Hi Rhoda,
As Harish has said the biomart.org and ensemble.org are working fine. The
problem is that when using Biomart from Taverna the attribute ID used in the
query is incorrect.
The correct query generated from biomart.org is
<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows
= "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_snp" interface = "default" >
<Filter name = "chr_name" value = "1"/>
<Attribute name = "illumina_human660wquad" />
</Dataset>
</Query>
The incorrect query generated from Taverna is
<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows
= "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_snp" interface = "default" >
<Filter name = "chr_name" value = "1"/>
<Attribute name = "Illumina_Human660Wquad" />
</Dataset>
</Query>
The difference is the attribute name; it should be illumina_human660wquad, not
Illumina_Human660Wquad
Taverna is getting the incorrect attribute ID from the dataset configuration
here
http://www.biomart.org/biomart/martservice?type=configuration&dataset=hsapiens_snp
It seems to me that either biomart.org uses a different dataset configuration
or there is some "convert to lower case" rule being applied somewhere.
David.
On 31 Aug 2012, at 12:02, <[email protected]> <[email protected]> wrote:
> Hi Rhoda,
> The Biomart web interface is working fine for all the Illumina related
> attributes (there are three of them), however, I am having trouble getting
> them (all three) to work through Taverna. David mentioned (see communication
> below) that Taverna is getting a wrong attribute for this dataset from the
> Biomart configuration, is that something that needs to be looked into? I have
> no idea how these things work internally, I am just a casual user, I guess it
> would prudent on my part not to offer any speculation but leave this for the
> myGrid/Biomart team to figure out. Please let me know if there is anything
> that I can do from my end to solve the problem.
> Best Regards,
> Harish.
> From: Rhoda Kinsella [[email protected]]
> Sent: Friday, August 31, 2012 11:16 AM
> To: Arek Kasprzyk
> Cc: myGrid Support; Dharuri, H.K. (HG); Biomart; Thomas Maurel
> Subject: Re: [BioMart Users] Problems with Biomart service
>
> Hi Harish,
> I have taken a look at our configuration and I am not sure why this
> particular Illumina attribute is causing an issue for you and the other
> Illumina attributes are fine. As you mention, the data can be retrieved from
> the interface so nothing is broken. The configuration for all the Illumina
> attributes are set up in the same way so right now I can't see why this one
> is causing problems. Can you please try your query again using the Ensembl
> BioMart databases at www.ensembl.org and see if you have the same issue
> there? You should also know that from release 69 (due to be released early
> October), the Illumina and Affy data will be moved to the variation set
> tables in the Ensembl variation schema and we will reflect this change in the
> variation mart database. This will mean that you will need to filter from the
> variation set filter section and the results will be retrieved from the
> Variation set attribute section. This change will be announced in the "What's
> new" section of the
Ensembl home page. Please let me know if you have the same issues when you run
your pipeline using the Ensembl martservice.
> Regards
> Rhoda
>
>
>
>
>>
>>
>>
>> On Thu, Aug 30, 2012 at 3:18 PM, myGrid Support <[email protected]>
>> wrote:
>> Hi Harish,
>>
>> The problem is that the attribute should be called illumina_human660wquad,
>> not Illumina_Human660Wquad.
>>
>> Taverna is getting the wrong attribute ID from the Biomart configuration for
>> this dataset -
>> http://www.biomart.org/biomart/martservice?type=configuration&dataset=hsapiens_snp
>>
>> I think it will require a fix from Biomart so I'm copying this to the
>> Biomart support list.
>>
>> David.
>>
>> On 30 Aug 2012, at 14:15, <[email protected]> <[email protected]> wrote:
>>
>> >
>> > Greetings Alan,
>> > Thank you for your prompt reply. Please find attached an example workflow
>> > that gives the error message that I was talking about. Basically, the
>> > workflow determines genomic location of the gene (provided as a constant
>> > input) and feeds it to the next biomart service that should return all the
>> > Illumina-chip specific snp ids, instead it issues the error message.
>> > Best Regards,
>> > Harish.
>> > ________________________________________
>> > From: Alan R Williams [[email protected]]
>> > Sent: Thursday, August 30, 2012 2:42 PM
>> > To: Dharuri, H.K. (HG)
>> > Cc: [email protected]
>> > Subject: Re: Problems with Biomart service
>> >
>> > On 30/08/2012 12:38, [email protected] wrote:
>> >> Hi,
>> >
>> > Hello
>> >
>> >> I am having issues with the Biomart service within Taverna. More
>> >> specifically, I am using the service to generate Illumina SNP IDs given
>> >> an input of chromosome name and start and end positions. This works well
>> >> with other "attributes" like the affy IDs. Also, I looked up the online
>> >> version of Biomart and it seems to be working fine, I am wondering if
>> >> this is a problem with Taverna. The error message issued was: "Query
>> >> ERROR: caught BioMart::Exception::Usage: Attribute
>> >> Illumina_Human660Wquad NOT FOUND".
>> >>
>> >> Please let me know what you think of this.
>> >
>> > Are you able to send the workflow or even better a smaller version of
>> > the workflow that just calls the service?
>> >
>> >> Best Regards,
>> >>
>> >> Harish.
>> >
>> > Alan<error_prone_biomart_service.t2flow>
>>
>> myGrid Support
>> [email protected]
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [email protected]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>>
>>
>> --
>> Arek Kasprzyk, MD, MSc, PhD
>> BioMart Project Lead
>> www.biomart.org
>
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge,
> CB10 1SD
>
>
>
>
myGrid Support
[email protected]
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