Re: [Obo-discuss] question about part_of inverse

[Jane L. <ja...@eb...>]

Yes - I think that's okay because the CV pore is part of both structures 
at the same time (if I understand the biology correctly)...

On Mon, 7 Nov 2005, Midori Harris wrote:

> There's at least one term (added very recently) that has two part-of 
> parents which I am assured are both biologically correct. See SF 1332635 
> for gory details.
> 
> https://sourceforge.net/tracker/?group_id=36855&atid=440764&func=detail&aid=1332635
> 
> m
> 
> On Fri, 4 Nov 2005, Chris Mungall wrote:
> 
> > 
> > Hmm, are they automatically wrong? We should take this over to the
> > relations list (it gets a bit more subtle in when you factor in time).
> > 
> > Whether or not they're automatically wrong, it may be a good way of
> > spotting problematic part_ofs. I can produce a report of these (it'll be
> > big!) and add it to the obo reports page, let you know when that's done.
> > John, this might be an idea for an OBO-Edit check too (remember to take
> > is-a into account here)
> > 
> > I notice this is also a good way of noticing unusual cases where part_of
> > crosses a boundary, for example "Golgi membrane part_of endomembrane
> > system". Here we have part_of crossing a boundary from a component to a
> > collection of components.
> > 
> > On Fri, 4 Nov 2005, Jane Lomax wrote:
> > 
> > >
> > > Someone generated a list for us once (Joel from MGI??) that was all the
> > > terms that had part_of relations to more than one parent - these are
> > > automatically wrong with our use of part_of - perhaps we could generate a
> > > another list? I know this doesn't catch all the incorrect uses of part_of,
> > > but it's a good place to start...
> > >
> > > jane
> > >
> > > On Fri, 4 Nov 2005, Chris Mungall wrote:
> > >
> > > >
> > > > Not automatically - this is down to curation and spotting the true path
> > > > violations..
> > > >
> > > > On Fri, 4 Nov 2005, Jane Lomax wrote:
> > > >
> > > > > Chris - is there a way you can figure out how many of these incorrect
> > > > > part_ofs we still have and what they are? Might be good to make a
> > > > > concerted effort to weed them out,
> > > > >
> > > > > thanks,
> > > > >
> > > > > Jane
> > > > >
> > > > > On Mon, 31 Oct 2005, Chris Mungall wrote:
> > > > >
> > > > > >
> > > > > > [cc-ing to GO also]
> > > > > >
> > > > > > Hi Alan
> > > > > >
> > > > > > The GO usage documentation precedes the OBO relations ontology; see
> > > > > > http://obo.sourceforge.net/relationship/
> > > > > >
> > > > > > "type 2", necessarily part_of is essentially the same as the definition
> > > > > > provided in the OBO relations ontology. The GO usage guide states that
> > > > > > this the way that part_of is "usually" used. I believe that since this was
> > > > > > written, most of the violations to the definition have been removed from
> > > > > > the ontology.
> > > > > >
> > > > > > Note that the OBO 1.2 format allows you to further qualify part_of
> > > > > > relationships between two classes, for example to state that A is part_of
> > > > > > B and B has_part A where A and B are classes. Currently this feature is
> > > > > > not used. This would be the same as placing two relationships, part_of and
> > > > > > has_part between both A and B.
> > > > > >
> > > > > > At this time, neither of these strategies are being used in any OBO
> > > > > > ontology. The main reason is that the part_of relation (as specified in
> > > > > > the OBO relations ontology) holds far more commonly than has_part.
> > > > > >
> > > > > > In answer to your question: can we infer that for any A which is the
> > > > > > object of the part_of relation for P1,P2,...,Pn, can we assume that A
> > > > > > has_part B where B is one of P1,P2,...,Pn? I don't think so. Even if we
> > > > > > were to assume that the knowledge provided in GO or any OBO ontology was
> > > > > > complete (which is definitely a dangerous assumption), we still could not
> > > > > > make this logical inference from the definitions provided.
> > > > > >
> > > > > > It may be still possible to logically infer that chromosome cannot have a
> > > > > > has_part relation to the ER class from other relations, but this would
> > > > > > probably rely on having additional spatial relations supplied in the
> > > > > > cellular component ontology.
> > > > > >
> > > > > > Thanks for the interesting question
> > > > > >
> > > > > > Cheers
> > > > > > Chris
> > > > > >
> > > > > > On Sat, 29 Oct 2005, Alan Ruttenberg wrote:
> > > > > >
> > > > > > > I've read http://www.geneontology.org/GO.usage.shtml#partof which
> > > > > > > describes part_of and the relationship to has_part, and specifies
> > > > > > > that in GO the meaning of part_of is that wherever the child exists,
> > > > > > > it is as part of the parent. I understand that it is not necessary
> > > > > > > that the parent has the child as a part whenever the parent exists.
> > > > > > >
> > > > > > > My question is about the possible values of has_part . Specifically I
> > > > > > > am wondering whether one can infer that whenever the parent has a
> > > > > > > part, that part must be one of those terms that is part_of the parent.
> > > > > > >
> > > > > > > Linking the question to the biological example in the documentation,
> > > > > > > consider those terms which are part_of chromosome:
> > > > > > >
> > > > > > > chromosome, pericentric region
> > > > > > > chromosome, telomeric region
> > > > > > > chromatin
> > > > > > > origin recognition complex
> > > > > > > cohesin complex
> > > > > > > provirus
> > > > > > > Rad17 RFC-like complex
> > > > > > > Ctf18 RFC-like complex
> > > > > > > Elg1 RFC-like complex
> > > > > > > Myb complex
> > > > > > >
> > > > > > > Would it be correct to infer that if a chromosome had parts, they
> > > > > > > could only things on of the above list, and not, for instance,
> > > > > > > GO_0005783:endoplasmic reticulum. If not, what lets us infer that an
> > > > > > > endoplasmic reticulum can't be part of a chromosome?
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Alan
> > > > > > >
> > > > > > >
> > > > > > >
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