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Appendix D - Publications

This appendix includes the following sections:

Additions to this List

To have a citation added please contact the NCI Help Desk.

Publications Citing caDSR and CDEs



  1. Rhee, David, Kevin Shieh, Julie Sullivan, Arron Golden. "Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies", Proceedings of the 2016 IEEE Tenth International Conference on Semantic Computing (ICSC 2016), April 2016.

  2. Lablans, Martin, Dennis Kadioglu, Sabastian Mate, Frank Ückert. "Strategies for Networking Biobanks",  Lablans,  Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz · January 2016, · DOI: 10.1007/s00103-015-2299-y
  3. Toga, Arthur W., Ivo D. Dinov. "Sharing big biomedical data", Journal of Big Data (2016) 2:7, DOI: 10.1186/s40537-015-0016-1.

  4. Chávez-Bosquez, Oscar, Pilar Pozos-Parra, "The Latin American Laws of Correct Nutrition: Review, Unified Interpretation, Model and Tools", Computers in Biology and Medicine 70 · January 2016, DOI: 10.1016/j.compbiomed.2015.12.019

  5. Mohd Noor, Aisyah, Lars Holmberg, Cheryl Gillett, Anita Girgoridis. "Big Data: The challenge for small research groups in the era of cancer genomics", British Journal of Cancer 113(10) · October 2015, DOI: 10.1038/bjc.2015.341.

  6. Renner, Robinette, John Carlis, Martin Maiers, et. al. "Integration of Hematopoietic Cell Transplantation Outcomes Data", "Data Integration in the Life Sciences", pp.139-146, DOI: 10.1007/978-3-319-21843-4_11  
  7. Quinlan, Philip, Martin Groves, Lee B. Jordan, Hilary Stobart, Colin Purdie, Alastair M. Thompson. "The Informatics Challenges Facing Biobanks: A Perspective from a United Kingdom Biobanking Network", Biopreservation and Biobanking 13(5) · September 2015, DOI: 10.1089/bio.2014.0099.
  8. Fedorov, Andriy, David Clunie, Ethan Ulrich, Christian Bauer, Andreas Wahle, Bartley Brown, Micheal Onken, Jörg Riesmeier, Steve Pieper, Ron Kikinis, John Buatii, Reinhard Beichel. "DICOM for quantitative imaging biomarker development: A standards based approach to sharing of clinical data and structured PET/CT analysis results in head and neck cancer research." (2015) Available from: https://www.researchgate.net/publication

  9. Lablans, M., D. Kadioglu, M. Muscholl, and F. Ückert. "Exploiting Distributed, Heterogeneous and Sensitive Data Stocks While Maintaining the Owner’s Data Sovereignty." Methods Inf Med Methods of Information in Medicine 54.4 (2015): 346-52. Web.

  10. Beaber, Elisabeth F., Jane J. Kim, Marilyn M. Schapira, Jasim A. Trio. "Unifying Screening Processes Within the PROSPR Consortium: A Conceptual Model for Breast, Cervical, and Colorectal Cancer Screening", Journal of the National Cancer Institute 107(6) · May 2015, DOI: 10.1093/jnci/djv120

  11. Toubiana, Laurent, Adrien Ugon, Allesandra Giavarini, et. al. "A "pivot" Model to set up Large Scale Rare Diseases Information Systems: Application to the Fibromuscular Dysplasia Registry", Studies in health technology and informatics 210:887-91 · May 2015, DOI: 10.3233/978-1-61499-512-8-887.
  12. Frantzi, Maria, Agnieszka Latosinska, Leif Flühe, et al. "Developing proteomic biomarkers for bladder cancer: Towards clinical application: Nature Reviews Urology 12(6) · May 2015. DOI: 10.1038/nrurol.2015.100.
  13. Ganzinger, Matthias, Petra Knaup-Gregori. "Requirements for data integration platforms in biomedical research networks: a reference model". PeerJ 3(7):e755 · February 2015. DOI: 10.7717/peerj.755.
  14. Biering-Sørensen, Sherita Alai, Kim D. Anderson, Lyn B. Jakeman. "Common data elements for spinal cord injury clinical research: A National Institute for Neurological Disorders and Stroke project". Spinal Cord 53(4) · February 2015. DOI: 10.1038/sc.2014.246.
  15. Goyet, Sophie. "Modelisation of the Knowledge Translation process between Research and Public Health". PhD, Thesis December 2014. DOI: 10.13140/2.1.4465.3609  
  16. Kicks, Karen A., James E Tcheng, Biykem Bozkurt, et. al. "2014 ACC/AHA Key Data Elements and Definitions for Cardiovascular Endpoint Events in Clinical Trials: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Data Standards (Writing Committee to Develop Cardiovascular Endpoints Data Standards)", Circulation 66(4) · December 2014. DOI: 10.1161/CIR.0000000000000156

  17. Lin C-H et al. "A multi-technique approach to bridge electronic case report form design and data standard adoption". J Biomed Inform (2014), http://dx.doi.org/10.1016/j.jbi.2014.08.013

  18. Lluch-Ariet, Magí, Albert Brugués, Francesc Vallverdú, Josep Pergueroes Vallés, "Knowledge sharing in the health scenario", Journal of Translational Medicine 12(2) · November 2014, DOI: 10.1186/1479-5876-12-S2-S8
  19. Senator Jeong, Hye Hyeon Kim, Yu Rang Park, Ju Han Kim. "Clinical Data Element Ontology for Unified Indexing and Retrieval of Data Elements across Multiple Metadata Registries", Healthcare Informatics Research, 2014 October;20(4):295-303. DOI:10.4258/hir.2014.20.4.295
  20. Church, Philip Clayton, Andrzej Goscinski, "A Survey of Cloud-Based Service Computing Solutions for Mammalian Genomics", IEEE Transactions on Services Computing 7(4):726-740 · September 2014. DOI: 10.1109/TSC.2014.2353645
  21. P Mongkolwat, V Kleper, S Talbot, D Rubin. "The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation Model." Journal of Digital Imaging, 2014. DOI:10.1107/s10278-014-9710-3
  22. Min H, Ohira R, Collins MA, et al. Sharing behavioral data through a grid infrastructure using data standards. Journal of the American Medical Informatics Association : JAMIA. 2014;21(4):642-649. doi:10.1136/amiajnl-2013-001763.
  23. Davies, Jim, Jeremy Gibbons, Steve Harris, and Charles Crichton. "The CancerGrid Experience: Metadata-based Model-driven Engineering for Clinical Trials." Science of Computer Programming 89 (2014):126-43. DOI: 10.1016/j.scico.2013.02.010
  24. Yu Rang Park, YJ Yoon, TH Jang, HJ Seo, JH Kim. "Establishing Semantic Interoperability of Biomedical Metadata Registries using Extended Semantic Relationships." Healthcare Informatics Research. 2014 January;20(1):39-44. DOI Exit Disclaimer logo pISSN 2093-3681
  25. A Anil Sinaci, Gokce B Laleci Erturkmen. "A Federated Semantic Metadata Registry Framework for Enabling Interoperability across Clinical Research and Care Domains." Journal of Biomedical Informatics (Impact Factor: 2.13). 06/2013; DOI:10.1016/j.jbi.2013.05.009
  26. Ngouongo, Sylvie M.n., Matthias Löbe, and Jürgen Stausberg. "The ISO/IEC 11179 Norm for Metadata Registries: Does It Cover Healthcare Standards in Empirical Research?" Journal of Biomedical Informatics 46.2 (2013): 318-27.
  27. Pascal Coorevits, Mats Sundgren, Gunnar O Klein, Anne Bahr, Brecht Claerhout, Christel Daniel, Martin Dugas, Danielle Dupont, Andreas Schmidt, Peter Singleton, Georges De Moor, Dipak Kalra. "Electronic health records: new opportunities for clinical research." Journal of Biomedical Informatics (Impact Factor: 2.13). 06/2013; DOI:10.1016/j.jbi.2013.05.00910
  28. Thibault JC, Frey L. Biomedical Terminology Mapper for UML projects . AMIA Summits on Translational Science Proceedings. 2013;2013:257-261.
  29. Vergara-Niedermayr C, Wang F, Pan T, Kurc T, Saltz J. Semantically Interoperable XML Data. International journal of semantic computing. 2013;7(3):237-255. doi:10.1142/S1793351X13500037.
  30. H. Vernon Anderson, William S. Weintraub, Martha J. Radford, Mark S. Kremers, Matthew T. Roe, Richard E. Shaw, Dana M. Pinchotti, James E. Tcheng. "Standardized Cardiovascular Data for Clinical Research, Registries, and Patient Care : A Report From the Data Standards Workgroup of the National Cardiovascular Research Infrastructure Project." Journal of the American College of Cardiology (Impact Factor: 14.09). 05/2013; 61(18):1835–1846. DOI:10.1016/j.jacc.2012.12.047
  31. Liu K, Acharya A, Alai S, Schleyer TK. Using Electronic Dental Record Data for Research: A Data-mapping Study. Journal of Dental Research. 2013;92(7 Suppl):S90-S96. doi:10.1177/0022034513487560.
  32. Pan H, Tryka KA, Vreeman DJ, et al. Using PhenX Measures to Identify Opportunities for Cross-Study Analysis. Human mutation. 2012;33(5):849-857. doi:10.1002/humu.22074.
  33. Wang H, Yatawara M, Huang S-C, et al. The Integrated Proactive Surveillance System for Prostate Cancer. The Open Medical Informatics Journal. 2012;6:1-8. doi:10.2174/1874431101206010001.
  34. Saver, J. L., S. Warach, S. Janis, J. Odenkirchen, K. Becker, O. Benavente, J. Broderick, A. W. Dromerick, P. Duncan, M. S. V. Elkind, K. Johnston, C. S. Kidwell, J. F. Meschia, and L. Schwamm. "Standardizing the Structure of Stroke Clinical and Epidemiologic Research Data: The National Institute of Neurological Disorders and Stroke (NINDS) Stroke Common Data Element (CDE) Project." Stroke 43.4 (2012): 967-73. DOI:10.1161/STROKEAHA.111.634352
  35. Richesson RL, Shereff D, Andrews JE. Standardization of Questions in Rare Disease Registries: The PRISM Library Project. El Emam K, Eysenbach G, eds. Interactive Journal of Medical Research. 2012;1(2):e10. doi:10.2196/ijmr.2107.
  36. S Hussain, D Ouagne, E Sadou, T Dart, MC Jaulent."EHR4CR: A semantic web based interoperability approach for reusing electronic healthcare records in protocol feasibility studies". (2012) Web. PDF Exit Disclaimer logo
  37. Zhu, Qian, Robert R. Freimuth, Zonghui Lian, Scott Bauer, Jyotishman Pathak, Cui Tao, Matthew J. Durski, and Christopher G. Chute. "Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study". Journal of Biomedical Informatics (2012) Web. DOI Exit Disclaimer logo
  38. Bruland P, B. Breil, F Fritz, M. Dugas. "Interoperability in clinical research: from metadata registries to semantically annotated CDISC ODM", Studies in Health Technology and Informatics [2012], 180:564-568]
  39. Hu, H., Correll, M., Kvecher, L., Osmond, M., Clark, J., Bekhash, A., Schwab, G., Gao, D., Gao, J., Kubatin, V., Shriver, C.D., Hooke, J.A., Maxwell, L.G., Kovatich, A.J., Sheldon, J.G., Liebman, M.N., Mural, R.J. "DW4TR: A Data Warehouse for Translational Research". Journal of Biomedical Informatics volume 44, issue 6, year 2011, pp. 1004 - 1019
  40. Hsu, Chien-Yeh, and Chi-Hung Huang. "Annotating Taiwan Cancer Registry with CaDSR for International Interoperability." Future Wireless Networks and Information Systems. By Shin-Bo Chen. Springer Verlag, 2012. 257-62. Print.
  41. Jiang G, Solbrig HR, Chute CG. Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups. Journal of the American Medical Informatics Association : JAMIA. 2012;19(e1):e129-e136. doi:10.1136/amiajnl-2011-000739.
  42. Martínez Costa, C., Menárguez-Tortosa, M., Fernández-Breis, J.T., "Clinical data interoperability based on archetype transformation". Journal of Biomedical Informatics volume 44, issue 5, year 2011, pp. 869 - 880
  43. Richesson, R. L., and P. Nadkarni. "Data Standards for Clinical Research Data Collection Forms: Current Status and Challenges." Journal of the American Medical Informatics Association 18.3 (2011): 341-46.
  44. James P. McCusker, Joanne Luciano, and Deborah L. McGuinness, "Towards an Ontology for Conceptual Modeling". Tetherless World Constellation Department of Computer Science Rensselaer Polytechnic Institute, PDF Exit Disclaimer logo
  45. Alejandra González-Beltrán, Ben Tagger, Anthony Finkelstein, "Federated Ontology-based Queries over Cancer Data". BMC Bioinformatics 2012, 13 (Suppl 1):S9  doi:10.1186/1471-2105-13-S1-S9
  46. Loring, David W., Daniel H. Lowenstein, Nicholas M. Barbaro, Brandy E. Fureman, Joanne Odenkirchen, Margaret P. Jacobs, Joan K. Austin, Dennis J. Dlugos, Jacqueline A. French, William Davis Gaillard, Bruce P. Hermann, Dale C. Hesdorffer, Steven N. Roper, Anne C. Van Cott, Stacie Grinnon, and Alexandra Stout. "Common Data Elements in Epilepsy Research: Development and Implementation of the NINDS Epilepsy CDE Project." Epilepsia 52.6 (2011): 1186-191. DOI:10.1111/j.1528-1167.2011.03018.x.
  47. Weintraub WS, Karlsberg RP, Tcheng JE, Buxton AE, Boris JR, Dove JT, Fonarow GC, Goldberg LR, Heidenreich P, Hendel RC, Jacobs AK, Lewis W, Mirro MJ, Shahian DM. ACCF/AHA 2011 key data elements and definitions of a base cardiovascular vocabulary for electronic health records: a report of the American College of Cardiology Foundation/American Heart Association Task Force on Clinical Data Standards. Circulation. 2011;124:103--123.
  48. Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG "Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience", JAMIA doi:10.1136/amiajnl-2010-000061, May 2011
  49. Yu Rang Park, Hye Hyeon Kim, Hwa Jeong Seo, Ju Han Kim.   CDISC Transformer: a metadata-based transformation tool for clinical trial and research data into CDISC standards. KSII Transactions on Internet and Information Systems (Impact Factor: 0.35). 10/2011; 5(10). DOI: 10.3837/tiis.2011.10.009
  50. Cui Tao, PhD, Guoqian Jiang, PhD, Weiqi Wei, MM, Harold R. Solbrig,and Christopher G. Chute MD, DrPH "Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies". AMIA Summit on Clinical Research Informatics (AMIA CRI 2011) Exit Disclaimer logo . San Francisco, CA, USA. March 11-12, 2011
  51. Informatics in radiology: an information model of the DICOM standard. Charles E CE Kahn, Curtis P CP Langlotz, David S DS Channin and Daniel L DL Rubin crossref 31(1):295-304 1 Jan 2011 PMID 20980665, doi: 10.1148/rg.311105085
  52. Krikov S, Price RC, Matney SA, Allen-Brady K, Facelli JC Enabling GeneHunter as a Grid Service. "A Case Study for Implementing Analytical Services in Biomedical Grids". Methods Inf Med. 2010 Oct 20;49(6).
  53. Park YR, Kim JH. Achieving interoperability for metadata registries using comparative object modeling. Stud Health Technol Inform. 2010;160(Pt 2):1136-9.
  54. Wang H, Bouzyk E, Kuehn A, et al. caGrid-Enabled caBIGTM Silver Level Compatible Head and Neck Cancer Tissue Database System. The Open Medical Informatics Journal. 2010;4:171-178. doi:10.2174/1874431101004010171.
  55. Tan W, Missier P, Foster I, Madduri R, Goble C. A Comparison of Using Taverna and BPEL in Building Scientific Workflows: the case of caGrid. Concurrency and computation : practice & experience. 2010;22(9):1098-1117. doi:10.1002/cpe.1547.
  56. Amin W, Singh H, Dzubinski LA, Schoen RE, Parwani AV. Design and utilization of the colorectal and pancreatic neoplasm virtual biorepository: "An early detection research network initiative." J Pathol Inform FIX (serial online Exit Disclaimer logo ) 20101:22.
  57. Frey LJ, Turner, S., et al. (2010 submitted - under review). "Obtaining Desiderata in the Common Terminology Criteria for Adverse Events: A Case Study", JAMIA
  58. Waqas Amin, Harpreet Singh, Andre K. Pople, Sharon Winters, Rajiv Dhir, Anil V. Parwani, and Michael J. Becich, "A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research.", J Pathol Inform. 2010; 1: 12. Published online 2010 August 10. doi: 10.4103/2153-3539.68314.
  59. Joshua Phillips, Alejandra González Beltrán, Anthony Finkelstein, Jyotishman Pathak "Exposing caGrid Data Services as Linked Data" In the proceedings of the 2010 AMIA Summit on Clinical Research Informatics (AMIA CRI 2010 Exit Disclaimer logo ). San Francisco, CA, USA. March 12-13, 2010.
  60. Alejandra González Beltrán, Anthony Finkelstein, J Max Wilkinson, Jeff Kramer "Domain Concept-Based Queries for Cancer Research Data Sources " In the proceedings of the 22nd IEEE International Symposium on Computer-Based Medical Systems 2009 (CBMS 2009 Exit Disclaimer logo ). Special track on HealthGrid Computing - Applications to Biomedical Research and Healthcare
  61. Sabados, William Thomas, Thesis: Comparing semantic matching results of schema matchers and metadata registry enabled systems. Pub date: 2010. Pages:xii, 164 leaves.
  62. Downing GJ. Policy perspectives on the emerging pathways of personalized medicine. Dialogues in Clinical Neuroscience. 2009;11(4):377-387.
  63. McCusker, James P., Joshua A. Phillips, Alejandra González Beltrán, Anthony Finkelstein, Michael Krauthammer, "Semantic web data warehousing for caGrid", BMC Bioinformatics, Vol 10, Supp 10, 2009.
  64. McCarthy J.L., Warzel D, Kendall E., Bargmeyer B., Solbrig H, Keck K, and Gey F., "Data Modeling and Harmonization with OWL: Opportunities and Lessons Learned", 5th International Workshop on Semantic Web Enabled Software Engineering, 8th International Semantic Web Conference Proceedings and Session, 2009, Virginia, USA.
  65. Sambit K Mohanty, Amita T Mistry, Waqas Amin, Anil V Parwani, Andrew K Pople, Linda Schmandt, Sharon B Winters, Erin Milliken, Paula Kim, Nancy B Whelan, Ghada Farhat, Jonathan Melamed, Emanuela Taioli, Rajiv Dhir, Harvey I Pass, and Michael J Becich., "The development and deployment of Common Data Elements for tissue banks for translational research in cancer – An emerging standard based approach for the Mesothelioma Virtual Tissue Bank", BMC Cancer. 2008; 8: 91. Published online 2008 April 8. doi: 10.1186/1471-2407-8-91.
  66. Thora Jonsdottir, Johann Thorsson, Ebba Thora Hvannberg, Jan-Eric Litton, Helgi Sigurdsson, "The Nordic Common Data Element repository for describing cancer data - International Journal of Metadata, Semantics and Ontologies" . Inderscience 232 Int. J. Metadata, Semantics and Ontologies, Vol. 4, No. 4, 2009.

  67. Stausberg, J, M Löbe, P Verplancke, J Drepper, H Herre, Markus Löffer. "Foundations of a Metadata Repository for Databases of Registers and Trials" Studies in health technology and informatics 150:409-13 · January 2009, DOI: 10.3233/978-1-60750-044-5-409

  68. Huang T, Shenoy PJ, Sinha R, Graiser M, Bumpers KW, Flowers CR. Development of the Lymphoma Enterprise Architecture Database: A caBIG(tm) Silver level compliant System. Cancer Informatics. 2009;8:45-64.
  69. Davies, J., Gibbons, J., Harris, S,, Warzel, D. "Evolving Health Informatics Semantic Frameworks and Metadata-Driven Architectures", Position Paper in Proceedings and session presented at Microsoft eScience Conference, (December 2008), Indiana, USA.
  70. Amin W, Parwani AV, Schmandt L, et al. National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer. 2008;8:236. doi:10.1186/1471-2407-8-236.
  71. Bodenreider, Olivier. "Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues." Data Integration in the Life Sciences Lecture Notes in Computer Science (2008): 1-4.
  72. Yong, M., B. Tolner, S. Nagl, R.b. Pedley, K. Chester, A.j. Green, A. Mayer, S. Sharma, and R. Begent. "Data Standards for Minimum Information Collection for Antibody Therapy Experiments." Protein Engineering Design and Selection 22.3 (2008): 221-24.
  73. Frey LJ, Maojo V and Mitchell JA. (2008). "Genome Sequencing: a Complex Path to Personalized Medicine". In Kim S, Tang H, Mardis ER (Eds.), Advances in Genome Sequencing Technology and Algorithms (pp. 53-75). Norwood, MA: Artech House Publishers, Inc.
  74. Waqas Amin, Anil V Parwani, Linda Schmandt, Sambit K Mohanty, Ghada Farhat, Andrew K Pople, Sharon B Winters, Nancy B Whelan, Althea M Schneider, John T Milnes, Federico A Valdivieso, Michael Feldman, Harvey I P, Rajiv Dhir, Jonathan Melamed and Michael J Becich., "National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research.", BMC Cancer 2008, 8:236doi:10.1186/1471-2407-8-236.
  75. Cryer, M and Frey LJ (2009) "Agent Based Modeling Supporting the Migration of Registry Systems to Grid Based Architectures." Proceedings of AMIA Summit on Translational Bioinformatics, San Francisco, CA.
  76. Komatsoulis, G.A., Warzel, D.B., Hartel, F.W., Shanbhag, K, Chilukuri, R, Fragoso, G., de Coronado, S, Reeves, D.M., Hadfield, J.B., Ludet, C., and P.A. Covitz (2007) "caCORE version 3: Implementation of an model driven, service-oriented architecture forsemantic interoperability."Journal of Biomed Informatics. 2008 February; 41(1): 106--123. Published online 2007 April 2. doi: 10.1016/j.jbi.2007.03.009.
  77. Ashokkumar A. Patel, John R. Gilbertson, Louise C. Showe, Jack W. London, Eric Ross, Michael Ochs, Joseph Carver, Andrea Lazarus, Anil V. Parwani, Rajiv Dhir, J. Robert Beck, Michael Liebman, Fernando U. Garcia, Jeff Prichard, Myra Wilkerson, Ronald B. Herberman, Michael J. Becich, and the PCABC, "A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)", Cancer Inform. 2007; 3: 255--274. Published online 2007 June 8.
  78. Oster, Scott, S. Langella,S. Hastings, D. Ervina, R. Madduri,J. Phillips, T. Kurca,F. Siebenlist, P. Covitz, K. Shanbhag, I. Foster, J. Saltz, "caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research." Journal of American Medical Informatics Association, 2008;15:138-149 doi:10.1197/jamia.M2522.
  79. Frey LJ, Maojo V and Mitchell JA. (2007). "Bioinformatics Linkage of Heterogeneous Clinical and Genomic Information in Support of Personalized Medicine." IMIA Yearbook of Medical Informatics, 21, 98 - 105.
  80. Crowley R, Wright L, Warzel D, Sioutos N, Mohanty S, Komatsoulis G, Chilukuri R, Tobias J, "The CAP cancer protocols - a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid", BMC Medical Informatics and Decision Making (June 20 2006) 6:25.
  81. Nadkarni PM, Brandt CA. The Common Data Elements for cancer research: remarks on functions and structure. Methods Inf Med 2006;45(6):594-601.
  82. Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz PA. The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services. BMC Medical Informatics and Decision Making. 2006;6:2. doi:10.1186/1472-6947-6-2.
  83. Ashokkumar A Patel, John R Gilbertson, Anil V Parwani, Rajiv Dhir, Milton W Datta, Rajnish Gupta, Jules J Berman, Jonathan Melamed, Andre Kajdacsy-Balla, Jan Orenstein, Michael J Becich and the Cooperative Prostate Cancer Tissue Resource (CPCTR), "An informatics model for tissue banks – Lessons learned from the Cooperative Prostate Cancer Tissue Resource", BMC Cancer 2006, 6:120doi:10.1186/1471-2407-6-120.

  84. Saltz, J., S. Oster, S. Hastings, S. Langella, T. Kurc, W. Sanchez, M. Kher, A. Manisundaram, K. Shanbhag, and P. Covitz. "CaGrid: Design and Implementation of the Core Architecture of the Cancer Biomedical Informatics Grid." Bioinformatics 22.15 (2006): 1910-916.

  85. Mougin F, Burgun A, Bodenreider O. Mapping data elements to terminological resources for integrating biomedical data sources. BMC Bioinformatics. 2006;7(Suppl 3):S6. doi:10.1186/1471-2105-7-S3-S6.
  86. Fenstermacher, D., C. Street, T. Mcsherry, V. Nayak, C. Overby, and M. Feldman. "The Cancer Biomedical Informatics Grid (caBIGTM)." 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference (2005).
  87. Ashokkumar A Patel, André Kajdacsy-Balla, Jules J Berman, Maarten Bosland, Milton W Datta, Rajiv Dhir, John Gilbertson, Jonathan Melamed, Jan Orenstein, Kuei-Fang Tai and Michael J Becich, "The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience.", BMC Cancer 2005, 5:108 doi:10.1186/1471-2407-5-108.
  88. Warzel D, Edelstein C, Lin C, Winget M, Thornquist M, "Proteomics Knowledge databases: facilitating collaboration and interaction between academia, industry, and federal agencies" in Informatics in Proteomics, Srivastava S, Zhang Z, Ravichandran V, Hanash S, Gangal R, Medjahed D, Lockett S, Crichton D, Fenyo D, Kowalski J, Eng J, Beer D, Hitt B, Taylor & Francis/CRC Press. 2005.
  89. Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ.. "caCORE: core architecture of bioinformation on cancer research in America" Beijing Da Xue Xue Bao 2006 Apr 18;38(2):218-21. Chinese.
  90. Winget MD, Baron JA, Spitz MR, Bremmer DE, Warzel D, Kincaid H, Thornquist M, Feng Z, "Development of common data elements: The experience of and recommendations from the early detection research network", International Journal of Medical Informatics, 2003, 70:41-48.
  91. Covitz P, Frank Hartel, Carl Schaefer, Sherri De Coronado, Gilberto Fragoso, Himanso Sahni, Scott Gustafson and Kenneth H. Buetow, "caCORE: A common infrastructure for cancer informatics", Bioinformatics, Vol. 19 no. 18 2003, pages 2404–2412, DOI: 10.1093/bioinformatics/btg335. PDF Exit Disclaimer logo
  92. Silva, J., Chute, C., Cancer informatics: essential technologies for clinical trials, 2002. Springer Verlag, New York.
  93. Silva, JS, Ball MJ, Douglas JV. "The Cancer Informatics Infrastructure (CII): an architecture for translating clinical research into patient care." Stud Health Technol Inform. 2001;84(Pt 1):114-7.
  94. Silva J, Wittes R. Role of clinical trials informatics in the NCI's cancer informatics infrastructure. Proc AMIA Symp. 1999:950-4. PubMed PMID: 10566501; PubMed Central PMCID: PMC2232686. [PubMed] [Free PMC Article]

Papers, Abstracts, Posters, and Talks

  1. Jiang G, Solbrig HR, Prud’hommeaux E, Tao C, Weng C, Chute CG. Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach. AMIA Annual Symposium Proceedings. 2015;2015:659-668.

  2. Warzel D., Carlin L;, Reeves D., Bondy J, REDX, Generating REDCap Data Dictionaries from NCI Standards, Poster, REDCap Annual Meeting, September, 2014

  3. Matthias Löbe, Magnus Knuth, Roland Mücke, TIM: A Semantic Web Application for the Specification of Metadata Items in Clinical Research, ResearchGate, May 2014.

  4. Pathak, J., Pan, H., Wang, J., Kashyap, S., Schad, P. A., Hamilton, C. M., … Chute, C. G. (2011). Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects. AMIA Summits on Translational Science Proceedings, 2011, 41–45.

  5. Topaloglu U., Jett T., Lane C., Hogan W., Hicks A., Kieber-Emmons T., Hutchins L., Curating All Data Elements in a Clinical Trial with CDEs from caDSR, Poster caBIG® Annual Meeting, September 13-15, 2010, Washington, D.C., U.S.A.
  6. Alejandra González Beltrán, Ben Tagger, Anthony Finkelstein "Ontology-based queries for the caGrid infrastructure", In "Building a Collaborative Biomedical Network", caBIG® Annual Meeting, September 13-15, 2010, Washington, D.C., U.S.A.
  7. Alejandra González Beltrán, May Yong, Richard Begent "Towards an unambiguous and formal description of cancer therapy experiments", In "Building a Collaborative Biomedical Network", caBIG® Annual Meeting, September 13-15, 2010, Washington, D.C., U.S.A.
  8. Warzel, D., Freimuth, R.R., Oniki TA., Reeves, DM, Chute, C.G, Huff, S.M., Approaches to Improving Clinical and Translational Biomedical Research Data Through Data Standards:  Registration of Clinical Element Models Using ISO/IEC 11179, AIMA CRI Symposium, May, 2013.

  9. Whitley, S., DM Reeves. "FormBuilder: A Tool For Promoting Data Sharing and Reuse Within the Cancer Community", 32nd Annual Oncology Nursing Society Congress, 2007, http://hdl.handle.net/10755/164909

  10. Warzel D. et al, "caCORE Evolves: Semantics II – Future Innovations", MIT Information Quality Symposium July, 2010
  11. Warzel, D., Reeves, D., Alley, R., Avdic, D., Mathur, A., Gagne, B., Harris, S and Tsui, A., "Cancer Informatics Research: for Recent advances in semantic interoperability cancer informatics", caBIG® Architecture and Vocabulary and Common Data Elements Face-To-Face, June 2010, Washington, DC.
  12. Warzel D, , "Semantics II – Future Innovations", Keynote Talk in ISO JTC1 SC32 WG2 Standards and Semantic Web,13 th Open Forum on Metadata Registries (May 2010), Kunming, China.
  13. Crichton, Charles, Jim Davies, Jeremy Gibbons, Steve Harris, Andrew Tsui, and James Brenton. "Metadata-driven Software for Clinical Trials." Proc. of SEHC '09 Proceedings of the 2009 ICSE Workshop on Software Engineering in Health Care, Vancouver, BC. Washington DC:
    IEEE, 2009. 1-11. Print.
  14. Alejandra González Beltrán, Anthony Finkelstein, J Max Wilkinson, Jeff Kramer, "Semantic concept-based queries for ONIX - caGrid case " in "Solving Basic and Clinical Research Challenges in Cancer and Beyond", caBIG® Annual Meeting, July 20-22, 2009, Washington, D.C., U.S.A.
  15. McCusker, James, Michael Krauthammer, Joshua Phillips, Alejandra González Beltrán, Anthony Finkelstein, "Semantic Web Data Warehousing for caGrid", In "Solving Basic and Clinical Research Challenges in Cancer and Beyond", caBIG® Annual Meeting, July 20-22, 2009, Washington, D.C., U.S.A.
  16. Warzel D., Crichton, C, Davies J. DPhl, Harris, S. PhD, Tsui A., Hastings S., Avdic D., Mathur A, Ludet, C, Elahi, B, "Recent advances in semantic interoperability for cancer informatics," Joint NCI/NCRI Informatics – caBIG® Conference (2009), London, UK
  17. Warzel D, "Emerging Semantic Technology Standards, Making Life Easier in the Information World", (June 2009), Keynote Talk in ISO JTC1 SC32 WG2 Standards and Semantic Web,12 th Open Forum on Metadata Registries, Seoul, Korea.
  18. Alejandra González Beltrán, Anthony Finkelstein, Jeff Kramer, J. Max Wilkinson. "ONIX Semantic Query Infrastructure", Poster NCI/NCRI Joint Conference: Biomedical Research Without Borders. Bethesda, USA. 2-3 September 2008
  19. Frey LJ, Stroup N, Cryer, M., He T, Meystre S, Rowe K, & Hartz A. Enabling Data Sharing across Borders with NAACCR and caBIG®. Poster session at Biomedical Informatics without Borders: Enabling Collaboration to Strengthen Research and Care, Bethesda, USA, September 2008
  20. Warzel D, "Using Vocabularies on the GRID." Abstract and session presented at NKOS/CENDI Joint Conference New Dimensions In Knowledge Organization Systems, (September 2008), Washington DC, USA
  21. Warzel D, Ludet, C, Davies J, Harris S, Tsui A, "cancerGrid cgMDR for decentralized development and registration of caBIG® compatible systems", Poster, NCRI/NCI Biomedical Informatics without Borders, September 2008, London, UK
  22. Alejandra González Beltrán, Anthony Finkelstein, J Max Wilkinson, "Platform Architecture and Requirements Testing (PART2) for ONIX Federated Queries" In "Getting Connected with caBI®, Poster, caBIG® Annual Meeting, June 23-25, 2008, Washington, D.C., U.S.A.
  23. Warzel D, Reeves D, Ludet, C, Davies J, Harris S, Tsui A, "Forms annotation and registration in caDSR facilitated by cancerGrid cgMDR", Poster, NCRI/NCI Biomedical Informatics without Borders, (September 2008), London, UK
  24. Kunz, Issac, Lin, Ming-Chin Lin, Frey, Lewis, "Metadata mapping and reuse in caBIG®, The First Summit on Translational Bioinformatics 2008 10--12 March 2008, San Francisco, CA, USA
  25. Kunz I, Lin, MC, and Frey LJ. (2008). "Population Studies for the Management of Colorectal Cancer using caBIG®.  Poster session presented at caBIG® Annual Meeting, September 2008, Washington, D.C.
  26. Frey LJ, He T, Stroup N, Meystre S, Rowe K, & Hartz A. "A Grid Demonstration Project Combining Colorectal Cancer Data Sets Across Utah to Examine Population-Based Health Issues". Annual Conference of the North American Association of Central Cancer Registries (NAACCR), Inc (2008).
  27. Warzel D, "Exchanging Components in Health Registries", Poster and Talk 11th Open Forum on Metadata Registries, Metadata Down Under, (May 2008), Sydney, Australia
  28. Macallum, Peter, Warzel, D, "Achieving International Interoperability: Distributed Metadata Registries" – Poster, Joint NCI/NCRI Informatics - caBIG® Conference (2007), Washington DC, USA

  29. Oster, S., Langella, S., Hastings, S., Ervin, D., Madduri, R., Kurc, T., … Saltz, J. (2007). caGrid 1.0: A Grid Enterprise Architecture for Cancer Research. AMIA Annual Symposium Proceedings, 2007, 573–577.

  30. Mougin, F., Anita Burgun, Olivier Bodenreider, "Data integration through data elements: Mapping data elements to terminological resources". Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM:2006) 52:59.

  31. Lin MC and Frey LJ. "Tooling to Support Reuse of CDEs in caBIG® UML Models".  Poster session presented at caBIG® Annual Meeting, 2007, Washington, D.C.
  32. Curtis T, Gundry K, Komatsoulis G, Warzel D, "Using Metadata For Semantic Interoperability: caCORE and the NCI's Cancer Biomedical Informatics Grid (caBIG®)", Poster and Talk, Data Managers Association (DAMA) 2006 Conference, Denver, Colorado
  33. Yu Rang Park, MS and Ju Han Kim, M.D., Ph.D."Metadata registry and management system based on ISO 11179 for cancer clinical trials information system", AMIA Annual Symposium, 2006
  34. Warzel D, "The NCI's cancer Data Standards Repository (caDSR): Harmonization of Ontology, Information Models and Metadata" 9th Open Forum on Metadata Registries Harmonization of Terminology, Ontology and Metadata, 2006, Abstract and Talk, Kobe, Japan
  35. Warzel D, Chilukuri R, De Coronado S, Fragoso G, "The NCI's caCORE: Leveraging Standards and Business Vocabulary for Semantic Interoperability", Abstract and Talk, Second Annual Semantic Technology Conference 2006 (STC06), San Jose, California
  36. Frey LJ. (2005). "Exploring Harmonization of UML models for caBIG®."  Poster session presented at Advancing Practice, Instruction and Innovation through Informatics (APII), Lake Tahoe, CA.
  37. Warzel DB, Andonyadis C, McCurry B, Chilukuri R, Ishmukhamedov S, Covitz P. Common Data Element (CDE) Management and Deployment in Clinical Trials. AMIA Annual Symposium Proceedings. 2003;2003:1048.
  38. Covitz P, Warzel D, "Metadata Management and Information Modeling", Systemics, Cybernetics and Informatics (SCI 2003), July 2003 Abstract and Talk at The 7th World Multiconference, Orlando, Florida
  39. "Metadata Management and Information Modeling", Systemics, Cybernetics and Informatics (SCI 2003), July 2003 Abstract and Talk at The 7thWorld Multiconference, Orlando, Florida.

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