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 LI1,3*
( 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,[email protected]