From eksi at wisc.edu  Mon Aug 10 11:32:18 2009
From: eksi at wisc.edu (RIDVAN EKSI)
Date: Mon, 10 Aug 2009 10:32:18 -0500
Subject: [DAS] gene annotation
Message-ID: <70c0e19318c7f.4a7ff732@wiscmail.wisc.edu>

Hello,
I want to have an annotation file that includes everything known about every genes for mouses. MGI database has a lot of field but it does not include some parts for example protein-protein interaction. So a couple of databases should be merged to have this kind of annotation file. I wonder is it possible with DAS, or is there any tool that already does that. 
Thanks in advance

Ridvan Eksi

From eksi at wisc.edu  Mon Aug 10 11:42:41 2009
From: eksi at wisc.edu (RIDVAN EKSI)
Date: Mon, 10 Aug 2009 10:42:41 -0500
Subject: [DAS] gene annotation
Message-ID: <6fb083cd1a7b3.4a7ff9a1@wiscmail.wisc.edu>

Hello,
I want to have an annotation file that includes everything known about every genes for mouses. MGI database has a lot of field but it does not include some parts for example protein-protein interaction. So a couple of databases should be merged to have this kind of annotation file. I wonder is it possible with DAS, or is there any tool that already does that. 
Thanks in advance

Ridvan Eksi

From andy.jenkinson at ebi.ac.uk  Tue Aug 11 04:53:14 2009
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Tue, 11 Aug 2009 09:53:14 +0100
Subject: [DAS] gene annotation
In-Reply-To: <6fb083cd1a7b3.4a7ff9a1@wiscmail.wisc.edu>
References: <6fb083cd1a7b3.4a7ff9a1@wiscmail.wisc.edu>
Message-ID: <1612220D-98B7-4BA7-9D12-51D7DD5CFD50@ebi.ac.uk>

Hi Ridvan,

There are certainly a significant number of DAS data sources providing  
gene and protein annotations (such as protein-protein interactions as  
you say). DAS is particularly well suited to the type of integration  
problem you illustrate, in that integrating many disparate data  
sources is not a scaleable task without a common data format such as  
DAS. However I suspect there is a fair amount not available through  
DAS sources, so any approach you take is likely to include other  
methods. I suggest you take a look at the data sources in the DAS  
Registry (http://www.dasregistry.org/) as a guide to what is  
available. I believe MGI may also operate a (genomic) DAS server in  
the future but cannot confirm that.

Cheers,
Andy

On 10 Aug 2009, at 16:42, RIDVAN EKSI wrote:

> Hello,
> I want to have an annotation file that includes everything known  
> about every genes for mouses. MGI database has a lot of field but it  
> does not include some parts for example protein-protein interaction.  
> So a couple of databases should be merged to have this kind of  
> annotation file. I wonder is it possible with DAS, or is there any  
> tool that already does that.
> Thanks in advance
>
> Ridvan Eksi
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das