[Ontology-editors] constituent part
Jane Lomax
jane at ebi.ac.uk
Tue Jul 8 06:40:05 PDT 2008
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
More information about the Ontology-editors
mailing list