title: Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature.
abstract: The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical information extraction system, BioIE, to address both of these needs by utilizing a full-fledged English grammar formalism, or a combinatory categorial grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, appositive structures, and anaphoric expressions. In order to deal with real-world syntactic variations of ontological terms, BioIE utilizes the syntactic dependencies between words in sentences as well, based on the observation that the component words in an ontological term usually appear in a sentence with known patterns of syntactic dependencies.
authors.affiliation: Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea. jjkim@nlp.kaist.ac.kr
authors.forename: Jung-Jae
authors.initials: JJ
authors.lastname: Kim
authors.forename: Jong C
authors.initials: JC
authors.lastname: Park
mesh_terms: D000043:Abstracting and Indexing; D003628:Database Management Systems; D016206:Databases, Bibliographic; D005786:Gene Expression Regulation / Q000502:physiology*; D016247:Information Storage and Retrieval / Q000379:methods*; D016239:MEDLINE; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods; D010506:Periodicals as Topic; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000378:metabolism*; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins