PIC-SURE

Overview

The Patient-centered Information Commons: Standard Unification of Research Elements (PIC-SURE) platform integrates different layers of clinical and genomic data from diverse data sources, providing a multifaceted approach to biomedical research.

The PIC-SURE platform was built on i2b2 (Informatics for Integrating Biology & the Bedside, a data model created for EHR data), with an Apache 2.0 license (open source). PIC-SURE has been deployed in both FISMA Moderate ATO and HI-TRUST environments.

PIC-SURE example user interface.

 

Features

PIC-SURE UI and API

The PIC-SURE platform provides both an intuitive graphical user interface (UI) and an application programming interface (API) to meet different use cases and levels of experience with data manipulation. The PIC-SURE UI allows for an investigator to search for variables of interest and to conduct feasibility queries. In this way, cohorts are built in real-time and results can be retrieved for analysis. 

 
 

PIC-SURE UI

PIC-SURE API

Advantages

Build queries using point-and-click interface to explore variables and aggregate counts

Build specific queries using code and extract data directly into workspace

Access point

PIC-SURE website

Didactic Jupyter notebooks in R and python, R Markdown files

Building queries

Query Builder tool

Python and R functions

Extracting data

Data can be downloaded or exported to an analysis workspace

Run query in python or R to export data to workspace

Data

Clinical and genomic data indexed at the variable level

Patient-level curation and ingestion of each phenotypic variable and genomic variant

Variable, table and study metadata ingested and indexed for search

Decoded variables from all studies made available to the user for 
cohort filtering and export

 

Query Builder

The Query Builder in the PIC-SURE UI allows users to interactively build queries and returns the counts of participants that meet the criteria. This tool functions similarly to a search engine, providing the ability to search a term of interest and returning variables that contain the search term. After determining a variable of interest, users can refine their query to filter participants with certain values and build a cohort. Both single and multiple criteria queries are supported.

 

Learn More

Videos 

PIC-SURE has a dedicated YouTube channel, where users can find video demonstrations of PIC-SURE features such as single criterion search, multiple criteria search, and harmonized variables. Users can find videos specific to certain PIC-SURE environments by viewing the ‘playlists’

GitHub

PIC-SURE is developed under an Apache 2.0 license; all code is open source and accessible on GitHub: https://github.com/hms-dbmi/pic-sure-all-in-one.

For users interested in the PIC-SURE API, we have developed several Jupyter notebooks (R and Python) and R Markdown files which contain PIC-SURE use-cases. These examples provide a starting point for users to get started with their own analyses, and are publicly available on GitHub: https://github.com/hms-dbmi/Access-to-Data-using-PIC-SURE-API

User Guide / Documentation

Written documentation for the PIC-SURE UI can be found here: PIC-SURE User Guide