Objective: The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System (UMLS) definition (Task 1a) and (ii) disorder mention normalization to an ontology (Task 1b). Such a community evaluation has not been previously executed. Task 1a included a total of 22 system submissions, and Task 1b included 17. Most of the systems employed a combination of rules and machine learners. Materials and methods: We used a subset of the Shared Annotated Resources (ShARe) corpus of annotated clinical text-199 clinical notes for training and 99 for testing (roughly 180 K words in total). We provided the community with the annotated gold standard training documents to build systems to identify and normalize disorder mentions. The systems were tested on a held-out gold standard test set to measure their performance. Results: For Task 1a, the best-performing system achieved an F1 score of 0.75 (0.80 precision; 0.71 recall). For Task 1b, another system performed best with an accuracy of 0.59. Discussion Most of the participating systems used a hybrid approach by supplementing machine-learning algorithms with features generated by rules and gazetteers created from the training data and from external resources. Conclusions: The task of disorder normalization is more challenging than that of identification. The ShARe corpus is available to the community as a reference standard for future studies.
|Number of pages||12|
|Journal||Journal of the American Medical Informatics Association|
|Publication status||Published - 2014|
Pradhan, S., Elhadad, N., South, B. R., Martínez, D., Christensen, L., Vogel, A., Suominen, H., Chapman, W. W., & Savova, G. (2014). Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. Journal of the American Medical Informatics Association, 22(1), 143-154. https://doi.org/10.1136/amiajnl-2013-002544