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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==


=== Specifying the stage at which a localization is observed ===
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.  
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.  


If a gene product is localized to the nuclear periphery in S phase, G2, and mitosis (S. pombe Ulp1; PMID:11884512):
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 5: GO:0034399 ! nuclear periphery
Line 11: Line 31:
   G2 phase of mitotic cell cycle, and mitosis respectively
   G2 phase of mitotic cell cycle, and mitosis respectively


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):
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 5: GO:0005816 ! spindle pole body
Line 20: Line 40:


   col5: GO:0005826 ! actomyosin contractile ring
   col5: GO:0005826 ! actomyosin contractile ring
  col 16: exists_during(GO:0007067) ! mitosis
  col5: GO:0005819 ! spindle
   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: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