Journal of Clinical and Translational Science (Jan 2023)
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
- Karamarie Fecho,
- Chris Bizon,
- Tursynay Issabekova,
- Sierra Moxon,
- Anne E. Thessen,
- Shervin Abdollahi,
- Sergio E. Baranzini,
- Basazin Belhu,
- William E. Byrd,
- Lawrence Chung,
- Andrew Crouse,
- Marc P. Duby,
- Stephen Ferguson,
- Aleksandra Foksinska,
- Laura Forero,
- Jennifer Friedman,
- Vicki Gardner,
- Gwênlyn Glusman,
- Jennifer Hadlock,
- Kristina Hanspers,
- Eugene Hinderer,
- Charlotte Hobbs,
- Gregory Hyde,
- Sui Huang,
- David Koslicki,
- Philip Mease,
- Sandrine Muller,
- Christopher J. Mungall,
- Stephen A. Ramsey,
- Jared Roach,
- Irit Rubin,
- Shepherd H. Schurman,
- Anath Shalev,
- Brett Smith,
- Karthik Soman,
- Sarah Stemann,
- Andrew I. Su,
- Casey Ta,
- Paul B. Watkins,
- Mark D. Williams,
- Chunlei Wu,
- Colleen H. Xu,
- The Biomedical Data Translator Consortium
Affiliations
- Karamarie Fecho
- ORCiD
- Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Copperline Professional Solutions, Pittsboro, NC, USA
- Chris Bizon
- ORCiD
- Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Tursynay Issabekova
- ORCiD
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Sierra Moxon
- ORCiD
- Biosystems Data Science Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Anne E. Thessen
- ORCiD
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Shervin Abdollahi
- ORCiD
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Sergio E. Baranzini
- ORCiD
- Department of Neurology, Weill Institute for Neuroscience, University of California - San Francisco, San Francisco, CA, USA
- Basazin Belhu
- Institute for Systems Biology, Seattle, WA, USA
- William E. Byrd
- ORCiD
- The Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
- Lawrence Chung
- ORCiD
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Andrew Crouse
- ORCiD
- The Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
- Marc P. Duby
- ORCiD
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stephen Ferguson
- ORCiD
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Aleksandra Foksinska
- ORCiD
- The Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
- Laura Forero
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA, USA University of California at San Diego, San Diego, CA, USA
- Jennifer Friedman
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA, USA University of California at San Diego, San Diego, CA, USA
- Vicki Gardner
- Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Gwênlyn Glusman
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- Jennifer Hadlock
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- Kristina Hanspers
- ORCiD
- Gladstone Institutes, University of California - San Francisco, San Francisco, CA, USA
- Eugene Hinderer
- ORCiD
- Tufts Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA
- Charlotte Hobbs
- ORCiD
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA, USA
- Gregory Hyde
- ORCiD
- Thayer School of Engineering at Dartmouth College, Hanover, NH, USA
- Sui Huang
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- David Koslicki
- ORCiD
- Departments of Computer Science and Engineering, Biology, and the Huck Institutes of the Life Sciences, Penn State University, University Park, PA, USA
- Philip Mease
- ORCiD
- Swedish Medical Center, St. Joseph Health, Seattle, WA, USA University of Washington, Seattle, WA, USA
- Sandrine Muller
- ORCiD
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Christopher J. Mungall
- ORCiD
- Biosystems Data Science Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Stephen A. Ramsey
- ORCiD
- Oregon State University, Corvallis, OR, USA
- Jared Roach
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- Irit Rubin
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- Shepherd H. Schurman
- ORCiD
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Anath Shalev
- ORCiD
- The Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
- Brett Smith
- ORCiD
- Institute for Systems Biology, Seattle, WA, USA
- Karthik Soman
- ORCiD
- Department of Neurology, Weill Institute for Neuroscience, University of California - San Francisco, San Francisco, CA, USA
- Sarah Stemann
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Andrew I. Su
- ORCiD
- The Scripps Research Institute, La Jolla, CA, USA
- Casey Ta
- ORCiD
- Columbia University Irving Medical Center, New York, NY, USA
- Paul B. Watkins
- ORCiD
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Mark D. Williams
- ORCiD
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Chunlei Wu
- ORCiD
- The Scripps Research Institute, La Jolla, CA, USA
- Colleen H. Xu
- ORCiD
- The Scripps Research Institute, La Jolla, CA, USA
- The Biomedical Data Translator Consortium
- DOI
- https://doi.org/10.1017/cts.2023.619
- Journal volume & issue
-
Vol. 7
Abstract
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph–based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly “Question-of-the-Month (QotM) Challenge” series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.
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