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Nominating openSNP for the ASAP Award

Posted by Russell on June 05, 2013 at 1:28 p.m.
So, there is this awesome new thing called the Accelerating Science Award Program (ASAP), which recognizes individuals who have used, applied, or remixed Open Access scientific research to create something new and cool. I can't think of a better example of remixing Open Access science than openSNP.

Here is my nomination.

Information About the Innovative Use

Describe the innovative use of scientific research published through Open Access you would like to nominate.

openSNP uses Open Access scientific research in several ways :

  1. It is itself and Open Access, user contributed dataset.
  2. It provides information about particular genetic variants through an innovative mashup of user contributed data with several other resources :
    1. SNPedia, a user created Open Access dataset that functions as a namespace for individual genetic variants (SNPs, or single-nucleotide polymorphisms) and a clearinghouse for references to the scientific literature relating to each SNP. Example and publication.
    2. PLOS, a major Open Access scientific publisher, is automatically scanned for references to each SNP. References and readership statistics are aggregated on for each SNP. Example.
    3. Mendeley, a social bookmarking and sharing site for scientific literature, is automatically scanned for papers containing references to each SNP. References and readership statistics are aggregated for each SNP. Example.
    4. The Personal Genome Project, an Open Access effort to improve genome annotation, is automatically scanned for data relating to each SNP. References are aggregated for each SNP.
    5. Genome.gov, the NIH-sponsored site for the National Human Genome Research Institute, is automatically scanned for data relating to each SNP. References, associated traits, and statistical confidence intervals are aggregated for each SNP. Example.
  3. BioDAS, a Open Access, distributed annotation protocol, is used to generate contextual, annotated visualizations of each SNP from DAS servers running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt.

Describe why you believe this work should be recognized.

openSNP serves more than one community. It is a community where the public can come to learn about and discuss their own health issues. Within that community, it allows people who are brave enough to step forward and share their genetic and health data for the benefit and education of the rest of the community. The community has been designed to encourage sharing of data with other users, which includes the scientific community. These activities have created a dataset that allows researchers to conduct genome wide association surveys (GWASs) inexpensively and largely free of the complexities usually associated with research involving human subjects.

There are other efforts that aim to accomplish similar objectives, but the creators of openSNP have taken what I feel is the most intellectually honest position. They accomplish this in two ways. First, they offer no pretense of privacy to people who elect to share their personal genomic data, and instead provide a clear warning of the real and potential hazards. Second, for those who choose to share their data despite this warning, they maximize the public good it can achieve by making it truly accessible. Data contributed to openSNP is indexed, annotated, linked, referenced, sorted and shared in as many ways as possible, making the contributions of participants as meaningful as possible.

Last of all, the creators of openSNP and its many contributors have elected to share everything they have produced under the least restrictive license possible. The entirety of this effort has been donated to the Public Domain. I strongly believe that this commitment to the common good deserves to be recognized.

For this reason, I think it is important not only to recognize Bastian, Helge, and Helge, but also the 1019 other people who have contributed personal data to openSNP. Bastian has also contributed his own genotype.

P.S. -- Others involved in openSNP may include Fabian Zimmer and Julia Reda.

Information About the Original Research

Please provide links or citations/references/DOIs to the articles, manuscripts, or datasets pertaining to the original scientific research published through Open Access on which the nomination for the innovative use is based, so that we may locate these online.

There are probably hundreds of thousands of publications referenced, indexed or linked from openSNP, far too many to enumerate here. Please see the links I have provided as various examples under "Information About the Innovative Use."

Bastian, Helge and Helge, as well as Fabian Zimmer and Julia Reda, are preparing a manuscript for submission describing openSNP. It is another measure of their commitment to Open Science that the progress with this manuscript can be viewed (and forked, and contributed to) among their public GitHub repositories.

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