title: Identifying respiratory findings in emergency department reports for biosurveillance using MetaMap.
abstract: Clinical conditions described in patients' dictated reports are necessary for automated detection of patients with respiratory illnesses such as inhalational anthrax and pneumonia. We applied MetaMap to emergency department reports to extract a set of 71 clinical conditions relevant to detection of a lower respiratory outbreak. We indexed UMLS terms in emergency department reports with MetaMap, filtered the indexed output with a specialized lexicon of UMLS terms for the domain, and mapped the clinical conditions of interest to concepts in the lexicon. We compared MetaMap's ability to accurately identify the conditions against a physician's manual annotations and evaluated incorrectly indexed features to determine what additional processing is necessary. MetaMap identified the clinical conditions with a recall of 0.72 and a precision of 0.56. Necessary processing beyond MetaMap's indexing includes finding validation, temporal discrimination, anatomic location discrimination, finding-disease discrimination, and contextual inference. Successful identification of clinical conditions in an emergency department report with MetaMap requires processing techniques specific to the clinical question of interest.
authors.affiliation: RODS Laboratory, Center for Biomedical Informatics, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213, USA. chapman@cbmi.pitt.edu
authors.forename: Wendy W
authors.initials: WW
authors.lastname: Chapman
authors.forename: Marcelo
authors.initials: M
authors.lastname: Fiszman
authors.forename: John N
authors.initials: JN
authors.lastname: Dowling
authors.forename: Brian E
authors.initials: BE
authors.lastname: Chapman
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Rindflesch
mesh_terms: D000043:Abstracting and Indexing; D023482:Bioterrorism; D004196:Disease Outbreaks / Q000517:prevention & control; D004636:Emergency Service, Hospital; D006801:Humans; D016247:Information Storage and Retrieval; D008499:Medical Records; D009323:Natural Language Processing; D011159:Population Surveillance; D012140:Respiratory Tract Diseases / Q000175:diagnosis*; D017432:Unified Medical Language System; D018875:Vocabulary, Controlled