Occurs in: Difference between revisions
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===What to capture with the occurs_in relation=== | ===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. | * '''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 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). | ||
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 annotation extensions for an annotation. | 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 annotation extensions for an annotation. | ||
Revision as of 11:25, 7 October 2021
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).
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 annotation extensions for an annotation.
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.
- 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.
- GO:0110165 cellular anatomical entity
- Cell Ontology (CL)
- Uberon
- 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)
- etc
Usage of occurs_in in annotation extensions versus GO-CAM
In annotation extensions
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
Review Status
Last reviewed: 2021-10-06
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