Methods Inf Med 2003; 42(05): 557-563
DOI: 10.1055/s-0038-1634383
Original Article
Schattauer GmbH

From Phenotype to Genotype: Issues in Navigating the Available Information Resources

J. A. Mitchell
1   Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
2   Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO, USA
,
A. T. McCray
1   Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
,
O. Bodenreider
1   Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
› Institutsangaben
Weitere Informationen

Publikationsverlauf

Publikationsdatum:
08. Februar 2018 (online)

Summary

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.

Conventions used in this paper: Gene names, gene products and gene symbols are in italics.


 
  • References

  • 1 The Human Genome.. Nature. 2001; 409 6822 813-958.
  • 2 Baxevanis AD. The Molecular Biology Database Collection: 2002 update. Nucleic Acids Res 2002; 30 (Suppl. 01) 1-12.
  • 3 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic Acids Res 2002; 30 (Suppl. 01) 17-20.
  • 4 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 (Suppl. 01) 27-30.
  • 5 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 (Suppl. 01) 21-6.
  • 6 Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU. et al. Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res 2002; 30 (Suppl. 01) 13-6.
  • 7 O’Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform 2002; 3 (Suppl. 03) 275-84.
  • 8 Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res 2002; 30 (Suppl. 01) 42-6.
  • 9 Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2002; 30 (Suppl. 01) 52-5.
  • 10 Miller N, Lacroix EM, Backus JE. MEDLINE-plus: building and maintaining the National Library of Medicine’s consumer health Web service. Bull Med Libr Assoc 2000; 88 (Suppl. 01) 11-7.
  • 11 McCray AT. Better access to information about clinical trials. Ann Intern Med 2000; 133 (Suppl. 08) 609-14.
  • 12 Pagon RA, Tarczy-Hornoch P, Baskin PK, Edwards JE, Covington ML, Espeseth M. et al. GeneTests-GeneClinics: genetic testing information for a growing audience. Hum Mutat 2002; 19 (Suppl. 05) 501-9.
  • 13 Bodenreider O, Mitchell JA, McCray AT. Evaluation of the UMLS as a Terminology and Knowledge Resource for Biomedical Informatics. Proc AMIA Symp. 2002: 61-5.
  • 14 Srinivasan P, Mitchell JA, Bodenreider O, Pant G, Menczer F. Web crawling agents for retrieving biomedical information. In: Proceedings of the International Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS 2002),. Bologna, Italy: July 15, 2002; 2002
  • 15 Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinform 2000; 1 (Suppl. 04) 398-414.
  • 16 Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB. Ontology development for a pharmacogenetics knowledge base. Pac Symp Biocomput. 2002: 65-76.
  • 17 Chen RO, Felciano R, Altman RB. RIBOWEB: linking structural computations to a knowledge base of published experimental data. Proc Int Conf Intell Syst Mol Biol 1997; 5: 84-7.
  • 18 Kazic T. Semiotes: a semantics for sharing. Bioinformatics 2000; 16 (Suppl. 12) 1129-44.
  • 19 Wroe C, Stevens R, Goble C, Ashburner M. An evolutionary methodology to migrate the gene ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput. 2003 (in press).
  • 20 Stevens R, Baker P, Bechhofer S, Ng G, Jacoby A, Paton NW. et al. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics 2000; 16 (Suppl. 02) 184-5.
  • 21 The Gene Ontology Consortium.. Creating the gene ontology resource: design and implementation. Genome Res 2001; 11 (Suppl. 08) 1425-33.