An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C)

no code implementations • 20 Oct 2021 • Sijia Liu, Andrew Wen, LiWei Wang, Huan He, Sunyang Fu, Robert Miller, Andrew Williams, Daniel Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-el-rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S Hong, Joel H Saltz, Thomas Schaffter, Emily Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu, Natural Language Processing, Subgroup, National COVID Cohort Collaborative

Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP.

Benchmarking

Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature

no code implementations • 24 Jun 2021 • Dalton Schutte, Jake Vasilakes, Anu Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang

MATERIALS AND METHODS: We created SemRepDS (an extension of SemRep), capable of extracting semantic relations from abstracts by leveraging a DS-specific terminology (iDISK) containing 28, 884 DS terms not found in the UMLS.

Drug Repurposing for COVID-19 via Knowledge Graph Completion

1 code implementation • 19 Oct 2020 • Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu

The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials.

Knowledge Graph Completion