[Biojava-l] Ontology OBO is_a TERMs

[JP]

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
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>
>
>  Peter E. Midford
> Mesquite Developer
> Peter.Midford at gmail.com
>
>
>
>
>