the occurs in relation. This usage captures subcellular or anatomical structures for which the more granular structure is part of the less granular structure, e.g. occurs_in(mitochondrion),occurs_in(neuron),occurs_in(brain). If a MF or a BP takes place at two different locations, this should be captured as independent annotations or independent annotation extensions for an annotation. (Note that in GO-CAM this is captured differently, i.e. structures that are part of other structures are linked to each other with the part of relation, while in annotation extensions, the GO term has a occurs in relation with each structure).

What not to capture

  • Localizations already present in the GO term label or definition; for example for GO:0050852 T cell receptor signaling pathway, occurs in T-cell does not need to be added as an extension.
  • 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.

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.


3. Specifying the cellular component in which a biological process takes place

Human ATP13A2 mediates autophagosome organization in cerebral cortex neurons, PMID:22186024

Annotation for ATP13A2
Gene product UniProtKB:Q9NQ11 ATP13A2
GP2term relation enables
GO term GO:1905037 autophagosome organization , occurs in(CL_0002609 neuron of cerebral cortex)
Evidence IDA
Reference PMID:22186024



Cross-reference to Relations Ontology (RO) term

BFO:0000066 occurs in

Review Status

Last reviewed: 2021-10-07

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