XP:cellular component xp self: Difference between revisions
No edit summary |
No edit summary |
||
(27 intermediate revisions by 2 users not shown) | |||
Line 1: | Line 1: | ||
'''OUT OF DATE''' | |||
* The basic part_of logical defs have been incorporated into the main ontology | |||
* Work is ongoing to add logical defs for lumens and membranes - see https://www.ebi.ac.uk/panda/jira/browse/GO-186 | |||
* Surrounds / surrounded_by in RO http://purl.obolibrary.org/obo/RO_0002219 are now different than what is proposed below - they are adjacency relations. Need a different relation that encompasses forming the boundary of and being part of | |||
Logical definitions for cellular component terms that reference only cellular component terms. Examples: | Logical definitions for cellular component terms that reference only cellular component terms. Examples: | ||
Line 34: | Line 41: | ||
In the [scratch/xps] directory: | In the [scratch/xps] directory: | ||
* [http://www.geneontology.org/scratch/xps/ | * [http://www.geneontology.org/scratch/xps/cellular_component_xp_self-imports.obo go/scratch/xps/cellular_component_xp_self-imports.obo] | ||
* [http://www.geneontology.org/scratch/xps/cellular_component_xp_self.obo go/scratch/xps/cellular_component_xp_self.obo] | * [http://www.geneontology.org/scratch/xps/cellular_component_xp_self.obo go/scratch/xps/cellular_component_xp_self.obo] | ||
Line 41: | Line 48: | ||
* [http://www.berkeleybop.org/ontologies/obo-all/cellular_component_xp_self/cellular_component_xp_self.xp.html Table] | * [http://www.berkeleybop.org/ontologies/obo-all/cellular_component_xp_self/cellular_component_xp_self.xp.html Table] | ||
* [http://www.berkeleybop.org/ontologies/obo-all/cellular_component_xp_self/cellular_component_xp_self.obo.html OBO-HTML] | * [http://www.berkeleybop.org/ontologies/obo-all/cellular_component_xp_self/cellular_component_xp_self.obo.html OBO-HTML] | ||
== Examples == | |||
The following XP matrix tables illustrate subsets of the CC XPs. | |||
* Each ''column'' in the matrix represents a genus term - the core building block for the more complex term | |||
* Each ''row'' in the matrix represents a term used in the ''differentium'' or ''discriminating characteristics'' of the XP term | |||
* Each ''cell'' in the matrix shows the XP def for an existing GO term. For now only terms with a single differentium are shown for simplicity. The relation used is also shown. | |||
Thus the definition of every XP term should read A ''cell-value'' [[is_a]] ''column-value'' '''that''' (relation) ''row-value'' | |||
=== Nuclear and mitochondrial lumen and membranes === | |||
{|class="wikitable" style="text-align:center" border="1" | |||
|- | |||
! | |||
! GO:0016020-membrane | |||
! GO:0019867-outer membrane | |||
! GO:0031965-nuclear membrane | |||
! GO:0031974-membrane-enclosed lumen | |||
! | |||
|- | |||
! GO:0005634-nucleus | |||
| GO:0031965-nuclear membrane<sub>[[surrounds]]</sub> | |||
| GO:0005640-nuclear outer membrane<sub>[[surrounds]]</sub> | |||
| GO:0005640-nuclear outer membrane<sub>[[surrounds]]</sub> | |||
| | |||
| | |||
! GO:0005634-nucleus | |||
|- | |||
! GO:0005637-nuclear inner membrane | |||
| | |||
| | |||
| | |||
| GO:0031981-nuclear lumen<sub>[[surrounded_by]]</sub> | |||
| | |||
! GO:0005637-nuclear inner membrane | |||
|- | |||
! GO:0005737-cytoplasm | |||
| | |||
| GO:0005640-nuclear outer membrane<sub>[[adjacent_to]]</sub> | |||
| GO:0005640-nuclear outer membrane<sub>[[adjacent_to]]</sub> | |||
| | |||
| | |||
! GO:0005737-cytoplasm | |||
|- | |||
! GO:0005739-mitochondrion | |||
| GO:0031966-mitochondrial membrane<sub>[[surrounds]]</sub> | |||
| GO:0005741-mitochondrial outer membrane<sub>[[surrounds]]</sub> | |||
| | |||
| GO:0031980-mitochondrial lumen<sub>[[surrounded_by]]</sub> | |||
| | |||
! GO:0005739-mitochondrion | |||
|- | |||
! GO:0005783-endoplasmic reticulum | |||
| GO:0005789-endoplasmic reticulum membrane<sub>[[surrounds]]</sub> GO:0042175-nuclear envelope-endoplasmic reticulum network<sub>[[has_part]]</sub> | |||
| | |||
| | |||
| GO:0005788-endoplasmic reticulum lumen<sub>[[surrounded_by]]</sub> | |||
| | |||
! GO:0005783-endoplasmic reticulum | |||
|- | |||
! GO:0031981-nuclear lumen | |||
| | |||
| | |||
| GO:0005637-nuclear inner membrane<sub>[[adjacent_to]]</sub> | |||
| | |||
| | |||
! GO:0031981-nuclear lumen | |||
|- | |||
! | |||
! | |||
|- | |||
! | |||
! GO:0016020-membrane | |||
! GO:0019867-outer membrane | |||
! GO:0031965-nuclear membrane | |||
! GO:0031974-membrane-enclosed lumen | |||
|} | |||
== Logical Definitions Structure == | == Logical Definitions Structure == | ||
Line 87: | Line 174: | ||
intersection_of: part_of GO:0030424 ! axon | intersection_of: part_of GO:0030424 ! axon | ||
</pre> | </pre> | ||
* [http://sourceforge.net/tracker/index.php?func=detail&aid=2019051&group_id=36855&atid=440764 tracker item] | |||
Using these XPs we can automatically place many CC terms. For example ''cortical microtubule'' [[is_a]] ''cell cortex part'' | |||
Because this is such a simple non-problematic set of XPs I have created a subset of the whole XP file called [http://www.geneontology.org/scratch/xps/cellular_component_xp_self_Xpart.obo cellular_component_xp_self_Xpart.obo]. From this, it is easy to generate [http://www.geneontology.org/scratch/xps/go_withXpart_links.obo go_withXpart_links.obo], a "repaired" version of GO with the missing links filled in. This file can be easily regenerated on demand from the latest GO - we can then use it to replace the existing file in GO. This is also easy for curators to do themselves. Here is the protocol: | |||
cd go/editors | |||
cvs update gene_ontology_write.obo | |||
cd ../../scratch/xps | |||
obo2obo -o -saveimpliedlinks cellular_component_xp_self_Xpart-implied.obo cellular_component_xp_self_Xpart-imports.obo | |||
grep -v ^intersection_of: cellular_component_xp_self_Xpart-imports.obo > go_withXpart_links.obo | |||
The last step is required because we do not yet save the xps in the main GO file. If it were not for this step the whole cycle could be performed in OBO-Edit. In fact within OBO-Edit, selected inferred links can be promoted. | |||
(use OE2 beta50 or greater for this) | |||
=== X membrane === | === X membrane === | ||
Line 134: | Line 237: | ||
=== X lumen === | === X lumen === | ||
lumens are defined by membranes. This is typically the membrane that surrounds the organelle, such as for example in lysosomes: | |||
<pre> | <pre> | ||
[Term] | [Term] | ||
id: GO:0043202 ! lysosomal lumen | id: GO:0043202 ! lysosomal lumen | ||
intersection_of: GO:0031974 ! membrane-enclosed lumen | |||
intersection_of: bounded_by GO:0005765 ! lysosomal membrane | |||
</pre> | |||
where organelles have two membranes, we must take care to distinguish the lumen between the two membranes vs the inner lumen: | |||
<pre> | |||
[Term] | |||
id: GO:0031981 ! nuclear lumen | |||
intersection_of: GO:0031974 ! membrane-enclosed lumen | intersection_of: GO:0031974 ! membrane-enclosed lumen | ||
intersection_of: | intersection_of: bounded_by GO:0005637 ! nuclear inner membrane | ||
</pre> | |||
<pre> | |||
[Term] | |||
id: GO:0005641 ! nuclear envelope lumen | |||
intersection_of: GO:0031970 ! organelle envelope lumen | |||
intersection_of: bounded_by GO:0005640 ! nuclear outer membrane | |||
intersection_of: bounds GO:0005637 ! nuclear inner membrane | |||
</pre> | |||
=== pores === | |||
<pre> | |||
[Term] | |||
id: GO:0005643 ! nuclear pore | |||
intersection_of: GO:0046930 ! pore complex | |||
intersection_of: perforates GO:0005635 ! nuclear envelope | |||
intersection_of: adjacent_to GO:0005637 ! nuclear inner membrane | |||
intersection_of: adjacent_to GO:0005640 ! nuclear outer membrane | |||
</pre> | </pre> | ||
=== cytoplasm === | === cytoplasm === | ||
Line 154: | Line 287: | ||
intersection_of: GO:0005575 ! cellular_component | intersection_of: GO:0005575 ! cellular_component | ||
intersection_of: bounded_by GO:0005886 ! plasma membrane | intersection_of: bounded_by GO:0005886 ! plasma membrane | ||
intersection_of: bounds GO: | intersection_of: bounds GO:0043226 ! organelle | ||
</pre> | </pre> | ||
i.e. the cytoplasm is the cellular component that is bounded by the plasma membrane | i.e. the cytoplasm is the cellular component that is bounded by the plasma membrane and bounds organelles | ||
=== host X === | === host X === | ||
Line 181: | Line 314: | ||
See the discussion of parasitophorous vacuole in this [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2019056&group_id=36855 SF tracker] item | See the discussion of parasitophorous vacuole in this [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2019056&group_id=36855 SF tracker] item | ||
'''NOTE:''' these have been moved to a separate file: | |||
* [http://www.geneontology.org/scratch/xps/cellular_component_xp_host.obo go/scratch/xps/cellular_component_xp_host.obo] | |||
== Results == | == Results == | ||
Line 206: | Line 343: | ||
See [[Cellular component disjoint classes]] | See [[Cellular component disjoint classes]] | ||
==Validation notes== | |||
* [[Notes_for_cc_xp_self|Jane's notes on validation of this file]] | |||
== See also == | == See also == |
Latest revision as of 13:28, 12 July 2013
OUT OF DATE
- The basic part_of logical defs have been incorporated into the main ontology
- Work is ongoing to add logical defs for lumens and membranes - see https://www.ebi.ac.uk/panda/jira/browse/GO-186
- Surrounds / surrounded_by in RO http://purl.obolibrary.org/obo/RO_0002219 are now different than what is proposed below - they are adjacency relations. Need a different relation that encompasses forming the boundary of and being part of
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:
Examples
The following XP matrix tables illustrate subsets of the CC XPs.
- Each column in the matrix represents a genus term - the core building block for the more complex term
- Each row in the matrix represents a term used in the differentium or discriminating characteristics of the XP term
- Each cell in the matrix shows the XP def for an existing GO term. For now only terms with a single differentium are shown for simplicity. The relation used is also shown.
Thus the definition of every XP term should read A cell-value is_a column-value that (relation) row-value
Nuclear and mitochondrial lumen and membranes
GO:0016020-membrane | GO:0019867-outer membrane | GO:0031965-nuclear membrane | GO:0031974-membrane-enclosed lumen | |||
---|---|---|---|---|---|---|
GO:0005634-nucleus | GO:0031965-nuclear membranesurrounds | GO:0005640-nuclear outer membranesurrounds | GO:0005640-nuclear outer membranesurrounds | GO:0005634-nucleus | ||
GO:0005637-nuclear inner membrane | GO:0031981-nuclear lumensurrounded_by | GO:0005637-nuclear inner membrane | ||||
GO:0005737-cytoplasm | GO:0005640-nuclear outer membraneadjacent_to | GO:0005640-nuclear outer membraneadjacent_to | GO:0005737-cytoplasm | |||
GO:0005739-mitochondrion | GO:0031966-mitochondrial membranesurrounds | GO:0005741-mitochondrial outer membranesurrounds | GO:0031980-mitochondrial lumensurrounded_by | GO:0005739-mitochondrion | ||
GO:0005783-endoplasmic reticulum | GO:0005789-endoplasmic reticulum membranesurrounds GO:0042175-nuclear envelope-endoplasmic reticulum networkhas_part | GO:0005788-endoplasmic reticulum lumensurrounded_by | GO:0005783-endoplasmic reticulum | |||
GO:0031981-nuclear lumen | GO:0005637-nuclear inner membraneadjacent_to | GO:0031981-nuclear lumen | ||||
GO:0016020-membrane | GO:0019867-outer membrane | GO:0031965-nuclear membrane | GO:0031974-membrane-enclosed lumen |
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
Using these XPs we can automatically place many CC terms. For example cortical microtubule is_a cell cortex part
Because this is such a simple non-problematic set of XPs I have created a subset of the whole XP file called cellular_component_xp_self_Xpart.obo. From this, it is easy to generate go_withXpart_links.obo, a "repaired" version of GO with the missing links filled in. This file can be easily regenerated on demand from the latest GO - we can then use it to replace the existing file in GO. This is also easy for curators to do themselves. Here is the protocol:
cd go/editors cvs update gene_ontology_write.obo cd ../../scratch/xps obo2obo -o -saveimpliedlinks cellular_component_xp_self_Xpart-implied.obo cellular_component_xp_self_Xpart-imports.obo grep -v ^intersection_of: cellular_component_xp_self_Xpart-imports.obo > go_withXpart_links.obo
The last step is required because we do not yet save the xps in the main GO file. If it were not for this step the whole cycle could be performed in OBO-Edit. In fact within OBO-Edit, selected inferred links can be promoted.
(use OE2 beta50 or greater for this)
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
lumens are defined by membranes. This is typically the membrane that surrounds the organelle, such as for example in lysosomes:
[Term] id: GO:0043202 ! lysosomal lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: bounded_by GO:0005765 ! lysosomal membrane
where organelles have two membranes, we must take care to distinguish the lumen between the two membranes vs the inner lumen:
[Term] id: GO:0031981 ! nuclear lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: bounded_by GO:0005637 ! nuclear inner membrane
[Term] id: GO:0005641 ! nuclear envelope lumen intersection_of: GO:0031970 ! organelle envelope lumen intersection_of: bounded_by GO:0005640 ! nuclear outer membrane intersection_of: bounds GO:0005637 ! nuclear inner membrane
pores
[Term] id: GO:0005643 ! nuclear pore intersection_of: GO:0046930 ! pore complex intersection_of: perforates GO:0005635 ! nuclear envelope intersection_of: adjacent_to GO:0005637 ! nuclear inner membrane intersection_of: adjacent_to GO:0005640 ! nuclear outer membrane
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:0043226 ! organelle
i.e. the cytoplasm is the cellular component that is bounded by the plasma membrane and bounds organelles
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
NOTE: these have been moved to a separate file:
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:
- prothylakoid is_a plastid thylakoid
- X part MPs - ongoing
- X membrane MPs - done?
- various
- integral to mitochondrial membrane
- integral to synaptic vesicle membrane
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
Validation notes
See also
XP:cellular_component_xp_go - CC to BP and MF