Affiliations: Department of Computational Biology, Graduate School
of Frontier Science, The University of Tokyo, Kiban-3A1(CB01) 5-1-5,
Kashiwanoha Kashiwa, Chiba, 277-8561, Japan | Central Research Laboratory, Hitachi Ltd. 1-280
Higashi-koigakubo Kokubunji city, Tokyo, 185-8601, Japan
Note: [] Corresponding author: Department of Computational Biology
Graduate School of Frontier Science, University of Tokyo Kiban-3A1(CB01) 1-5-1
Kashiwanoha Kashiwa, Chiba, 277-8561, Japan. Tel.: +81 4 7136 3982; Fax: +81 4
7136 3975; E-mail: [email protected]
Abstract: With the exponentially increasing amount of information in the
biomedical field, the significance of advanced information retrieval and
information extraction, as well as the role of databases, has been increasing.
PRIME is an integrated gene/protein informatics database based on natural
language processing. It provides automatically extracted
protein/family/gene/compound interaction information including both physical
and genetic interactions, gene ontology based functions, and graphic pathway
viewers. Gene/protein/family names and functional terms are recognized based on
dictionaries developed in our laboratory. The interaction and functional
information are extracted by syntactic dependencies and various phrase
patterns. We have included about 920,000 (non-redundant) protein interactions
and 360,000 annotated gene-function relationships for major eukaryotes. By
combining the sequence and text information, the pathway comparison between two
organisms and simple pathway deduction based on other organism interaction
data, and pathway filtering using tissue expression data, are also available.
This database is accessible at
http://prime.ontology.ims.u-tokyo.ac.jp:8081.
Keywords: protein interaction, biological process, pathway database, natural language processing
