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. 2003;42(5):557-63.
doi: 10.1267/meth03050557.

From phenotype to genotype: issues in navigating the available information resources

J A Mitchell  1 , A T McCray, O Bodenreider
Affiliations

From phenotype to genotype: issues in navigating the available information resources

J A Mitchell et al. Methods Inf Med. 2003.

Abstract

Objectives: As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases.

Methods: We focused on a set of single gene diseases selected from main topics in MEDLINEplus, the NLM's principal resource focused on consumers. We used publicly available websites to investigate specific questions about the genes and gene products associated with the diseases. We also investigated questions of knowledge and data representation for the information resources and navigational issues.

Results: Many online resources are available but they are complex and technical. The major challenges encountered when navigating from phenotype to genotype were (1) complexity of the data, (2) dynamic nature of the data, (3) diversity of foci and number of information resources, and (4) lack of use of standard data and knowledge representation methods.

Conclusions: Three major informatics issues arise from the navigational challenges. First, the official gene names are insufficient for navigation of these web resources. Second, navigational inconsistencies arise from difficulties in determining the number and function of alternate forms of the gene or gene product and maintaining currency with this information. Third, synonymy and polysemy cause much confusion. These are severe obstacles to computational navigation from phenotype to genotype, especially for individuals who are novices in the underlying science. Tools and standards to facilitate this navigation are sorely needed.

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Figures

Fig. 1
Fig. 1
Navigation path from phenotype to genotype through the information resources used to answer the questions of the study as they pertain to Marfan syndrome
See this image and copyright information in PMC

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References

    1. The Human Genome. Nature. 2001;409 (6822):813–958. - PubMed
    1. Baxevanis AD. The Molecular Biology Database Collection: 2002 update. Nucleic Acids Res. 2002;30 (1):1–12. - PMC - PubMed
    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic Acids Res. 2002;30 (1):17–20. - PMC - PubMed
    1. Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H, et al. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res. 2002;30 (1):27–30. - PMC - PubMed
    1. Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 2002;30 (1):21–6. - PMC - PubMed

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