[Bioperl-l] Bio::OntologyIO

Sohel Merchant s-merchant at northwestern.edu
Mon Aug 28 10:45:06 EDT 2006

Hi Heikki,
  I like the idea of using the Bio::Ontology::OBOterm for implementing this
functionality. I think you can add a type associated with the add_synonymn
method. We have nice tests written to make sure the code does not break. I
would like you to run the tests locally before you commit any changes.


-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki at sanbi.ac.za] 
Sent: Monday, August 28, 2006 6:08 AM
To: bioperl-l at lists.open-bio.org
Cc: Sohel Merchant
Subject: Re: [Bioperl-l] Bio::OntologyIO


This is great. I've used to module and it works well.

I am trying to see if I could create write_ontology method so that I could 
recreate the obo file already read in. So far, there is one big snag:

Synonyms are all read in into one structure. The methods dealing with
in Bio::Ontology::Term all work with lists of strings. The problem is that
obo files there are four different types of synonyms: 

	broad, exact, narrow, related

What would be the best way, at code and interface levels, to associate these

categories to synonyms?

Currently, add_synonym() accepts a list of synonym strings as an argument. 
Most of the time only one synonym gets passed to the method. If that were
rule, I could add an other argument and store the category in an other 
internal array. Bio::Ontology::OBOterm inherits from Bio::Ontology::Term, so

I could do the changes there. Would this change break anything? In 


On Thursday 01 June 2006 19:17, Sohel Merchant wrote:
> Hi Everyone,
>     I would like to announce the availability of an obo format parser
> which can parse GO, PO, PATO and other ontology files in obo format. The
> parser can be used through the Bio::OntologyIO module. Thanks to HIlamar
> Lapp and Chris Mungall for their invaluable contributions.
> Thanks,
> Sohel Merchant.
> Sohel Merchant
> dictyBase
> Bioinformatics Software Engineer
> Center for Genetic Medicine
> Northwestern University
> 676 St. Clair Street, Suite 1206
> Chicago IL 60611
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
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