[BioC] biomaRt and ensembl tables

Tue Apr 25 10:30:55 CEST 2006

Thank you for your help. I am now using the 1.5.17 biomaRt package to 
use the webservice mode but using the webservice mode i still have 
problems with the getHomolog fonction :
/> getHomolog(id="NM_000015", from.type="refseq", to.type="refseq", 
from.mart=martHs, to.mart=martMm)
                                               V1
1       ERROR::Attribute gene_stable_id NOT FOUND
2 ERROR::Attribute transcript_stable_id NOT FOUND

/and also with the "hsapiens_gene_ensembl_structure.exon_stable_id_v" 
attribute I get an error whereas it works with others attributes :
/(getBM(attributes="hsapiens_gene_ensembl_structure.exon_stable_id_v", 
filters="refseq_dna", values="NM_000015", mart=martHs))/
/<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
2                                                                      
<HTML><HEAD>
3                                          <TITLE>500 Internal Server 
Error</TITLE>
4                                                                     
</HEAD><BODY>
5                                                    <H1>Internal Server 
Error</H1>
6                                       The server encountered an 
internal error or
7                                       misconfiguration and was unable 
to complete
8                                                                  your 
request.<P>
9                                          Please contact the server 
administrator,
10  webmaster&amp;#064;mydomain.org and inform them of the time the 
error occurred,
11                                   and anything you might have done 
that may have
12                                                             caused 
the error.<P>
13                               More information about this error may 
be available
14                                                      in the server 
error log.<P>
15                                                                   
</BODY></HTML>/

Is it coming from the ensembl databases ?
regards,

Tabaré Mourot

Wolfgang Huber a écrit :
> Dear Tabare,
>
> we recommend to use the biomaRt package in the webservice mode. The 
> direct access to the Ensembl database tables via MySQL relies one some 
> hard coded assumptions which may not apply to the particular table you 
> are looking at, also there has recently been a new Ensembl release, 
> which might complicate things.
>
> For this reason please use the webservice access to biomarts, which is 
> not prone to these problems.
>
> Best wishes
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
> -------------------------------------
>
>
> TM wrote:
>> Hi
>> I am having some trouble in using the biomart package.
>> I get this error message :
>> /Error in mysqlExecStatement(conn, statement, ...) :    RS-DBI 
>> driver: (could not run statement: Table 
>> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't exist)/
>> when executing  this command 
>> *getBM(attributes=listAttributes(martMm)[202], 
>> filters=listFilters(martMm)[15], values=listT , mart=martMm)
>> with 
>> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.exon_stable_id_v" 
>>
>> and **listFilters(martMm)[15] = *
>> where martMm has been created this way :* martMm <- useMart(biomart = 
>> "ensembl", dataset="mmusculus_gene_ensembl", 
>> host="ensembldb.ensembl.org", mysql=TRUE)
>>
>> *Can someone help me please
>> thank you.
>>
>

-- 
MOUROT Tabaré
Stagiaire Master Pro BioInfo
Plateforme transcriptome
Institut de Génomique Fonctionnelle
141, rue de la Cardonille
34094 Montpellier Cedex 5

Tel : +33 (0)4 67 14 29 64
E-mail : tabare.mourot at igf.cnrs.fr

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