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[biomart-users] Access request to hsapiens_gene_ensembl GRCh37 fails

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[biomart-users] Access request to hsapiens_gene_ensembl GRCh37 fails

'Bernard Thienpont' via biomart-users
Hi everyone,

Access request to GRCh37 version of ENSEMBL with BioMart fails as follows: 

BIOMARVERSION="feb2014.archive.ensembl.org"
ensembl
=biomaRt::useMart("ENSEMBL_MART_ENSEMBL",host=BIOMARVERSION)
mart
= biomaRt::useDataset("hsapiens_gene_ensembl",mart=ensembl)
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

Above code used to work just fine up until about a week ago. Also, access to any other archive published after the Feb. 2014 version above, works now as well. Unfortunately, later versions already contain the GRCh38 version. 
Looks like the link to GRCh37 BioMart does not work any more.
Will need to update my application to GRCh38 anyways, but until then I would be grateful for any suggestions on how to fix above issue.

Thanks,

Noemi

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Re: [biomart-users] Access request to hsapiens_gene_ensembl GRCh37 fails

Thomas Maurel
Dear Noemi,

I’ve tried your code and it’s working fine for me. Maybe it was a glitch or our website was temporarily down.
We also maintain a GRCh37 archive on the following website: http://grch37.ensembl.org/index.html. The gene set is the same as the one from the February 14 archive but we have updated the Variation and Regulation data.
You can access this website by running:

> BIOMARVERSION="grch37.ensembl.org"
> ensembl=biomaRt::useMart("ENSEMBL_MART_ENSEMBL",host=BIOMARVERSION)
> mart = biomaRt::useDataset(“hsapiens_gene_ensembl",mart=ensembl)

Hope this helps,
Kind Regards,
Thomas
On 20 Mar 2017, at 20:09, 'Noemi' via biomart-users <[hidden email]> wrote:

Hi everyone,

Access request to GRCh37 version of ENSEMBL with BioMart fails as follows: 

BIOMARVERSION="feb2014.archive.ensembl.org"
ensembl
=biomaRt::useMart("ENSEMBL_MART_ENSEMBL",host=BIOMARVERSION)
mart
= biomaRt::useDataset("hsapiens_gene_ensembl",mart=ensembl)
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

Above code used to work just fine up until about a week ago. Also, access to any other archive published after the Feb. 2014 version above, works now as well. Unfortunately, later versions already contain the GRCh38 version. 
Looks like the link to GRCh37 BioMart does not work any more.
Will need to update my application to GRCh38 anyways, but until then I would be grateful for any suggestions on how to fix above issue.

Thanks,

Noemi

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Access request to hsapiens_gene_ensembl GRCh37 fails

'Bernard Thienpont' via biomart-users
Dear Thomas,

Access to the Feb. 2014 version still doesn't work for me, but access to the alternative: http://grch37.ensembl.org/index.html, does. So this solves my problem.

Thank you!

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