Hi Josh, We will change the attribute names to use the species latin names for the next release due in early October. Thank you for your feedback. Regards Rhoda
On 30 Aug 2012, at 23:46, "Stein, Joshua" <[email protected]> wrote: > Hi, > > I'm trying to parse available homolog information from the attribute metadata > tables, e.g. available at > http://www.biomart.org/biomart/martservice?type=attributes&dataset=oanatinus_gene_ensembl > > I don't understand why in the case of ensembl_mart_68 the name given to a > gene dataset (e.g. "mmusculus_gene_ensembl") has no correspondence with the > attribute names of target homolog gene sets, which tend to use common names > instead of scientific names (e.g. "mouse_ensembl_gene"). There is not > sufficient information in the attribute file to parse species, assembly, etc. > for the target homolog gene set. > > This problem does not exist for other Mart services such as metazoa_mart_14, > wherein the gene dataset names match with homolog gene attribute names. In > this case it is possible to get richer metadata for the homolog attribute > name by consulting the dataset metadata file. For example > "amellifera_eg_gene" appears both as a dataset and as an attribute. > > Is there a way to mitigate this Ensembl main? I'm trying to automate > ortholog retrieval given a query species and target species and think I can > only do this easily with Ensembl Genomes marts given the structure of the > metadata. > > Thanks, > Josh > > > Joshua Stein, PhD > Manager, Sci. Informatics III > Cold Spring Harbor Laboratory > [email protected] > http://ware.cshl.org/ > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
