title: Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction.
abstract: Clinical Natural Language Processing (NLP) systems require a semantic schema comprised of domain-specific concepts, their lexical variants, and associated modifiers to accurately extract information from clinical texts. An NLP system leverages this schema to structure concepts and extract meaning from the free texts. In the clinical domain, creating a semantic schema typically requires input from both a domain expert, such as a clinician, and an NLP expert who will represent clinical concepts created from the clinician's domain expertise into a computable format usable by an NLP system. The goal of this work is to develop a web-based tool, Knowledge Author, that bridges the gap between the clinical domain expert and the NLP system development by facilitating the development of domain content represented in a semantic schema for extracting information from clinical free-text.
  
  
  
  Knowledge Author is a web-based, recommendation system that supports users in developing domain content necessary for clinical NLP applications. Knowledge Author's schematic model leverages a set of semantic types derived from the Secondary Use Clinical Element Models and the Common Type System to allow the user to quickly create and modify domain-related concepts. Features such as collaborative development and providing domain content suggestions through the mapping of concepts to the Unified Medical Language System Metathesaurus database further supports the domain content creation process. Two proof of concept studies were performed to evaluate the system's performance. The first study evaluated Knowledge Author's flexibility to create a broad range of concepts. A dataset of 115 concepts was created of which 87 (76 %) were able to be created using Knowledge Author. The second study evaluated the effectiveness of Knowledge Author's output in an NLP system by extracting concepts and associated modifiers representing a clinical element, carotid stenosis, from 34 clinical free-text radiology reports using Knowledge Author and an NLP system, pyConText. Knowledge Author's domain content produced high recall for concepts (targeted findings: 86 %) and varied recall for modifiers (certainty: 91 % sidedness: 80 %, neurovascular anatomy: 46 %).
  
  
  
  Knowledge Author can support clinical domain content development for information extraction by supporting semantic schema creation by domain experts.
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84108, USA.
authors.forename: William
authors.initials: W
authors.lastname: Scuba
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84108, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Tharp
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84108, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Mowery
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, USA.
authors.forename: Eugene
authors.initials: E
authors.lastname: Tseytlin
authors.affiliation: University of California, San Diego, CA, 92093, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Psychology, University of Utah, Salt Lake City, UT, 84108, USA.
authors.forename: Frank A
authors.initials: FA
authors.lastname: Drews
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84108, USA. wendy.chapman@utah.edu.
authors.forename: Wendy W
authors.initials: WW
authors.lastname: Chapman
mesh_terms: D064229:Biological Ontologies; D057225:Data Mining / Q000379:methods*; D020407:Internet; D009323:Natural Language Processing; D012660:Semantics; D012984:Software; D014584:User-Computer Interface
keywords: Information extraction; Knowledge representation; Natural Language Processing; Semantics; Unified Medical Language System