[BioMart Users] Problem with HGNC attributes

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[BioMart Users] Problem with HGNC attributes

Kristian Gray
Hi,

A user has notified us of a problem on the biomart central site. The user has pointed out that for the HGNC dataset,
it is no longer possible to select the "Approved Symbol" attribute as seen in the url below. 

http://central.biomart.org/martwizard/#!/Gene_annotation?mart=Hugo+Gene+Nomenclature+%28HGNC%29+%28EBI%2C+UK%29&step=3

On our own biomart server (http://www.genenames.org/biomart/martview) has the "Approved Symbol" set as
default as this is arguably the most important attribute. If this could be correct it would be very much appreciated.

Many thanks,

Kristian Gray
Scientific Programmer
HUGO Gene Nomenclature Committee (HGNC)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD, UK
fax: +44 (0)1223 494468
email: [hidden email]
http://www.genenames.org







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Re: [BioMart Users] Problem with HGNC attributes

Arek Kasprzyk
Hi Krisitian,
we are happy to fix it if this is available in the latest Ensembl release. Rhoda, could you confirm?


a


On 9 May 2013 16:44, Kristian Gray <[hidden email]> wrote:
Hi,

A user has notified us of a problem on the biomart central site. The user has pointed out that for the HGNC dataset,
it is no longer possible to select the "Approved Symbol" attribute as seen in the url below. 

http://central.biomart.org/martwizard/#!/Gene_annotation?mart=Hugo+Gene+Nomenclature+%28HGNC%29+%28EBI%2C+UK%29&step=3

On our own biomart server (http://www.genenames.org/biomart/martview) has the "Approved Symbol" set as
default as this is arguably the most important attribute. If this could be correct it would be very much appreciated.

Many thanks,

Kristian Gray
Scientific Programmer
HUGO Gene Nomenclature Committee (HGNC)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD, UK
fax: <a href="tel:%2B44%20%280%291223%20494468" value="+441223494468" target="_blank">+44 (0)1223 494468
email: [hidden email]
http://www.genenames.org








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Re: [BioMart Users] Problem with HGNC attributes

Rhoda Kinsella
Hi Arek
HGNC is a separate project and they produce their own BioMart databases (see link that Kris added below). Therefore this issue is not related to the Ensembl mart databases or Ensembl release.
Hope that helps
Rhoda

On 9 May 2013, at 20:36, Arek Kasprzyk <[hidden email]> wrote:

Hi Krisitian,
we are happy to fix it if this is available in the latest Ensembl release. Rhoda, could you confirm?


a


On 9 May 2013 16:44, Kristian Gray <[hidden email]> wrote:
Hi,

A user has notified us of a problem on the biomart central site. The user has pointed out that for the HGNC dataset,
it is no longer possible to select the "Approved Symbol" attribute as seen in the url below. 

http://central.biomart.org/martwizard/#!/Gene_annotation?mart=Hugo+Gene+Nomenclature+%28HGNC%29+%28EBI%2C+UK%29&step=3

On our own biomart server (http://www.genenames.org/biomart/martview) has the "Approved Symbol" set as
default as this is arguably the most important attribute. If this could be correct it would be very much appreciated.

Many thanks,

Kristian Gray
Scientific Programmer
HUGO Gene Nomenclature Committee (HGNC)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD, UK
fax: <a href="tel:%2B44%20%280%291223%20494468" value="+441223494468" target="_blank">+44 (0)1223 494468
email: [hidden email]
http://www.genenames.org








Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




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