Using semantic web technologies for the generation of domain-specific templates to support clinical study metadata standards

Journal of Biomedical Semantics

Volumn 7, Issue 1, 2016, Pages

  Jiang, Guoqian ^a   Evans, Julie ^b   Endle, Cory M ^a   Solbrig, Harold R ^a   Chute, Christopher ^c  

^a MAYO CLINIC   (United States)

^b Clinical Data Interchange Standards Consortium   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

BRIDG; CIMI; Clinical study meta data standards; Detailed clinical model; Doman analysis model; RDF; Semantic web technologies

Indexed keywords

HUMAN; INTERNET; MEDICAL INFORMATICS; MEDICAL RESEARCH; PROCEDURES; SEMANTICS; STANDARD; STANDARDS; THEORETICAL MODEL;

BIOMEDICAL RESEARCH; HUMANS; INTERNET; MEDICAL INFORMATICS; MODELS, THEORETICAL; REFERENCE STANDARDS; SEMANTICS;

EID: 85008406157     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/S13326-016-0053-5     Document Type: Article

References (27)

1. The Biomedical Research Integrated Domain Group (BRIDG) Model [cited 2012 November 19, 2013]. Available from: http://www.bridgmodel.org/.
2. Fridsma DB, Evans J, Hastak S, Mead CN. The BRIDG project: a technical report. J Am Med Inform Assoc. 2008;15(2):130-7. doi:10.1197/jamia.M2556. PubMed PMID: 18096907, PubMed Central PMCID: PMC2274793, Epub 2007/12/22M2556 [pii].
3. The CDISC [November 6, 2012]. Available from: http://www.cdisc.org/.
4. The CDISC CSHARE [May 15, 2013]. Available from: http://www.cdisc.org/cdisc-share.
5. The Clinical Information Modeling Initiative (CIMI) [cited 2012 November 6, 2012]. Available from: http://www.opencimi.org/.
6. CIMI-initial public statement [cited 2012 November 6, 2012]. Available from: http://omowizard.wordpress.com/2011/12/14/cimi-initial-publicstatement/.
7. Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood Jr WD, et al. Development of the logical observation identifier names and codes (LOINC) vocabulary. J Am Med Inform Assoc. 1998;5(3):276-92. PubMed PMID: 9609498, PubMed Central PMCID: PMC61302, Epub 1998/06/03.
8. Dolin RH, Huff SM, Rocha RA, Spackman KA, Campbell KE. Evaluation of a "lexically assign, logically refine" strategy for semi-automated integration of overlapping terminologies. J Am Med Inform Assoc. 1998;5(2):203-13. PubMed PMID: 9524353, PubMed Central PMCID: PMC61291, Epub 1998/04/03.
9. Davies J, CGibbons J, Harris S, Crichton C. The CancerGrid Experience: Metadata-Based Model-Driven Engineering for Clinical Trials. Sci Compt Programming. 2014;89:126-143.
10. Komatsoulis GA, Warzel DB, Hartel FW, Shanbhag K, Chilukuri R, Fragoso G, et al. caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inform. 2008;41(1):106- 23. doi:10.1016/j.jbi.2007.03.009. PubMed PMID: 17512259, PubMed Central PMCID: PMC2254758, Epub 2007/05/22S1532-0464(07)00029-9 [pii].
11. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009;37(Web Server issue):W170-3. Epub 2009/06/02. doi: gkp440 [pii] 10.1093/nar/gkp440. PubMed PMID: 19483092; PubMed Central PMCID: PMC2703982.
12. Nadkarni PM, Brandt CA. The common data elements for cancer research: remarks on functions and structure. Methods Inf Med. 2006;45(6):594-601. PubMed PMID: 17149500, PubMed Central PMCID: PMC2980785, Epub 2006/12/07doi: 06060594 [pii].
13. HL7 Detailed Clinical Models [cited 2012 November 6, 2012]. Available from: http://wiki.hl7.org/index.php?title=Detailed_Clinical_Models.
14. ISO/IEC 11179, Information Technology-Metadata registries (MDR) [cited 2012 November 6, 2012]. Available from: http://metadata-standards.org/11179/.
15. Tao C, Jiang G, Oniki TA, Freimuth RR, Pathak J, Zhu Q, et al. A Semantic- Web Oriented Representation of the Clinical Element Model for Secondary Use of Electronic Health Records Data. J Am Med Inform Assoc 2012;(doi:10.1136/amiajnl-2012-001326).
16. Tao C, Jiang G, Wei WQ, Solbrig H, Chute CG. Towards Semantic-Web based representation and harmonization of standard metadata models for clinical studies. AMIA Summits Transl Sci Proc. 2011;2011:59-63.
17. The Simple Knowledge Organization System (SKOS) [November 6, 2012]. Available from: http://www.w3.org/TR/skos-reference/.
18. Jiang G, Solbrig HR, Iberson-Hurst D, Kush RD, Chute CG. A collaborative framework for representation and harmonization of clinical study data elements using semantic MediaWiki. AMIA Summits Transl Sci Proc. 2010; 2010:11-5. PubMed PMID: 21347136, PubMed Central PMCID: PMC3041544, Epub 2011/02/25.
19. The RDF Schema vocabulary (RDFS) [November 6, 2012]. Available from: http://www.w3.org/2000/01/rdf-schema.
20. The OWL 2 [November 6, 2012]. Available from: http://www.w3.org/TR/ owl2-syntax/.
21. The SPARQL Query Language for RDF [November 6, 2012]. Available from: http://www.w3.org/TR/rdf-sparql-query/.
22. SPARQL Inference Notation (SPIN) [November 1, 2012]. Available from: http://spinrdf.org/.
23. HL7 OWL Project [April 10, 2013]. Available from: http://gforge.hl7.org/gf/ project/hl7owl/.
24. 4Store Website [May 8, 2013]. Available from: https://github.com/garlik/ 4store.
25. Jena ARQ API [May 15, 2013]. Available from: http://jena.apache.org/ documentation/query/.
26. SmartGWT API [May 15, 2013]. Available from: https://github.com/isomorphic-software/smartgwt.
27. Freemind [May 15, 2013]. Available from: http://freemind.sourceforge.net/ wiki/index.php/Main_Page.