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
[email protected]
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