Great. Thanks for the information. --Josh On Aug 31, 2012, at 3:57 AM, Rhoda Kinsella wrote:
> 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 > > > 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
