ARAX: a graph-based modular reasoning tool for translational biomedicine

Glen, A. K.; Ma, C.; Mendoza, L.; Womack, F.; Wood, E. C.; Sinha, M.; Acevedo, L.; Kvarfordt, L. G.; Peene, R. C.; Liu, S.; Hoffman, A. S.; Roach, J. C.; Deutsch, E. W.; Ramsey, S. A.; Koslicki, D.

doi:10.1101/2022.08.12.503810

bioRxiv · 10.1101/2022.08.12.503810

ARAX: a graph-based modular reasoning tool for translational biomedicine

Glen, A. K.·Ma, C.·Mendoza, L.·Womack, F.·Wood, E. C.·Sinha, M.·Acevedo, L.·Kvarfordt, L. G.·Peene, R. C.·Liu, S.·Hoffman, A. S.·Roach, J. C.·Deutsch, E. W.·Ramsey, S. A.·Koslicki, D.

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Abstract

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSWith the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but progress has been hindered by the lack of an expressive analysis workflow language for translational reasoning and by the lack of a reasoning engine--supporting that language--that federates semantically integrated knowledge-bases. ResultsWe introduce ARAX, a new reasoning system for translational biomedicine that provides a web browser user interface and an application programming interface. ARAX enables users to encode translational biomedical questions and to integrate knowledge across sources to answer the users query and facilitate exploration of results. For ARAX, we developed new approaches to query planning, knowledge-gathering, reasoning, and result ranking and dynamically integrate knowledge providers for answering biomedical questions. To illustrate ARAXs application and utility in specific disease contexts, we present several use-case examples. Availability and ImplementationThe source code and technical documentation for building the ARAX server-side software and its built-in knowledge database are freely available online (https://github.com/RTXteam/RTX). We provide a hosted ARAX service with a web browser interface at arax.rtx.ai and a web application programming interface (API) endpoint at arax.rtx.ai/api/arax/v1.3/ui/. Contactdmk333@psu.edu

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Glen, A. K., Ma, C., Mendoza, L., Womack, F., Wood, E. C., Sinha, M., Acevedo, L., Kvarfordt, L. G., Peene, R. C., Liu, S., Hoffman, A. S., Roach, J. C., Deutsch, E. W., Ramsey, S. A., Koslicki, D.. 2022-08-16. ARAX: a graph-based modular reasoning tool for translational biomedicine. https://doi.org/10.1101/2022.08.12.503810

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