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
