Mastermind data availability in UCSC Genome Browser

[Mark Kiel]

Hello-

I wonder if I could be connected to someone at UCSC to discuss the possibility of making some of our data available in UCSC data tracks.

In brief, we have a very large collection of genomic variants extracted from the medical literature that are currently available to users in our free software - Mastermind. We would like to make this data more readily available to researchers and think a data integration with UCSC browser functionality would be a great way to do that.

Looking forward to chatting about a possible way forward!

Mark

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Mark J. Kiel MD PhD

CSO || VP of Product Strategy

GENOMENON Inc.

C: (734) 223-2519 || O: (734) 794-3075 

www.genomenon.com

[Brian Lee]

Dear Mark,

Thank you for contacting the UCSC Genome Browser and your question about adding data.

We have a mechanism available where external groups can build and package data to display on the UCSC Genome Browser called "Public Hubs."

Here is a link to our Public Hubs page to help show how people can find such data, in this case around variants from other groups: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hubSearchTerms=variants

Track Hubs require external groups both to format their data to display in the browser and to host the data remotely. The data is often formatted into bigBeds or one of the big* formats (http://genome.ucsc.edu/FAQ/FAQformat.html), where a theme is that the first four fields define chromosome, start coordinate, end coordinate, and name, unless it is in another format such as VCF.

To have a finished Track Hub added as a Public Hub, we also require it meet certain documentation requirements (track descriptions and only a minimal number of tracks displayed). Here is a link to the Public Hub''s Guidelines page: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines

Our mailing list archives may also provide some assistance in troubleshooting issues to the bioinformatician who may be transforming your data into a track hub if that is an approach your group decides to pursue: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/track$20hubs%7Csort:date

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public 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.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

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