An efficient prototype method to identify and correct misspellings in clinical text

OBJECTIVE: Misspellings in clinical free text present challenges to natural language processing. With an objective to identify misspellings and their corrections, we developed a prototype spelling analysis method that implements Word2Vec, Levenshtein edit distance constraints, a lexical resource, and corpus term frequencies. We used the prototype method to process two different corpora, surgical pathology reports, and emergency department progress and visit notes, extracted from Veterans Health Administration resources. We evaluated performance by measuring positive predictive value and performing an error analysis of false positive output, using four classifications. We also performed an analysis of spelling errors in each corpus, using common error classifications. RESULTS: In this small-scale study utilizing a total of 76,786 clinical notes, the prototype method achieved positive predictive values of 0.9057 and 0.8979, respectively, for the surgical pathology reports, and emergency department progress and visit notes, in identifying and correcting misspelled words. False positives varied by corpus. Spelling error types were similar among the two corpora, however, the authors of emergency department progress and visit notes made over four times as many errors. Overall, the results of this study suggest that this method could also perform sufficiently in identifying misspellings in other clinical document types. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13104-019-4073-y) contains supplementary material, which is available to authorized users.