[Ontology-editors] Disjointness [was Re: constituent part]
Chris Mungall
cjm at berkeleybop.org
Tue Aug 5 11:13:56 PDT 2008
For now I'm maintaining the disjoint statements in a separate file and
running the reasoner in batch and generating reports.
Added a tracker item for:
http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes#Extracellular_and_cell
I have not yet added a tracker item for:
http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes#X_part_and_X
There is a section in the OE reasoner paper on disjoint_from (shared
on google docs under the geneontology account - let me know if you
want individual access)
Do you think the following example is a good one:
---
In 2007 we made some high-level changes to the GO and introduced three
high level mutually disjoint classes within the biological process
ontology: cellular process, multi-cellular process and multi-organism
process.
The editors used a configurable disjointness check in OboEdit to help
organize the graph such that these mutual exclusivity constraints
held. At first there were multiple violations of the disjointness
constraint. For example "conjugation with cellular fusion" was an is_a
child of both cellular process and multi-organism process. On closer
examination the definition of the class was found to be problematic,
the definition was changed and the disjointness violation was resolved
by removing the is_a link between 'conjugation with cellular fusion'
and 'reproductive process in single-celled organism'. [Can a GO editor
check this? See email thread Re: fixing non-disjoint violations Feb 5
2007]
---
On Jul 8, 2008, at 6:40 AM, Jane Lomax wrote:
> That would be good. However, we still have the problem that we can't
> hide disjoint relations in OE1, so I'd be a bit wary about adding
> any more until we're using OE2 as it makes the graph view very
> tangled...
>
>
>
> Chris Mungall wrote:
>>
>> I think we should add a disjoint relation between "cell part" and
>> "extracellular region part" (to allow OE to auto-detect other
>> errors of this sort)
>>
>> See:
>> http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes
>>
>> On Jul 8, 2008, at 12:41 PM, Jane Lomax wrote:
>>
>>> Looks like this is the offending relationship:
>>>
>>> / GO:0005576 extracellular region
>>> po GO:0020008 rhoptry {via is_a extracellular region part}
>>>
>>> I can't find anything in the literature to indicate that the
>>> rhoptry is extracellular (see http://www.nature.com/nrmicro/journal/v6/n1/fig_tab/nrmicro1800_F3.html)
>>> . Anyone object if I go ahead and delete this relationship?
>>>
>>> Jane
>>>
>>>
>>>
>>> Chris Mungall wrote:
>>>>
>>>> Actually if constituent has no special meaning then the reasoner
>>>> is correct (the links are not asserted & the reasoner is
>>>> inferring the links)
>>>>
>>>> / GO:0005576 extracellular region
>>>> po GO:0020008 rhoptry {via is_a extracellular region part}
>>>> / GO:0005623 cell
>>>> po GO:0045177 apical part of cell {via is_a cell part}
>>>> po GO:0020007 apical complex
>>>> po GO:0020008 rhoptry
>>>>
>>>>
>>>> On Jul 8, 2008, at 11:48 AM, Jane Lomax wrote:
>>>>
>>>>> Chris - I don't think 'constituent part' has any special meaning
>>>>> in these defs - we could drop it. The reasoner is right to throw
>>>>> up those "rhoptry lumen" relationships - they are dodgy, how can
>>>>> it be both a cell part and extracellular?
>>>>>
>>>>> Jane
>>>>>
>>>>> Chris Mungall wrote:
>>>>>> We use the phrase "constituent part" in (almost) all the "X
>>>>>> part" terms; e.g.:
>>>>>>
>>>>>> axoneme part [DEF: "Any constituent part of an axoneme, the
>>>>>> bundle of microtubules and associated proteins that forms the
>>>>>> core of cilia and flagella in eukaryotic cells and is
>>>>>> responsible for their movements."]
>>>>>>
>>>>>> What exactly does "constituent" mean here?
>>>>>>
>>>>>> I recall being part of the discussion that lead to this, but
>>>>>> can't find the relevant emails. Did we just import this term
>>>>>> from the FMA? It seems to have a specific meaning in anatomy. I
>>>>>> can't really find a solid definition in the FMA papers.
>>>>>>
>>>>>> I don't see anything in the component docs either.
>>>>>>
>>>>>> I think we should either document this or drop it
>>>>>>
>>>>>> Here's why I'm interested - I define X part generically as a
>>>>>> cellular component that is part_of X.
>>>>>>
>>>>>> This means the reasoner throws up:
>>>>>>
>>>>>> "rhoptry lumen" [GO:0034591] is_a "extracellular region
>>>>>> part" [GO:0044421]
>>>>>> "rhoptry lumen" [GO:0034591] is_a "cell part" [GO:0044464]
>>>>>>
>>>>>> Is there something subtle in the "constituent" qualifier that
>>>>>> is missing from my xp definition, that simultaneously excludes
>>>>>> the above links?
>>>>>> _______________________________________________
>>>>>> Ontology-editors mailing list
>>>>>> Ontology-editors at geneontology.org
>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>
>>>>>
>>>>> --
>>>>> Dr Jane
>>>>> Lomax
>>>>> GO
>>>>> Editorial
>>>>> Office
>>>>> EMBL
>>>>> -
>>>>> EBI
>>>>> Wellcome
>>>>> Trust Genome
>>>>> Campus
>>>>> Hinxton
>>>>> Cambridgeshire
>>>>> ,
>>>>> UK
>>>>> CB10
>>>>>
>>>>> 1SD
>>>>> p
>>>>> : +44 1223
>>>>> 492516
>>>>> f
>>>>> : +44 1223 494468
>>>>>
>>>>>
>>>
>>>
>>> --
>>> Dr Jane
>>> Lomax
>>> GO
>>> Editorial
>>> Office
>>> EMBL
>>> -
>>> EBI
>>> Wellcome
>>> Trust Genome
>>> Campus
>>> Hinxton
>>> Cambridgeshire
>>> ,
>>> UK
>>> CB10
>>>
>>> 1SD
>>> p
>>> : +44 1223
>>> 492516
>>> f
>>> : +44 1223 494468
>>>
>>>
>
>
> --
> Dr Jane
> Lomax
> GO
> Editorial
> Office
> EMBL
> -
> EBI
> Wellcome
> Trust Genome
> Campus
> Hinxton
> Cambridgeshire
> ,
> UK
> CB10
>
> 1SD
> p
> : +44 1223
> 492516
> f
> : +44 1223 494468
>
>
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