XP:cellular component xp self: Difference between revisions

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==== surrounded_by and surrounds vs part_of ====
==== surrounded_by and surrounds vs part_of ====
THE SECTION BELOW IS OUT OF DATE


Often [[part_of]] is not specific enough to make N+S conditions in an xp def.
Often [[part_of]] is not specific enough to make N+S conditions in an xp def.

Revision as of 12:06, 16 July 2008

Logical definitions for cellular component terms that reference only cellular component terms. Examples:

  • cellular bud neck contractile ring
  • nuclear envelope
  • lysosomal membrane

Methods

Obol was used to generate the initial version of the file. This was then vetted by cjm. Obol grammar: obol_cellular_component_xp prolog grammar

ontologies used

  • GO (CC)
  • RO
  • ro_proposed

availability

In the [scratch/xps] directory:

Also on the OBO xp page:

Results

Examples

[Term]
id: GO:0000142 ! cellular bud neck contractile ring
intersection_of: GO:0005826 ! contractile ring
intersection_of: part_of GO:0005935 ! cellular bud neck

[Term]
id: GO:0005641 ! nuclear envelope lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: surrounded_by GO:0005635 ! nuclear envelope

Relations

surrounded_by and surrounds vs part_of

THE SECTION BELOW IS OUT OF DATE

Often part_of is not specific enough to make N+S conditions in an xp def.

For example, if we say

  • cytoplasmic chromosome = chromosome THAT part_of cytoplasm
  • mitochondrial chromosome = chromosome THAT part_of mitochondrion

Then a reasoner will infer:

  • mitochondrial chromosome is_a cytoplasmic chromosome

(because of the transitivity of part_of)

[Term]
id: GO:0000229 ! cytoplasmic chromosome
intersection_of: GO:0005694 ! chromosome
intersection_of: OBO_REL:surrounded_by GO:0005737 ! cytoplasm

Also, at this time Obol generated xp defs like this:

 [Term]
 id: GO:0005640 ! nuclear outer membrane
 intersection_of: GO:0019867 ! outer membrane
 intersection_of: part_of GO:0005634 ! nucleus

This is probably not specific enough. We probably want the grammar rule

  • X outer membrane = membrane THAT surrounds X

X part

X part terms get xp definitions of the form:

  • A cellular_component that part_of a X

X membrane

X membrane terms are either defined as:

or

It is necessary to examine the text definition to check which one. There may be some errors.

lumen

Each lumen is surrounded_by (enclosed within) some membrane. TODO - this for all

host

This is a tricky one. It would be natural to say:

  • GO:0020002 host cell plasma membrane = plasma membrane THAT part_of host cells

i.e. all host cell plasma membranes are plasma membranes that are part of a host cell

However, in GO the following relation does NOT hold.

  • GO:0020002 host cell plasma membrane is_a plasma membrane

This is because the host part of CC represents locations, specifically relative locations. It can be argued that all of CC represents relative locations...

We get round this by saying that host cell plasma membrane is an extracellular region that inheres_in a plasma membrane. inheres_in is a general relation between a dependent continuant and an independent continuant - e.g. between a relative location and what that location is relative to. This is somewhat abstract but I can't think of a better way.

 [Term]
 id: GO:0020002 ! host cell plasma membrane
 intersection_of: GO:0044421 ! extracellular region part
 intersection_of: OBO_REL:inheres_in GO:0005886 ! plasma membrane

missing links

disjoint classes

We can use the xp defs to generate disjoint links of the form:

e.g. to say the X and Y have no parts in common - they are spatially disconnected

See Cellular component disjoint classes

See also

XP:cellular_component_xp_go