Mirroring annotations with software release

[Viraj Deshpande]

Hello,

I am planning to release an open source software which analyses human genome sequence variants. My software uses the human genome assembly and annotations like genes, exons, Duke35 mappability scores and segmental duplications that I downloaded from the UCSC genome brower or linked websites. I am wondering if I can included the data that I use as part of my software. Do I need to included any licenses or acknowledgements while hosting of the data and in what form?

Thank you,

Viraj

[Christopher Lee]

Hi Viraj,

Thank you for your question about including UCSC data in your software. Please see the following page for more information about data use and acknowledgements:
http://genome.ucsc.edu/license/

From that page:
"The data displayed by the browser is freely available for both public and commercial use with a few exceptions. The README.txt file in the download directory of each assembly shows the use restrictions pertaining to that data set."

For instance, if you wanted to include the file:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgEncodeDukeMapabilityRegionsExcludable.txt.gz

then you would check http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/README.txt for information about data use and restrictions. In this case, the README states:
All the files and tables in this directory are freely usable for any purpose.

I hope this helps!

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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