[Bioperl-l] bioperl based database infrastucture for directed graphs

Scott Cain cain.cshl at gmail.com
Wed Jan 9 22:15:29 EST 2008

Hi Robson,

I seem to be perennially working on the 1.0 release of Chado.  The
schema itself is quite stable but I'm always working on the tools to
make them handle more cases and be as stable as possible.  For the time
being, you need to get Chado from cvs; see 


I removed the 0.003 release from the SourceForge site because the schema
in it is out of date relative to what we've been working on for the last


On Wed, 2008-01-09 at 22:28 -0200, Robson Francisco de Souza wrote:
> Hi,
> 2008/1/9, Chris Mungall <cjm at fruitfly.org>:
> > [cc-d to gmod-schema]
> >
> > Chado does have some views and pg functions for interval-based
> > retrieval. AFAIK there are no accelerators for deep feature graphs,
> > as most chado users have relatively shallow gene-model/SO feature
> > graphs. It may not be so hard to extend cvterm code for doing this,
> > depending on the characteristics of your graphs (the closure of
> > feature neighbourhood graphs may be particularly large)
> Great! I'm studing Chado and I will have a look at the interval optimizations.
> Did any of you compared BioSQL and Chado for huge feature and feature
> graph storage/retrieval efficiency? As Sendu pointed to limitations in
> Bio::DB::SeqFeature's schema, I'm thinking which of these plataforms
> (or maybe another one?) would be best suited for these tasks... for
> the moment, I will either extend Sendu's hack of Lincon's modules or
> adapt the binning algorithm of Bio::DB::SeqFeature::DBI::mysql to
> Chado, if it turns out to be more efficient than the pg functions.
> Best,
> Robson
> PS: I could not find the most recent version of gmod by following the
> Download link to gmod(Chado) from GMOD's site to the Sourceforge
> download page. Did I miss the right link on the download site or is
> this unexpected? Is the version available at IUBio's mirror (0.003-10)
> the most recent one?
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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