1 code implementation • 11 Jul 2023 • Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr, Lawrence E. Hunter
Translational research requires data at multiple scales of biological organization.
1 code implementation • 24 Sep 2022 • Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
NP-KG is a heterogeneous KG with biomedical ontologies, linked data, and full texts of the scientific literature, constructed with the Phenotype Knowledge Translator framework and the semantic relation extraction systems, SemRep and Integrated Network and Dynamic Reasoning Assembler.
1 code implementation • 10 Sep 2022 • Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne-Davies, James A. Feinstein, Melissa A. Haendel, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin Reese, Jessica Sinclair, Sanya B. Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew Williams, Xingman A. Zhang, Joshua C. Denny, Peter N. Robinson, Patrick Ryan, George Hripcsak, Tellen D. Bennett, Lawrence E. Hunter, Michael G. Kahn
Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping.
1 code implementation • NAACL (TeachingNLP) 2021 • Sanya B. Taneja, Richard D. Boyce, William T. Reynolds, Denis Newman-Griffis
Introducing biomedical informatics (BMI) students to natural language processing (NLP) requires balancing technical depth with practical know-how to address application-focused needs.