title: A common type system for clinical natural language processing.
abstract: BACKGROUND
  One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings.
  
  
  RESULTS
  We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later.
  
  
  CONCLUSIONS
  We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types.
authors.affiliation: Mayo Clinic, Rochester, Rochester, MN, USA. wu.stephen@mayo.edu.
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Wu
authors.forename: Vinod C
authors.initials: VC
authors.lastname: Kaggal
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Dligach
authors.forename: James J
authors.initials: JJ
authors.lastname: Masanz
authors.forename: Pei
authors.initials: P
authors.lastname: Chen
authors.forename: Lee
authors.initials: L
authors.lastname: Becker
authors.forename: Wendy W
authors.initials: WW
authors.lastname: Chapman
authors.forename: Guergana K
authors.initials: GK
authors.lastname: Savova
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Chute