Annotation Extension Relation:exists during

From GO Wiki
Jump to: navigation, search

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