EliIE: An open-source information extraction system for clinical trial eligibility criteria.

ABSTRACT:

Objective

To develop an open-source information extraction system called Eligibility Criteria Information Extraction (EliIE) for parsing and formalizing free-text clinical research eligibility criteria (EC) following Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) version 5.0.

Materials and methods

EliIE parses EC in 4 steps: (1) clinical entity and attribute recognition, (2) negation detection, (3) relation extraction, and (4) concept normalization and output structuring. Informaticians and domain experts were recruited to design an annotation guideline and generate a training corpus of annotated EC for 230 Alzheimer's clinical trials, which were represented as queries against the OMOP CDM and included 8008 entities, 3550 attributes, and 3529 relatio

SUBMITTER: Kang T 

PROVIDER: S-EPMC6259668 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature