EVIDARA: Automated Evidential Support from Raw Data for relay agents in Biomedical KG Queries

Institute For Systems Biology, Seattle WA

Investigators

Linked publications, trials & patents

Abstract

1. Rationale for the joint effort as a multi-PI (MPI) team. At the core of the is pilot project is the combination of two sets of resources and expertise that each of the two principal investigators (PIs), Dr. Sergio Baranzini (UCSF) and Dr. Sui Huang (ISB) will contribute to develop, test and deliver a computational tool (?Automatic Relay Agent?, ARA) as defined by the FOA of Biomedical Translator program of NCATS as a milestone for the ?First Segment? (January- March, 2020). The ARA envisioned by this team is EVIDARA, a system that extracts knowledge from a knowledge graph (KG) and evaluates it against multi-omics raw data of a large cohort for evidential support. The evidenced-tested knowledge is then relaying it to the Biomedical Translator. The two resources that will be combined to build EVIDARA are: (i) A novel knowledge graph, SPOKE and (ii) a new genre of multi-omics data sets from scientific wellness studies. The two PIs will bring these two resources and thus play complementary role: Dr. Sergio Baranzini, with his team at UCSF, is the developer of SPOKE and Dr. Sui Huang provides subject matter expertise in multiomics studies and has access to data from a cohort studied at ISB that he has been analyzing. Dr. Baranzini will bring expertise in all computational aspects of SPOKE and its new applications and Dr. Huang will also act as subject matter expert in multi-omics driven medical practice and research to guide product development and testing. 2. Goal of project and continuation. The pilot project id defined by the common goal of delivering the milestone product, EVIDARA as described in the proposal. If the pilot project is successful and this team is selected to continue to the ?Second Segment? (an up to five project) the two PIs will work again as an MPI team and jointly design the expansion of the project into this second phase and jointly prepare the new research plan to NCATS. 3. Management and coordination. Dr. Huang, is the contact-MPI and will coordinate the project and directly communicate with Dr. Baranzini to ensure that both MPIs are kept informed about the project?s technical progress and all administrative matters. Each MPI will assume fiscal and administrative management of their own team, as reflected in the budget and consortium subcontract. Dr. Huang will be responsible for communication with NCATS Program manager team. The two MPIs and their team members and institutional collaborators agree to work jointly as a group towards the milestone product. Should publications result, both will be co-senior authors and their team members included as authors based on their contribution, following common academic practice. If there are any conflicts in the course of the project, both PIs and collaborators will meet in person and work in a spirit of cooperation to resolve any conflicts. Given that Drs. Huang and Baranzini have interacted academically for almost two decades, share the same scholarly perspective and the complementary and synergistic nature of their expertise that is required for the project it is highly unlikely a neutral arbitration committee would be required to resolve conflicts. 4. Intellectual Property. For intellectual property issue, the Technology Transfer Offices at each of the PI?s institutions will be responsible for agreements relating to the research and the outcome of the work.