I regularly use biomaRt, the R package, to query archived versions of Ensembl. I had been querying Ensembl 65 for over a year with no issues, and I've tried Ensembl 72 and 74 and they work fine, too.
However, for my current project, I want to use Ensembl 73 (the rest of the project uses Gencode v18), and when I obtain this mart, I cannot identify any datasets in it (using the same commands that work for the other archives).
Could someone please advise me on what I might be doing wrong or if the archived version of Ensembl 73 is known to have problems with biomaRt? Does it work just fine for others? Some code and version information below:
R version, etc: R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit)
Here is some sample code/output: Ensembl 65 querying:
> library(biomaRt) ## from biomaRt_2.18.0.tgz > listMarts(host="dec2011.archive.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 65 2 ENSEMBL_MART_SNP Ensembl Variation 65 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 65 4 ENSEMBL_MART_VEGA Vega 45 5 REACTOME REACTOME (CSHL US) 6 pride PRIDE (EBI UK) > mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",host="dec2011.archive.ensembl.org")#,dataset="hsapiens_gene_ensembl") > listDatasets(mart) dataset description 1 oanatinus_gene_ensembl Ornithorhynchus anatinus genes (OANA5) 2 tguttata_gene_ensembl Taeniopygia guttata genes (taeGut3.2.4) 3 cporcellus_gene_ensembl Cavia porcellus genes (cavPor3) 4 gaculeatus_gene_ensembl Gasterosteus aculeatus genes (BROADS1) 5 lafricana_gene_ensembl Loxodonta africana genes (loxAfr3) 6 mlucifugus_gene_ensembl Myotis lucifugus genes (myoLuc2) 7 hsapiens_gene_ensembl Homo sapiens genes (GRCh37.p5) ## etc. - it loads just fine
Ensembl 73 querying:
> library(biomaRt) > listMarts(host="sep2013.archive.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 73 2 ENSEMBL_MART_SNP Ensembl Variation 73 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 73 4 ENSEMBL_MART_VEGA Vega 53 5 pride PRIDE (EBI UK) > mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",host="sep2013.archive.ensembl.org") > listDatasets(mart)  dataset description version <0 rows> (or 0-length row.names)
Note that I get an empty query with the "sep2013.archive.ensembl.org" while other archives appear to work fine.
Thank you in advance for your help!