JP,
No, these are not just annotations to terms, and the code
jumbles together several things that should be separated. 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 assume the other key values
that look like set operations are for building restrictions.
Peter
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
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Peter E. Midford
Mesquite Developer
[email protected]
Peter E. Midford
Mesquite Developer
[email protected]
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