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Distribution of immunodeficiency fact files with XML – from Web to WAP

By Jouni Väliaho, Pentti Riikonen and Mauno Vihinen

Abstract

BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at . A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at

Topics: Research Article
Publisher: BioMed Central
Year: 2005
DOI identifier: 10.1186/1472-6947-5-21
OAI identifier: oai:pubmedcentral.nih.gov:1184081
Provided by: PubMed Central

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Citations

  1. (2004). 4.0: towards genomic data integration. Nucleic Acids Res
  2. (2003). Alizadeh AA: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res
  3. (2004). Apweiler R: The EMBL Nucleotide Sequence Database. Nucleic Acids Res
  4. (2001). Barillot E: XML, bioinformatics and data integration. Bioinformatics
  5. (2001). BioWAP, mobile Internet service for bioinformatics. Bioinformatics
  6. (2003). CA: Bioinformatics and medical informatics: collaborations on the road to genomic medicine?
  7. (2003). CA: myGrid: personalised bioinformatics on the information grid. Bioinformatics
  8. (2001). CI: Primary immunodeficiency mutation databases. Adv Genet
  9. (2002). Collins FS: Genomic medicine - a primer.
  10. (2001). DR: RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res
  11. (2002). E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res
  12. (2004). Ensembl 2004. Nucleic Acids Res
  13. (1999). Etzioni A: Diagnostic criteria for primary immunodeficiencies. Clin Immunol
  14. (2002). Etzold T: The EBI SRS servernew features. Bioinformatics
  15. (2002). euGenes: a eukaryote genome information system.
  16. (2003). From biological databases to platforms for biomedical discovery. Trends in Biotechnol
  17. (1998). Genatlas database, genes and development defects.
  18. (2000). GeneClinics: a hybrid text/data electronic publishing model using XML applied to clinical genetic testing.
  19. (2004). Genew: the Human Gene Nomenclature Database,
  20. Genome Database [http://www.gdb.org/]
  21. (2002). IDR: the ImmunoDeficiency Resource. Nucleic Acids Res
  22. (2003). Information storage and management in large web-based applications using XML.
  23. Integrating relational database schemas using a standardized dictionary: ; Las Vegas,
  24. International Organization for Standardization: Standard Generalized Markup Language (SGML).
  25. Lancet D: GeneCards: encyclopedia for genes, proteins and diseases. [http://bioinformat ics.weizmann.ac.il/cards].
  26. (2002). Majoros WH: Genomics and natural language processing. Nat Rev Genet
  27. (2002). Mining the bibliome: searching for a needle in a haystack? New computing tools are needed to effectively scan the growing amount of scientific literature for useful information. EMBO Rep
  28. (2002). Mobile access to biological databases on the Internet.
  29. (2003). MS: A vision for the future of genomics research.
  30. Nicull D: ebXML Technical Architecture Specification
  31. (2000). Novel immunodeficiency data servers. Immunol Rev
  32. (2004). Online Registry of Genetic and Clinical Immunodeficiency Diagnostic Laboratories, IDdiagnostics.
  33. (2003). P: LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem
  34. (2002). P: PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform
  35. (1997). Pieces of the puzzle: expressed sequence tags and the catalog of human genes.
  36. (2002). ProDom: automated clustering of homologous domains. Brief Bioinform
  37. (2003). SM: Standards for detailed clinical models as the basis for medical data exchange and decision support.
  38. (2002). Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res
  39. Tarczy-Hornoch P: A model for data integration systems of biomedical data applied to online genetic databases.
  40. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures.
  41. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res
  42. (2002). VA: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res
  43. (2003). Vaughan R,Publish with BioMed Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime."
  44. Web Consortium:
  45. Web Consortium: Document Object Model (DOM)
  46. Web Consortium: Extensible Markup Language (XML)
  47. Web Consortium: Namespaces in XML.
  48. Web Consortium: RDF/XML Syntax Specification (Revised).
  49. (2001). WW: GeneLynx: a gene-centric portal to the human genome. Genome Res
  50. (2001). YJ: Initial sequencing and analysis of the human genome. Nature

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