Contestants in this combined datathon/hackathon are challenged with providing a user interface data exploration tool fed by PIC-SURE queries. Any data manipulations must be performed either inside the web browser or through the new PIC-SURE Scripted Query functionality (JS and possibly Python or R). Each team should contain at least one scientist (PostDoc, PhD student, etc.) and at least two developers.
This contest is focused on using the new Scripted Query beta feature of the PIC-SURE API, which allows users to submit code that can be used to perform arbitrary transformations on data retrieved through PIC-SURE as part of their query. This will not require contestants to modify the PIC-SURE API itself.
Visualization of available genomic and phenotypic data (patient counts, number of variables, etc. )
Select demographic and clinical variables to run a query and get back patient counts
Integration of UpSet visualization approach to visualize intersecting sets of patients
Create a dashboard to visualize quantitative data (lab values, expression levels, etc.) in histograms, scatter plots, or other basic plots and stratified by categorical variables (genotype, race, etc.)
List not exhaustive, be creative!
DFCI is currently working on using the PIC-SURE API in development of a replacement front-end for I2B2. Additionally work has been done in accessing genotype and phenotype data via the PIC-SURE API through Jupyter Notebooks utilizing R and Python. For example, an R library (R-Cupcake) has been developed at HMS DBMI which facilitates access to the API through R kernels in Jupyter Notebooks. It is hoped that through this datathon/hackathon, next level functionality will be built using the PIC-SURE API for data access.
HMS DBMI is developing an open-source infrastructure that will foster the incorporation of multiple heterogeneous patient-level clinical, omics and environment datasets. This system embraces the idea of decentralized datasets of varying types, and the protocols used to access them, while still providing a simple communication layer that can handle querying, joining, and computing. The BD2K PIC-SURE RESTful API implementation is called Inter Resource Communication Tool (IRCT).