Developing a corpus of clinical notes manually annotated for part-of-speech.
OBJECTIVE
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.


CONCLUSIONS
Our preliminary experimental results indicate the necessity for adapting state-of-the-art POS taggers to the sublanguage domain of clinical text.
Pakhomov
Serguei V
SV
Division of Biomedical Informatics, Mayo College of Medicine, Rochester, MN 55905, USA. Pakhomov.Serguei@mayo.edu
Coden
Anni
A
Chute
Christopher G
CG
D000043:Abstracting and Indexing / Q000379:methods*; D001185:Artificial Intelligence; D015510:Clinical Medicine; D003628:Database Management Systems; D016206:Databases, Bibliographic; D016247:Information Storage and Retrieval / Q000379:methods; D008037:Linguistics; D009323:Natural Language Processing; D012660:Semantics; D009626:Terminology as Topic; D018875:Vocabulary, Controlled