Integration of CRAVAT and CIViC

malachig commented 6 years ago

There is interest in integration of CRAVAT and CIViC (possibly bi-directional?). In what specific ways? To be discussed with the Karchin Lab (https://github.com/KarchinLab).

mryaninsilico commented 6 years ago

Possible items for CRAVAT / CIVIC hackathon:

implement a new Open-CRAVAT (https://github.com/KarchinLab/open-cravat/wiki) annotator for integrating CIVIC information into CRAVAT variant processing (maybe make this a new kind of annotator that uses a web service to get data rather than a pre-compute so CIVIC data will always be fresh)
implement a Open-CRAVAT visualization widget for CIVIC results including a link-out to the CIVIC site for variant annotation details
Add a linkout from the CIVIC variant details page to the CRAVAT website Single Variant Page (example: http://www.cravat.us/CRAVAT/variant.html?variant=chr21_34859485_+_C_T)

malachig commented 5 years ago

For inspiration for current visualizations one could look at the integration of CIViC in existing portals for inspiration. e.g. CBioPortal, ICGC data portal.

kmoad commented 5 years ago

https://drive.google.com/file/d/11kYlo_Es9rghYSYCQVdSdV9ooUMU5Z8V/view?usp=sharing

griffithlab / civic-meeting

Integration of CRAVAT and CIViC #32