Happens during: Difference between revisions
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Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation usage examples for each annotation extension relation] | |||
==Definition== | ==Definition== | ||
Identifies a | Identifies a temporal phase during which a molecular function or biological process occurs. | ||
==Comment== | ==Comment== | ||
* Temporal phases can be either a child of GO:0044848 (biological phase) or UBERON:0000105 (life cycle stage). | |||
To link a physical entity to a process by duration, use exists_during. | * This extension is no longer used to add a ''biological process'' to the annotation extension field when the role of the gene product in the process is unclear, but its activity appears to coincide with another process. If the function or process is known to definitely be part of a process, use the 'part of' extension relation. | ||
* To link a physical entity (''cellular component'') to a process by duration, use the relationship exists_during. Note, however, that exists_during is not currently in the Relations Ontology and its usage may be addressed in future work. | |||
==Synonym== | ==Synonym== | ||
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==Child terms== | ==Child terms== | ||
* None | * None | ||
==Scope of use== | ==Scope of use== | ||
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===Domain=== | ===Domain=== | ||
BFO:0000007 ! process ( | BFO:0000007 ! process (biological_process or molecular_function) | ||
===Range=== | ===Range=== | ||
GO:0044848 ! biological phase | |||
UBERON:0000105 ! life cycle stage | |||
==Annotation Extension Usage Examples== | ==Annotation Extension Usage Examples== | ||
'''1 | '''1. A process occurring during a cell cycle phase''' | ||
Statement from paper: | Statement from paper: | ||
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== Using examples to demonstrate [[Folding_and_Unfolding]] using the relationship happens_during == | == Using examples to demonstrate [[Folding_and_Unfolding]] using the relationship happens_during == | ||
'''1. A process occurring during a cell cycle phase''' | |||
Cdc14 targets Yen1 to the nucleus in early anaphase, PMID:24626187 | |||
{| class="wikitable" border="1" | {| class="wikitable" border="1" | ||
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|PMID:24626187 | |PMID:24626187 | ||
| | | | ||
| | |is a GO:0034504 <span style="color:red">protein localization to nucleus</span> AND part_of<span style="color:red">??</span> GO:0048471 <span style="color:red">mitotic anaphase</span> | ||
|- | |- | ||
|} | |} | ||
'''OWL class expression:''' GO:0034504 <span style="color:red">protein localization to nucleus</span> AND happens_during SOME GO:0000090 <span style="color:red">mitotic anaphase</span> | |||
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[[Category:relations]] | [[Category:relations]] | ||
[[Category:annotation extension]] | [[Category:annotation extension]] | ||
[[Category: GO-CAM Relations]] |
Revision as of 11:05, 9 September 2019
Back to Annotation usage examples for each annotation extension relation
Definition
Identifies a temporal phase during which a molecular function or biological process occurs.
Comment
- Temporal phases can be either a child of GO:0044848 (biological phase) or UBERON:0000105 (life cycle stage).
- This extension is no longer used to add a biological process to the annotation extension field when the role of the gene product in the process is unclear, but its activity appears to coincide with another process. If the function or process is known to definitely be part of a process, use the 'part of' extension relation.
- To link a physical entity (cellular component) to a process by duration, use the relationship exists_during. Note, however, that exists_during is not currently in the Relations Ontology and its usage may be addressed in future work.
Synonym
occurs_during (EXACT)
Child terms
- None
Scope of use
Domain
BFO:0000007 ! process (biological_process or molecular_function)
Range
GO:0044848 ! biological phase
UBERON:0000105 ! life cycle stage
Annotation Extension Usage Examples
1. A process occurring during a cell cycle phase
Statement from paper:
We here show that the mitotic master phosphatase Cdc14 targets Yen1 to the nucleus in early anaphase through the FEAR network. In Figure 2, Yen1 re-localizes back to the nucleus in early anaphase in a Cdc14-dependent manner.
Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) |
---|---|---|---|---|
Q00684 cdc14 | GO:0034504 protein localization to nucleus | PMID:24626187 | happens_during(GO:0000090 mitotic anaphase) |
Using examples to demonstrate Folding_and_Unfolding using the relationship happens_during
1. A process occurring during a cell cycle phase Cdc14 targets Yen1 to the nucleus in early anaphase, PMID:24626187
Folded/unfolded | DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) | Parent terms for new folded GO term |
---|---|---|---|---|---|---|
Unfolded | Q00684 | cdc14 | GO:0034504 protein localization to nucleus | PMID:24626187 | happens_during(GO:0000090 mitotic anaphase) | |
Folded | Q00684 | cdc14 | New potential GO term protein localisation to nucleus during mitotic anaphase | PMID:24626187 | is a GO:0034504 protein localization to nucleus AND part_of?? GO:0048471 mitotic anaphase |
OWL class expression: GO:0034504 protein localization to nucleus AND happens_during SOME GO:0000090 mitotic anaphase
Back to Annotation usage examples for each annotation extension relation