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 <[email protected]> > > 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 - [email protected] > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > Peter E. Midford > > Mesquite Developer > > [email protected] > > Peter E. Midford > Mesquite Developer > [email protected] > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Dipl. Inf. Florian Mittag Universität Tuebingen WSI-RA, Sand 1 72076 Tuebingen, Germany Phone: +49 7071 / 29 78985 Fax: +49 7071 / 29 5091 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
