[biomart-users] Incorrect link to the HGNC BioMart service on community page

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[biomart-users] Incorrect link to the HGNC BioMart service on community page

Kristian Gray-2
Hi,

Could someone please change the HGNC link to the HGNC BioMart server from http://www.genenames.org/biomart/martview to http://biomart.genenames.org/ on the http://www.biomart.org/community.html page.

Many thanks

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Re: [biomart-users] Incorrect link to the HGNC BioMart service on community page

Arek Kasprzyk

done!

sorry about the delay

a.

On 1 August 2016 at 17:17, Kristian Gray <[hidden email]> wrote:
Hi,

Could someone please change the HGNC link to the HGNC BioMart server from http://www.genenames.org/biomart/martview to http://biomart.genenames.org/ on the http://www.biomart.org/community.html page.

Many thanks

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Re: [biomart-users] Incorrect link to the HGNC BioMart service on community page

Julian Spagnuolo
The updated link doesn't appear to work with the biomaRt package.

> listMarts(host="http://biomart.genenames.org/")
returns:
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.
Error: XML content does not seem to be XML: 

do you have any advice?

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Re: [biomart-users] Incorrect link to the HGNC BioMart service on community page

Steffen Durinck-2
Hi Julian,

The genenames.org BioMart appears to be v0.9 and the biomaRt package currently only works with v0.7.
We're upgrading biomaRt to work with both versions but they are quite different and up until recently most BioMarts were running v0.7 .  Having some v0.9 BioMarts online, should help speedup upgrading the biomaRt code.

Cheers,
Steffen

On Thu, Oct 27, 2016 at 12:47 AM, Julian Spagnuolo <[hidden email]> wrote:
The updated link doesn't appear to work with the biomaRt package.

> listMarts(host="http://biomart.genenames.org/")
returns:
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.
Error: XML content does not seem to be XML: 

do you have any advice?

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Re: [biomart-users] Incorrect link to the HGNC BioMart service on community page

Julian Spagnuolo
Ok, thanks Steffen, shame about that, I was looking forward to using biomaRt - I wasn't able to during my PhD because the E.coli marts were deprecated, but now I am working in human functional genetics so it is a great tool to have in the box.

On 27 October 2016 at 20:27, Steffen Durinck <[hidden email]> wrote:
Hi Julian,

The genenames.org BioMart appears to be v0.9 and the biomaRt package currently only works with v0.7.
We're upgrading biomaRt to work with both versions but they are quite different and up until recently most BioMarts were running v0.7 .  Having some v0.9 BioMarts online, should help speedup upgrading the biomaRt code.

Cheers,
Steffen

On Thu, Oct 27, 2016 at 12:47 AM, Julian Spagnuolo <[hidden email]> wrote:
The updated link doesn't appear to work with the biomaRt package.

> listMarts(host="http://biomart.genenames.org/")
returns:
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.
Error: XML content does not seem to be XML: 

do you have any advice?

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