Microbiology result events in microbiology report sentences [To be released in Jan 2015]
This corpus includes sentences from 1442 de-identified microbiology reports. Each report has been annotated for microbiology result events defined with several entities including (1) organism—a microorganism found in a culture (e.g., bacteria, flora, fungus, yeast), (2) organism quantity—a measurement of the amount of the organisms found in a culture (e.g., >10,000 col/ml, one colony, no, isolated), (3) rating—a qualitative measurement of the amount of organisms found in a culture (e.g., 1+,2+,3+,4+), (4) drug—a drug that was tested on an organism (e.g., penicillin), (5) drug resistance—a susceptibility of an organism to the drug (e.g., susceptible, intermediate, resistant, no CLSI interpretive criteria), and (6) MIC—minimum inhibitory concentration of an antimicrobial that inhibited the growth of a microorganism after overnight incubation (e.g., 2.0 µcg/ml).
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Details of the corpus can be found in the following papers:
W. Yim, X. Engle, H.L. Evans, M. Yetisgen. A New Corpus for Structured Microbiology Results. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'14). Washington DC, November, 2014.
W. Yim, H.L. Evans, M. Yetisgen. Structuring Free-text Microbiology Culture Reports for Secondary Use. Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'15). San Francisco, CA, March, 2015.