[Biojava-l] Ontology OBO is_a TERMs

[Florian Mittag]

On Thursday, 23. July 2009 17:39, Peter Midford wrote:
> [...] To properly handle the IS_A key, you will have to build the hierarchy,
> which you can do OBO style using links or restrictions (which I believe are
> a  subclass of links in OBO, rather than adding an intermediate class to
> the ontology) or OWL style using triples (Subject, Predicate, Object)
> where is_a would be your predicate.  [...]

I think you mean RDF style triples, no need to make it more complicated than 
necessary ;-)
Although there are some restriction you need OWL for expressing them.

Regards,
  Florian


> On Jul 23, 2009, at 11:29, JP wrote:
> > I never quite got this Peter, what is a triple ?
> > Could these simply be considered as annotations ?  Or are you
> > thinking in the lines of building hierarchies out of these (I take
> > it this is the most common task).
> >
> > These relationships are *fundamental* for any work of ontology.
> >
> > 2009/7/23 Peter Midford <peter.midford at gmail.com>
> > JP,
> >        Looking at the code for OboFileHandler.java, fresh from svn,
> > it looks like they're presently being dropped on the floor.  Perhaps
> > someone should either implement obo restrictions or links or build
> > some triples here, as they seem to be used for the rest of the
> > ontology code.
> >
> >
> >
> > 			} else if (key.equals(IS_A) ||
> > 					key.equals(RELATIONSHIP) ||
> > 					key.equals(DISJOINT_FROM) ||
> > 					key.equals(INTERSECTION_OF) ||
> > 					key.equals(SUBSET)) {
> > 				//TODO: deal with relationships
> >
> >
> > 			} else if (key.equals(COMMENT)){
> >
> >
> > Peter
> >
> > On Jul 23, 2009, at 7:15, JP wrote:
> >> Hi there at Biojava,
> >>
> >> I have an ontology file (from www.geneontology.org, gene_ontology.
> >> 1_2.obo).
> >> A typical entry for a term is:
> >>
> >> [Term]
> >> id: GO:0000025
> >> name: maltose catabolic process
> >> namespace: biological_process
> >> def: "The chemical reactions and pathways resulting in the
> >> breakdown of the
> >> disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-
> >> glucopyranose)." [GOC:jl,
> >> ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular
> >> Biology"]
> >> subset: gosubset_prok
> >> synonym: "malt sugar catabolic process" EXACT []
> >> synonym: "malt sugar catabolism" EXACT []
> >> synonym: "maltose breakdown" EXACT []
> >> synonym: "maltose degradation" EXACT []
> >> synonym: "maltose hydrolysis" NARROW []
> >> xref: MetaCyc:MALTOSECAT-PWY
> >> is_a: GO:0000023 ! maltose metabolic process
> >> is_a: GO:0046352 ! disaccharide catabolic process
> >>
> >> I am reading this with the code suggested in:
> >> http://biojava.open-bio.org/wiki/BioJava:CookBook:OBO:parse
> >> I would like to get the is_a entries (as Term) - is this possible ?
> >> I tried
> >> to find this everywhere (annotations?) but find it (google searches
> >> included).
> >>
> >> Many Thanks
> >> JP
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > Peter E. Midford
> > Mesquite Developer
> > Peter.Midford at gmail.com
>
> Peter E. Midford
> Mesquite Developer
> Peter.Midford at gmail.com
>
>
>
>
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-- 
Dipl. Inf. Florian Mittag
Universität Tuebingen
WSI-RA, Sand 1
72076 Tuebingen, Germany
Phone: +49 7071 / 29 78985  Fax: +49 7071 / 29 5091