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

Martin, Tiphaine tiphaine.martin at kcl.ac.uk
Tue Dec 19 16:16:25 CET 2017


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.

 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



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

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