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The Synapse Commons Repository is a Synapse project that provides access to raw data and corresponding phenotypic information for tens of thousands of distinct genomic data sets. All analyses of these data exist outside this project.  Note that any data set available through this project is available with no restrictions on use. The figure to the right shows how the Synapse Commons Repository lets analytical projects like the metaGenomics project make use of publicly available data. In reality, contributed data can be obtained through public repositories like NCBI GEO, ArrayExpress from EBI, and TCGA, as well as any source that can be accessed through the web, including a URL made available through an individual lab, a core facility, or a cloud based storage site like an Amazon S3 bucket. Consult the figure for more information.

Existing Data

Currently we have crawlers that gather data from a variety of publicly available data repositories, including:

• NCBI GEO
• Array Express
• TCGA
  
• TG Gate

Contributing Data

Do you know of any data that isn't yet available in the SCR? If so, then we hope you'll take the time to contact us or follow the links below to learn how you can use our software to contribute data directly.

• from R
• from the Web

Contributing metaData

A massive limitation of publicly available genomic data is the lack of standards around the vocabulary used to define experimental and biological concepts. We have begun a process to standardize these data, which we refer to as metadata. Please read here for more information and do no hesitate to contact us if you are interested in contributing to this effort.