[Bioc-devel] Update in BioMart/ENSEMBL alters coMET

[Markus List]

I've also had trouble accessing hsapiens_gene_ensembl yesterday without
updating the biomaRt package. I think ENSEMBL is making changes on the
server side. Does anyone know more about this?

Best,
Markus



On Tue, 19 Dec 2017 at 16:17 Martin, Tiphaine <tiphaine.martin at kcl.ac.uk>
wrote:

> Hi,
>
>
> Could you inform me which modification you did in biomaRt ? or in ENSEMBL ?
>
> Indeed, I have my R package (coMET) use biomaRt to access to data. From
> the last update in BiomaRt (12/14/2017), I have a new error message.
>
>
> Do you change the name of database associated with ENSEMBL ?
>
>
> This is my error message
>
> Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
>
> http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
>
>  When I look at the list of dataset, I have
>
> <MartURLLocation database="ensembl_mart_91" default="1"
> displayName="Ensembl Genes 91" host="grch37.ensembl.org"
> includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL"
> path="/biomart/martservice" port="80" serverVirtualSchema="default"
> visible="1" />
>
>
> however, previously, the database name was hsapiens_gene_ensembl.
>
> Does it mean that you are going to change the name of database for each
> new release ?
>
> How, I can have the name of databases from ENSEMBL stable between
> different releases of ENSEMBL
>
>
> Regards,
>
> Tiphaine
>
>
> ----------------------------
> Tiphaine Martin
> Research Associate | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics &
> Molecular Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> Bioinformatician | The University of Western Australia,
> Endocrinology & Diabetes,
> Sir Charles Gairdner Hospital.
> School of Medicine & Pharmacology,
> The University of Western Australia,
> Nedlands, Western Australia 6009.
>
> email : tiphaine.martin at kcl.ac.uk
> Fax: +44 (0) 207 188 6761 <+44%2020%207188%206761>
>
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