SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps

Journal of the American Medical Informatics Association

Volumn 22, Issue 6, 2015, Pages 1173-1178

  Alterovitz, Gil ^a,b,c   Warner, Jeremy ^d,e   Zhang, Peijin ^f   Chen, Yishen ^g   Ullman Cullere, Mollie ^h   Kreda, David ^b   Kohane, Isaac S ^a,b,c  

^a Harvard Medical School ^*  (United States)

^b Harvard Medical School Center for Biomedical Informatics   (United States)

^c USA   (United States)

^d VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^e VANDERBILT UNIVERSITY   (United States)

^f Carnegie Mellon University   (United States)

^g NONE   (United States)

^h DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

Clinicogenomics; Data sharing; Data warehouse; EHR; EMR; FHIR; Genomics; HL7; I2b2; SMART; Standards

Indexed keywords

ELECTRONIC MEDICAL RECORD; FEASIBILITY STUDY; GENOMICS; HEALTH LEVEL 7; HOSPITAL; PERSONALIZED MEDICINE; ELECTRONIC HEALTH RECORD; GENETIC DATABASE; HUMAN; INFORMATION DISSEMINATION; INTERNET; SOFTWARE; STANDARDS;

DATABASES, GENETIC; ELECTRONIC HEALTH RECORDS; GENOMICS; HEALTH LEVEL SEVEN; HUMANS; INFORMATION DISSEMINATION; INTERNET; SOFTWARE;

EID: 84954505162     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1093/jamia/ocv045     Document Type: Article

References (18)

1. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet. 2010;11(1):31-46.
2. Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009;360(13):1278-81.
3. Mandl KD, Mandel JC, Murphy SN, et al. The SMART Platform: early experience enabling substitutable applications for electronic health records. J Am Med Inform Assoc. 2012;19(4):597-603.
4. Field D, Sansone SA, Collis A, et al. Megascience. 'Omics data sharing. Science. 2009;326(5950):234-6.
5. Wooley JC, Field D, Glockner FO. Extending standards for genomics and metagenomics data: a Research Coordination Network for the Genomic Standards Consortium (RCN4GSC). Stand Genomic Sci. 2009;1(1):87-90.
6. Tenenbaum JD, Sansone SA, Haendel M. A sea of standards for omics data: sink or swim? J Am Med Inform Assoc. 2014;21(2):200-3.
7. Raths D. Trend: standards development. Catching FHIR. A new HL7 draft standard may boost web services development in healthcare. Healthcare Informatics. 2014;31(2):13,6.
8. den Dunnen JT, Antonarakis SE. Nomenclature for the description of human sequence variations. Hum Genet. 2001;109(1):121-4.
9. Pruitt KD, Harrow J, Harte RA, et al. The Consensus Coding Sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009;19(7):1316-23.
10. Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H. The HUGO Gene Nomenclature Committee (HGNC). Hum Genet. 2001;109(6):678-80.
11. Bender D, Sartipi K. HL7 FHIR: An agile and RESTful approach to healthcare information exchange. In: Proceedings of the IEEE 26th International Symposium on Computer-Based Medical Systems (CBMS 2013). 2013:326-31.
12. Procedure Resource, HL7 FHIR DSTU1 v0082 2015. Health Level 7 International website. http://www.hl7.org/implement/standards/fhir/procedure.html. Accessed February 8, 2015.
13. Observation Resource, HL7 FHIR DSTU1 v0082 2015. Health Level 7 International website. http://www.hl7.org/implement/standards/fhir/observation.html. Accessed February 8, 2015.
14. Danciu I, Cowan JD, Basford M, et al. Secondary use of clinical data: The Vanderbilt approach. J Biomed Inform. 2014;52:28-35.
15. Goldberg HS, Paterno MD, Rocha BH, et al. A highly scalable, interoperable clinical decision support service. J Am Med Inform Assoc. 2014;21(e1): e55-62.
16. Pathak J, Bailey KR, Beebe CE, et al. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 2013;20(e2):e341-8.
17. Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015.
18. Rioth M, Staggs D, Warner J. Incorporation of externally generated next-generation tumor genotyping into clinical and research workflows: successes and lessons learned. J Clin Oncol. 2014;32 suppl 30:abstr 156.