Hi Jonathan,
When biomart.org <http://biomart.org> is updated we announce it on
this mailing list. For specifics of changes made to individual
datasets, you will need to contact the individual data providers.
OK.
Your specific problem with Ensembl Plant is a little bit more
complicated: the issue is that within one registry dataset names must
be unique. In Biomart.org <http://Biomart.org>, we have two marts that
use the same dataset names for A. Thaliana and O. sativa: Ensembl
Plant and Gramene 30 Ensembl Genes. In order to accommodate this, we
have a concept of "virtualSchema"; each of these two marts is
contained in a virtualSchema. If the dataset name is unique then the
virtualSchema can be ignored; however, in this case, because it is not
unique, the query must be qualified with the virtualSchema name.
To see this, you may use the XML button in the upper right corner of
the query page. For example, for the same query against Ensembl Plant
and Gramene 30 you will get the following XMLs:
ENSEMBL PLANT:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count=""
datasetConfigVersion="0.7">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>
GRAMENE:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default2" formatter="TSV" header="0" uniqueRows="0" count=""
datasetConfigVersion="0.6">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>
Notice that for Ensembl Plant, the property is set as
virtualSchemaName="default", whereas for Gramene is is "default2".
I imagine that this is also the cause of your problem for Dictostelium
and Plasmodium genomes, because they are also still contained at
biomart.org <http://biomart.org>.
This was indeed one of the problems. I also found that (for rice) I
needed to point the BioMart at
http://plants.ensembl.org/biomart/martservice, rather than at
http://www.biomart.org/biomart/martservice, as we had originally being
doing.
One thing that I noticed was that the virtual schema we had to use was
plant_mart_9. Will this always remain the same, or is the "9" some kind
of release or version number that could change with time?
Cheers,
David Croft.
Is there any kind of centralized point of distribution for alerts on
changes to the various BioMarts? We have been going to
http://www.biomart.org/biomart/martservice to get information about
ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
changed - as far as I can work out, we now need to get this data from
http://plants.ensembl.org/biomart/martservice. We are also having
problems with Dictostelium and Plasmodium genomes, I guess they have
also moved to some more specialized location?
Cheers,
David Croft.
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