View source for Cellular component disjoint classes


'''NOTE:''' the disjointness axioms are being moved to the [[Ontology extensions]] directory


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 done

== Working area ==

We use the scratch/ directory in cvs

* [http://www.geneontology.org/scratch/disjointness_constraints/ go/scratch/disjointness_constraints]

== Results ==

=== Top level disjoint pairs ===

I found it helped by creating 4 new top level classes. Note that I am not necessarily recommending this for GO, for hypothesis-testing purposes it makes sense to start with the more extreme case:

 / GO:0005575 cellular_component
  is_a GO:0005576 extracellular region
  is_a GO:0031975 envelope
  is_a GO_CJM:0000001 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.

"part" is somewhat troublesome. I'm not sure how useful the X-part terms are (they were introduced for is_a complete, perhaps something like "portion" and "whole" as an upper level term would have helped). On reflection these should be treated as grouping classes.

The resulting obo file is [http://www.geneontology.org/scratch/disjointness_constraints/cellular_component_disj.obo cellular_component_disj.obo], it can be loaded in conjunction with the GO.

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  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. Also problems with root detection. Solution: maintain disjoint_from separately

=== 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].

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:0005856-cytoskeleton	GO:0044430-cytoskeletal part
#	GO:0001740-Barr body	GO:0005694-chromosome	GO:0044427-chromosomal part
#	GO:0005637-nuclear inner membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0005637-nuclear inner membrane	GO:0031965-nuclear membrane	GO:0044453-nuclear membrane part
#	GO:0005640-nuclear outer membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0005640-nuclear outer membrane	GO:0031965-nuclear membrane	GO:0044453-nuclear membrane part
#	GO:0005741-mitochondrial outer membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0005778-peroxisomal membrane	GO:0042579-microbody	GO:0044438-microbody part
#	GO:0005789-endoplasmic reticulum membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0009276-Gram-negative-bacterium-type cell wall	GO:0030312-external encapsulating structure	GO:0044462-external encapsulating structure part
#	GO:0009707-chloroplast outer membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0012507-ER to Golgi transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0012507-ER to Golgi transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0012508-Golgi to ER transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0012508-Golgi to ER transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0012509-inter-Golgi transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0012509-inter-Golgi transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0012510-trans-Golgi network transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0012510-trans-Golgi network transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0020006-parasitophorous vacuolar membrane network	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0020017-flagellar membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0030485-smooth muscle contractile fiber	GO:0043292-contractile fiber	GO:0044449-contractile fiber part
#	GO:0030671-clathrin-coated phagocytic vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0030671-clathrin-coated phagocytic vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0030673-axolemma	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0030864-cortical actin cytoskeleton	GO:0005856-cytoskeleton	GO:0044430-cytoskeletal part
#	GO:0031676-plasma membrane-derived thylakoid membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0031900-chromoplast outer membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0032159-septin cap	GO:0005856-cytoskeleton	GO:0044430-cytoskeletal part
#	GO:0032160-septin filament array	GO:0005856-cytoskeleton	GO:0044430-cytoskeletal part
#	GO:0032169-prospore septin ring	GO:0005856-cytoskeleton	GO:0044430-cytoskeletal part
#	GO:0032174-cellular bud neck septin collar	GO:0044430-cytoskeletal part	GO:0005856-cytoskeleton
#	GO:0032177-cellular bud neck split septin rings	GO:0044430-cytoskeletal part	GO:0005856-cytoskeleton
#	GO:0046861-glyoxysomal membrane	GO:0042579-microbody	GO:0044438-microbody part
#	GO:0055038-recycling endosome membrane	GO:0044440-endosomal part	GO:0005768-endosome
#	GO:0060201-clathrin sculpted acetylcholine transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0060201-clathrin sculpted acetylcholine transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane
#	GO:0060203-clathrin sculpted glutamate transport vesicle membrane	GO:0016020-membrane	GO:0044425-membrane part
#	GO:0060203-clathrin sculpted glutamate transport vesicle membrane	GO:0044425-membrane part	GO:0016020-membrane

See [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2019056&group_id=36855 sf: various organelles and complexes] for a discussion of parasitophorous vacuole

== Spatial disjointness: Disconnected from ==

As noted before, X [[disjoint_from]] Y means that is no class that [[is_a]] X and [[is_a]] Y. It does not mean that X and are Y are spatially disconnected. Nothing is both a cell and a cytoplasm - but obviously these spatially overlap.

If we want to asserted spatially nob-overlapping we state disjoint_from between parts.

E.g.

<pre>
[Term]
id: GO:0044428 ! nuclear part
disjoint_from: GO:0044444 ! cytoplasmic part
</pre>

Many "X part" terms are pre-coordinated in GO. Terms can be automatically classified under these terms (many manual assertions are lagging bahind the reasoner, see [[XP:cellular_component_xp_self#X_part]]

For spatial disjointness between classes that don't have an "X part" class pre-coordinated we can introduce a shortcut relation non_overlapping_with

Here are some obvious ones, and the reasoner inconsistency reports that follow:

I then added additional constraints such as

=== Extracellular and cell ===

* extracellular part [[disjoint_from]] cell part

This gave the following violations:

<pre>
GO:0005607-laminin-2 complex
GO:0009549-cellulose microfibril
GO:0016010-dystrophin-associated glycoprotein complex
GO:0016011-dystroglycan complex
GO:0016456-X chromosome located dosage compensation complex, transcription activating
GO:0020003-parasitophorous vacuole
GO:0020004-parasitophorous vacuolar space
GO:0020005-parasitophorous vacuolar membrane
GO:0020006-parasitophorous vacuolar membrane network
GO:0020006-parasitophorous vacuolar membrane network
GO:0020008-rhoptry
</pre>

See [http://sourceforge.net/tracker/index.php?func=detail&aid=2039153&group_id=36855&atid=440764 sf item]

=== Cytosol and nucleus ===

* cytosolic part [[disjoint_from]] nuclear part

No violations found

=== Cytosol and organelle ===

* cytosolic part [[disjoint_from]] organelle part

one violation - cytosolic ribosome - see https://sourceforge.net/tracker/?func=detail&aid=2872739&group_id=36855&atid=440764

== Tracker items resulting from this work ==

* [http://sourceforge.net/tracker/index.php?func=detail&aid=1960729&group_id=36855&atid=440764 Golgi membrane TPV]
* [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=2039153&group_id=36855&atid=440764 Extracellular disconnected-from cell violations]

See also the discussion of parasitophorous vacuole in this [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2019056&group_id=36855 SF tracker] item - in particular what this means for disjointness of [[XP:cellular_component_xp_self#host_X|Host_X]] terms

== Future ==

=== Region Connection Calculus ===

See

http://en.wikipedia.org/wiki/Region_Connection_Calculus

- reasoning about protein localization. If a protein is localized to X, what does it have to pass through on its way?

=== SAO ===

The [http://ccdb.ucsd.edu/CCDBWebSite/sao.html subcellular anatomy ontology] (SAO) has lots of overlap with GO. It is developed with OWL as the primary representation language. It makes heavy use of disjointness axioms to keep the ontology consistent.

Many of these would not apply to GO-CC as it is now, since SAO is much more specific in the realm of subcellular anatomy. For example, SAO has:

 [Term]
 id: sao:sao-188049490
 name: Node Of Ranvier Axon
 is_a: sao:sao1791490892  ! Regional Part Of Myelinated Axon
 relationship: sao:sao152994059 __file:///Users/cjm/cvs/go/scratch/disjointness_constraints/SAO.owl#__Description81
 disjoint_from: sao:sao1191319089  ! Juxta Paranode Axon
 disjoint_from: sao:sao830092290  ! Internode Axon
 disjoint_from: sao:sao936144858  ! Paranode Axon

Whereas GO has only one subtype of axon, "giant axon" (hmm, single is_a child, not so good!)

However, there may be areas where we can share axioms

== See also ==

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


[[Category: Cellular component]]
[[Category: Ontology]]