The CALBC Silver Standard Corpus for Biomedical Named Entities — A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers

Dietrich Rebholz-Schuhmann, Antonio José Jimeno Yepes, Erik M. van Mulligen, Ning Kang, Jan Kors, David Milward, Peter Corbett, Ekaterina Buyko, Katrin Tomanek, Elena Beisswanger, Udo Hahn


Abstract
The production of gold standard corpora is time-consuming and costly. We propose an alternative: the ‚silver standard corpus‘ (SSC), a corpus that has been generated by the harmonisation of the annotations that have been delivered from a selection of annotation systems. The systems have to share the type system for the annotations and the harmonisation solution has use a suitable similarity measure for the pair-wise comparison of the annotations. The annotation systems have been evaluated against the harmonised set (630.324 sentences, 15,956,841 tokens). We can demonstrate that the annotation of proteins and genes shows higher diversity across all used annotation solutions leading to a lower agreement against the harmonised set in comparison to the annotations of diseases and species. An analysis of the most frequent annotations from all systems shows that a high agreement amongst systems leads to the selection of terms that are suitable to be kept in the harmonised set. This is the first large-scale approach to generate an annotated corpus from automated annotation systems. Further research is required to understand, how the annotations from different systems have to be combined to produce the best annotation result for a harmonised corpus.
Anthology ID:
L10-1609
Volume:
Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC'10)
Month:
May
Year:
2010
Address:
Valletta, Malta
Venue:
LREC
SIG:
Publisher:
European Language Resources Association (ELRA)
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URL:
http://www.lrec-conf.org/proceedings/lrec2010/pdf/888_Paper.pdf
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http://www.lrec-conf.org/proceedings/lrec2010/pdf/888_Paper.pdf