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
http://uswest.ensembl.org/biomart/martservice
gets sent with "Content-Type: text/plain", which causes the browser to
render the raw HTML. The same thing happens even if one visits
http://uswest.ensembl.org/biomart/martservice/index.html , or if one
replaces the host name with www.biomart.org.
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
http://uswest.ensembl.org/biomart/martservice?type=registry
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
