Ensembles of natural language processing systems for portable phenotyping solutions.

ABSTRACT:

Background

Manually curating standardized phenotypic concepts such as Human Phenotype Ontology (HPO) terms from narrative text in electronic health records (EHRs) is time consuming and error prone. Natural language processing (NLP) techniques can facilitate automated phenotype extraction and thus improve the efficiency of curating clinical phenotypes from clinical texts. While individual NLP systems can perform well for a single cohort, an ensemble-based method might shed light on increasing the portability of NLP pipelines across different cohorts.

Methods

We compared four NLP systems, MetaMapLite, MedLEE, ClinPhen and cTAKES, and four ensemble techniques, including intersection, union, majority-voting and machine learning, for extracting generic phenotypic concepts. We add

SUBMITTER: Liu C 

PROVIDER: S-EPMC6899194 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature