Modern Software Experience

2011-12-07

openSNP Logo

open genetic data

open data

OpenSNP is a non-profit, open source and open data platform for sharing genetic and phenotypic information. The goal is simply to build an open database of freely accessible genetic data.

The openSNP project is open source. The openSNP project is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0) license. The openSNP source code is available on github as the SNPr project.

The openSNP project may be open source, but openSNP really is about open data. The openSNP platform invites you to help build the openSNP database by uploading the data you received from your genetic test.
You should read the openSNP disclaimer before doing so. The openSNP database is truly open. Everything but your email address is available to everyone under a Creative Commons Zero (CC0) license: No Rights Reserved. You may delete your data at any time, but others may have downloaded it already, and are free to republish it somewhere else.
The openSNP teams believes the disclaimer to be so important that they repeat it on the sign-up page.

openSNP Home Page

FAQ

The website has a FAQ, but it currently only discusses uploading and downloading data. It does not answer basic questions such as where the openSNP name comes from. Briefly, SNP (pronounced snip) is an abbreviation of Single-Nucleotide Polymorphism, a single nucleotide (commonly represented by the letters A, T, C or G) difference between two DNA fragments. The SNPedia provides a detailed explanation. The platform is called openSNP because it maintains a open database of SNP-based genetic test results.

openSNP SNPs

An important question the upload FAQ does answer is where to get your data. It provides direct links to the download pages of the Direct-to-Consumer (DtC) genetic testing companies. You will need the login credentials for the company you used to access their download page.

students

OpenSNP was started by three German students; Bastian Greshake, Fabian Zimmer and Philipp Bayer. They finished their undergraduate studies of Life Sciences, and now Bastian is studying Ecology & Evolution, Fabian is studying Biology and Philipp is studying Computer Science. They got help building the openSNP site from web developer Helge Rausch. None of them is working full-time on the site.

Bastian came up with the idea for SNP after having his DNA genotyped by 23andMe. Playing around with the data, he found it too difficult to find interesting data, and decided that things would be easier if he access to more DNA test results. That's how he came up with the idea for openSNP.

supported file formats

The openSNP platform started with 23andMe data, but already supports the formats used by deCODEme and FamilyTreeDNA as well. A quick overview of currently supported file types can be found on the openSNP file types pages.

openSNP phenotypes

phenotypes

The creators of openSNP encourage uploaders to provide phenotype data. The current list of phenotypes varies from obvious characteristics such as eye colour, hair colour and height, through blood type, handedness, and colour blindness to less obvious phenotypes such as Interest in Spirituality and Mysticism and Ability to find a bug in openSNP. The hope is that researchers will find significant relationships between the genetic data and the phenotype.

openSNP user 23: Philipp Bayer

Philipp Bayer's page shows that he is a right-handed lactose-intolerant non-smoker with blue eyes and blonde wavy hair.

annotation

The SNP data uploaded to openSNP is annotated using information from SNPedia, and links to publications found through PLoS and Mendeley, a crowd-sourced repository of scientific publications.

ysearch

Readers may be familiar with ysearch, a free service run by FamilyTreeDNA. The ysearch data is not open and does not include any phenotype information, and the ysearch service is focussed on finding genealogical relationships.

API

The openSNP server does not offer an API, at least not yet. Researchers interested in the data can select a phenotype to mass-download all SNP-data for that phenotype, and then subscribe to an RSS feed for data matching that phenotype.

updates

2012-01-02: openSNP presentations

The openSNP presentations given at the 28th Chaos Communication Congress in Berlin are now available on YouTube and as MP4 downloads.

links

openSNP

supported genetic testing services