TY - JOUR
T1 - Developing a corpus of clinical notes manually annotated for part-of-speech
AU - Pakhomov, Serguei V.
AU - Coden, Anni
AU - Chute, Christopher G.
N1 - Funding Information:
We would like to thank our medical index experts Barbara Abbot, Pauline Funk and Debora Albrecht for their persistent efforts in the difficult task of corpus annotation. This work was done in part under the NLM Training grant (# T15 LM07041-19 ) .
PY - 2006/6
Y1 - 2006/6
N2 - Purpose: This paper presents a project whose main goal is to construct a corpus of clinical text manually annotated for part-of-speech (POS) information. We describe and discuss the process of training three domain experts to perform linguistic annotation. Methods: Three domain experts were trained to perform manual annotation of a corpus of clinical notes. A part of this corpus was combined with the Penn Treebank corpus of general purpose English text and another part was set aside for testing. The corpora were then used for training and testing statistical part-of-speech taggers. We list some of the challenges as well as encouraging results pertaining to inter-rater agreement and consistency of annotation. Results: We used the Trigrams'n'Tags (TnT) [T. Brants, TnT-a statistical part-of-speech tagger, In: Proceedings of NAACL/ANLP-2000 Symposium, 2000] tagger trained on general English data to achieve 89.79% correctness. The same tagger trained on a portion of the medical data annotated for this project improved the performance to 94.69%. Furthermore, we find that discriminating between different types of discourse represented by different sections of clinical text may be very beneficial to improve correctness of POS tagging. Conclusion: Our preliminary experimental results indicate the necessity for adapting state-of-the-art POS taggers to the sublanguage domain of clinical text.
AB - Purpose: This paper presents a project whose main goal is to construct a corpus of clinical text manually annotated for part-of-speech (POS) information. We describe and discuss the process of training three domain experts to perform linguistic annotation. Methods: Three domain experts were trained to perform manual annotation of a corpus of clinical notes. A part of this corpus was combined with the Penn Treebank corpus of general purpose English text and another part was set aside for testing. The corpora were then used for training and testing statistical part-of-speech taggers. We list some of the challenges as well as encouraging results pertaining to inter-rater agreement and consistency of annotation. Results: We used the Trigrams'n'Tags (TnT) [T. Brants, TnT-a statistical part-of-speech tagger, In: Proceedings of NAACL/ANLP-2000 Symposium, 2000] tagger trained on general English data to achieve 89.79% correctness. The same tagger trained on a portion of the medical data annotated for this project improved the performance to 94.69%. Furthermore, we find that discriminating between different types of discourse represented by different sections of clinical text may be very beneficial to improve correctness of POS tagging. Conclusion: Our preliminary experimental results indicate the necessity for adapting state-of-the-art POS taggers to the sublanguage domain of clinical text.
KW - Domain adaptation
KW - Manual text annotation
KW - Medical domain
KW - Natural language processing
KW - Statistical part-of-speech tagging
KW - Text analysis
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U2 - 10.1016/j.ijmedinf.2005.08.006
DO - 10.1016/j.ijmedinf.2005.08.006
M3 - Article
C2 - 16169769
AN - SCOPUS:33646159049
SN - 1386-5056
VL - 75
SP - 418
EP - 429
JO - International Journal of Medical Informatics
JF - International Journal of Medical Informatics
IS - 6
ER -