XP:cellular component xp self
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
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:
- A membrane that surrounds a X
or
- A plasma membrane part that surrounds a X
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:
- X part disjoint from Y part
e.g. to say the X and Y have no parts in common - they are spatially disconnected
See Cellular component disjoint classes