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Authors: Jyh-Jong Tsay ; Bo-Liang Wu and Hou-Ji Dai

Affiliation: National Chung-Cheng University, Taiwan

Keyword(s): Pathway Database Integration, Data Matching, KEGG, MetaCyc.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Data Mining and Machine Learning ; Databases and Data Management ; Web Services in Bioinformatics

Abstract: Most of biological databases provide cross links that point to data records describing the same object in other databases. However, as more and more databases are available, manually creating and maintaining cross links becomes very time consuming, if not impossible. Existing databases provide only a small portion of all possible links. In this paper, we present a database cross link server BioDBLink that can automatically collect and generate cross links among biological databases. The core of BioDBLink is a data matching technique that identifies and matches data records or elements describing the same object among pathway databases. Experiment on a data set collected from several pathway, enzyme and compound databases shows that our approach is able to identify most of the cross links provided by current databases, discover a large number of missing links, and detect inconsistency and duplicate errors.

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Paper citation in several formats:
Tsay, J.; Wu, B. and Dai, H. (2011). BIODBLINK: MULTI-LEVEL DATA MATCHING FOR AUTOMATIC GENERATION OF CROSS LINKS AMONG BIOCHEMICAL PATHWAY DATABASES. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 125-130. DOI: 10.5220/0003136601250130

@conference{bioinformatics11,
author={Jyh{-}Jong Tsay. and Bo{-}Liang Wu. and Hou{-}Ji Dai.},
title={BIODBLINK: MULTI-LEVEL DATA MATCHING FOR AUTOMATIC GENERATION OF CROSS LINKS AMONG BIOCHEMICAL PATHWAY DATABASES},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={125-130},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003136601250130},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - BIODBLINK: MULTI-LEVEL DATA MATCHING FOR AUTOMATIC GENERATION OF CROSS LINKS AMONG BIOCHEMICAL PATHWAY DATABASES
SN - 978-989-8425-36-2
IS - 2184-4305
AU - Tsay, J.
AU - Wu, B.
AU - Dai, H.
PY - 2011
SP - 125
EP - 130
DO - 10.5220/0003136601250130
PB - SciTePress