Arek,
Thanks for the pointer. Using that information, I found the following URL for
my mart which gave me the dataset-name/patch-version. Thanks again!
http://www.biomart.org/biomart/martservice?type=datasets&mart=ensembl
________________________________
From: Arek Kasprzyk <[email protected]>
To: pip pipster <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Wednesday, September 14, 2011 10:47 PM
Subject: Re: [BioMart Users] Patch version determination
Hi Philippe,
you need to look at the individual datasets not marts. There is an assembly
version included in the dataset name.
Please let me know if you need more info
a
On Wed, Sep 14, 2011 at 10:25 PM, pip pipster <[email protected]> wrote:
Arek,
>Thanks for the reply. Even on the ENSEMBL mart, it says 63 (but no indication
>of patch level). For coordinates I suspect it's not all that important, but
>for sequences it would be. If there's no other way then one would have to
>manually determine the patch level by looking for a nucleotide that's 'new' in
>a given patch. That's the approach I'll take if there's no other way. But to
>do that everytime you pull data from a mart seems overkill.
>
>
>Regards,
>Phillipe
>
>
>
>
>________________________________
>From: Arek Kasprzyk <[email protected]>
>To: pip pipster <[email protected]>
>Cc: "[email protected]" <[email protected]>
>Sent: Wednesday, September 14, 2011 5:51 PM
>Subject: Re: [BioMart Users] Patch version determination
>
>
>
>Hi Philippe,
>there is no explicit support for assembly version. The individual
>administrators can of course use
>place holders such a mart name or dataset name or description to put the names
>there as you can see in ensembl or icgc examples
>
>a
>
>
>On Wed, Sep 14, 2011 at 3:28 PM, pip pipster <[email protected]> wrote:
>
>Does anyone know how to determine what patch level a given mart is using? For
>example, if I use the following Mart, is it using GRCh37, GRCh37 Patch 3,
>GRCh37 Patch 5, etc. ? I'm hoping there is a command you can issue in Bioperl
>where the Mart tells you exactly which Assembly it's using but open to any
>other avenue that would work.
>>
>>
>>
>> <MartURLLocation database="ensembl_mart_63" default="1"
>>displayName="ENSEMBL GENES 63 (SANGER UK)" host="www.biomart.org"
>>includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice"
>>port="80" serverVirtualSchema="default" visible="1" />
>>
>>
>>Thank you,
>>Phillipe
>>
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>>
>>
>
>
>
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