XP:cellular component xp self

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Revision as of 19:07, 16 July 2008 by Cjm (talk | contribs) (→‎Results)
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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

Cytoplasmic X

If we define terms cytoplasmic X and mitochondrial X such that:

  • 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

This is correct according to the xp definition.

If we wish to avoid this, we can define it as "cytosolic chromosome"


X part

X part terms get xp definitions of the form:

  • A cellular_component that part_of a X
[Term]
id: GO:0033267 ! axon part
intersection_of: GO:0005575 ! cellular_component
intersection_of: part_of GO:0030424 ! axon

X membrane

parthood relations are not enough to make necessary and sufficient definitions.

We use the surrounds relation for when a part_of b and the area within a contains b

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.


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

[Term]
id: GO:0005740 ! mitochondrial envelope
intersection_of: GO:0031975 ! envelope
intersection_of: surrounds GO:0005739 ! mitochondrion

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

The following tracker items were submitted based on running the reasoner over the xp definitions:

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