Yearbook of Medical Informatics, Table of Contents Yearb Med Inform 2014; 23(01): 206-211DOI: 10.15265/IY-2014-0006 Original Article Georg Thieme Verlag KG Stuttgart EHR Big Data Deep Phenotyping Contribution of the IMIA Genomic Medicine Working Group L. J. Frey 1 Chair IMIA Genomic Medicine WG, Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC, USA , L. Lenert 2 Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC, USA , G. Lopez-Campos 3 Vice-Chair IMIA Genomic Medicine WG, Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria, Australia › Author Affiliations Recommend Article Abstract Full Text PDF Download Keywords KeywordsDeep phenotype - ontology - big data - genome - electronic health record References References 1 Cases M, Fulong LI, Albanell J, Altman RB, Bellazzi R, Boyer S. et al. Improving data and knowledge management to better integrate health care and research.. J Intern Med 2013; 321-8. 2 Starren J, Williams MS, Bottinger EP. Crossing the omic chasm: a time for omic ancillary systems.. JAMA 2013; Mar 27; 309 (12) 1237-8. 3 Masys DR, Jarvik GP, Abernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN. et al. Technical desiderata for the integration of genomic data into Electronic Health Records.. J Biomed Inform 2012; Jun 45 (03) 419-22. 4 Stead WW, Kelly BJ, Kolodner RM. Achievable Steps Toward Building a National Health Information Infrastructure in the United States.. J Am Med Inform Assoc 2005; 12 (02) 113-21. 5 Rabbani B, Mahdieh N, Hosomichi K, Nakaoka H, Inoue I. Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders.. J Hum Genet 2012; July: 621-32. 6 Robinson PN. Deep Phenotyping for Precision Medicine.. Hum Mutat 2012; 33 (05) 777-80. 7 Dawkins R. The Extended Phenotype.. Oxford: Oxford University Press; 1989 8 Hripcsak G, Albers DJ. Next-generation phenotyping of electronic health records.. J Am Med Inform Assoc 2013; 20 (01) 117-21. 9 Darvasi A. Experimental strategies for the genetic dissection of complex traits in animal models.. Nat Genet 1998; 18: 19-24. 10 Doelken SC, Mungall CJ, Bauer S, Firth HV, Bail-leul-Forestier I, Black GCM. et al. The Human Phenotype Ontology project : linking molecular biology and disease through phenotype data.. Nucleic Acids Res 2013; 1-9. 11 Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chitayat D. et al. PhenoTips: Patient Phenotyping Software for Clinical and Research Use.. Hum Mutat 2013; 34 (08) 1057-65. 12 Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology.. Nucleic Acids Res 32 (Database issue). 2004; 267-70. 13 Bodenreider O, Burgun A. Aligning knowledge sources in the UMLS: methods, quantitative results, and applications.. Medinfo Proc 2004; 327-31. 14 Wilson PS, Scichilone RA. LOINC as a data standard: how LOINC can be used in electronic environments.. J AHMIA 2011; 82 (07) 44-47. 15 Nelson SJ, Zeng K, Kilbourne J, Powell T, Moore R. Normalized names for clinical drugs: RxNorm at 6 years.. J Am Med Inform Assoc 2011; 8: 441-8. 16 International Classification of Diseases version 9.. [15 December 2013];. http://www.icd9data.com/2006/Volume1/ 17 Melton GB, Parsons S, Morrison FP, Rothschild AS, Markatou M, Hripcsak G. Inter-patient distance metrics using SNOMED CT defining relationships.. J Biomed Inform 2006; 39: 697-705. 18 Robinson PN, Mundlos S. The Human Phenotype Ontology.. Clin Genet 2010; 77: 525-34. 19 McKusick VA. Mendelian Inheritance in Man.. A Catalog of Human Genes and Genetic Disorders. Baltimore:: Johns Hopkins University Press;; 1998. (12th edition). 20 Köhler S, Schulz MH, Krawitz P, Bauer S, Dölken S, Ott CE. et al. Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies.. Am J Hum Genet 2009; 85: 457-64. 21 Hajihashemi Z, Popescu M. An Early Illness Recognition Framework Using a Temporal Smith Waterman Algorithm and NLP.. Proc AMIA Fall Symp 2013; 549-57. 22 Wang TD, Plaisant C. et al. Aligning Temporal Data by Sentinel Events: Discovering Patterns in Electronic Health Records.. CHI 2008 Proceedings: Health and Wellness,; Florence, Italy;: 2008 23 Wongsuphasawat K, Gomez JAG. et al. LifeFlow: Visualizing an Overview of Event Sequences.. CHI 2011,; Vancouver,; BC, Canada;: 2011 24 Wongsuphasawat K, Gotz DH. Outflow: Visualizing Patient Flow by Symptoms and Outcome.. IBM;; 2011. p. 1-4. 25 Lee WN, Das AK. Local Alignment Tool for Clinical History: Temporal Semantic Search of Clinical Databases.. AMIA Annu Symp Proc 2010; 437-41. 26 Lee WN, Bridewell W, Das AK. Alignment and Clustering of Breast Cancer Patients by Longitudinal Treatment History.. AMIA Annu Symp Proc 2011; 2011: 760-7. 27 Ayres J, Gehrke J, Yiu T, Flannick J. Sequential Pattern Mining using a Bitmap Representation.. In: SIGKDD’02,; Edmonton,; Canada;: 2002. July. 28 Papapetrou P, Kollios G, Sclaroff S, Gunopulos D. Mining frequent arrangements of temporal intervals.. Knowl Inf Syst 2009; 21 (02) 133-71. 29 Shahar Y, Goren-Bar D, Boaz D, Tahan G. Distributed, intelligent, interactive visualization and exploration of time-oriented clinical data.. Artif Intell Med 2006; 38 (02) 115-35. 30 Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM. et al. Exome sequencing identifies the cause of a mendelian disorder.. Nat Genet 2010; Jan 42 (01) 30-5. 31 Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT. et al. A standard variation file format for human genome sequences.. Genome Biol 2010; 11 (08) R88. 32 McCarty CA, Chisholm RL, Chute CG, Kullo IJ, Jarvik GP, Larson EB. et al. The eMERGE Network : A consortium of biorepositories linked to electronic medical records data for conducting genomic studies.. BMC Med Genomics 2011; 4 (01) 13. 33 Newton KM, Peissig PL, Kho AN, Bielinski SJ, Berg RL, Choudhary V. et al. Validation of electronic medical record-based phenotyping algorithms : results and lessons learned from the eMERGE network.. Medical Informatics 2013; 20: e147-e154. 34 Ghemawat S, Gobioff H. et al. The Google File System.. SOSP’03, Bolton Landing,; New York, USA;: 2003 35 Chang F, Dean J. et al. Bigtable: A Distributed Storage System for Structured Data.. OSDI ‘06: 7th USENIX Symposium on Operating Systems Design and Implementation;; 2006. p. 205-18. 36 Borthakur D, Sarma JS. et al. Apache Hadoop Goes Realtime at Facebook.. SIGMOD ‘11, Athens,; Greece.: 2011 37 Seoane JA, Dorado J, Pazos A. Data Integration in Genomic Medicine: Trends and Applications.. IMIA Yearbook 2012: Personal Health Informatics 2012; 117-25.
