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Homologene converter?

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Homologene converter?

Joel Richardson-2

Is there a converter for Homologene? Also, is there a consensus on the preferred source of orthologues?

Thanks,
Joel

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Re: Homologene converter?

Julie Sullivan


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
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: Homologene converter?

Benjamin Hitz-2

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
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]





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Re: Homologene converter?

Todd Harris-2
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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Homologene converter?

Benjamin Hitz-2

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
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
>> Stanford University ** [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]





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Re: Homologene converter?

Josh Goodman
In reply to this post by Todd Harris-2
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 <[hidden email]> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Homologene converter?

Benjamin Hitz-2

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 <[hidden email]> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]





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