A Common Dialect for Infrastructure and Services in Translator

Melissa Haendel, Julie McMurry, Anne Thessen, Chris Bizon, Nomi Harris, Chris Mungall
2019 Zenodo  
1) We will build a robust, dynamic Translator Standards and Reference Implementations Component (SRI) that integrates the collaborations and investments that the NCATS Translator has made to date. This component will consist of a suite of standards and products, a model for their governance, and processes to coordinate integration and shared implementation: Community governance coordination will be developed with community buy-in to ensure an effective collaborative environment, and drive
more » ... tium-wide consensus on the other components. Architecture and API specifications will drive community efforts to define details of project architecture and communication protocols across Translator Knowledge Providers (KPs), Autonomous Relay Agents (ARAs), and the Autonomous Relay System (ARS). The BioLink model will define the standard entity types, relationship types, and a schema shared by all Translator components. This includes related utility libraries and a novel approach to accommodate multiple alternate data modeling perspectives. Integrated reference ontologies will provide BioLink-compliant terms and relationships. We will draw on the ROBOKOP Ubergraph framework [1], the Monarch integrated ontologies, and other ontologies from Open Biological and Biomedical Ontologies (OBO) [2]. A continually-updated knowledge graph and data lake will provide Translator with a standardized and integrated global view of the whole information landscape. Next-generation Shared Translator Services will integrate features of ROBOKOP [3], Monarch [4], BioLink [5], and the reasoner APIs to remove integration barriers. These services will provide validation, lookup, and mapping functionality for use across Translator. A registry of Translator KPs, ARAs, and shared services will increase efficiency, eliminate duplication of effort, and promote collaboration. 2) Our proposed SRI will address the problem of connecting together different components and data/information sources at scale, with community buy-in, and with a plan for sustainabil [...]
doi:10.5281/zenodo.3546914 fatcat:uzgj6bckgbdyxb43a4yneu3kcm