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J Biomed Inform. 2018 Dec;88:62-69. doi: 10.1016/j.jbi.2018.11.004. Epub 2018 Nov 7.

A method for harmonization of clinical abbreviation and acronym sense inventories.

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Department of Biomedical Informatics, Columbia University, New York, NY, USA; College of Physicians and Surgeons, Columbia University, New York, NY, USA. Electronic address:
Department of Biomedical Informatics, Columbia University, New York, NY, USA.
Department of Biomedical Informatics, Columbia University, New York, NY, USA; Value Institute, NewYork-Presbyterian Hospital, New York, NY, USA.



Previous research has developed methods to construct acronym sense inventories from a single institutional corpus. Although beneficial, a sense inventory constructed from a single institutional corpus is not generalizable, because acronyms from different geographic regions and medical specialties vary greatly.


Develop an automated method to harmonize sense inventories from different regions and specialties towards the development of a comprehensive inventory.


The method involves integrating multiple source sense inventories into one centralized inventory and cross-mapping redundant entries to establish synonymy. To evaluate our method, we integrated 8 well-known source inventories into one comprehensive inventory (or metathesaurus). For both the metathesaurus and its sources, we evaluated the coverage of acronyms and their senses on a corpus of 1 million clinical notes. The corpus came from a different institution, region, and specialty than the source inventories.


In the evaluation using clinical notes, the metathesaurus demonstrated an acronym (short form) micro-coverage of 94.3%, representing a substantial increase over the two next largest source inventories, the UMLS LRABR (74.8%) and ADAM (68.0%). The metathesaurus demonstrated a sense (long form) micro-coverage of 99.6%, again a substantial increase compared to the UMLS LRABR (82.5%) and ADAM (55.4%).


Given the high coverage, harmonizing acronym sense inventories is a promising methodology to improve their comprehensiveness. Our method is automated, leverages the extensive resources already devoted to developing institution-specific inventories in the United States, and may help generalize sense inventories to institutions who lack the resources to develop them. Future work should address quality issues in source inventories and explore additional approaches to establishing synonymy.


Acronymsandabbreviations; Consumer health informatics; Knowledge representation; Vocabulary and terminology

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