[InterMine Dev] Homologene converter?

Benjamin Hitz hitz at stanford.edu
Fri Mar 16 23:02:37 GMT 2012


From Paul Foster the PI (also a GOC PI):

> We're going to keep a yearly release cycle.  The release was delayed
> because of issues in switching over to the UniProt reference proteome set
> (http://www.ebi.ac.uk/reference_proteomes/).  The next update will begin
> in April when the new release of reference proteomes is available, and
> will be done before the end of this year.
> 
> Paul.

On Mar 16, 2012, at 12:40 PM, Josh Goodman wrote:

> 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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> >>
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> >
> > --
> > Ben Hitz
> > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> > Stanford University ** hitz at stanford.edu
> >
> >
> >
> >
> >
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> > dev at intermine.org
> > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> 
> 
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--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** hitz at stanford.edu




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