PASBio: predicate-argument structures for event extraction in molecular biology |
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Authors: | Tuangthong?Wattarujeekrit Parantu?K?Shah Email author" target="_blank">Nigel?CollierEmail author |
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Institution: | (1) National Institute of Informatics (NII), National Center of Sciences, Hitotsubashi 2-1-2, Chiyoda-ku, Tokyo 101-8430, Japan;(2) Structural and Computational Biology Program, European Molecular Biology Laboratory, Heidelberg, Germany;(3) Max Delbruck Center for Molecular Medicine, Berlin-Buch, Germany |
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Abstract: | Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from
free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest
results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences
but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A
consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the
relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically
correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component
is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several
projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas
where sentence understanding is required like machine translation and text summarization. In this article, we explore the
need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require
consideration in their construction. |
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