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ISSN 0582-9879 Acta Biochim et Biophysica Sinica 2004, 36(5):365-370 CN 31-1300/Q

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Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

Shun-Liang CAO, Lei QIN¹, Wei-Zhong HE¹, Yang ZHONG², Yang-Yong ZHU, and Yi-Xue LI^1,3*
( Department of Computing and Information Technology, Fudan University, Shanghai 200433, China;
¹Shanghai Center for Bioinformation Technology, Shanghai 200235, China;
²School of Life Sciences, Fudan University, Shanghai 200433, China;
³Bioinformation Center of Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031, China )

Abstract Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

Key words Gene Ontology; semantic search; BioDW

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Received: January 16, 2004 Accepted: March 9, 2004
This work was supported by the grants from the National High Technology and Development Program of China (No. 2002AA231011, No.2002AA231041), the National Key Project for Basic Research (No. 2002CB512801) and the Major Project of Shanghai Commission of Scienceand Technology (No. 02DJ14013)
*Corresponding author: Tel, 86-21-64836199; Fax, 86-21-64838882; Email,yxli@scbit.org