One of our pride points for being able to pool, standardize, and share gene and variant annotation data as a service, is that our service is fast! The reason that MyGene.info and MyVariant.info are made with speed in mind is because we want them to be useful to bioinformaticians and tool/resource developers alike! How can we tell if we’ve successfully provided a useful service?
One measure we LOVE, is when a user builds something useful or amazing with our service--and Colin has done just that! Without further ado, we’d like to introduce Colin Diesh and the jbrowse plugin he’s built.
In one tweet or less, introduce us to your tool:
MyVariantViewer is a jbrowse plugin that visualizes #bioinformatics data from the mygene.info and myvariant.info APIs!
If I recall correctly, you started working on this plugin during a Hackathon. What inspired you to continue working on it, even keeping it up-to-date with the latest versions of MyGene/MyVariant?
Indeed, we started the idea at Apollo Hackathon 2016. The hackathon was really great, and I really liked the Scripps Institute La Jolla campus. There were definitely some very productive integrations between Apollo, jbrowse, and the Su Lab projects (MyGene/MyVariant and WikiGenomes) throughout the meeting!
As far as the motivation for continuing work, I really liked using MyGene/MyVariant as a data source, and I added additional features to view different data sources (ClinVar, dbSNP) as different genome browser tracks, added the ability to query both hg38 and hg19, and even loaded data from other species that are in MyGene like zebrafish!
In building it as a jbrowse plugin, you enable users to consume data from MyGene/MyVariant in a visual and intuitive fashion. Did you start (or continue working on) this with a target audience in mind? If so, who is your target audience?
I knew that the MyGene/MyVariant APIs were good for accessing programmatically, but making everything available in the genome browser means that even non-technical users would be able to use it.
I imagine health and human disease researchers can benefit from the plugin, for example, you can view ClinVar data (clinical variant associations) and Grasp data (genotype-phenotype links) that might be around a region of interest in the genome browser.
Another audience that can benefit would be users who are starting their own jbrowse instances, and they could use the plugin tracks along with their own data. This way, they get a ton of annotation data automatically that would be very hard to gather and load yourself!
The code for this plugin is available openly on github along with an excellent demo. Any idea on how many people have viewed your demo?
It appears that about 6350 page views were recorded, but 2000 or more page views were probably from me!
Do you have any improvements planned for your plugin, or will you leave future features up to the open source community on github?
I think there are lots of additional ways to enhance the plugin further, for example, adding color for severity of variants, improving ability to do searches within the genome browser, etc. I may leave it up to the community to contribute and make suggestions!
Link to the github repository for the jbrowse plugin: MyVariantViewer
Demo--see this nifty thing in action!
Follow Colin on github or twitter to see the other great tools he’s building or check out his most recent work and publications.