IDPredictor: predict database links in biomedical database

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doi doi:10.2390/biecoll-jib-2012-190
submission May 16, 2012
published June 26, 2012
NCBI PubMed PubMed ID 22736059

Hendrik Mehlhorn, Matthias Lange, Uwe Scholz and Falk Schreiber

Correspondence should be addressed to:
Hendrik Mehlhorn
Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466 Gatersleben, Germany
ed.nebelsretag-kpi@nullnrohlhem


Abstract

Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data is spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a semi-automated data exploration in information retrieval environments, an integrated view to databases is essential. Search engines have the potential of assisting in data retrieval from these structured sources, but fall short of providing a comprehensive knowledge excerpt out of the interlinked databases. A prerequisit of supporting the concept of an integrated data view is to acquire insights into cross-references among database entities. This issue is being hampered by the fact, that only a fraction of all possible cross-references are explicitely tagged in the particular biomedical informations systems. In this work, we investigate to what extend an automated construction of an integrated data network is possible. We propose a method that predicts and extracts cross-references from multiple life science databases and possible referenced data targets. We study the retrieval quality of our method and report on first, promising results. The method is implemented as the tool IDPredictor, which is published under the DOI 10.5447/IPK/2012/4 and is freely available using the URL: http://dx.doi.org/10.5447/IPK/2012/4.

Reference

Hendrik Mehlhorn, Matthias Lange, Uwe Scholz and Falk Schreiber. IDPredictor: predict database links in biomedical database. Journal of Integrative Bioinformatics, 9(2):190, 2012. Online Journal: http://journal.imbio.de/index.php?paper_id=190
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