Cellular component disjoint classes

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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.

We could go ahead and put these in the GO. We don't need to keep the hokey GO_CJM terms. We can move the space-whole DF down to 2x6 statements on the children.

One consideration here is that people typically have disjoint_from links turned on in graphviz displays in OE. This works fine for the 3 disjoint classes we currently have, but could result in nasty hairballs if we extend this further. Easily fixed in OE2 - OE1 too? How much warning?

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.

I think many of the remaining DF statements are still valid. I checked 2 and made tracker items (see next section).

I didn't check the rest; here they are, verbatim:

  1. GO:0000144-cellular bud neck septin ring GO:0005940-septin ring GO:0032161-cleavage apparatus septin structure GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
  2. GO:0001740-Barr body GO:0000805-X chromosome GO:0001739-sex chromatin GO:0005694-chromosome GO:0044427-chromosomal part
  3. GO:0005637-nuclear inner membrane GO:0019866-organelle inner membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
  4. GO:0005637-nuclear inner membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
  5. GO:0005637-nuclear inner membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0031965-nuclear membrane GO:0044453-nuclear membrane part
  6. GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0031968-organelle outer membrane GO:0016020-membrane GO:0044425-membrane part
  7. GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
  8. GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0031965-nuclear membrane GO:0044453-nuclear membrane part
  9. GO:0005640-nuclear outer membrane GO:0031968-organelle outer membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
  10. GO:0005741-mitochondrial outer membrane GO:0031966-mitochondrial membrane GO:0031968-organelle outer membrane GO:0016020-membrane GO:0044425-membrane part
  11. GO:0005778-peroxisomal membrane GO:0031903-microbody membrane GO:0044439-peroxisomal part GO:0042579-microbody GO:0044438-microbody part
  12. GO:0005789-endoplasmic reticulum membrane GO:0031090-organelle membrane GO:0044425-membrane part GO:0016020-membrane GO:0044425-membrane part
  13. GO:0009276-Gram-negative-bacterium-type cell wall GO:0009274-peptidoglycan-based cell wall GO:0044462-external encapsulating structure part GO:0030312-external encapsulating structure GO:0044462-external encapsulating structure part
  14. GO:0009707-chloroplast outer membrane GO:0009527-plastid outer membrane GO:0031969-chloroplast membrane GO:0044425-membrane part GO:0016020-membrane
  15. GO:0012507-ER to Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  16. GO:0012507-ER to Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  17. GO:0012507-ER to Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030662-coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  18. GO:0012507-ER to Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030662-coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  19. GO:0012507-ER to Golgi transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030662-coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  20. GO:0012507-ER to Golgi transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030662-coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  21. GO:0012508-Golgi to ER transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  22. GO:0012508-Golgi to ER transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  23. GO:0012508-Golgi to ER transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  24. GO:0012508-Golgi to ER transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  25. GO:0012508-Golgi to ER transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  26. GO:0012508-Golgi to ER transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  27. GO:0012509-inter-Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  28. GO:0012509-inter-Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  29. GO:0012509-inter-Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  30. GO:0012509-inter-Golgi transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  31. GO:0012509-inter-Golgi transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  32. GO:0012509-inter-Golgi transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030663-COPI coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  33. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  34. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  35. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  36. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  37. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  38. GO:0012510-trans-Golgi network transport vesicle membrane GO:0030660-Golgi-associated vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  39. GO:0020006-parasitophorous vacuolar membrane network GO:0005774-vacuolar membrane GO:0044425-membrane part GO:0016020-membrane GO:0044425-membrane part
  40. GO:0020017-flagellar membrane GO:0031090-organelle membrane GO:0044459-plasma membrane part GO:0016020-membrane GO:0044425-membrane part
  41. GO:0030485-smooth muscle contractile fiber GO:0043292-contractile fiber GO:0044449-contractile fiber part GO:0043292-contractile fiber GO:0044449-contractile fiber part
  42. GO:0030671-clathrin-coated phagocytic vesicle membrane GO:0030669-clathrin-coated endocytic vesicle membrane GO:0030670-phagocytic vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  43. GO:0030671-clathrin-coated phagocytic vesicle membrane GO:0030669-clathrin-coated endocytic vesicle membrane GO:0030670-phagocytic vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  44. GO:0030673-axolemma GO:0016020-membrane GO:0032589-neuron projection membrane GO:0016020-membrane GO:0044425-membrane part
  45. GO:0030864-cortical actin cytoskeleton GO:0030863-cortical cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
  46. GO:0031676-plasma membrane-derived thylakoid membrane GO:0042651-thylakoid membrane GO:0044459-plasma membrane part GO:0016020-membrane GO:0044425-membrane part
  47. GO:0031900-chromoplast outer membrane GO:0009527-plastid outer membrane GO:0046862-chromoplast membrane GO:0044425-membrane part GO:0016020-membrane
  48. GO:0032159-septin cap GO:0032156-septin cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
  49. GO:0032160-septin filament array GO:0032156-septin cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
  50. GO:0032169-prospore septin ring GO:0005940-septin ring GO:0032161-cleavage apparatus septin structure GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
  51. GO:0032174-cellular bud neck septin collar GO:0032161-cleavage apparatus septin structure GO:0032173-septin collar GO:0044430-cytoskeletal part GO:0005856-cytoskeleton
  52. GO:0032177-cellular bud neck split septin rings GO:0032161-cleavage apparatus septin structure GO:0032176-split septin rings GO:0044430-cytoskeletal part GO:0005856-cytoskeleton
  53. GO:0046861-glyoxysomal membrane GO:0031903-microbody membrane GO:0044438-microbody part GO:0042579-microbody GO:0044438-microbody part
  54. GO:0055038-recycling endosome membrane GO:0010008-endosome membrane GO:0055037-recycling endosome GO:0044440-endosomal part GO:0005768-endosome
  55. GO:0060201-clathrin sculpted acetylcholine transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  56. GO:0060201-clathrin sculpted acetylcholine transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane
  57. GO:0060203-clathrin sculpted glutamate transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0016020-membrane GO:0044425-membrane part
  58. GO:0060203-clathrin sculpted glutamate transport vesicle membrane GO:0030658-transport vesicle membrane GO:0030665-clathrin coated vesicle membrane GO:0044425-membrane part GO:0016020-membrane

Tracker items resulting from this work

Future

Region Connection Calculus

See also

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