XP:biological process xp cellular component
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
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
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
- various closed