Happens during: Difference between revisions

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==Definition==
==Definition==


Identifies a process during which a biological process occurs
Identifies a temporal phase during which a molecular function or biological process occurs.


==Comment==
==Comment==
This relationship can be used in two ways:
* Temporal phases can be either a child of GO:0044848 (biological phase) or UBERON:0000105 (life cycle stage).
* To add a '''PHASE''' to the annotation extension field of a biological processes the '''ONLY''' relationship to use is ‘happens_during’ (not part_of)
* 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 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 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.
 
To link a '''physical entity''' (''cellular component'') to a process by duration, use the relationship '''exists_during.'''


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


===Range===
===Range===


GO:0008150 ! Biological Process
GO:0044848 ! biological phase
 
UBERON:0000105 ! life cycle stage


==Annotation Extension Usage Examples==
==Annotation Extension Usage Examples==


'''1. A process occurring during cell development'''
'''1. A process occurring during a cell cycle phase'''
 
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).''
 
 
 
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| P22003  <span style="color:green">BMP5</span>
| GO:0010862 <span style="color:green">positive regulation of pathway-restricted SMAD protein phosphorylation</span>
| PMID:11580864
| IDA
| happens_during(GO:0016358 <span style="color:green">dendrite development</span>)
 
|}
 
 
'''2. 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 ==


'''2. A process occurring during a cell cycle phase'''
'''1. A process occurring during a cell cycle phase'''
Cdc14 targets Yen1 to the nucleus in early anaphase, PMID:24626187
Cdc14 targets Yen1 to the nucleus in early anaphase, PMID:24626187


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|PMID:24626187
|PMID:24626187
|
|
|happens_during GO:0048471 <span style="color:red">mitotic anaphase</span>
|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>
|-
|}
 
'''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
 
{| class="wikitable" border="1"
! 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 <span style="color:green">canonical Wnt signaling pathway</span>
|PMID: ID
|happens_during (GO:0035108 <span style="color:green">limb morphogenesis</span>)
|
|-
|Folded
|ID
|Protein A
|New GO term <span style="color:green">canonical Wnt signaling pathway during limb morphogenesis </span>
|PMID: ID
|
|is_a GO:0060070 <span style="color:red">canonical Wnt signaling pathway</span> AND <span style="color:red">?? </span> GO:0035108 <span style="color:red">limb morphogenesis</span>
|-
|-
|}
|}


'''OWL class expression:''' GO:0060070 <span style="color:red">canonical Wnt signaling pathway</span> AND <span style="color:red">?? </span> GO:0035108 <span style="color:red">limb morphogenesis</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>


Note that in this example the GO term GO:0035108 <span style="color:green">limb morphogenesis</span> is not directly associated with Protein A, whereas in the part_of [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:part_of#Using_examples_.28from_above.29_to_demonstrate_Folding_and_Unfolding_using_the_relationship_part_of] example it is known that Protein A plays a role in limb morphogenesis and therefore the additional annotation GO:0035108 <span style="color:green">limb morphogenesis</span> is directly associated with Protein A.
----




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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