Semantic processing of EHR data for clinical research

Journal of Biomedical Informatics

Volumn 58, Issue , 2015, Pages 247-259

  Sun, Hong ^a   Depraetere, Kristof ^a   De Roo, Jos ^a   Mels, Giovanni ^a   De Vloed, Boris ^a   Twagirumukiza, Marc ^a   Colaert, Dirk ^a  

^a Agfa HealthCare   (Belgium)

Author keywords

Clinical research; EHR; N3 rules; RESTful; Semantic interoperability; Semantic web stack

Indexed keywords

DATA HANDLING; REUSABILITY;

CLINICAL RESEARCH; EHR; N3 RULES; RESTFUL; SEMANTIC INTEROPERABILITY;

SEMANTIC WEB;

ARTICLE; CLINICAL RESEARCH; COMPUTER INTERFACE; DATA ANALYSIS; ELECTRONIC MEDICAL RECORD; HUMAN; MEDICAL INFORMATION SYSTEM; MEDICAL ONTOLOGY; NATURAL LANGUAGE PROCESSING; PRIORITY JOURNAL; PROBABILITY; SEMANTICS; ELECTRONIC HEALTH RECORD; MEDICAL RESEARCH;

BIOMEDICAL RESEARCH; ELECTRONIC HEALTH RECORDS; SEMANTICS;

EID: 84947923608     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2015.10.009     Document Type: Article

References (41)

1. Health Level Seven. <> (accessed July 2015). http://www.hl7.org.
2. OpenEHR. <> (accessed July 2015). http://www.openehr.org.
3. ISO 13606 Standard. <> (accessed July 2015). http://www.iso.org/iso/home.html.
4. Schober D., Boeker M., Bullenkamp J., Huszka C., Depraetere K., Teodoro D., Nadah N., Choquet R., Daniel C., Schulz S. The DebugIT core ontology: semantic integration of antibiotics resistance patterns. Stud. Health Technol. Inform. 2010, 160(Pt 2):1060-1064.
5. Debug-IT Project. <> (accessed July 2015). http://www.debugit.eu/.
6. H. Sun, K. Depraetere, J. De Roo, B. De Vloed, G. Mels, D. Colaert, Semantic Integration and Analysis of Clinical Data. Available from: arxiv:1210.4405.
7. Salus Project. <> (accessed July 2015). http://www.salusproject.eu/.
8. CREAM, Clinical Research Entities Patterns: Advanced Model. <> (accessed July 2015). http://www.srdc.com.tr/projects/salus/blog/?p=342.
9. M. Twagirumukiza, K. Depraetere, H. Sun, A. Sinaci, SALUS Deliverable D4.3.2 SALUS Harmonized Ontology for Post Market Safety Studies-R2. <> (accessed July 2015). http://www.srdc.com.tr/projects/salus/docs/D4.3.2.pdf.
10. Informatics for Integrating Biology and the Bedside. <> (accessed July 2015). http://https://www.i2b2.org.
11. Observational Medical Outcomes Partnership Project Vocabularies. <> (accessed July 2015). http://omop.org.
12. J. De Roo, Euler Yet Another Proof Engine, 2013. <>. http://eulersharp.sourceforge.net.
13. T. Berners-Lee, et al., Cwm: A General Purpose Data Processor for the Semantic Web. <>. http://www.w3.org/2000/10/swap/doc/cwm.html.
14. Costa C.M., Menárguez-Tortosa M., Fernández-Breis J.T. Clinical data interoperability based on archetype transformation. J. Biomed. Inform. 2011, 44(5):869-880.
15. Gonçalves B., Guizzardi G., Pereira Filho J.G. Using an ECG reference ontology for semantic interoperability of ECG data. J. Biomed. Inform. 2011, 44(1):126-136.
16. C. Martínez-Costa, D. Kalra, S. Schulz, Improving EHR semantic interoperability. Future vision and challenges, in: Proceedings of MIE, 2014.
17. Berges I., Bermúdez J., Illarramendi A. Toward semantic interoperability of electronic health records. IEEE Trans. Inf. Technol. Biomed. 2012, 16(3):424-431.
18. Martínez-Costa C., Cornet R., Karlsson D., Schulz S., Kalra D. Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case. J. Am. Med. Inform. Assoc. 2015, ocu013.
19. Presutti V., Gangemi A. Content ontology design patterns as practical building blocks for web ontologies. Conceptual Modeling-ER 2008 2008, 128-141. Springer.
20. Clinical Information Modeling Initiative (CIMI). <> (accessed July 2015). http://informatics.mayo.edu/CIMI/index.php/Main_Page.
21. PCORnet Common Data Model (CDM). <> (accessed July 2015). http://www.pcornet.org/wp-content/uploads/2015/06/2015-06-01-PCORnet-Common-Data-Model-v3dot0-RELEASE.pdf.
22. Pathak J., Bailey K.R., Beebe C.E., Bethard S., Carrell D.S., Chen P.J., Dligach D., Endle C.M., Hart L.A., Haug P.J. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J. Am. Med. Inform. Assoc. 2013, 20(e2):e341-e348.
23. Rea S., Pathak J., Savova G., Oniki T.A., Westberg L., Beebe C.E., Tao C., Parker C.G., Haug P.J., Huff S.M. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project. J. Biomed. Inform. 2012, 45(4):763-771.
24. EHR4CR Project. <> (accessed July 2015). http://www.ehr4cr.eu/.
25. Doods J., Bache R., McGilchrist M., Daniel C., Dugas M., Fritz F., et al. Piloting the EHR4CR feasibility platform across Europe. Methods Inf. Med. 2014, 53(4):264-268.
26. M. Arenas, A. Bertails, E. Prud'hommeaux, J. Sequeda, A Direct Mapping of Relational Data to RDF.
27. Hussain S., Sun H., Erturkmen G.B.L., Yuksel M., Mead C., Gray A.J., Forsberg K., Batchelor C.R. A justification-based semantic framework for representing, evaluating and utilizing terminology mappings. Context 2014, 98-113.
28. Heath T., Bizer C. Linked data: evolving the web into a global data space. Synth. Lect. Semantic Web: Theory Technol. 2011, 1(1):1-136.
29. S. Das, S. Sundara, R. Cyganiak, R2RML: RDB to RDF Mapping Language.
30. Holford M.E., McCusker J.P., Cheung K.-H., Krauthammer M. A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinform. 2012, 13(suppl. 1):S10.
31. H.M. Villazón-Terrazas B, RDB2RDF Implementation Report. <> (accessed July 2015). http://www.w3.org/TR/rdb2rdf-implementations/.
32. C. Bizer, A. Seaborne, D2RQ-treating non-RDF databases as virtual RDF graphs, in: Proceedings of the 3rd International Semantic Web Conference (ISWC2004), vol. 2004, 2004.
33. OMOP Common Data Model. <> (accessed July 2015). http://omop.org/CDM.
34. H. Knublauch, SPINMap: SPARQL-based Ontology Mapping with a Graphical Notation. <> (accessed July 2015). http://composing-the-semantic-web.blogspot.com/2011/04/spinmap-sparql-based-ontology-mapping.html.
35. EYE Builtins. <> (accessed July 2015). http://eulersharp.sourceforge.net/2003/03swap/eye-builtins.
36. Sample Conversion Rules and Proofs. <> (accessed July 2015). http://https://github.com/hongsun502/jbi_sample_conversions.
37. Log Ontology. <> (accessed July 2015). http://www.w3.org/2000/10/swap/log#.
38. A. Polleres, H. Boley, M. Kifer, RIF Datatypes and Built-ins 1.0, W3C Working Draft. <>. http://www.w3.org/2005/rules/wiki/DTB.
39. S. Bratt. Semantic Web and Other W3C Technologies to Watch, 2007. <> (accessed July 2015). http://www.w3.org/2007/Talks/0130-sb-W3CTechSemWeb/0130-sb-W3CTechSemWeb.
40. i2b2 Software Architecture: Ontology Management (ONT) Cell. <> (accessed July 2015). http://https://www.i2b2.org/software/files/PDF/current/Ontology_Architecture.pdf.
41. K. Depraetere, SALUS D4.4.2 SALUS Semantic Mediation Framework-R2. <> (accessed July 2015). http://www.srdc.com.tr/projects/salus/docs/D4.4.2.pdf.