[Bioperl-l] Bio::Ontology::OntologyI

[Naama Menda]

My main problem is that go-perl does not handle updates, so if I want  
to update GO I need an empty schema. We find it more complicated to  
re-load our annotations than to update cvterms and their related data.
Our loading script compares an existing load of an ontology to the  
obo file and updates/insets/deletes accordingly.
We are now in the process of committing this code to GMOD, and  
thought this will be a good opportunity for adding the Typedef  
parsing option.

Thanks,
-Naama


On Sun, Mar 9, 2008 at 5:37 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
Naama -

it is the OntologyIO::obo parser that omits the typedefs. Parsing
rather than skipping those could be added to the code; I also once
started and almost completed a project to integrated the go-perl .obo
parser into the Bio::OntologyIO framework, but the final touches fell
victim to moving jobs and the ensuing upheaval.

If all you need to do is parsing a .obo-formatted ontology and
traversing it in some way, go-perl might have all you need. If you
need more than that, could you elaborate?

        -hilmar

On Mar 8, 2008, at 11:48 AM, Naama Menda wrote:

 > Hi Hilmar,
 >
 > I have a loading script that uses Bio::Ontology::OntologyI  for
 > parsing  obo files and loading terms  into chado schema.
 > I'm trying to find all relationship types, and it seems that the
 > parser looks at the distinct relationship types used by the terms
 > in the file,
 > but not at the ' [Typedef] ' fields (I used 'get_predicate_terms 
()' ).
 > This is important for storing the relationships in the right
 > context , for example all relationships types defined by Sequence
 > Ontology should be stored in
 > the chado schema using the SO cv_id, while other relationship
 > types, not defined as Typedef in the obo file, should be stored
 > using the 'relationship' cv_id.
 > Without a way to parse Typedefs, I also cannot use Bio::Ontology
 > for parsing OBO_REL file (http://www.obofoundry.org/ro/ro.obo).
 >
 > Is there another function in Bio::Ontology that handles Typedefs?
 > If not can one be added?
 >
 > Thanks!
 > -Naama Menda

--
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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