Difference between revisions of "XP:biological process xp cellular component"

From GO Wiki
Jump to: navigation, search
Line 1: Line 1:
 
XPs defining biological processes in terms of cellular components; example:
 
XPs defining biological processes in terms of cellular components; example:
  
  [Term]
+
<pre>
  id: GO:0000054 ! ribosome export from nucleus
+
[Term]
  intersection_of: GO:0051168 {namespace=biological_process_xp_cellular_component} ! nuclear export
+
id: GO:0010020 ! chloroplast fission
  intersection_of: OBO_REL:results_in_transport_of GO:0005840 {namespace=biological_process_xp_cellular_component} ! ribosome
+
intersection_of: GO:0048285  ! organelle fission
 +
intersection_of: OBO_REL:results_in_division_of GO:0009507 ! chloroplast
 +
</pre>
  
i.e. ribosome export from nucleus = nuclear export THAT results_in_transport_of ribosome
+
i.e. '''chloroplast fission''' <sub>=def</sub> '''organelle fission''' THAT [[results_in_division_of]] '''chloroplast'''
  
(Experimenting with the use of namespace tags as an easy way to separate out xp content from main GO)
+
== Availability ==
  
 
See the [http://www.geneontology.org/scratch/xps/ go/scratch/xps] directory
 
See the [http://www.geneontology.org/scratch/xps/ go/scratch/xps] directory
Line 20: Line 22:
 
* [http://www.berkeleybop.org/ontologies/obo-all/bp_xp_cellular_component/bp_xp_cellular_component.xp.html HTML]
 
* [http://www.berkeleybop.org/ontologies/obo-all/bp_xp_cellular_component/bp_xp_cellular_component.xp.html HTML]
  
Missing Link Reports:
+
== Methods ==
 +
 
 +
=== 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.
 +
 
 +
<pre>
 +
[Term]
 +
id: GO:0000963 ! mitochondrial RNA processing
 +
intersection_of: GO:0006396 ! RNA processing
 +
intersection_of: OBO_REL:unfolds_in GO:0005739 ! mitochondrion
 +
</pre>
 +
 
 +
See [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2020664&group_id=36855 this sf item] for clarification on RNA processing terms
 +
 
 +
== Results ==
 +
 
 +
=== Missing Parentage Reports ===
  
 
* http://sourceforge.net/tracker/index.php?func=detail&aid=1939817&group_id=36855&atid=440764
 
* http://sourceforge.net/tracker/index.php?func=detail&aid=1939817&group_id=36855&atid=440764

Revision as of 11:51, 17 July 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

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

Availability

See the go/scratch/xps directory

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

Methods

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

Results

Missing Parentage Reports