Happens during: Difference between revisions

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==Comment==
==Comment==
This relationship can be used in two ways:  
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 capture the temporal '''PHASE''' during which a Molecular Function is executed.
* 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 [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:part_of part_of] if it is known that the process is definitely part of the biological process.
* 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 [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:part_of part_of] if it is known that the process is definitely part of the biological process.



Revision as of 17:58, 18 June 2019

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Definition

Identifies a process during which a biological process occurs

Comment

This relationship can be used in two ways:

  • To capture the temporal PHASE during which a Molecular Function is executed.
  • 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.

Synonym

occurs_during (EXACT)

Child terms

  • None.

Scope of use

Domain

BFO:0000007 ! process (Biological Process or Molecular Function)

Range

GO:0008150 ! Biological Process

Annotation Extension Usage Examples

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 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

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 [1] 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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