[Bioperl-l] GO ontology browser module available

Chris Mungall cjm@fruitfly.bdgp.berkeley.edu
Wed, 31 Jan 2001 10:02:05 -0800 (PST)

Hi Mark

Sorry you haven't heard back from us GO people, all the GO developers are
working full time on another project at the moment, just keep at us and
we'll respond eventually.

We should fix the problem of the SGML embedded within XML - Brad, can you
see to this?

In the meantime, have you tried using either the flat files or the mysql
database? there are perl modules for using either of these in the GO

As to where you deposit your code, I'd love to keep all the GO code
together in one cvs repository. Unfortunately, the stanford cvs server is
highly restricted. I was considering moving the perl software portion of
GO away from the stanford cvs server into the Berkeley one, for this
reason. Another option would be to use bioperl cvs for all of GO-perl, if
people are willing.

if anyone's interested the GO module docs are here:

On Wed, 31 Jan 2001, Mark Wilkinson wrote:

> Ewan Birney wrote:
> > > > Wouldn't it make sense to add it to bioperl-gui?
> > > >
> > > >     Hilmar
> > > >
> > > Inasmuch as it is completely separate from SeqCanvas, and we are still
> > > thinking bioperl-gui=SeqCanvas, no; but since bioperl-gui could be greater
> > > than SeqCanvas, maybe.  Mark?  I think it would be okay.
> >
> > Sounds like the right place to me....
> indeed - that was where I intended to put it when it was a little more
> "polished"... I am just hesitant to use the BioPerl CVS repository to store my
> half-baked code.
> There are several things which "don't work right" (tm).  I think a lot of this
> has to do with the fact that I can not get my hands on the GO.dtd - it isn't
> available on the GO website, though all of the other XML files are (yet they
> reference the DTD in these same XML files).   Neither do I receive a response to
> inquiries sent to the consortium e-mail address.
> The consequence is that XML::Parser doesn't know what to do with the HTML-like
> formatting tags that they are using in some of their "free text", and in some
> cases tries to treat them as sub-level tags (for example,  what should be a
> subscript or superscript will become a sub-element of the preceeding word, so
> Carbon<down>14</down> parses as $GO->{Carbon}->{14}... which is ridiculous of
> course....).  In addition they use HTML designations for the greek alpha, beta,
> gamma, and so on, preceeded with an ampersand and ending with a semicolon  These
> can not be parsed by XML::Parser *at all* unless it is specifically told that
> these are going to be #CDATA elements... which requires a DTD.... which I don't
> have.
> So, GO_Browser (for the time being) hacks away at the XML in its first parsing
> pass, replacing these tags with things that will not break XML::Parser, and then
> reads from this hacked data.  As a result, what you get is not "strict" GO
> ontology, but a slightly modified version of the same.... which effectively
> defeats the purpose of GO which is that everyone should use a consensus
> nomenclature.  :-(
> In any case, after all that griping, I am perfectly willing to cvs add this
> module to bioperl-gui, so long as I am not judged too harshly by it - I know it's
> a hack!!   :-)
> I'll get on to that later this afternoon.
> b.t.w. If anyone can assist me in getting ahold of a GO.dtd please speak up!  It
> would make my miserable life a bit brighter!!
> --
> ---
> Dr. Mark Wilkinson
> Bioinformatics Group
> National Research Council of Canada
> Plant Biotechnology Institute
> 110 Gymnasium Place
> Saskatoon, SK
> Canada
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