Where Can I Download The Public Version Of The The Human Gene Mutation Database (Hgmd)

Question

[star.bioinformatics]

Hi,

I would like to download "HGMD public version" . could you please let me know how i can do that?

Thank you

[Neilfws]

Come on, this information can be found via a simple Web search. You register here using an academic email address.

[PGreen]

Hi, I'm registered and I can access to the public version of HGMD but how can I download it? Thanks

Answer 1

[stensonpd]

HGMD data are not available for bulk download from the HGMD Public website. hg19 coordinates for HGMD variants are available as part of Ensembl, but are limited to coordinates only and are 3 years out of date. The full dataset is available without restriction under license from Qiagen/Biobase.

Answer 2

[Istvan Albert]

Just adding the comment by Neilfws as an answer, as the page says:

Please note that the public version of our database is free only for registered users from academic institutions/non-profit organisations. Commercial users are required to purchase a license from BIOBASE, our commercial partner. The HGMD Professional license is available to both commercial and academic/non-profit users wishing to access the most up-to-date version of the database. HGMD mutation data are made available via the public site 3 years after initial inclusion.

The URL is: http://www.hgmd.cf.ac.uk/docs/register.html

Answer 3

[ajingnk]

I still have the same problem. I am an academic user (PhD student). But, after login, I still cannot find any link for download. I have no problem to search or browse, but I need the whole data set.

[Ram]

You will have to check with BioBase - they offer a different license to access the data through MySQL, and you'll need that for bulk download. If you try bots, they block your IP.

[Shicheng Guo]

So anyway to download the whole dataset in VCF format?

[Ram]

Did you try emailing them? I'm not sure they even have it all in VCF format.

[Shicheng Guo]

Okay. any format will be fine, is there any way to get the whole list?

[Michael]

As has been stated before, you should contact the owner of the resource. Or get a quote from Quiagen for the commercial version.