Natalia Grabar1,2, Clément Dalloux3, Vincent Claveau3. 1. CNRS, UMR 8163, Lille, F-59000, France. natalia.grabar@univ-lille.fr. 2. Univ. Lille, UMR 8163 - STL - Savoirs Textes Langage, Lille, F-59000, France. natalia.grabar@univ-lille.fr. 3. Univ Rennes, Inria, CNRS, IRISA, Rennes, F-35000, France.
Abstract
BACKGROUND: Textual corpora are extremely important for various NLP applications as they provide information necessary for creating, setting and testing those applications and the corresponding tools. They are also crucial for designing reliable methods and reproducible results. Yet, in some areas, such as the medical area, due to confidentiality or to ethical reasons, it is complicated or even impossible to access representative textual data. We propose the CAS corpus built with clinical cases, such as they are reported in the published scientific literature in French. RESULTS: Currently, the corpus contains 4,900 clinical cases in French, totaling nearly 1.7M word occurrences. Some clinical cases are associated with discussions. A subset of the whole set of cases is enriched with morpho-syntactic (PoS-tagging, lemmatization) and semantic (the UMLS concepts, negation, uncertainty) annotations. The corpus is being continuously enriched with new clinical cases and annotations. The CAS corpus has been compared with similar clinical narratives. When computed on tokenized and lowercase words, the Jaccard index indicates that the similarity between clinical cases and narratives reaches up to 0.9727. CONCLUSION: We assume that the CAS corpus can be effectively exploited for the development and testing of NLP tools and methods. Besides, the corpus will be used in NLP challenges and distributed to the research community.
BACKGROUND: Textual corpora are extremely important for various NLP applications as they provide information necessary for creating, setting and testing those applications and the corresponding tools. They are also crucial for designing reliable methods and reproducible results. Yet, in some areas, such as the medical area, due to confidentiality or to ethical reasons, it is complicated or even impossible to access representative textual data. We propose the CAS corpus built with clinical cases, such as they are reported in the published scientific literature in French. RESULTS: Currently, the corpus contains 4,900 clinical cases in French, totaling nearly 1.7M word occurrences. Some clinical cases are associated with discussions. A subset of the whole set of cases is enriched with morpho-syntactic (PoS-tagging, lemmatization) and semantic (the UMLS concepts, negation, uncertainty) annotations. The corpus is being continuously enriched with new clinical cases and annotations. The CAS corpus has been compared with similar clinical narratives. When computed on tokenized and lowercase words, the Jaccard index indicates that the similarity between clinical cases and narratives reaches up to 0.9727. CONCLUSION: We assume that the CAS corpus can be effectively exploited for the development and testing of NLP tools and methods. Besides, the corpus will be used in NLP challenges and distributed to the research community.
Entities:
Keywords:
Corpus with clinical cases; Medical area; Morpho-syntactic and semantic annotation; Natural language processing; Reproducibility; Sustainability
Authors: Wendy W Chapman; Prakash M Nadkarni; Lynette Hirschman; Leonard W D'Avolio; Guergana K Savova; Ozlem Uzuner Journal: J Am Med Inform Assoc Date: 2011 Sep-Oct Impact factor: 4.497