Extraction of biomedical knowledge from literature and its systematization

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It is indispensable to develop databases of gene and protein interactions and their functions extracted from literature so that we can systematically understand lives based on flood of biological data such as genome sequences, gene expressions, and interactions between molecules. From this perspective, we have been tackling two challenges, that is, 1) automatically extracting knowledge of biological functions from literature and 2) representing and utilizing the extracted knowledge on computers. Followings are brief descriptions of our efforts.a)We developed a knowledge extraction system. We almost established a method of extracting information of gene / protein / chemical compounds interaction from literature. Our system achieved a recall of about 50 % and a precision of about 90 %.b)We developed dictionaries of gene names and gene family names that are used for identifying those names in literature. GENA, one of the dictionaries, stores about 880,000-gene names and, depending on organisms, covers 90-95 % of all the genes appearing in literature). By using the dictionaries and the above mentioned extraction system, we developed and published an interaction database called PRIME and a dictionary of biological functional terms. PRIME stores about three million interactions of six eukaryotes such as human and rat.c)We prepared a corpus and an ontology for knowledge extraction. To develop and evaluate a knowledge extraction system, a tagged corpus and an ontology of defining domain specific terms are needed. We, therefore, developed and published the GENIA corpus that is composed from 2,000 MEDLINE abstracts whose terms are given semantic and part-of-speech tags accordingly. In addition, we developed the GENIA ontology to be used for adding semantic tags to terms in literature.