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orthologues

Benjamin Hitz-2
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 ** [hidden email]





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Re: orthologues

Suzanna Lewis
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 ** [hidden email]
>
>
>
>
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
> about Cisco certifications, training, and career opportunities.
> http://p.sf.net/sfu/cisco-dev2dev
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel


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Re: orthologues

Josh Goodman
In reply to this post by Benjamin Hitz-2
Hi Ben,

The bulk of the interoperability discussion focused on the API issue.  What I think we all agreed
upon is that a RESTful/RPC type API was the way to go and that we need to make adoption as easy as
possible.  Ideas to drive adoption included keeping it simple and easy to use/install, bundling it
with some other desirable GMOD tool and publishing a proof of concept type article that highlights
its usefulness.

I've cc'd Alex Kalderimis (InterMine) because he and I have agreed to try to spearhead an attempt to
get something functional within the next couple of months.  I'm working on a Perl implementation
using Dancer that will work with Chado out of the box.  The design uses a modular plugin approach
for each service, so if you don't use Chado you simply extend the base code for each service to fit
your data model.  Alex whipped up a small demo in Python at the meeting that utilized existing
InterMine APIs and I believe he plans to either further develop that or implement an InterMine
module for the Perl version.  Either way there should be code you could utilize with SGD's InterMine
instance.

We didn't talk much about the issue of common orthologies even though that was Scott's original
topic idea.  Partly because it was right before dinner and interest was waning and partly because
this is a discussion that needs to happen with more than just developers involved.

Thanks to you and Suzi for pointing out the reference proteome set, I wasn't aware of this project.

Cheers,
Josh

On 10/20/2011 02:04 PM, 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 ** [hidden email]
>
>
>
>

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Re: orthologues

Thomas, Paul
In reply to this post by Suzanna Lewis
Yes, and my group is planning to set up a web service for querying and
retrieving orthologs.  The basic functionality would be to take a query
organism and list of gene ID's, as well as the target organism; for each
query ID, the ID's of ortholog(s) in the target organism, if any, would be
returned.  Would this address the requirements for this group, or are
there additional requests?

Thanks,
Paul.
--
Paul D. Thomas, Ph.D.
Associate Professor and Director
Division of Bioinformatics
Department of Preventive Medicine
University of Southern California
1450 Biggy Street, NRT 2502
Los Angeles, CA 90089-9601
* please use zip code 90033 for FedEx deliveries
ph.: (323) 442-7799
fax: (323) 442-7995
email: [hidden email]



On 10/20/11 1:30 PM, "Suzanna Lewis" <[hidden email]> 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 ** [hidden email]
>>
>>
>>
>>
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>


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Re: orthologues

Richard Smith
In reply to this post by Suzanna Lewis
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 ** [hidden email]
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
> about Cisco certifications, training, and career opportunities.
> http://p.sf.net/sfu/cisco-dev2dev
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>


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Re: orthologues

Thomas, Paul
The GO Consortium is using trees and orthologs from the PANTHER database.

Paul

Sent from my iPhone

On Oct 24, 2011, at 5:59 AM, "Richard Smith" <[hidden email]> 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 ** [hidden email]
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The demand for IT networking professionals continues to grow, and the
>>> demand for specialized networking skills is growing even more rapidly.
>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>> about Cisco certifications, training, and career opportunities.
>>> http://p.sf.net/sfu/cisco-dev2dev
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>> ------------------------------------------------------------------------------
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>

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Re: orthologues

Josh Goodman
In reply to this post by Suzanna Lewis
Hi Suzi,

I would suggest adding the assembly and annotation release numbers used for the various reference
set species when possible.

Josh


On 10/20/2011 04:30 PM, 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 ** [hidden email]
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
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Re: orthologues

Suzanna Lewis
Good idea. I'll pass it on to Tony and Eleanor at UniProt.

On Oct 24, 2011, at 7:46 AM, Josh Goodman wrote:

> Hi Suzi,
>
> I would suggest adding the assembly and annotation release numbers used for the various reference
> set species when possible.
>
> Josh
>
>
> On 10/20/2011 04:30 PM, 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 ** [hidden email]
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The demand for IT networking professionals continues to grow, and the
>>> demand for specialized networking skills is growing even more rapidly.
>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>> about Cisco certifications, training, and career opportunities.
>>> http://p.sf.net/sfu/cisco-dev2dev
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>> ------------------------------------------------------------------------------
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>


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Re: orthologues

Thomas, Paul
In reply to this post by Richard Smith
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" <[hidden email]> 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 ** [hidden email]
>>>
>>>
>>>
>>>
>>>
>>>
>>>------------------------------------------------------------------------
>>>------
>>> The demand for IT networking professionals continues to grow, and the
>>> demand for specialized networking skills is growing even more rapidly.
>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>> about Cisco certifications, training, and career opportunities.
>>> http://p.sf.net/sfu/cisco-dev2dev
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> The demand for IT networking professionals continues to grow, and the
>> demand for specialized networking skills is growing even more rapidly.
>> Take a complimentary Learning@Cisco Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> http://p.sf.net/sfu/cisco-dev2dev
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>


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Re: orthologues

Richard Smith
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"<[hidden email]>  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 ** [hidden email]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>> ------
>>>> The demand for IT networking professionals continues to grow, and the
>>>> demand for specialized networking skills is growing even more rapidly.
>>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>>> about Cisco certifications, training, and career opportunities.
>>>> http://p.sf.net/sfu/cisco-dev2dev
>>>> _______________________________________________
>>>> Gmod-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>>
>>>
>>> -------------------------------------------------------------------------
>>> -----
>>> The demand for IT networking professionals continues to grow, and the
>>> demand for specialized networking skills is growing even more rapidly.
>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>> about Cisco certifications, training, and career opportunities.
>>> http://p.sf.net/sfu/cisco-dev2dev
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>
>
>


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Re: orthologues

Thomas, Paul
They're generated yearly.  The proteome sets were generated using the
prototype process we developed prior to the release of the EBI reference
proteomes.  The gp2protein files are available at
ftp://ftp.pantherdb.org/genome (version 7.0).  We will be in synch with
the EBI sets no later than July of 2012.

Chris Mungall pointed out that there is currently an extra column for
paralogs, and we'll be fixing that soon, please keep that in mind as you
design your parser (the two flanking species events for paralogs will be
pipe-separated in a single column).

Thanks,
Paul.

On 10/25/11 3:16 AM, "Richard Smith" <[hidden email]> wrote:

>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"<[hidden email]>  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 ** [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>----------------------------------------------------------------------
>>>>>--
>>>>> ------
>>>>> The demand for IT networking professionals continues to grow, and the
>>>>> demand for specialized networking skills is growing even more
>>>>>rapidly.
>>>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>>>> about Cisco certifications, training, and career opportunities.
>>>>> http://p.sf.net/sfu/cisco-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-devel mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>
>>>>
>>>>
>>>>
>>>>-----------------------------------------------------------------------
>>>>--
>>>> -----
>>>> The demand for IT networking professionals continues to grow, and the
>>>> demand for specialized networking skills is growing even more rapidly.
>>>> Take a complimentary Learning@Cisco Self-Assessment and learn
>>>> about Cisco certifications, training, and career opportunities.
>>>> http://p.sf.net/sfu/cisco-dev2dev
>>>> _______________________________________________
>>>> Gmod-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>
>>>
>>
>>
>


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