[BioC] ensembl biomart

[Rhoda Kinsella]

Hi Javier and Steffen,
Ensembl has been updated to version 52 on the central service at  
biomart.org. In the mean time, I will
look into why the martservice is not working at ensembl.org/biomart.
Regards,
Rhoda


On 19 Dec 2008, at 03:38, steffen at stat.Berkeley.EDU wrote:

> 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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>>>>
>>>
>>>
>>
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.