[BioC] biomaRt and ensembl tables
sdurinck at ebi.ac.uk
sdurinck at ebi.ac.uk
Fri Apr 28 10:36:23 CEST 2006
Dear Tabare,
biomaRt tries to contain as minimal as possible hard coded information on
the BioMart databases and as such to be robust to new BioMart database
releases. The getBM function contains no hard-coded information on the
databases and should always work. The 'simpler' biomaRt functions such as
getGene and getHomolog do contain hard-coded information on the attributes
to query and as such are prone to database changes.
The new release of Ensembl (which this time contained quite some changes)
co-incided with a new release of Bioconductor. I've had to change the
biomaRt code so it could work with the old and new Ensembl version.
The biomaRt version (1.6.0) that is included in Bioconductor release 1.8
can deal with both Ensembl releases and your getHomolog query works:
> martHs = useMart("ensembl",dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> martMm = useMart("ensembl",dataset="mmusculus_gene_ensembl")
Checking attributes and filters ... ok
> getHomolog(id="NM_000015", from.type="refseq", to.type="refseq",
+ from.mart=martHs, to.mart=martMm)
V1 V2 V3
1 ENSMUSG00000051147 ENSMUST00000070766
2 ENSMUSG00000051147 ENSMUST00000093470 NM_010874
The second error you give is a bug.
The attribute "hsapiens_gene_ensembl_structure.exon_stable_id_v" should
not be present in the output of listAttributes as it involves multiple
BioMart datasets to be combined to make the query. Currently only the
getHomolog function can combine two datasets (i.e. two species).
Best,
Steffen
> 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&#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
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> Tel : +33 (0)4 67 14 29 64
> E-mail : tabare.mourot at igf.cnrs.fr
>
>
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