Cellular component disjoint classes: Difference between revisions

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=== Top level disjoint pairs ===
=== Top level disjoint pairs ===
I found it helped by creating 4 new top level classes:
/ GO:0005575 cellular_component
  is_a GO:0005576 extracellular region
  is_a GO:0031975 envelope
  is_a GO_CJM:0000001 fiat part
  is_a GO:0044420 extracellular matrix part
  is_a GO:0044421 extracellular region part
  is_a GO:0044422 organelle part
  is_a GO:0044423 virion part
  is_a GO:0044456 synapse part
  is_a GO:0044464 cell part
  is_a GO_CJM:0000002 external
  is_a GO_CJM:0000003 space
  is_a GO:0031974 membrane-enclosed lumen
  is_a GO:0045202 synapse
  is_a GO_CJM:0000004 whole
  is_a GO:0005623 cell
  is_a GO:0019012 virion
  is_a GO:0031012 extracellular matrix
  is_a GO:0032991 macromolecular complex
  is_a GO:0043226 organelle
  is_a GO:0055044 symplast
These may or may not be meaningful or consistent with the GO - it's a starting point.
See [http://www.geneontology.org/scratch/disjointness_constraints/cellular_component_disj.obo cellular_component_disj.obo].
I declared space disjoint from whole. Really this was just a convenient alternative to making 2 x 6 pairwise DF statements for each is_a child.
I then used the "make is_a children mutually disjoint" menu option in OE2beta on "whole" and "space"
At this point I saw no violations in GO. The declarations so far are fairly conservative.
=== X part and X ===
Using the [[XP:cellular_component_xp_self CC xps]] I created a [[disjoint_from]] statements for all pairs "X" and "X part"
This proved too extreme. I manually removed the disjoint_from statement between organelle and organelle part (whilst nothing can be both an organelle and a proper part of the '''same''' organelle, something can be both a whole organelle and part of a larger different kind of organelle).
See [http://www.geneontology.org/scratch/disjointness_constraints/cc_part_whole_disjoint.obo cc_part_whole_disjoint.obo].


== Tracker items resulting from this work ==
== Tracker items resulting from this work ==
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* [http://sourceforge.net/tracker/index.php?func=detail&aid=1960642&group_id=36855&atid=440764 Barr body TPV]
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1960642&group_id=36855&atid=440764 Barr body TPV]


== Region Connection Calculus ==
== Future ==
 
=== Region Connection Calculus ===


== See also ==
== See also ==


* [http://www.geneontology.org/GO.component.guidelines.shtml GO CC guidelines]
* [http://www.geneontology.org/GO.component.guidelines.shtml GO CC guidelines]

Revision as of 17:03, 9 May 2008

The GO CC hierarchy contains many classes that should probably be declared disjoint. For example, nothing is both an intracellular region and an extracellular space. Similarly nothing is both a cell and a cytoplasm (of course cell and cytoplasm spatially overlap. disjoint_from is about set-disjointness, not spatial disjointness). Addng disjoint_from links prevents TPVs (for evidence see below_

But we don't want to add disjoint_from links willy-nilly. We should be methodical to reduce the amount of work that needs don

Working area

We use the scratch/ directory in cvs

Results

Top level disjoint pairs

I found it helped by creating 4 new top level classes:

/ GO:0005575 cellular_component
 is_a GO:0005576 extracellular region
 is_a GO:0031975 envelope
 is_a GO_CJM:0000001 fiat part
  is_a GO:0044420 extracellular matrix part
  is_a GO:0044421 extracellular region part
  is_a GO:0044422 organelle part
  is_a GO:0044423 virion part
  is_a GO:0044456 synapse part
  is_a GO:0044464 cell part
 is_a GO_CJM:0000002 external
 is_a GO_CJM:0000003 space
  is_a GO:0031974 membrane-enclosed lumen
  is_a GO:0045202 synapse
 is_a GO_CJM:0000004 whole
  is_a GO:0005623 cell
  is_a GO:0019012 virion
  is_a GO:0031012 extracellular matrix
  is_a GO:0032991 macromolecular complex
  is_a GO:0043226 organelle
  is_a GO:0055044 symplast

These may or may not be meaningful or consistent with the GO - it's a starting point.

See cellular_component_disj.obo.

I declared space disjoint from whole. Really this was just a convenient alternative to making 2 x 6 pairwise DF statements for each is_a child.

I then used the "make is_a children mutually disjoint" menu option in OE2beta on "whole" and "space"

At this point I saw no violations in GO. The declarations so far are fairly conservative.

X part and X

Using the XP:cellular_component_xp_self CC xps I created a disjoint_from statements for all pairs "X" and "X part"

This proved too extreme. I manually removed the disjoint_from statement between organelle and organelle part (whilst nothing can be both an organelle and a proper part of the same organelle, something can be both a whole organelle and part of a larger different kind of organelle).

See cc_part_whole_disjoint.obo.


Tracker items resulting from this work

Future

Region Connection Calculus

See also