Progress toward a universal biomedical data translator

Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well‐being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline‐...

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Vydáno v:Clinical and translational science Ročník 15; číslo 8; s. 1838 - 1847
Hlavní autoři: Thessen, Anne E., Roper, Ryan T., Southall, Noel, Ta, Casey, Xu, Hao, Byrd, William, Dančík, Vlado, Duby, Marc P., Dumontier, Michel, Glusman, Gustavo, Hinderer, Eugene W., Johs, Adam, Su, Andrew I., Qin, Guangrong, Zhu, Qian, Dougherty, Jennifer, Magis, Andrew, Smith, Brett, Chen, Zhehuan, Azevedo, Ricardo De Miranda, Lee, Jay, Weng, Chunhua, Yilmaz, Arif, Santos, Eugene, Yakaboski, Chase, Deutsch, Eric, Koslicki, David, Kvarfordt, Lindsey, Ma, Chunyu, Wood, Erica, Roach, Jared, Williams, Andrew, Gormley, Joseph, Zisk, Tom, Hoatlin, Maureen, Pico, Alexander, Riutta, Anders, Xu, Colleen, Ahalt, Stanley C., Knowles, Michael, Krishnamurthy, Ashok, Mandal, Meisha, Peden, David B., Cox, Steven, Vaidya, Gaurav, Wang, Max, Alkanaq, Ahmed, Costanzo, Maria, Koesterer, Ryan, Flannick, Jason, Kluge, Alexandria, Strasser, Michael “ Michi”, Chung, Lawrence, Kang, Jimin, Mantilla, Michelle, Muller, Sandrine, Persaud, Bria, Wei, Qi, Dai, Cheng, Duvvuri, Venkata, Mauldin, Denise, Korn, Daniel, Mesbah, Abrar, Tropsha, Alexander, Mersmann, Marian, Morton, Kenny, Lin, Jason, Avila, Ricardo, Wu, Chunlei, Cano, Marco Alvarado, Issabekova, Tursynay, McMurry, Julie, Cohen, Kevin, He, Kaiwen, Mamidi, Tarun, Might, Matthew, Osborne, John, Tran‐Nguyen, Thi, Crouse, Andrew, Belhu, Basazin, Stillwell, Lisa, Grotthuss, Marcin, Wang, Patrick, Zhou, Xinghua, Sinha, Meghamala, Raj, Shruti, Peene, R. Carter, McClelland, Jason, Leigh, Margaret, Zhou, Eric, Amin, Nada, Fehrmann, Nathaniel, Foksinska, Aleksandra M., Jenkins, Lindsay, Jarrell, Matthew, Pollard, Elizabeth, Rucka, Sienna, Tinglin, Jillian, Zheng, Marissa
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States John Wiley & Sons, Inc 01.08.2022
Wiley
John Wiley and Sons Inc
Témata:
Application programming interface
Consortia
Electronic health records
Interoperability
Knowledge discovery
Knowledge representation
Mini‐review
Natural language
Ontology
Pain
Queries
Research & Experimental Medicine
Reviews
Science
Software
Terminology
Translation
Well being
ISSN:1752-8054, 1752-8062, 1752-8062
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Popis
Shrnutí:Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well‐being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline‐specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph‐based “Translator” system capable of integrating existing biomedical data sets and “translating” those data into insights intended to augment human reasoning and accelerate translational science. Having demonstrated feasibility of the Translator system, the Translator program has since moved into development, and the Translator Consortium has made significant progress in the research, design, and implementation of an operational system. Herein, we describe the current system’s architecture, performance, and quality of results. We apply Translator to several real‐world use cases developed in collaboration with subject‐matter experts. Finally, we discuss the scientific and technical features of Translator and compare those features to other state‐of‐the‐art, biomedical graph‐based question‐answering systems.
Bibliografie:Funding information
This work was supported by the National Center for Advancing Translational Sciences, Biomedical Data Translator Program (Other Transaction Awards OT2TR003434, OT2TR003436, OT2TR003428, OT2TR003448, OT2TR003427, OT2TR003430, OT2TR003433, OT2TR003450, OT2TR003437, OT2TR003443, OT2TR003441, OT2TR003449, OT2TR003445, OT2TR003422, OT2TR003435, OT3TR002026, OT3TR002020, OT3TR002025, OT3TR002019, OT3TR002027, OT2TR002517, OT2TR002514, OT2TR002515, OT2TR002584, and OT2TR002520; Contract number 75N95021P00636). Additional funding was provided by the National Center for Advancing Translational Sciences, Intramural Research Program (ZIA TR000276‐05) and the National Institute of Diabetes and Digestive and Kidney Diseases (5U01DK065201).
Consortial/collaborative authors.
These authors served as co‐first authors.
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USDOE
AC02-05CH11231
None
Funding informationThis work was supported by the National Center for Advancing Translational Sciences, Biomedical Data Translator Program (Other Transaction Awards OT2TR003434, OT2TR003436, OT2TR003428, OT2TR003448, OT2TR003427, OT2TR003430, OT2TR003433, OT2TR003450, OT2TR003437, OT2TR003443, OT2TR003441, OT2TR003449, OT2TR003445, OT2TR003422, OT2TR003435, OT3TR002026, OT3TR002020, OT3TR002025, OT3TR002019, OT3TR002027, OT2TR002517, OT2TR002514, OT2TR002515, OT2TR002584, and OT2TR002520; Contract number 75N95021P00636). Additional funding was provided by the National Center for Advancing Translational Sciences, Intramural Research Program (ZIA TR000276‐05) and the National Institute of Diabetes and Digestive and Kidney Diseases (5U01DK065201).
ISSN:1752-8054
1752-8062
1752-8062
DOI:10.1111/cts.13301