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BMC Medical Informatics and Decision Making

, 5:21

First Online: 26 June 2005Received: 11 March 2004Accepted: 26 June 2005

Abstract

BackgroundAlthough 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.

MethodsHere 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.

ResultsIDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource IDR available at http:-bioinf.uta.fi-idr-. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases.

ConclusionThe 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 http:-bioinf.uta.fi-idml-.

List of abbreviationsAxKitAn XML Delivery Toolkit for Apache

BioWAPBioinformatics service for portable devices

DOMDocument Object Model

DTDDocument Type Definition

ebXMLElectronic Business XML

EDDNALEuropean Directory of DNA Diagnostic Laboratories

EMBLGenetic sequence database by European Molecular Biology Laboratory

GDBGenome Database

GenBankGenetic sequence database by National Center for Biotechnology Information

HTMLHypertext Markup Language

IDMLInherited Disease Markup Language

IDRImmunoDeficiency Resource

IEInformation extraction

IFNγInterferon gamma

NLPNatural language processing

OMIMOnline Mendelian Inheritance in Man

OMIMxPrimary Immunodeficiency

PDBProtein DataBank

PDFPortable Document Format

PfamProtein Families Database

ProDomProtein Domain Database

PROSITEDatabase of Protein Families and Domains

RDFResource Description Framework

SGMLStandard Generalized Markup Language

SMARTSimple Modular Architecture Research Tool

SNPSingle nucleotide polymorphism

SOAPSimple Object Access Protocol

SOURCEGenomic resource in the Internet

Swiss-ProtProtein knowledgebase

UDDIUniversal Description, Discovery, and Integration

URLUnified Resource Locator

W3CWorld Wide Web Consortium

WAPWireless Application Protocol

WMLWireless Markup Language

WSDLWeb Services Definition-Description Language

XMLExtensible Markup Language

XPSXPathScript

XSLExtensible Style Language

XSLTXSL Transformations

XSPeXtensible Server Pages

Electronic supplementary materialThe online version of this article doi:10.1186-1472-6947-5-21 contains supplementary material, which is available to authorized users.

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Autor: Jouni Väliaho - Pentti Riikonen - Mauno Vihinen

Fuente: https://link.springer.com/



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