biomart attribute "external_gene_id"

[josegarciamanteiga]

Hi,
I was trying to retrieve data for Rattus Norvegicus 79 from ensembl using the get_data.sh
I found that the file ensembl1.txt gives the error:
Query ERROR: caught BioMart::Exception::Usage: Attribute external_gene_id NOT FOUND
Indeed, the attribute has changed some time ago to "external_gene_name"
Same for the ensembl2.txt:
Query ERROR: caught BioMart::Exception::Usage: Attribute uniprot_swissprot_accession
should it be: "uniprot_swissprot"?

[mgonzalezporta]

Hi Jose,

Thanks a lot for your constructive comment. I've now updated ensembl1.xml and ensembl2.xml with the new keys.

[josegarciamanteiga]

Hi Mar,
My suggestions were right but not for al ensembl versions. I have realized that depending on the annotation version, the attributes are still your original ones (for instance hsa.72). This is an annoying issue always with biomaRt when they update/change some fields in new versions. Unfortunately all packages using them have to be maintained to support it.
I would add also that when you run get_data.sh and something goes wrong, you do not have any error message. It could come handy to have a check of the files (ensembl1.txt and ensembl2.txt) not to be empty and also the protein sequences retrieval.
Thanks!
Jose