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MOLECULAR EVENT EXTRACTION FROM LINK GRAMMAR PARSE TREES IN THE BIONLP’09 SHARED TASK
Author(s) -
Hakenberg Jörg,
Solt Illés,
Tikk Domonkos,
Nguyên Võ Há,
Tari Luis,
Nguyen Quang Long,
Baral Chitta,
Leser Ulf
Publication year - 2011
Publication title -
computational intelligence
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.353
H-Index - 52
eISSN - 1467-8640
pISSN - 0824-7935
DOI - 10.1111/j.1467-8640.2011.00404.x
Subject(s) - computer science , natural language processing , parsing , event (particle physics) , task (project management) , biomedical text mining , artificial intelligence , benchmark (surveying) , sentence , text mining , physics , management , geodesy , quantum mechanics , economics , geography
The BioNLP’09 Shared Task deals with extracting information on molecular events, such as gene expression and protein localization, from natural language text. Information in this benchmark are given as tuples including protein names, trigger terms for each event, and possible other participants such as bindings sites. We address all three tasks of BioNLP’09: event detection, event enrichment, and recognition of negation and speculation. Our method for the first two tasks is based on a deep parser; we store the parse tree of each sentence in a relational database scheme. From the training data, we collect the dependencies connecting any two relevant terms of a known tuple, that is, the shortest paths linking these two constituents. We encode all such linkages in a query language to retrieve similar linkages from unseen text. For the third task, we rely on a hierarchy of hand‐crafted regular expressions to recognize speculation and negated events. In this paper, we added extensions regarding a post‐processing step that handles ambiguous event trigger terms, as well as an extension of the query language to relax linkage constraints. On the BioNLP Shared Task test data, we achieve an overall F1‐measure of 32%, 29%, and 30% for the successive Tasks 1, 2, and 3, respectively.