[InterMine Dev] Homologene converter?

Josh Goodman jogoodma at indiana.edu
Fri Mar 16 19:40:11 GMT 2012


My only concern with Panther are the dates listed on
http://pantherdb.org/panther/summaryStats.jsp.  3+ years is far too long to
go without updating gene models from the various MODs.  Does anyone know if
they have plans to do an update?  It looks like their grant runs out this
month as well.

Josh

On Fri, Mar 16, 2012 at 1:47 PM, Todd Harris <todd at wormbase.org> wrote:

> I second on Panther.
>
> But why settle on a single algorithm? It's useful to cross-correlate
> approaches.
>
> Todd
>
> On Mar 16, 2012, at 11:31 AM, Benjamin Hitz wrote:
>
> >
> > Panther?  That is what GO is moving to.
> >
> >>
> >>
> >> On 16/03/12 10:47, Joel Richardson wrote:
> >>>
> >>> Is there a converter for Homologene?
> >>
> >> No but I can write one!  I looked at a data file briefly a few years
> ago but it wasn't clear to me how to model the data.  Can you send me
> information on which data file you are loading and how you think it should
> be modeled?
> >>
> >> Also, is there a consensus on the preferred source of orthologues?
> >>>
> >>
> >> No, I think that's going to be a topic of discussion at the annual
> meeting. Currently we in Cambridge are using Ensembl Compara because
> TreeFam hasn't updated since 2009.
> >>
> >>> Thanks,
> >>> Joel
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> >>
> >> _______________________________________________
> >> dev mailing list
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> >
> > --
> > Ben Hitz
> > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO
> Consortium
> > Stanford University ** hitz at stanford.edu
> >
> >
> >
> >
> >
> > _______________________________________________
> > dev mailing list
> > dev at intermine.org
> > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
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