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---------------Text extracted from ontology: DO NOT EDIT---------------
- OWL ID: RO_0002092
- label: happens during
- synonyms [u'occurs_during', u'during']
Identifies a process or life stage during which a molecular function or biological process occurs. This is weaker than parthood. So, for example, various processes occur during gastrulation without being part of it.
Previous definition "p happens_during q if and only if the temporal extent of p is part_of the temporal extent of q." Note that part_of between processes implies happens_during (we must use OWL to express this), but happens_during does not imply part_of. Note also that this relation holds between two processes. To link a physical entity to a process by duration, use exists_during. [BFO:cjm] Note that in order to express that part_of between processes implies during, we must use OWL.
[AE_biological_process, valid_for_annotation_extension, ro-eco, AE_developmental_stages, display_for_curators]
##local domain {u'BFO:0000015': u'process'}
{u'GO:0008150': u'biological_process', u'WBls:0000075': u'Nematoda Life Stage', u'ZFS:0100000': u'ZFS:0100000', u'UBERON:0000105': ''}
---------------END AUTO GENERATED SECTION---------------
This relationship can be used in two ways:
- To add a PHASE to the annotation extension field of a biological processes the ONLY relationship to use is happens_during (not part_of)
- To add a biological process to the annotation extension field when the role of the gene product in the process is unclear, but occurs during this specific biological process. Consider the use of the relationship part_of if it is known that the process is definitely part of the biological process.
To link a physical entity (cellular component) to a process by duration, use the relationship exists_during.
occurs_during (EXACT)
1. A process occurring during cell development
Statement from paper:
In most cell systems that have been examined, the primary signal transduction pathway for BMPs involves phosphorylation of Smad-1 [22]... To determine if BMP-5 initiates similar signaling events in sympathetic neurons, cultured sympathetic neurons grown in the absence of glial cells were treated with BMP-5 for 30 or 60 min then analyzed by Western blotting using Abs specific for total Smad-1 or for phosphorylated Smad-1. Phosphorylation of Smad-1 is evident within 30 min after exposure to BMP-5 (Figure 4A) with significantly increased pSmad-1 levels apparent at 60min. In contrast, treatment with BMP-5 did not alter levels of total Smad-1 (Figure 4B).
| Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) |
|---|---|---|---|---|
| P22003 BMP5 | GO:0010862 positive regulation of pathway-restricted SMAD protein phosphorylation | PMID:11580864 | IDA | happens_during(GO:0016358 dendrite development) |
2. 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
2. 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 GO term: protein localization to nucleus during mitotic anaphase | PMID:24626187 | is a GO:0034504 protein localization to nucleus AND part_of GO:0000090 mitotic anaphase | |
OWL class expression: GO:0034504 protein localization to nucleus AND happens_during SOME GO:0000090 mitotic anaphase
3. Specifying the developmental process during which another biological process is occurs, but where the role of the biological process in the developmental processes is unknown. No usage examples for this currently exist
| Folded/unfolded | DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) | Parent terms of new folded GO term |
|---|---|---|---|---|---|---|
| Unfolded | ID | Protein A | GO:0060070 canonical Wnt signaling pathway | PMID: ID | happens_during (GO:0035108 limb morphogenesis) | |
| Folded | ID | Protein A | New GO term: canonical Wnt signaling pathway during limb morphogenesis | PMID: ID | is_a GO:0060070 canonical Wnt signaling pathway AND part_of GO:0035108 limb morphogenesis | |
OWL class expression: GO:0060070 canonical Wnt signaling pathway AND happens_during SOME GO:0035108 limb morphogenesis
Note that in this example the GO term GO:0035108 limb morphogenesis is not directly associated with Protein A, whereas in the part_of example it is known that Protein A plays a role in limb morphogenesis and therefore the additional annotation GO:0035108 limb morphogenesis is directly associated with Protein A.
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