This week’s video tip comes to us from Google–it’s about their participation in the “Global Alliance for Genomics and Health” coalition. Global Alliance is aimed at developing genomic data standards for interoperability, and they’ve been working on creating the framework (some background links below in the references will provide further details). It has over 170 members, and one of these members is Google. Although Google talked about this earlier this year when they joined this group, more recently pieces have begun to emerge about the directions and specific tools. Google’s efforts made the mainstream news recently in their announcement about working on a project to examine genomic data associated with autism.
Although this video doesn’t talk about a single specific tool like we usually cover, it provides more detail about this framework for building tools which is important to understand. And in this video I learned about a new browser developed under this project that I did have a quick look at, and I’ll add below.
They browser that they reference is called GAbrowse–I assume that means Global Alliance browse–but there’s not a lot of detail. Their “about” dialog box says this:
GABrowse is a sample application designed to demonstrate the capabilities of the GA4GH API v0.1.
Currently, you can view data from Google, NCBI and EBI.
- Use the button on the left to select a Readset or Callset.
- Once loaded, choose a chromosome and zoom or drag the main graph to explore Read data.
- Individual bases will appear once you zoom in far enough.
The code for this application is in GitHub and is a work in progress. Patches welcome!
I kicked the tires a bit, but it’s clearly not fully fleshed out at this point. When I tried to zoom up from the nucleotide level it went up a bit, but eventually you hit a point that says “This zoom level is coming soon!” So certainly there’s more to come, and a lot more functionality that would be necessary. But it’s early. And it’s just a demo. I have no idea if it’s intended to become a stand-alone public browser.
So if you are interested in issue of cross-compatibility of human genomic data (and as far as I can tell this is all human-centric, I’d like to see a wider conversation on this), it’s probably worth knowing what Google is offering here. You should also be aware of what the Global Alliance is working on. Below I’ve added some of the publications and media I’ve seen about their efforts.
Hat tip to Can Holyavkin on Google+ for the link to the video. https://plus.google.com/u/0/114690993717100405711/posts/gwNy5E7E6Vb?cfem=1
Global Alliance for Genomics and Health: http://genomicsandhealth.org/
Google genomics: https://developers.google.com/genomics/
(2013). Global Alliance to Create Standards For Sharing Genomic Data, American Journal of Medical Genetics Part A, 161 (9) xi-xi. DOI: http://dx.doi.org/10.1002/ajmg.a.36168
Callaway E. (2014). Global genomic data-sharing effort kicks off, Nature, DOI: http://dx.doi.org/10.1038/nature.2014.14826
White paper 2013: http://www.broadinstitute.org/files/news/pdfs/GAWhitePaperJune3.pdf
Framework for Responsible Sharing of Genomic and Health-Related Data – DRAFT # 7 http://genomicsandhealth.org/our-work/work-products/framework-responsible-sharing-genomic-and-health-related-data-draft-7
Terry S.F. (2014). The Global Alliance for Genomics , Genetic Testing and Molecular Biomarkers, 18 (6) 375-376. DOI: http://dx.doi.org/10.1089/gtmb.2014.1555 [available here from GA: http://genomicsandhealth.org/files/public/gtmb%252E2014%252E1555%5B2%5D.pdf]