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Open Access Highly Accessed Research article

Corpus annotation for mining biomedical events from literature

Jin-Dong Kim1*, Tomoko Ohta1 and Jun'ichi Tsujii123

Author Affiliations

1 Department of Computer Science, School of Information Science and Technology, University of Tokyo, Tokyo, Japan

2 School of Computer Science, University of Manchester, Manchester, UK

3 National Centre for Text Mining, University of Manchester, Manchester, UK

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BMC Bioinformatics 2008, 9:10  doi:10.1186/1471-2105-9-10

Published: 8 January 2008

Abstract

Background

Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation.

Results

We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation.

Conclusion

The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain.