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Share your genotype: openSNP wins Mendeley/PLoS API Binary Battle

2 Dec, 11 | by BMJ

The winner of the Mendeley/PLoS API Binary Battle has been announced, after two months of shortlisting, public voting and expert panel deliberation (by the likes of Werner Vogels, Juan Enriquez, Tim O’Reilly, James Powell, and John Wilbanks).

The overall grand prize of the 2011 Mendeley-PLoS Binary Battle, receiving $10,001 and $1,000 of Amazon Web Service credits, went to openSNP.

openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.

openSNP is a community-driven platform for publicly sharing genetic information, designed to enable crowdsourcing of associations between genetic traits and the physical manifestation of those traits, such as eye colour or propensity for some diseases. With openSNP, you can share your personal genome from 23andMe (personal genomics and biotechnology company helping customers understand their own genetic information) or deCODEme (biopharmaceutical company) to find the latest relevant research and let scientists discover new genetic associations.

There are 4 basic areas of interest for genotyping users…

  1. Upload your genotyping profile
    Upload the genotyping raw-data you get from 23andMe or deCODEme to the database of openSNP to make it publicly available.
  2. Share Phenotypes and traits
    Share phenotypes, characteristics and traits with other openSNP users and find others with similar characteristics. This is your chance to help scientists discover new genetic associations.
  3. Share stories on variations and phenotypes
    Share stories on your own genetic variations and phenotypes with others and discover what others have to say .
  4. Find literature on genetic variation
    openSNP pulls in the latest open access journal articles on genetic variations from the PLoS. Popular articles are also indexed via Mendeley. Summaries are provided by SNPedia.

And for the scientists…

  1. Search for phenotypes
    Many diseases and traits are suspected of having genetical components. Now you can easily find people specific variations  via openSNP. If the variation you are looking for hasn’t been entered yet, you can add it yourself.
  2. Easily download datasets
    The mass download-function of openSNP allows you to easily download the full genotyping raw-data in the file formats that are provided by 23andMe and deCODEme. As the files can be grouped by their variations for specific phenotypes, it is easy to get datasets that are already usable for association studies.
  3. Get notified about new data
    OpenSNP offers an RSS feed for each phenotype. This means you can be notified of  new datasets when made available for the phenotypes of your interest, without having to check for new entries by hand. For all data junkies that need more data: There is also a feed that carries all new datasets.

Werner Vogels, Amazon CTO and one of the judges commented that, “OpenSNP is cool. I have uploaded my genotype, and it is interesting to see it at work.”

Read an interview with the openSNP team at the Mendeley blog.

The runner up prize went to Paper Critic, which allows post-publication peer review in an open environment by rating papers, writing critical reviews or reading those from others. A special extra prize of $1000 awarded to rOpenSci for the best Mendeley/PLoS mashup.

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