Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition

Philip Ogren, Guergana Savova, Christopher Chute


Abstract
We report on the construction of a gold-standard dataset consisting of annotated clinical notes suitable for evaluating our biomedical named entity recognition system. The dataset is the result of consensus between four human annotators and contains 1,556 annotations on 160 clinical notes using 658 unique concept codes from SNOMED-CT corresponding to human disorders. Inter-annotator agreement was calculated on annotations from 100 of the documents for span (90.9%), concept code (81.7%), context (84.8%), and status (86.0%) agreement. Complete agreement for span, concept code, context, and status was 74.6%. We found that creating a consensus set based on annotations from two independently-created annotation sets can reduce inter-annotator disagreement by 32.3%. We found little benefit to pre-annotating the corpus with a third-party named entity recognizer.
Anthology ID:
L08-1366
Volume:
Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08)
Month:
May
Year:
2008
Address:
Marrakech, Morocco
Venue:
LREC
SIG:
Publisher:
European Language Resources Association (ELRA)
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Pages:
Language:
URL:
http://www.lrec-conf.org/proceedings/lrec2008/pdf/796_paper.pdf
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http://www.lrec-conf.org/proceedings/lrec2008/pdf/796_paper.pdf