[Biojava-l] Ontology OBO is_a TERMs

[Peter Midford]

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