This project houses the milestones and deliverables for the Connections Hypothesis Provider (CHP) service built by Dartmouth College (PI – Dr. Eugene Santos) and Tufts University (Co-PI – Joseph Gormley) in collaboration with the National Center for Advancing Translational Sciences (NCATS). CHP aims to leverage clinical data along with structured biochemical knowledge to derive a computational representation of pathway structures and molecular components to support human and machine-driven interpretation, enable pathway-based biomarker discovery, and aid in the drug development process. In its current version, CHP supports queries relating to genetic, therapeutic, and patient clinical features (e.g. tumor staging) contribution toward patient survival, as computed within the context of our test pilot: a robust breast cancer dataset from The Cancer Genome Atlas (TCGA). We are using this as a proving ground for our system’s basic operations as we work to incorporate structured pathway knowledge and pathway analysis methods into the tool.
For more details about the service CHP provides please see here: https://github.com/di2ag/chp_api
We encourage anyone looking for tooling/instructions, to interface with our API, to the following repository, CHP Client, https://github.com/di2ag/chp_client. CHP Client is a lightweight Python client that interfaces CHP. It is meant to be an easy-to-use wrapper utility to both run and build TRAPI queries that the CHP web service will understand.
Other notable links:
Our API Repository: https://github.com/di2ag/chp_api
Our CHP Client repository: https://github.com/di2ag/chp_client
A repository for our reasoning code: https://github.com/di2ag/chp
Our NCATS Wiki Page: https://github.com/NCATSTranslator/Translator-All/wiki/Connections-Hypothesis-Provider
Dr. Eugene Santos (PI): Eugene.Santos.Jr@dartmouth.edu
Joseph Gormley (Co-PI): jgormley@tuftsmedicalcenter.org