Exists 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 process or stage during which a cellular component is present. | |||
==Child terms== | ==Child terms== | ||
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===Range=== | ===Range=== | ||
GO:0008150 ! Biological Process, WBls:0000075 ! nematode life stage, ZFS:0100000 ! Zebrafish stage | |||
==Annotation Extension Usage Examples== | ==Annotation Extension Usage Examples== | ||
=== Enhancing Cell Component Annotations === | === Enhancing Cell Component Annotations === | ||
Cellular component annotations can be enhanced by specifying that localization is observed during a cell cycle or developmental stage, or in the context of a specific biological process. | Cellular component annotations can be enhanced by specifying that localization is observed during a cell cycle or developmental stage, or in the context of a specific biological process. | ||
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col5: GO:0005826 ! actomyosin contractile ring | col5: GO:0005826 ! actomyosin contractile ring | ||
col 16: exists_during(GO:0007067) ! mitosis | col 16: exists_during(GO:0007067) ! mitosis | ||
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Also see the [http://fafner.stanford.edu/pipermail/go-discuss/2011-March/005560.html go-discuss mailing list] for more information. | Also see the [http://fafner.stanford.edu/pipermail/go-discuss/2011-March/005560.html go-discuss mailing list] for more information. | ||
== Using examples to demonstrate [[Folding_and_Unfolding]] using the relationship exists_during == | |||
'''Specifying that a gene product is localized to the spindle pole body (SPB) and nucleolus in interphase.''' PMID:16085490 | |||
{| class="wikitable" border="1" | |||
! 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 | |||
| SPAC1782.09c | |||
| Clp1 | |||
| GO:0005816 <span style="color:green">spindle pole body</span> | |||
| PMID:16085490 | |||
| exists_during(GO:0051329 <span style="color:green">interphase of mitotic cell cycle</span>) | |||
| | |||
|- | |||
| Folded | |||
| SPAC1782.09c | |||
| Clp1 | |||
| New GO term <span style="color:green">spindle pole body during interphase of mitotic cell cycle</span> | |||
| PMID:16085490 | |||
| | |||
| is_a GO:0005816 <span style="color:red">spindle pole body</span> | |||
|- | |||
|} | |||
'''OWL class expression:''' GO:0005816 <span style="color:red">spindle pole body</span> AND exists_during SOME GO:0051329 <span style="color:red">interphase of mitotic cell cycle</span> | |||
{| class="wikitable" border="1" | |||
! 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 | |||
| SPAC1782.09c | |||
| Clp1 | |||
| GO:0005730 <span style="color:green">nucleolus</span> | |||
| PMID:16085490 | |||
| exists_during(GO:0051329 <span style="color:green">interphase of mitotic cell cycle</span>) | |||
| | |||
|- | |||
| Folded | |||
| SPAC1782.09c | |||
| Clp1 | |||
| New GO term <span style="color:green">nucleolus during interphase of mitotic cell cycle</span> | |||
| PMID:16085490 | |||
| | |||
| is_a GO:0005730 <span style="color:red">nucleolus</span> | |||
|- | |||
|} | |||
'''OWL class expression:''' GO:0005730 <span style="color:red">nucleolus</span> AND exists_during SOME GO:0051329 <span style="color:red">interphase of mitotic cell cycle</span> | |||
---- | |||
Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation usage examples for each annotation extension relation] | |||
[[Category:relations]] | [[Category:relations]] | ||
[[Category:annotation extension]] | [[Category:annotation extension]] |
Revision as of 08:10, 5 March 2015
Back to Annotation usage examples for each annotation extension relation
Definition
Identifies a process or stage during which a cellular component is present.
Child terms
- None.
Scope of use
Domain
BFO:0000004 ! independent continuant (Cellular Component)
Range
GO:0008150 ! Biological Process, WBls:0000075 ! nematode life stage, ZFS:0100000 ! Zebrafish stage
Annotation Extension Usage Examples
Enhancing Cell Component Annotations
Cellular component annotations can be enhanced by specifying that localization is observed during a cell cycle or developmental stage, or in the context of a specific biological process.
1. If a gene product is localized to the nuclear periphery in S phase, G2, and mitosis (S. pombe Ulp1; PMID:11884512):
col 5: GO:0034399 ! nuclear periphery col 16: exists_during(GO:0000084)|exists_during(GO:0000085)|exists_during(GO:0007067) ! S phase of mitotic cell cycle, G2 phase of mitotic cell cycle, and mitosis respectively
2. If a gene product is localized to the spindle pole body (SPB) and nucleolus in interphase and to the actin contractile ring, the mitotic spindle, and kinetochores during mitosis (S. pombe Clp1; PMID:16085490):
col 5: GO:0005816 ! spindle pole body col 16: exists_during(GO:0051329) ! interphase of mitotic cell cycle
col 5: GO:0005730 ! nucleolus col 16: exists_during(GO:0051329) ! interphase of mitotic cell cycle
col5: GO:0005826 ! actomyosin contractile ring col 16: exists_during(GO:0007067) ! mitosis
col5: GO:0000777 ! condensed chromosome kinetochore col 16: exists_during(GO:0007067) ! mitosis
Note that an experiment that supports 'CC exists_during BP' may also support an annotation of the 'BP occurs_in CC' pattern.
Also see the go-discuss mailing list for more information.
Using examples to demonstrate Folding_and_Unfolding using the relationship exists_during
Specifying that a gene product is localized to the spindle pole body (SPB) and nucleolus in interphase. PMID:16085490
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 | SPAC1782.09c | Clp1 | GO:0005816 spindle pole body | PMID:16085490 | exists_during(GO:0051329 interphase of mitotic cell cycle) | |
Folded | SPAC1782.09c | Clp1 | New GO term spindle pole body during interphase of mitotic cell cycle | PMID:16085490 | is_a GO:0005816 spindle pole body |
OWL class expression: GO:0005816 spindle pole body AND exists_during SOME GO:0051329 interphase of mitotic cell cycle
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 | SPAC1782.09c | Clp1 | GO:0005730 nucleolus | PMID:16085490 | exists_during(GO:0051329 interphase of mitotic cell cycle) | |
Folded | SPAC1782.09c | Clp1 | New GO term nucleolus during interphase of mitotic cell cycle | PMID:16085490 | is_a GO:0005730 nucleolus |
OWL class expression: GO:0005730 nucleolus AND exists_during SOME GO:0051329 interphase of mitotic cell cycle
Back to Annotation usage examples for each annotation extension relation