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:
Logical Definitions Structure
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:
- 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.
[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
X inner membrane
We define inner membranes using a combination of the surrounds relation (to indicate the organelle or component that is within the membrane), and the adjacent_to relation to indicate that this membrane is on the inside. For example:
[Term] id: GO:0009528 ! plastid inner membrane intersection_of: GO:0016020 ! membrane intersection_of: surrounds GO:0009536 ! plastid intersection_of: adjacent_to GO:0031974 ! membrane-enclosed lumen
TODO: clarify outer membranes
X lumen
Example:
[Term] id: GO:0043202 ! lysosomal lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: surrounded_by GO:0005764 ! lysosome
host X
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 it is difficult to find another way that does not lead to unwanted logical entailments (e.g. host cell plasma membrane is_a plasma membrane)
[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
Results
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:
- 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
See also
XP:cellular_component_xp_go - CC to BP and MF