[InterMine Dev] Homologene converter?

Benjamin Hitz hitz at stanford.edu
Fri Mar 16 19:00:06 GMT 2012


It's a classic "user" trade off.  On the one hand you want to provide as much information as possible so that the user can make an informed decision.
On the other hand, presenting a myriad of confusing relationships with no clear or obvious way to distinguish them is not helpful.

Probably some sort of "default/advanced user" interface would work for this.

Ben

On Mar 16, 2012, at 10:47 AM, Todd Harris 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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>> 
>> --
>> Ben Hitz 
>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
>> Stanford University ** hitz at stanford.edu
>> 
>> 
>> 
>> 
>> 
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> 

--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** hitz at stanford.edu







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