Hello David, 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.
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>. I hope that helps! Sincerely, Jonathan Guberman, PhD Application Programmer Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7818 Toll-free: 1-866-678-6427 www.oicr.on.ca<http://www.oicr.on.ca> On 2011-06-09, at 9:33 AM, David Croft wrote: Hi, 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. _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users
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