Extracting secondary bio-event arguments with extraction constraints

Yutaka Sasaki, Xinglong Wang, Sophia Ananiadou

    Research output: Contribution to journalArticlepeer-review


    This paper describes our bio-event extraction system developed for the BioNLP 2009 Shared Task 2, with focus on its capability of extracting secondary biological event arguments from literature. Shared Task 2 is particularly interesting because when browsing literature, biologists often need to understand conditions surrounding biological events, which are usually expressed by secondary event arguments (e.g., binding sites). To achieve our goal, we take an approach that extracts n-ary relations from text using event extraction constraints automatically generated from a training corpus. Event constraints consist of sequences of trigger words and semantic roles which we automatically identify using Conditional Random Fields (CRFs). Unlike most other systems participating in this shared task, our system is light-weight and relies on neither external resources (e.g., Ontologies and dictionaries) nor natural language processing software (e.g., POS taggers and parsers). The official test results show that our approach performed well on extracting secondary arguments in Task 2, yielding the highest precision at 76.62% and the second highest F-measure at 43.22%. © 2011 Wiley Periodicals Inc.
    Original languageEnglish
    Pages (from-to)702-721
    Number of pages19
    JournalComputational Intelligence
    Issue number4
    Publication statusPublished - Nov 2011


    • bio-event extraction
    • BioNLP shared task
    • information extraction


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