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This appendix includes the following sections:

Publications Citing caDSR and CDEs

  1. 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. http://ceur-ws.org/Vol-952/paper_31.pdf.
  2. S Ngouongo, M Löbe, J Stausberg. "The ISO/IEC 11179 norm for metadata registries: Does it cover healthcare standards in empirical research". Journal of Biomedical Informatics (2012). Web. http://dx.doi.org/10.1016/j.jbi.2012.11.008
  3. 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. http://dx.doi.org/10.1016/j.jbi.2012.11.004
  4. 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
  5. 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.
  6. 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
  7. 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, http://tw.rpi.edu/media/2011/03/14/da62/cmo.pdf
  8. Alejandra González-Beltrán, Ben Tagger, Anthony Finkelstein, "Federated Ontology-based Queries over Cancer Data". Accepted for publication BMC Bioinformatics
  9. 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.
  10. 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
  11. Guoqian Jiang, Harold R. Solbrig, Christopher G. Chute "Quality Evaluation of Cancer Study Common Data Elements Using the UMLS Semantic Network". MIA Summit on Clinical Research Informatics (AMIA CRI 2011)|http://proceedings.amia.org/]. San Francisco, CA, USA, March 11-12, 2011
  12. 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)|http://proceedings.amia.org]. San Francisco, CA, USA. March 11-12, 2011
  13. 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
  14. 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).
  15. Park YR, Kim JH. Achieving interoperability for metadata registries using comparative object modeling. Stud Health Technol Inform. 2010;160(Pt 2):1136-9.
  16. 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 [serial online] 20101:22. Available from: http://www.jpathinformatics.org/text.asp?2010/1/1/22/70831
  17. 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.
  18. Frey LJ, Turner, S., et al. (2010 submitted - under review). "Obtaining Desiderata in the Common Terminology Criteria for Adverse Events: A Case Study", JAMIA
  19. 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.
  20. 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)|http://crisummit2010.amia.org/]. San Francisco, CA, USA. March 12-13, 2010.
  21. 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)|http://cvial.ece.ttu.edu/cbms2009/]. Special track on HealthGrid Computing - Applications to Biomedical Research and Healthcare
  22. Sabados, William Thomas, Thesis: Comparing semantic matching results of schema matchers and metadata registry enabled systems. Pub date:2010. Pages:xii, 164 leaves
  23. 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
  24. 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.
  25. 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
  26. 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
  27. 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.
  28. 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
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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
  34. Covitz P, Warzel D, Fragoso G, Chilukuri R, Phillips J, "The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services.", BMC Medical Informatics and Decision Making (2006) 6:2
  35. 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
  36. 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
  37. 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
  38. 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.
  39. 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
  40. Silva, J., Chute, C., Cancer informatics: essential technologies for clinical trials, 2002. Springer Verlag, New York

Abstracts, Posters, and Talks

  1. 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.
  2. 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.
  3. 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.
  4. Warzel D. et al, "caCORE Evolves: Semantics II – Future Innovations", MIT Information Quality Symposium July, 2010
  5. 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+
  6. Warzel D, , "Semantics II – Future Innovations", Keynote Talk in ISO JTC1 SC32 WG2 Standards and Semantic Web,13th Open Forum on Metadata Registries (May 2010), ,Kunming, China.
  7. 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.
  8. 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.
  9. 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
  10. 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,12th Open Forum on Metadata Registries, Seoul, Korea
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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.
  16. 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
  17. 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
  18. 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.
  19. 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).
  20. Warzel D, "Exchanging Components in Health Registries", Poster and Talk 11th Open Forum on Metadata Registries, Metadata Down Under, (May 2008), Sydney, Australia
  21. Macallum, Peter, Warzel, D, "Achieving International Interoperability: Distributed Metadata Registries" – Poster, Joint NCI/NCRI Informatics - caBIG® Conference (2007), Washington DC, USA
  22. 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.
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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.
  28. Warzel D, Andonyadis C, McCurry C, Chilukuri R, Ishmukhamedov S, Covitz P, "Common Data Element (CDE) Management and Deployment in Clinical Trials", Poster presented at American Medical Informatics Association (AMIA), Annual Symposium, September 2003, Washington DC, USA
  29. 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

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