The purpose of annotation extensions is described in the main Annotation_Extension documentation page.
What to capture with the occurs_in relation
occurs inis 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 inrelation. 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 ofrelation, while in annotation extensions, the GO term has a
occurs inrelation 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.
occurs infor 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 refers to the GO terms that can be further specified with the relation.
Range describes the types of entities that can be used with the relation.
- GO:0110165 cellular anatomical entity
- Cell Ontology (CL)
- Mouse Developmental Anatomy Ontology (EMAPA)
- Drosophila Anatomy Ontology (DAO)
- C. elegans gross anatomy ontology (WBbt)
- Plant Trait Ontology (TO)
- Xenopus anatomical entity
- Zebrafish anatomy and development ontology (ZFA)
Usage examples for the occurs_in extension
1. Specifying the cellular location in which a molecular function takes place
|Annotation for LIG3|
|Gene product||UniProtKB:P23743 LIG3|
|GO term||GO:0003909 DNA ligase activity, occurs in(GO:0005739 mitochondrion)|
2. Specifying both the cellular location and the cell type in which a molecular function takes place
|Annotation for CASQ2|
|Gene product||UniProtKB:O14958 CASQ2|
|GO term||GO:0140314 calcium ion sequestering activity, occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)|
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
|Annotation for ATP13A2|
|Gene product||UniProtKB:Q9NQ11 ATP13A2|
|GO term||GO:1905037 autophagosome organization , occurs in(CL_0002609 neuron of cerebral cortex)|
Cross-reference to Relations Ontology (RO) term
Last reviewed: 2021-10-07
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