[Biojava-l] Ontology OBO is_a TERMs

[Peter Midford]

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 <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
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> Peter E. Midford
> Mesquite Developer
> Peter.Midford at gmail.com
>
>
>
>
>

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