Cellular component disjoint classes
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:
- GO:0000144-cellular bud neck septin ring GO:0005940-septin ring GO:0032161-cleavage apparatus septin structure GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
- GO:0001740-Barr body GO:0000805-X chromosome GO:0001739-sex chromatin GO:0005694-chromosome GO:0044427-chromosomal part
- GO:0005637-nuclear inner membrane GO:0019866-organelle inner membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0005637-nuclear inner membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0005637-nuclear inner membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0031965-nuclear membrane GO:0044453-nuclear membrane part
- GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0031968-organelle outer membrane GO:0016020-membrane GO:0044425-membrane part
- GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0005640-nuclear outer membrane GO:0031965-nuclear membrane GO:0044453-nuclear membrane part GO:0031965-nuclear membrane GO:0044453-nuclear membrane part
- GO:0005640-nuclear outer membrane GO:0031968-organelle outer membrane GO:0044453-nuclear membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0005741-mitochondrial outer membrane GO:0031966-mitochondrial membrane GO:0031968-organelle outer membrane GO:0016020-membrane GO:0044425-membrane part
- GO:0005778-peroxisomal membrane GO:0031903-microbody membrane GO:0044439-peroxisomal part GO:0042579-microbody GO:0044438-microbody part
- GO:0005789-endoplasmic reticulum membrane GO:0031090-organelle membrane GO:0044425-membrane part GO:0016020-membrane GO:0044425-membrane part
- 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
- GO:0009707-chloroplast outer membrane GO:0009527-plastid outer membrane GO:0031969-chloroplast membrane GO:0044425-membrane part GO:0016020-membrane
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- GO:0020006-parasitophorous vacuolar membrane network GO:0005774-vacuolar membrane GO:0044425-membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0020017-flagellar membrane GO:0031090-organelle membrane GO:0044459-plasma membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0030485-smooth muscle contractile fiber GO:0043292-contractile fiber GO:0044449-contractile fiber part GO:0043292-contractile fiber GO:0044449-contractile fiber part
- 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
- 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
- GO:0030673-axolemma GO:0016020-membrane GO:0032589-neuron projection membrane GO:0016020-membrane GO:0044425-membrane part
- GO:0030864-cortical actin cytoskeleton GO:0030863-cortical cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
- GO:0031676-plasma membrane-derived thylakoid membrane GO:0042651-thylakoid membrane GO:0044459-plasma membrane part GO:0016020-membrane GO:0044425-membrane part
- GO:0031900-chromoplast outer membrane GO:0009527-plastid outer membrane GO:0046862-chromoplast membrane GO:0044425-membrane part GO:0016020-membrane
- GO:0032159-septin cap GO:0032156-septin cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
- GO:0032160-septin filament array GO:0032156-septin cytoskeleton GO:0044430-cytoskeletal part GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
- GO:0032169-prospore septin ring GO:0005940-septin ring GO:0032161-cleavage apparatus septin structure GO:0005856-cytoskeleton GO:0044430-cytoskeletal part
- GO:0032174-cellular bud neck septin collar GO:0032161-cleavage apparatus septin structure GO:0032173-septin collar GO:0044430-cytoskeletal part GO:0005856-cytoskeleton
- 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
- GO:0046861-glyoxysomal membrane GO:0031903-microbody membrane GO:0044438-microbody part GO:0042579-microbody GO:0044438-microbody part
- GO:0055038-recycling endosome membrane GO:0010008-endosome membrane GO:0055037-recycling endosome GO:0044440-endosomal part GO:0005768-endosome
- 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
- 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
- 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
- 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
TODO - write something clever here
http://en.wikipedia.org/wiki/Region_Connection_Calculus
Use cases:
- reasoning about protein localization. If a protein is localized to X, what does it have to pass through on its way?