[BioC] are older versions of Ensembl accessible with biomaRt?

[Steffen Durinck]

Dear Lynn,

Yes it has but it is only available using biomaRt in MySQL mode.
Here's how to get access:

1) Check which archives are available

library(biomaRt)
listMarts(archive=TRUE, mysql=TRUE)

this will give the following Ensembl archives

23              ensembl_mart_29
24              ensembl_mart_30
25              ensembl_mart_31
26              ensembl_mart_32
27              ensembl_mart_33
28              ensembl_mart_34
29              ensembl_mart_35
30              ensembl_mart_36
31              ensembl_mart_37
32              ensembl_mart_38
33              ensembl_mart_39
34              ensembl_mart_40
35              ensembl_mart_41
36              ensembl_mart_42
37              ensembl_mart_43
38              ensembl_mart_44
39              ensembl_mart_45
40              ensembl_mart_46
41              ensembl_mart_47


2)  Connect to the archive (e.g. let's connect to Ensembl 44):

ensembl = useMart("ensembl_mart_44", dataset="hsapiens_gene_ensembl",archive=TRUE, mysql=TRUE)


3) Perform your biomaRt queries as you usually do.  I would recommend using the getBM function as this doesn't contain hard-coded attribute and filter names.  getGene, getGO etc might fail on older Ensembl versions as attributes might be renamed in the meantime.

Cheers,
Steffen

----- Original Message -----
From: Lynn Amon <lamon at fhcrc.org>
Date: Tuesday, October 23, 2007 3:27 pm
Subject: [BioC] are older versions of Ensembl accessible with biomaRt?
To: bioconductor at stat.math.ethz.ch

> Hello Steffen and others,
> Has the capability of searching older versions of Ensembl been 
> added to
> the R version of biomaRt yet?
> Thanks,
> Lynn Amon
> 
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