XP:biological process xp cellular component: Difference between revisions
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Revision as of 14:08, 3 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.
- chloroplast fission =def organelle fission THAT results_in_division_of chloroplast
- plastid fission =def organelle fission THAT results_in_division_of plastid
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
- xp obo file
- imports file - point oboedit at this
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
biogenesis, organization etc
Awaiting clarification. See: Cellular_component_processes
Existing xp defs may be changed once this is resolved
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
Results
Missing Parentage Reports
- missing links 14 added. closed.
- http://sourceforge.net/tracker/index.php?func=detail&aid=2015221&group_id=36855&atid=440764 -- made after it was clarified CCs are anatomical structures. See also Cellular_component_processes. Open
- cellular processes