Answers.Body: <p>Most genomics data that is published should be available in <a href="https://www.ncbi.nlm.nih.gov/geo/summary/" rel="nofollow noreferrer">GEO</a> (or SRA). Usually in the paper they mention the accession number. However, not every study ends up in there, and sometime studies that are in GEO are not reproducible (poor description of the samples, or design). But if you look at the original papers, most of the times you'll find an accession number.</p>
  
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Answers.CreationDate: 2018-06-15T14:22:01.903Z
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Answers.UserDisplayName: benn
Answers.Body: <p>Yet another place I find useful is provided by <a href="https://repositive.io/" rel="nofollow noreferrer">Repositive</a>. 
  You can think of it as a meta-search engine which includes most of the databases already stated and links hits to relevant papers.</p>
  
  <p>With respect to your question about bipolar, <a href="https://discover.repositive.io/datasets/search?query=bipolar" rel="nofollow noreferrer">this search</a> could get you started.</p>
  
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Answers.CreationDate: 2018-06-22T11:12:16.337Z
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Answers.UserDisplayName: Sebastian Müller
Answers.Body: <p>Another places you could look for SNP data would be <a href="http://www.internationalgenome.org/" rel="nofollow noreferrer">1000 genomes</a>, <a href="http://exac.broadinstitute.org/" rel="nofollow noreferrer">the ExACT database</a> and the <a href="http://gnomad.broadinstitute.org/" rel="nofollow noreferrer">genomAD</a> database. Cancer specific data is available at the <a href="https://gdc.cancer.gov/" rel="nofollow noreferrer">GDC</a> and <a href="https://dcc.icgc.org/" rel="nofollow noreferrer">ICGC</a> data portal.</p>
  
  <p>Unfortunately a lot of what you'd like to work with is probably covered by restricted access due to privacy concerns. Lots of this data is stored in the <a href="https://www.ncbi.nlm.nih.gov/gap" rel="nofollow noreferrer">dbGap</a> database and the <a href="https://www.ebi.ac.uk/ega/home" rel="nofollow noreferrer">EGA</a>. If you are an academic or employed by a company with a legitimate interest in the data you can usually apply for access to the restricted data, and I've never known anyone to be turned down if you have a legitimate reaons to access the data and can demonstrate your computer systems meet the required security standards. </p>
  
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Answers.CreationDate: 2018-06-20T17:26:37.043Z
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Answers.UserDisplayName: Ian Sudbery
Body: <p>I'm a statistician, and am interested in applying the theory of algebraic Markov models to genomics. Here's one paper I'm interested in: <a href="https://www.nature.com/articles/ng.943" rel="nofollow noreferrer">Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4</a>. I'm also interested in other diseases (i.e. not just bipolar). </p>
  
  <p>Are there any genomics databases that I can access publicly? </p>
  
  <p>There are some links in <a href="http://www.humanconnectomeproject.org/data/hcp-project/" rel="nofollow noreferrer">Human Connectome Project</a>, but I'm not sure if these are genomics databases (or which papers have used their research).</p>
  
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Comments.CreationDate: 2018-06-15T14:41:10.400Z
Comments.Text: You're going to struggle to find public databases with genotype data for individuals because of concerns about de-identification. You can request access to the server where the data from that paper is stored [here](http://www.med.unc.edu/pgc/shared-methods/how-to). If it's possible to run your analyses on summary statistics, these can usually be [downloaded](http://www.med.unc.edu/pgc/results-and-downloads/downloads) without restrictions.
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-16T12:32:46.360Z
Comments.Text: Could you clarify what kind of data you need? "genomics databases" is a very broad term and most of what I would call genomics data is publicly available. It would be helpful if you could [edit] your question and explain exactly what sort of dataset you would want to work on.
Comments.UserDisplayName: terdon
Tags: <database><human-genome>
Title: Public access to genomics databases
ThreadText: # Public access to genomics databases
  
  (Asked by: username_0 on 2018-06-15)
  
  I'm a statistician, and am interested in applying the theory of algebraic Markov models to genomics. Here's one paper I'm interested in: [Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4](https://www.nature.com/articles/ng.943). I'm also interested in other diseases (i.e. not just bipolar).
  
  Are there any genomics databases that I can access publicly?
  
  There are some links in [Human Connectome Project](http://www.humanconnectomeproject.org/data/hcp-project/), but I'm not sure if these are genomics databases (or which papers have used their research).
  
  **Tags:** database, human-genome
  
  > **Comments:**
  > **username_1**: You're going to struggle to find public databases with genotype data for individuals because of concerns about de-identification. You can request access to the server where the data from that paper is stored [here](http://www.med.unc.edu/pgc/shared-methods/how-to). If it's possible to run your analyses on summary statistics, these can usually be [downloaded](http://www.med.unc.edu/pgc/results-and-downloads/downloads) without restrictions.  
  > **username_2**: Could you clarify what kind of data you need? "genomics databases" is a very broad term and most of what I would call genomics data is publicly available. It would be helpful if you could [edit] your question and explain exactly what sort of dataset you would want to work on.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2018-06-15. Score: 3
  
  Most genomics data that is published should be available in [GEO](https://www.ncbi.nlm.nih.gov/geo/summary/) (or SRA). Usually in the paper they mention the accession number. However, not every study ends up in there, and sometime studies that are in GEO are not reproducible (poor description of the samples, or design). But if you look at the original papers, most of the times you'll find an accession number.
  
  
  ---
  
  ### Answer by username_4 on 2018-06-22. Score: 0
  
  Yet another place I find useful is provided by [Repositive](https://repositive.io/).
  You can think of it as a meta-search engine which includes most of the databases already stated and links hits to relevant papers.
  
  With respect to your question about bipolar, [this search](https://discover.repositive.io/datasets/search?query=bipolar) could get you started.
  
  
  ---
  
  ### Answer by username_5 on 2018-06-20. Score: 0
  
  Another places you could look for SNP data would be [1000 genomes](http://www.internationalgenome.org/), [the ExACT database](http://exac.broadinstitute.org/) and the [genomAD](http://gnomad.broadinstitute.org/) database. Cancer specific data is available at the [GDC](https://gdc.cancer.gov/) and [ICGC](https://dcc.icgc.org/) data portal.
  
  Unfortunately a lot of what you'd like to work with is probably covered by restricted access due to privacy concerns. Lots of this data is stored in the [dbGap](https://www.ncbi.nlm.nih.gov/gap) database and the [EGA](https://www.ebi.ac.uk/ega/home). If you are an academic or employed by a company with a legitimate interest in the data you can usually apply for access to the restricted data, and I've never known anyone to be turned down if you have a legitimate reaons to access the data and can demonstrate your computer systems meet the required security standards.
  
  
  ---
  
  