title: A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
abstract: OBJECTIVE
  The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems' capability to handle abbreviations in clinical narratives.
  
  
  METHODS
  We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations. We applied CARD to clinical corpora from Vanderbilt University Medical Center (VUMC) and generated 2 comprehensive sense inventories for abbreviations in discharge summaries and clinic visit notes. Furthermore, we developed a wrapper that integrates CARD with MetaMap, a widely used general clinical NLP system.
  
  
  CONCLUSIONS
  CARD detected 27 317 and 107 303 distinct abbreviations from discharge summaries and clinic visit notes, respectively. Two sense inventories were constructed for the 1000 most frequent abbreviations in these 2 corpora. Using the sense inventories created from discharge summaries, CARD achieved an F1 score of 0.755 for identifying and disambiguating all abbreviations in a corpus from the VUMC discharge summaries, which is superior to MetaMap and Apache's clinical Text Analysis Knowledge Extraction System (cTAKES). Using additional external corpora, we also demonstrated that the MetaMap-CARD wrapper improved MetaMap's performance in recognizing disorder entities in clinical notes. The CARD framework, 2 sense inventories, and the wrapper for MetaMap are publicly available at https://sbmi.uth.edu/ccb/resources/abbreviation.htm . We believe the CARD framework can be a valuable resource for improving abbreviation identification in clinical NLP systems.
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.|Department of Medicine, Vanderbilt University School of Medicine.
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Denny
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.|Department of Medicine, Vanderbilt University School of Medicine.
authors.forename: S
authors.initials: S
authors.lastname: Trent Rosenbloom
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.|Department of Medicine, Vanderbilt University School of Medicine.
authors.forename: Randolph A
authors.initials: RA
authors.lastname: Miller
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.
authors.forename: Dario A
authors.initials: DA
authors.lastname: Giuse
authors.affiliation: Department of Medicine, Vanderbilt University School of Medicine.
authors.forename: Lulu
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Medicine, University of Alabama at Birmingham, Birmingham.
authors.forename: Carmelo
authors.initials: C
authors.lastname: Blanquicett
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston.
authors.forename: Ergin
authors.initials: E
authors.lastname: Soysal
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston.
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston.
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
mesh_terms: D000004:Abbreviations as Topic; D057286:Electronic Health Records; D006801:Humans; D000069550:Machine Learning; D009323:Natural Language Processing; D010351:Patient Discharge
keywords: clinical abbreviation; clinical natural language processing; machine learning; sense clustering