XP:biological process xp cellular component: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 91: Line 91:
intersection_of: OBO_REL:results_in_transport_to GO:0005739 ! mitochondrion
intersection_of: OBO_REL:results_in_transport_to GO:0005739 ! mitochondrion
</pre>
</pre>
== Examples ==
{|class="wikitable" style="text-align:center" border="1"
|-
!
! GO:0016043-cellular component organization
! GO:0022411-cellular component disassembly
! GO:0022607-cellular component assembly
! GO:0031555-transcriptional attenuation
! GO:0051168-nuclear export
!
|-
! GO:0005840-ribosome
| GO:0042254-ribosome biogenesis<sub>[[results_in_organization_of]]</sub>
| GO:0032790-ribosome disassembly<sub>[[OBO_REL:results_in_breakdown_of]]</sub>
| GO:0042255-ribosome assembly<sub>[[OBO_REL:results_in_formation_of]]</sub>
| GO:0031556-transcriptional attenuation by ribosome<sub>[[OBO_REL:mediated_by]]</sub>
| GO:0000054-ribosome export from nucleus<sub>[[OBO_REL:results_in_transport_of]]</sub>
|
! GO:0005840-ribosome
|-
! GO:0015934-large ribosomal subunit
| GO:0042273-ribosomal large subunit biogenesis<sub>[[results_in_organization_of]]</sub>
|
|
|
| GO:0000055-ribosomal large subunit export from nucleus<sub>[[OBO_REL:results_in_transport_of]]</sub>
|
! GO:0015934-large ribosomal subunit
|-
! GO:0015935-small ribosomal subunit
| GO:0042274-ribosomal small subunit biogenesis<sub>[[results_in_organization_of]]</sub>
|
|
|
| GO:0000056-ribosomal small subunit export from nucleus<sub>[[OBO_REL:results_in_transport_of]]</sub>
|
! GO:0015935-small ribosomal subunit
|-
! GO:0033279-ribosomal subunit
|
|
| GO:0042257-ribosomal subunit assembly<sub>[[OBO_REL:results_in_formation_of]]</sub>
|
|
|
! GO:0033279-ribosomal subunit
|-
!
!
|-
!
! GO:0016043-cellular component organization
! GO:0022411-cellular component disassembly
! GO:0022607-cellular component assembly
! GO:0031555-transcriptional attenuation
! GO:0051168-nuclear export
|}


== Results ==
== Results ==

Revision as of 17:51, 8 October 2008

XPs defining biological processes in terms of cellular components; example: 

[Term]
id: GO:0010020 ! chloroplast fission
intersection_of: GO:0048285  ! organelle fission
intersection_of: OBO_REL:results_in_division_of GO:0009507 ! chloroplast

[Term]
id: GO:0043572 ! plastid fission
intersection_of: GO:0048285  ! organelle fission
intersection_of: OBO_REL:results_in_division_of GO:0009536 ! plastid

i.e.

This allows a reasoner to compute the is_a relation between the two BP terms (based on the definition and the is_a relation between the CCs)

Availability

See the go/scratch/xps directory

This xp file has been registered in the OBO xps metadata so it is available here:

Methods

An initial parse was made using Obol. The results were then manually vetted by cjm, and new xp defs manually added

mitochondrial X

Terms of the form "mitochondrial X" are typically defined as 

* An X that unfolds_in a mitochondrion

Here unfolds_in is a relation between a process and the location of the participants throughout the process

E.g. 

[Term]
id: GO:0000963 ! mitochondrial RNA processing
intersection_of: GO:0006396 ! RNA processing
intersection_of: OBO_REL:unfolds_in GO:0005739 ! mitochondrion

See this sf item for clarification on RNA processing terms

Cellular X

Cellular X means X is executed at the level of the cell.

See sf item for clarification

For now we define cellular X using the has_level relation, but this is difficult to define

biogenesis, organization etc

Awaiting clarification. See: Cellular_component_processes

Existing xp defs may be changed once this is resolved

The current plan is to get replace "organization and biogenesis" with "organization". See above page for details.

export terms

Examples: 

[Term]
id: GO:0000056 ! ribosomal small subunit export from nucleus
intersection_of: GO:0051168 ! nuclear export
intersection_of: OBO_REL:results_in_transport_of GO:0015935 ! small ribosomal subunit

[Term]
id: GO:0006608 ! snRNP protein import into nucleus
intersection_of: GO:0006606 ! protein import into nucleus
intersection_of: OBO_REL:results_in_transport_of GO:0030532 ! small nuclear ribonucleoprotein complex

[Term]
id: GO:0006626 ! protein targeting to mitochondrion
intersection_of: GO:0006605 ! protein targeting
intersection_of: OBO_REL:results_in_transport_to GO:0005739 ! mitochondrion

Examples

GO:0016043-cellular component organization GO:0022411-cellular component disassembly GO:0022607-cellular component assembly GO:0031555-transcriptional attenuation GO:0051168-nuclear export
GO:0005840-ribosome GO:0042254-ribosome biogenesisresults_in_organization_of GO:0032790-ribosome disassemblyOBO_REL:results_in_breakdown_of GO:0042255-ribosome assemblyOBO_REL:results_in_formation_of GO:0031556-transcriptional attenuation by ribosomeOBO_REL:mediated_by GO:0000054-ribosome export from nucleusOBO_REL:results_in_transport_of GO:0005840-ribosome
GO:0015934-large ribosomal subunit GO:0042273-ribosomal large subunit biogenesisresults_in_organization_of GO:0000055-ribosomal large subunit export from nucleusOBO_REL:results_in_transport_of GO:0015934-large ribosomal subunit
GO:0015935-small ribosomal subunit GO:0042274-ribosomal small subunit biogenesisresults_in_organization_of GO:0000056-ribosomal small subunit export from nucleusOBO_REL:results_in_transport_of GO:0015935-small ribosomal subunit
GO:0033279-ribosomal subunit GO:0042257-ribosomal subunit assemblyOBO_REL:results_in_formation_of GO:0033279-ribosomal subunit
GO:0016043-cellular component organization GO:0022411-cellular component disassembly GO:0022607-cellular component assembly GO:0031555-transcriptional attenuation GO:0051168-nuclear export

Results

Missing Parentage Reports

Retrieved from "https://wiki.geneontology.org/index.php?title=XP:biological_process_xp_cellular_component&oldid=15909"