Semantic search among heterogeneous biological databases based on gene ontology.

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by Shun-Liang Cao, Lei Qin, Wei-Zhong He, Yang Zhong, Yang-Yong Zhu, Yi-Xue Li
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.
Reference:
Semantic search among heterogeneous biological databases based on gene ontology. (Shun-Liang Cao, Lei Qin, Wei-Zhong He, Yang Zhong, Yang-Yong Zhu, Yi-Xue Li), In Acta biochimica et biophysica Sinica, volume 36, 2004.
Bibtex Entry:
@article{Cao2004,
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.},
author = {Cao, Shun-Liang and Qin, Lei and He, Wei-Zhong and Zhong, Yang and Zhu, Yang-Yong and Li, Yi-Xue},
issn = {1672-9145},
journal = {Acta biochimica et biophysica Sinica},
keywords = {Database Management Systems,Databases, Factual,Databases, Genetic,Documentation,Information Storage and Retrieval,Information Storage and Retrieval: methods,Natural Language Processing,Phylogeny,SML-LIB-BIBLIO,Semantics,Systems Integration,Terminology as Topic,Vocabulary, Controlled,lang:ENG},
mendeley-tags = {SML-LIB-BIBLIO,lang:ENG},
month = may,
number = {5},
pages = {365--70},
pmid = {15156279},
title = {{Semantic search among heterogeneous biological databases based on gene ontology.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15156279},
volume = {36},
year = {2004}
}
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