Hi Ken,
Yes, this is confusing. Here is how it works. As the central portal, biomart.org federates databases from different data providers. With more data sources to be federated, it is unavoidable that datasets from different sources may have the same name. In such case, we have to put these data sources in different virtual schemas. When a dataset name is globally uniquely in biomart server, you don't need to specify which virtualSchema in order to access its configuration. This is why http://www.gramene.org/biomart/martservice?type=configuration&dataset=alyra ta_eg_gene works without virtualSchema=default. But in the case of biomart.org, since there are two datasets are named as alyrata_eg_gene, when you access configuration you will have to specify the virtualSchema. In biomart.org, alyrata_eg_gene exists in default and default2 virtualSchema: http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyra ta_eg_gene&virtualschema=default http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyra ta_eg_gene&virtualschema=default2 BTW, it is the second one (default2) that is the same as http://www.gramene.org/biomart/martservice?type=configuration&dataset=alyra ta_eg_gen One thing to note is that when a dataset name is globally unique, and can be access without specifying the virtualSchema does not mean that dataset is under virtaulSchema. Here is one example: http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p ancreas (this works) http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p ancreas&virtualSchema=default2 (this works) http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p ancreas&virtualSchema=default (this doesn't work) Junjun On 11-08-26 11:57 AM, "Youens-Clark, Ken" <[email protected]> wrote: >BioMart developers, > >A user describes a problem with programmatic access to BioMart as >follows: > >> When accessing the data sets for the mart ENSEMBL_MART_PLANT via the >>MartService at biomart.org, an error is being generated if the >>virtualschema=default parameter is not included. >> >> Example: >> >> this isn't working >> >>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly >>rata_eg_gene >> >> and this is >> >>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly >>rata_eg_gene&virtualschema=default >> >> The services are accessed via the MartService urls. To access the mart >>in question we are using the url: >> >> >>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly >>rata_eg_gene >> >> which currently responds: >> Dataset name conflict for alyrata_eg_gene. Need to further qualify with >>the virtualSchema param as well >> >> If I add the virtualschema parameter as default, the correct >>information is retrieved: >> >> >>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly >>rata_eg_gene&virtualschema=default >> >> However, based upon the documentation, the virtualschema is 'default' >>by default. Do we have to alter the client code to include the >>virtualschema=default parameter? Based on our reading of the docs it >>shouldn't be required, e.g. accessing >>http://www.gramene.org/biomart/martservice?type=configuration&dataset=aly >>rata_eg_gene it is unnecessary. >> >> If this doesn't make sense, let me know. > >I would appreciate any advice you could provide. > >-- >Ken Youens-Clark >[email protected] >Gramene.org Project Manager >Ware Lab/CSHL/USDA-ARS > > > >_______________________________________________ >Users mailing list >[email protected] >https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
