World Scientific
Skip main navigation

Cookies Notification

We use cookies on this site to enhance your user experience. By continuing to browse the site, you consent to the use of our cookies. Learn More
×
Our website is made possible by displaying certain online content using javascript.
In order to view the full content, please disable your ad blocker or whitelist our website www.worldscientific.com.

System Upgrade on Mon, Jun 21st, 2021 at 1am (EDT)

During this period, the E-commerce and registration of new users may not be available for up to 6 hours.
For online purchase, please visit us again. Contact us at [email protected] for any enquiries.

SEMANTICALLY INTEROPERABLE XML DATA

    XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups.

    References

    • "cabig". , https://cabig.nci.nih.gov/ . Google Scholar
    • caGrid XML Data Service Framework (xService). https://web.cci.emory.edu/confluence/display/xmlds/ . Google Scholar
    • Cancer data standards registry and repository (cadsr). https://cabig.nci.nih.gov/concepts/caDSR/ . Google Scholar
    • CQL: Common/caGrid Query Language. http://cagrid.org/display/dataservices/CQL . Google Scholar
    • DB2 Express-C Overview. http://www-306.ibm.com/software/data/db2/express/ . Google Scholar
    • Enterprise vocabulary services (evs). https://cabig.nci.nih.gov/concepts/EVS/ . Google Scholar
    • eXist XML Database. http://www.exist-db.org/ . Google Scholar
    • Health Level Seven International (HL7) . Google Scholar
    • Integrating the healthcare enterprise (ihe). http://wiki.ihe.net/ . Google Scholar
    • Introduce: The cagrid service creation toolkit. http://cagrid.org/display/introduce/Home . Google Scholar
    • The mobius project at osu bmi. http://www.projectmobius.org . Google Scholar
    • OpenMDR. http://cagrid.org/display/MDR/ . Google Scholar
    • Oracle Berkeley DB XML. http://www.oracle.com/database/berkeley-db/xml/ . Google Scholar
    • Oracle XML DB. http://www.oracle.com/technology/tech/xml/xmldb . Google Scholar
    • owl-s: Semantic markup for web services. http://www.w3.org/Submission/OWL-S/ . Google Scholar
    • Semantic integration workbench (siw). https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Semantic_Integration_Workbench_%28SIW%29 . Google Scholar
    • Tamino: The XML database. www.softwareag.com/us/products/wm/tamino/ . Google Scholar
    • "uml model browser". , https://wiki.nci.nih.gov/display/caDSR/UML+ Model+Browser . Google Scholar
    • Xsl transformations (xslt). http://www.w3.org/TR/xslt . Google Scholar
    • Semantic integration of xservice for the creation of cabig compatible xml data services. https://web.cci.emory.edu/confluence/download/attachments/1015923/CristobalThesis.pdf, 2010 . Google Scholar
    • Aim data service at emory university. https://web.cci.emory.edu/confluence/display/IVI/AIME, 2011 . Google Scholar
    • Pathology analytical imaging standards. https://web.cci.emory.edu/confluence/display/PAIS, 2011 . Google Scholar
    • Tcga enterprise use case. https://wiki.nci.nih.gov/display/Imaging/TCGA+ Enterprise+Use+Case, 2011 . Google Scholar
    • Xsd2uml svn repository. https://scm.cci.emory.edu/svn/xservice/branches/xService_1.3.5_caBIGSemanticIntegration/projects/caBIGSemanticIntegration, 2011 . Google Scholar
    • N. Baleset al., A framework for xml-based integration of data, visualization and analysis in a biomedical domain, XSym (2005) pp. 207–221. Google Scholar
    • M. Bernauer, G. Kappel and G. Kramler, Web Engineering, Lecture Notes in Computer Science 3140, eds. N. Koch, P. Fraternali and M. Wirsing (Springer, Berlin Heidelberg, 2004) pp. 440–444. CrossrefGoogle Scholar
    • G. Booch, M. Christerson, M. Fuchs and J. Koistinen, UML for XML schema mapping specification, White paper, Rational, 1999 . Google Scholar
    • D.   Carlson , Modeling XML Applications with UML: Practical e-Business Applications ( Addison-Wesley , 2001 ) . Google Scholar
    • D. Channinet al., Journal of Digital Imaging  (2009). Google Scholar
    • E. Domínguezet al., A survey of UML models to XML schemas transformations, Web Information Systems Engineering (2007) pp. 184–195. Google Scholar
    • D. J. Foranet al., JAMIA 18(4), 403 (2011). ISIGoogle Scholar
    • D. Marcuset al., Neuroinformatics 11 (2007). Google Scholar
    • J.   McCarthy et al. , Data modeling and harmonization with OWL: Opportunities and lessons learned , Fifth International Workshop on Semantic Web Enabled Software Engineering ( 2009 ) . Google Scholar
    • M. Mesitiet al., BMC Bioinformatics 10(S7), (2009), DOI: 10.1186/1471-2105-10-S12-S7. Google Scholar
    • W. Provost, Ml for w3c xml schema design, 2002 . Google Scholar
    • N. Routledge, L. Bird and A. Goodchild, UML and XML schema, ADC (2002) pp. 157–166. Google Scholar
    • A. Shabo, S. Rabinovici-Cohen and P. Vortman, IBM Syst. J. 45(2), 361 (2006), DOI: 10.1147/sj.452.0361. Crossref, ISIGoogle Scholar
    • F. Wanget al., Sciport: An adaptable scientific data integration platform for collaborative scientific research, VLDB (2007) pp. 1310–1313. Google Scholar
    • F. Wanget al., Journal of Pathology Informatics 2(32), (2011), DOI: 10.4103/2153-3539.92037. Google Scholar
    • F.   Wang , P.   Liu and J.   Pearson , Database Technology for Life Sciences and Medicine , SciPort: An Extensible Data Management Platform for Biomedical Research   6 ( World Scientific , 2010 ) . Google Scholar
    • F.   Wang et al. , Experiment management with metadata based integration for collaborative scientific research , ICDE ( 2006 ) . Google Scholar
    • F.   Wang et al. , Managing and querying image annotation and markup in XML , SPIE Medical Imaging ( 2010 ) . Google Scholar
    • F.   Wang et al. , An adaptable XML based approach for scientific data management and integration , SPIE Medical Imaging 6919 ( 2008 ) . Google Scholar
    Remember to check out the Most Cited Articles!

    Check out our titles in Semantic Computing!