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Open Access Database

PADB : Published Association Database

Hwanseok Rhee1 and Jin-Sung Lee123*

Author Affiliations

1 Department of Clinical Genetics, Yonsei University College of Medicine, Seoul, Korea

2 Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea

3 Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea

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BMC Bioinformatics 2007, 8:348  doi:10.1186/1471-2105-8-348

Published: 19 September 2007

Abstract

Background

Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in any association databases.

Description

We have developed a published association database (PADB; http://www.medclue.com/padb webcite) that includes both the genetic associations and the environmental risk factors available in PubMed database. Each genetic risk factor is linked to a molecular pathway database and the HapMap database through human gene symbols identified in the abstracts. And the risk measures such as odds ratios or hazard ratios are extracted automatically from the abstracts when available. Thus, users can review the association data sorted by the risk measures, and genetic associations can be grouped by human genes or molecular pathways. The search results can also be saved to tab-delimited text files for further sorting or analysis. Currently, PADB indexes more than 1,500,000 PubMed abstracts that include 3442 human genes, 461 molecular pathways and about 190,000 risk measures ranging from 0.00001 to 4878.9.

Conclusion

PADB is a unique online database of published associations that will serve as a novel and powerful resource for reviewing and interpreting huge association data of complex human diseases.