[BioC] ensembl biomart

[steffen at stat.Berkeley.EDU]

We'll have to wait till the Ensembl version is updated to version 52 on
the central service at biomart.org.

I'll investigate why we can't use the alternate host I suggested earlier.

Cheers,
Steffen


> Hi Steffen,
> listMarts(host="www.ensembl.org/biomart/martservice") works, but not
> useMart, that returns this error message:
>>Error in file(file, "r") : cannot open the connection
>>In addition: Warning message:
>>In file(file, "r") : cannot open: HTTP status was '404 Not Found'
> Best
> Javi
>
> On Wed, Dec 17, 2008 at 6:11 AM, <steffen at stat.berkeley.edu> wrote:
>
>> That's indeed the default host as it is the central registry which keeps
>> track of the available BioMarts and from there a dispatch happens to
>> other
>> hosts depending on the BioMart you use.
>>
>> You probably wanted to access the 52 version of Ensembl which is not yet
>> available from biomart.org.  52 was released last week and it takes a
>> few
>> days to get that update into the central registry.
>>
>> Try this:
>>
>> > listMarts(host="www.ensembl.org/biomart/martservice")
>>               biomart      version
>> 1 ENSEMBL_MART_ENSEMBL   Ensembl 52
>> 2     ENSEMBL_MART_SNP Variation 52
>>
>> > mart = useMart("ENSEMBL_MART_ENSEMBL",
>> dataset="hsapiens_gene_ensembl",
>> host="www.ensembl.org/biomart/martservice")
>>
>>
>> Cheers,
>> Steffen
>>
>> > 15/12/2008 17:09 Javier Díez scripsit
>> >> Hi,
>> >> Do you know how could I query the *martdb.ensembl.org* server,
>> instead
>> >> of
>> >> the default server biomart.org ( I think this is the default server,
>> >> isn't
>> >> it?).
>> >> Best
>> >> Javi
>> >>
>> >
>> > Have you tried typing
>> >
>> >  ? useMart
>> >
>> > and reading it?
>> >
>> >
>> > The default value for 'host' is
>> > "http://www.biomart.org/biomart/martservice"
>> >
>> > Best wishes
>> >  Wolfgang
>> >
>> > ------------------------------------------------------------------
>> > Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>> >
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>> >
>>
>>
>