XP:cellular component xp self: Difference between revisions

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* [http://sourceforge.net/tracker/index.php?func=detail&aid=2019056&group_id=36855&atid=440764 various]
* [http://sourceforge.net/tracker/index.php?func=detail&aid=2019056&group_id=36855&atid=440764 various]
* [http://sourceforge.net/tracker/index.php?func=detail&aid=2097069&group_id=36855&atid=440764 integral to mitochondrial membrane]
* [http://sourceforge.net/tracker/index.php?func=detail&aid=2097069&group_id=36855&atid=440764 integral to mitochondrial membrane]
* [http://sourceforge.net/tracker/index.php?func=detail&aid=2097117&group_id=36855&atid=440764 integral to synaptic vesicle membrane]


=== disjoint classes ===
=== disjoint classes ===

Revision as of 12:19, 6 September 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

Relations used

TODO: needs written up more

Many trivial N+S conditions can be stated using nothing more than the part_of relation.

Other relations required included:

  • adjacent_to
  • continuous_with
  • surrounds / surrounded_by
  • bounds / bounded_by

Having surrounds and bounds may seem odd. This is because we have two cases: where the larger piece encloses the smaller piece and is part of it (e.g plasma membrane and cell), and the case where it encloses it but is not part of it (e.g. plasma membrane and cytosol)

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:

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

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

cytoplasm

Although the focus of the xp project is to provide logical definitions for combinatorial terms, we can also provide logical definitions for some of the high level terms too.

Here is a candidate definition for cytoplasm:

[Term]
id: GO:0005737 ! cytoplasm
intersection_of: GO:0005575 ! cellular_component
intersection_of: bounded_by GO:0005886 ! plasma membrane
intersection_of: bounds GO:0005634 ! nucleus

i.e. the cytoplasm is the cellular component that is bounded by the plasma membrane but excludes the nucleus. Unfortunately this only works for nucleated cells

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

See the discussion of parasitophorous vacuole in this SF tracker item

Results

One thing I observed in making these xps is the lack of suitable is_a parents in CC. Definitions refer to networks, bundles, gels/matrix, spaces/regions, pores etc as their genus, but there is no corresponding term defined. Humans and computers could benefit from such a collection of upper level terms being realized in CC (these terms could themselves be defined via CARO)

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 - CC to BP and MF