Re: [GMOD-devel] orthologues

[Richard S. <ri...@fl...>]

Thanks Paul.  We'll add a parser to InterMine.

How often are these generated?  I notice the file date is June 2011 and
the reference proteomes at the EBI are from April 2011, so are they
generated from those gp2protein files?

However, this page on pantherdb lists genome dates as January 2009:

	http://pantherdb.org/panther/summaryStats.jsp

Cheers,
Richard.


On 24/10/2011 19:18, Thomas, Paul wrote:
> Here's the link to the ftp directory for the files with pairwise orthologs
> across the GO Reference Genomes:
> ftp://ftp.pantherdb.org/ortholog
>
> Paul.
>
> On 10/24/11 5:59 AM, "Richard Smith"<ri...@fl...>  wrote:
>
>> Hi all,
>> I can see the reference proteomes for download but only a link to
>> InParanoid for orthologs.  Have other methods been used on the
>> reference proteomes and is there a plan for a blessed set of
>> ortholog predictions?
>>
>> At InterMine we're working with several MODs and interoperability
>> between the Mines is a big part of the project.  We would like to
>> load in the most widely accepted ortholog predictions.
>>
>> As Josh says, Alex is working on an InterMine implementation of the
>> GMOD REST API, which will be available for the MODs that are
>> deploying InterMine instances (SGD, RGD, ZFIN, WormBase, MGI).
>>
>>
>> Thanks,
>> Richard.
>>
>>
>> On 20/10/2011 21:30, Suzanna Lewis wrote:
>>> Yes, Ben is absolutely right. For more information you can look here:
>>> http://www.ebi.ac.uk/reference_proteomes/
>>>
>>> And of course we really want to hear from all of you. Involvement and
>>> feedback are really wanted!
>>>
>>> I think the phylogenetic trees GO is using are soon to be available
>>> programmatically, if not today then certainly by the end of the year.
>>> the new GO architecture (all the behind the scenes stuff) is all
>>> services based.
>>>
>>> -S
>>>
>>> On Oct 20, 2011, at 11:04 AM, Benjamin Hitz wrote:
>>>
>>>> Hi gmod.  Hope everyone had a good time in Toronto; sorry I couldn't
>>>> make it.
>>>> Kalpana gave us a report on the meeting and something stuck out at us
>>>> that I though we should follow up on - the discussion on MOD
>>>> interoperation by Josh Goodman.
>>>>
>>>> There were no notes to confirm, but message we received back at SGD
>>>> was that it was difficult for MODs to communicate without some common
>>>> ortholog discussion.
>>>> I know there is not a huge overlap in meeting attendees between GMOD
>>>> meeting and GO consortium meetings, BUT all the major and most minor
>>>> mods are part of GO - and GO has essentially "solved" this problem, or
>>>> at least has decided on common protein sets and a set of orthologs
>>>> across model organisms.  I am not personally part of this GO
>>>> subproject, but certainly we should work together with GO on this.
>>>>
>>>> We are planning to re-do SGD's software in the next couple years and I
>>>> would like to use whatever GMOD common REST API (and I suppose might as
>>>> well implement SADI as well) from the beginning... whatever that API
>>>> happens to be.  Oh, but I can 99% guarentee we won't use CHADO - and I
>>>> know worm, mouse, zfin, etc. don't either, so we should think about
>>>> generic implemention of the REST API (as a group)
>>>>
>>>> Ben
>>>> --
>>>> Ben Hitz
>>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO
>>>> Consortium
>>>> Stanford University ** hi...@st...
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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