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] > > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
