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

i.e. chloroplast fission _=def organelle fission THAT results_in_division_of chloroplast

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:

• downloads page
• HTML

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
• http://sourceforge.net/tracker/index.php?func=detail&aid=2016121&group_id=36855&atid=440764