s-merchant at northwestern.edu
Mon Aug 28 10:45:06 EDT 2006
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.
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.
> Sohel Merchant.
> Sohel Merchant
> 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
______ _/ _/_____________________________________________________
_/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
_/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of Western Cape, South Africa
_/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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