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. 2007 Sep 19:8:348.
doi: 10.1186/1471-2105-8-348.

PADB: published association database

Hwanseok Rhee  1 , Jin-Sung Lee
Affiliations

PADB: published association database

Hwanseok Rhee et al. BMC Bioinformatics. .

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) 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.

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Figures

Figure 1
Figure 1
Sorting associations by the risk measures. PADB automatically extracts the odds ratio, hazard ratio, risk ratio and relative risk data if they are available in sentences. When multiple associations are reported in a single sentence, those multiple association data are indexed as separate records.
Figure 2
Figure 2
Linking genetic risks to molecular pathway and HapMap information. PADB can help biomedical researchers to review and interpret genetic risk factors more effectively along with molecular pathway and HapMap information.
Figure 3
Figure 3
Median risk measures of 'risk' and 'protective' associations during the past 25 years. (A) The median strengths of risk associations remain quite stable around 2.5 (0.4 when log-transformed) in spite of the exponential increase of published association data during the past 25 years. (B) The median strengths of protective associations also remain stable around 0.6 (-0.2 when log-transformed).
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References

    1. Becker KG, Barnes KC, Bright TJ, Wang SA. The genetic association database. Nat Genet. 2004;36:431–432. doi: 10.1038/ng0504-431. - DOI - PubMed
    1. Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, Khoury MJ. Tracking the Epidemiology of Human Genes in the Literature: The HuGE Published Literature Database. Am J Epidemiol. 2006;164:1–4. doi: 10.1093/aje/kwj175. - DOI - PubMed
    1. Altman RB. PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet. 2007;39:426. doi: 10.1038/ng0407-426. - DOI - PMC - PubMed
    1. Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE. Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet. 2007;39:17–23. doi: 10.1038/ng1934. - DOI - PubMed
    1. Hulbert EM, Smink LJ, Adlem EC, Allen JE, Burdick DB, Burren OS, Cavnor CC, Dolman GE, Flamez D, Friery KF, Healy BC, Killcoyne SA, Kutlu B, Schuilenburg H, Walker NM, Mychaleckyj J, Eizirik DL, Wicker LS, Todd JA, Goodman N. T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res. 2007;35:D742–6. doi: 10.1093/nar/gkl933. - DOI - PMC - PubMed

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