title: Food entries in a large allergy data repository.
abstract: OBJECTIVE
  Accurate food adverse sensitivity documentation in electronic health records (EHRs) is crucial to patient safety. This study examined, encoded, and grouped foods that caused any adverse sensitivity in a large allergy repository using natural language processing and standard terminologies.
  
  
  METHODS
  Using the Medical Text Extraction, Reasoning, and Mapping System (MTERMS), we processed both structured and free-text entries stored in an enterprise-wide allergy repository (Partners' Enterprise-wide Allergy Repository), normalized diverse food allergen terms into concepts, and encoded these concepts using the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) and Unique Ingredient Identifiers (UNII) terminologies. Concept coverage also was assessed for these two terminologies. We further categorized allergen concepts into groups and calculated the frequencies of these concepts by group. Finally, we conducted an external validation of MTERMS's performance when identifying food allergen terms, using a randomized sample from a different institution.
  
  
  RESULTS
  We identified 158 552 food allergen records (2140 unique terms) in the Partners repository, corresponding to 672 food allergen concepts. High-frequency groups included shellfish (19.3%), fruits or vegetables (18.4%), dairy (9.0%), peanuts (8.5%), tree nuts (8.5%), eggs (6.0%), grains (5.1%), and additives (4.7%). Ambiguous, generic concepts such as "nuts" and "seafood" accounted for 8.8% of the records. SNOMED-CT covered more concepts than UNII in terms of exact (81.7% vs 68.0%) and partial (14.3% vs 9.7%) matches.
  
  
  CONCLUSIONS
  Adverse sensitivities to food are diverse, and existing standard terminologies have gaps in their coverage of the breadth of allergy concepts.
  
  
  CONCLUSIONS
  New strategies are needed to represent and standardize food adverse sensitivity concepts, to improve documentation in EHRs.
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Plasek
authors.affiliation: Department of Emergency Medicine and Clinical Decision Making, Tufts Medical Center, Boston, MA, USA Department of Emergency Medicine, University of Colorado, Aurora, CO, USA.
authors.forename: Foster R
authors.initials: FR
authors.lastname: Goss
authors.affiliation: Clinical & Quality Analysis, Partners HealthCare System, Boston, MA, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Lai
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Lau
authors.affiliation: Clinical & Quality Analysis, Partners HealthCare System, Boston, MA, USA.
authors.forename: Diane L
authors.initials: DL
authors.lastname: Seger
authors.affiliation: Allergy and Immunology, Massachusetts General Hospital, Boston, MA, USA.
authors.forename: Kimberly G
authors.initials: KG
authors.lastname: Blumenthal
authors.affiliation: Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Paige G
authors.initials: PG
authors.lastname: Wickner
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA Division of Pharmacy, School of Medicine, Pharmacy and Health, Durham University, Durham, UK.
authors.forename: Sarah P
authors.initials: SP
authors.lastname: Slight
authors.affiliation: Clinical Informatics, Partners eCare, Partners HealthCare System, Boston, MA, USA.
authors.forename: Frank Y
authors.initials: FY
authors.lastname: Chang
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA Harvard Medical School, Boston, MA, USA.
authors.forename: Maxim
authors.initials: M
authors.lastname: Topaz
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA Harvard Medical School, Boston, MA, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Bates
authors.affiliation: Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA Clinical Informatics, Partners eCare, Partners HealthCare System, Boston, MA, USA Harvard Medical School, Boston, MA, USA lzhou2@partners.org.
authors.forename: Li
authors.initials: L
authors.lastname: Zhou
mesh_terms: D000485:Allergens; D019992:Databases as Topic; D005512:Food Hypersensitivity; D006801:Humans; D009323:Natural Language Processing; D039061:Systematized Nomenclature of Medicine; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
chemical_list: D000485:Allergens
keywords: allergy and immunology; controlled; electronic health records; food hypersensitivity; natural language processing; systematized nomenclature of medicine; vocabulary