datasetConfigVersion; metazoa & plant marts

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datasetConfigVersion; metazoa & plant marts

Gabriel Berriz
Hi!  I have 2 questions.

1. Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like

<!DOCTYPE Query>
<Query completionStamp="1" count=""
datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
<Dataset interface="default" name="btaurus_gene_ensembl">
  <Attribute name="ensembl_gene_id" />
  <Attribute name="description" />
</Dataset>
</Query>

Until some months ago, I used to get this information with the following query:

/biomart/martservice?mart=btaurus_gene_ensembl&virtualschema=default&type=version

But now this query fails with the following error message:

Mart name btaurus_gene_ensembl not found on server for the serverVirtualSchema specified
non-BioMart die(): Can't call method "version" on an undefined value at /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martservice line 424.

(BTW, from the error message I infer that this is an unexpected exception, so may there's a bug somewhere.)

(BTW #2: the page one sees when one visits


gets sent with "Content-Type: text/plain", which causes the browser to render the raw HTML.  The same thing happens even if one visits


Also, this page refers to the URL http://www.ensembl.org/martservice, which appears to be dead.)



2. Where did the following datasets go?

aaegypti_gene_ensembl
agambiae_gene_ensembl
athaliana_gene_ensembl

They are not in any of the marts listed in response to


More importantly: how can my code discover the location of these datasets programmatically?

TIA!




=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557





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Re: datasetConfigVersion; metazoa & plant marts

Dan Staines
Hi Gabriel,

> 2. Where did the following datasets go?
>
> aaegypti_gene_ensembl
> agambiae_gene_ensembl
> athaliana_gene_ensembl
>
> They are not in any of the marts listed in response to
>
> http://uswest.ensembl.org/biomart/martservice?*type=registry*

The Ensembl databases and corresponding marts for these organisms are
now provided by the Ensembl Genomes group (and in the case of A.
thaliana, by our colleauges at Gramene as well) - Ensembl Genomes is now
responsible for providing ensembl resources for non-vertebrate
organisms, including plants and metazoa. For various reasons, this has
necessitated a change in dataset name to be aaegypti_eg_gene,
agambiae_eg_gene and athaliana_eg_gene, and can be found via the mart
installs at the individual Ensembl Genomes sites e.g.:
http://plants.ensembl.org/biomart/martview
http://metazoa.ensembl.org/biomart/martview

Hope this helps!

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
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Re: datasetConfigVersion; metazoa & plant marts

Gabriel Berriz

On 100816M, at 04:44, Dan Staines wrote:

Hi Gabriel,

2. Where did the following datasets go?

aaegypti_gene_ensembl
agambiae_gene_ensembl
athaliana_gene_ensembl

They are not in any of the marts listed in response to

http://uswest.ensembl.org/biomart/martservice?*type=registry*

The Ensembl databases and corresponding marts for these organisms are
now provided by the Ensembl Genomes group (and in the case of A.
thaliana, by our colleauges at Gramene as well) - Ensembl Genomes is now
responsible for providing ensembl resources for non-vertebrate
organisms, including plants and metazoa. For various reasons, this has
necessitated a change in dataset name to be aaegypti_eg_gene,
agambiae_eg_gene and athaliana_eg_gene, and can be found via the mart
installs at the individual Ensembl Genomes sites e.g.:
http://plants.ensembl.org/biomart/martview
http://metazoa.ensembl.org/biomart/martview


Thanks for the info!

G.



=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557





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Re: datasetConfigVersion

Gabriel Berriz
In reply to this post by Gabriel Berriz
Bump?

On 100813F, at 16:30, Gabriel Berriz wrote:

Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like

<!DOCTYPE Query>
<Query completionStamp="1" count=""
datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
<Dataset interface="default" name="btaurus_gene_ensembl">
  <Attribute name="ensembl_gene_id" />
  <Attribute name="description" />
</Dataset>
</Query>

Until some months ago, I used to get this information with the following query:

/biomart/martservice?mart=btaurus_gene_ensembl&virtualschema=default&type=version

But now this query fails with the following error message:

Mart name btaurus_gene_ensembl not found on server for the serverVirtualSchema specified
non-BioMart die(): Can't call method "version" on an undefined value at /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martservice line 424.






=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557





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Re: datasetConfigVersion

Richard Holland
btaurus_gene_ensembl is a dataset name, not a mart name. The parameter 'mart' requires a mart name. In this case (admittedly I did this by process of guessing) the mart name for the mart that contains the dataset btaurus_gene_ensembl is 'ensembl'. Therefore the following works the way you are probably expecting it to:

http://www.biomart.org/biomart/martservice?mart=ensembl&type=version

cheers,
Richard

On 26 Aug 2010, at 14:59, Gabriel Berriz wrote:

> Bump?
>
> On 100813F, at 16:30, Gabriel Berriz wrote:
>
>> Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like
>>
>> <!DOCTYPE Query>
>> <Query completionStamp="1" count="" datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
>> <Dataset interface="default" name="btaurus_gene_ensembl">
>>   <Attribute name="ensembl_gene_id" />
>>   <Attribute name="description" />
>> </Dataset>
>> </Query>
>>
>> Until some months ago, I used to get this information with the following query:
>>
>> /biomart/martservice?mart=btaurus_gene_ensembl&virtualschema=default&type=version
>>
>> But now this query fails with the following error message:
>>
>> Mart name btaurus_gene_ensembl not found on server for the serverVirtualSchema specified
>> non-BioMart die(): Can't call method "version" on an undefined value at /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martservice line 424.
>
>
>
>
>
>
> =============================================================
> Gabriel F. Berriz, PhD
> Senior Bioinformatics Developer
> Roth Lab
> Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
> 250 Longwood Avenue
> Seeley G. Mudd Building 322B
> Boston, MA 02115-5701
> Telephone: 617.432.3555
> Fax: 617.432.3557
>
>
>
>
>

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [hidden email]
http://www.eaglegenomics.com/

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Re: datasetConfigVersion

Gabriel Berriz
On 100826T, at 10:08, Richard Holland wrote:

On 100813F, at 16:30, Gabriel Berriz wrote:

Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like

<!DOCTYPE Query>
<Query completionStamp="1" count="" datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
<Dataset interface="default" name="btaurus_gene_ensembl">
 <Attribute name="ensembl_gene_id" />
 <Attribute name="description" />
</Dataset>
</Query>

btaurus_gene_ensembl is a dataset name, not a mart name. The parameter 'mart' requires a mart name. In this case (admittedly I did this by process of guessing) the mart name for the mart that contains the dataset btaurus_gene_ensembl is 'ensembl'.

Hi.  Thanks for the correction.

Therefore the following works the way you are probably expecting it to:

http://www.biomart.org/biomart/martservice?mart=ensembl&type=version


When I visit this URL, I get the value 0.6, but the BioMart documentation (p. 68) suggests that the value for the datasetConfigVersion attribute should be at least 0.7:

<?xml version="1.0" encoding="UTF-8"?> 
<!DOCTYPE Query> 
<Query virtualSchemaName = "default" uniqueRows = "" count = "" datasetConfigVersion = "0.7" > 
  <Dataset name = "mytest" interface = "default" > 
    <Attribute name = "ensembl_transcript_id" /> 
    <Attribute name = "chromosome_name" /> 
    <Filter name = "chromosome_name" value= "22"/> 
  </Dataset> 
</Query>


I'm not sure how to make sense of this.

My goal here is to find a programmatic way to determine the most current value for the datasetConfigVersion attribute.

If anyone knows how to do this, please let me know.

TIA!

Gabriel



=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557





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Re: datasetConfigVersion

Richard Holland
I _think_ (not 100% certain) that doing this will get you the info you need:

 http://www.biomart.org/biomart/martservice?type=configuration&dataset=btaurus_gene_ensembl

and look for the softwareVersion attribute in the DatasetConfig tag (very near the top).

However I think the datasetConfigVersion in Query is not really that important and I'm pretty sure it is never actually checked. Mostly it is checking that the query format you are using is the same as the version of MartService you are talking to - i.e. when talking to a 0.6 server, don't use any tags that weren't introduced until 0.7, for instance.

But when all's said and done I'm not a huge BioMart expert at the moment so I'll leave it to Syed and co. to correct me if I'm wrong!

cheers,
Richard

On 26 Aug 2010, at 17:01, Gabriel Berriz wrote:

> On 100826T, at 10:08, Richard Holland wrote:
>
>>> On 100813F, at 16:30, Gabriel Berriz wrote:
>>>
>>>> Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like
>>>>
>>>> <!DOCTYPE Query>
>>>> <Query completionStamp="1" count="" datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
>>>> <Dataset interface="default" name="btaurus_gene_ensembl">
>>>>  <Attribute name="ensembl_gene_id" />
>>>>  <Attribute name="description" />
>>>> </Dataset>
>>>> </Query>
>>>
>
>> btaurus_gene_ensembl is a dataset name, not a mart name. The parameter 'mart' requires a mart name. In this case (admittedly I did this by process of guessing) the mart name for the mart that contains the dataset btaurus_gene_ensembl is 'ensembl'.
>
> Hi.  Thanks for the correction.
>
>> Therefore the following works the way you are probably expecting it to:
>>
>> http://www.biomart.org/biomart/martservice?mart=ensembl&type=version
>
>
> When I visit this URL, I get the value 0.6, but the BioMart documentation (p. 68) suggests that the value for the datasetConfigVersion attribute should be at least 0.7:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" uniqueRows = "" count = "" datasetConfigVersion = "0.7" >
>   <Dataset name = "mytest" interface = "default" >
>     <Attribute name = "ensembl_transcript_id" />
>     <Attribute name = "chromosome_name" />
>     <Filter name = "chromosome_name" value= "22"/>
>   </Dataset>
> </Query>
>
>
> I'm not sure how to make sense of this.
>
> My goal here is to find a programmatic way to determine the most current value for the datasetConfigVersion attribute.
>
> If anyone knows how to do this, please let me know.
>
> TIA!
>
> Gabriel
>
>
>
> =============================================================
> Gabriel F. Berriz, PhD
> Senior Bioinformatics Developer
> Roth Lab
> Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
> 250 Longwood Avenue
> Seeley G. Mudd Building 322B
> Boston, MA 02115-5701
> Telephone: 617.432.3555
> Fax: 617.432.3557
>
>
>
>
>

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [hidden email]
http://www.eaglegenomics.com/

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Re: datasetConfigVersion

Syed Haider
Hi Gabriel,

please let the datasetConfigVersion out or setting it to 0.6 or 0.7
means the same. hope this helps.

Best
Syed

On 26/08/2010 17:42, Richard Holland wrote:

> I _think_ (not 100% certain) that doing this will get you the info you need:
>
>   http://www.biomart.org/biomart/martservice?type=configuration&dataset=btaurus_gene_ensembl
>
> and look for the softwareVersion attribute in the DatasetConfig tag (very near the top).
>
> However I think the datasetConfigVersion in Query is not really that important and I'm pretty sure it is never actually checked. Mostly it is checking that the query format you are using is the same as the version of MartService you are talking to - i.e. when talking to a 0.6 server, don't use any tags that weren't introduced until 0.7, for instance.
>
> But when all's said and done I'm not a huge BioMart expert at the moment so I'll leave it to Syed and co. to correct me if I'm wrong!
>
> cheers,
> Richard
>
> On 26 Aug 2010, at 17:01, Gabriel Berriz wrote:
>
>> On 100826T, at 10:08, Richard Holland wrote:
>>
>>>> On 100813F, at 16:30, Gabriel Berriz wrote:
>>>>
>>>>> Is there a programmatic way to get the correct value of the datasetConfigVersion attribute, for queries like
>>>>>
>>>>> <!DOCTYPE Query>
>>>>> <Query completionStamp="1" count="" datasetConfigVersion="0.6" requestId="biomart-client" uniqueRows="1" virtualSchemaName="default">
>>>>> <Dataset interface="default" name="btaurus_gene_ensembl">
>>>>>   <Attribute name="ensembl_gene_id" />
>>>>>   <Attribute name="description" />
>>>>> </Dataset>
>>>>> </Query>
>>>>
>>
>>> btaurus_gene_ensembl is a dataset name, not a mart name. The parameter 'mart' requires a mart name. In this case (admittedly I did this by process of guessing) the mart name for the mart that contains the dataset btaurus_gene_ensembl is 'ensembl'.
>>
>> Hi.  Thanks for the correction.
>>
>>> Therefore the following works the way you are probably expecting it to:
>>>
>>> http://www.biomart.org/biomart/martservice?mart=ensembl&type=version
>>
>>
>> When I visit this URL, I get the value 0.6, but the BioMart documentation (p. 68) suggests that the value for the datasetConfigVersion attribute should be at least 0.7:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName = "default" uniqueRows = "" count = "" datasetConfigVersion = "0.7">
>>    <Dataset name = "mytest" interface = "default">
>>      <Attribute name = "ensembl_transcript_id" />
>>      <Attribute name = "chromosome_name" />
>>      <Filter name = "chromosome_name" value= "22"/>
>>    </Dataset>
>> </Query>
>>
>>
>> I'm not sure how to make sense of this.
>>
>> My goal here is to find a programmatic way to determine the most current value for the datasetConfigVersion attribute.
>>
>> If anyone knows how to do this, please let me know.
>>
>> TIA!
>>
>> Gabriel
>>
>>
>>
>> =============================================================
>> Gabriel F. Berriz, PhD
>> Senior Bioinformatics Developer
>> Roth Lab
>> Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
>> 250 Longwood Avenue
>> Seeley G. Mudd Building 322B
>> Boston, MA 02115-5701
>> Telephone: 617.432.3555
>> Fax: 617.432.3557
>>
>>
>>
>>
>>
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: [hidden email]
> http://www.eaglegenomics.com/
>
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Re: datasetConfigVersion

Gabriel Berriz

On 100828S, at 08:27, Syed Haider wrote:

Hi Gabriel,

please let the datasetConfigVersion out or setting it to 0.6 or 0.7
means the same. hope this helps.

Thanks!

Gabriel



=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557