Hashtag: #TBICRI11 - AMIA | Informatics Professionals. · PDF file · 2016-04-18Distributed Electronic Data Interchange and ... Chen, Indiana University-Purdue University Indianapolis

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Dear Colleagues and Friends,

Along with the Track Chairs and the rest of the Scientific Program Committee, I am delighted to welcome you to the Fourth AMIA Summit on Translational Bioinformatics! With such high attendance, this year’s Summit promises to be a true confluence of the very best minds in translational bioinformatics. And, thanks to the number of high-quality submissions, we have assembled a terrific program that we are sure you will find enriching.

Your participation in the Summit is an essential component towards galvanizing the next generation of trans-disciplinary innovations required for the success of translational bioinformatics. We hope you find this to be a fruitful experience from which to gain new insights, new contacts, and perhaps even new hires.

Interacting with others in attendance, you will find a unique blend of expertise from academia, industry, government, and non-profit sectors with equal interest in forging new opportunities that undoubtedly will lead to the future of translational bioinformatics, and therefore to the future of medicine. With your help, we will continue exploring the nature and scope of this now burgeoning research field by creating a unique learning environment that bridges innovations in biomedical research to patient care.

The future of translational bioinformatics relies on your professional dedication and your individual and collective leadership. Together, we will continue to make great strides and promote the advancement of this exciting field. I am truly honored to have each and every one of you at this event, and look forward to witnessing the next breakthroughs that you will help enable. Best wishes to each of you!

Enjoy the Summit and all that you gain from it.

All the best,

Indra Neil Sarkar, PhD, MLISChair, 2011 Scientific Program Committee

Hashtag: #TBICRI11

Neil Sarkar, PhD, MLIS

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TBI Summit at a Glance .................................................................................................... 3

AMIA Board of Directors .................................................................................................. 5

Scientific Program Committee Members ............................................................................. 6

Track Descriptions .......................................................................................................... 7

Keynote Presentations ..................................................................................................... 8

Program Chronology

Monday, March 7 .................................................................................................... 10

Tuesday, March 8 .................................................................................................... 13

Wednesday, March 9—‘Bridge Day’ .......................................................................... 19

Posters .......................................................................................................................... 24

TaBLe of CoNTeNTS

March 7–9, 2011• Parc 55 hotel San FranciSco 3

MoNDay, MaRCh 7

7:30 – 8:30 am Coffee & Pastries

7:30 am – 5:30 pm Registration open

8:30 am – 12:00 pm Tutorials T01: Introduction to Translational Bioinformatics t02: ontology Services for translational research in the i2b2 Workbench T03: Statistics Concepts for Translational Researchers

10:00 – 10:30 am Coffee Break

12:15 – 1:15 pm IDBS Lunch-and-Learn: Lung Genomics Research Consortium: Building a Translational Research Portal to Improve the Molecular Understanding of Lung Disease

1:30 – 3:00 pm opening Session and Keynote Presentation: lincoln Stein, Platform leader, informatics and Bio-computing, ontario institute for Cancer Research

3:00 – 3:30 pm Coffee Break

3:30 – 5:00 pm Scientific Sessions TBI-01: Text Mining and Pharmacogenomics TBI-02: Analysis of Complex Disorders TBI-03: Bioinformatic Knowledge Clustering TBI-04: Therapy-relevant Stratification of Breast Cancer: Integrating Pathology and Quantitative Biomarker Analyses

5:00 – 6:30 pm Poster Session 1 and Reception

TueSDay, MaRCh 8



8:30 – 10:00 am Scientific Sessions TBI-05: Complex Analytics of Bioinformatics Data TBI-06: Knowledge Representation and Mining of Primary Biological Data TBI-07: Insights to Disease Etiology Using Gene Expression TBI-08: Current Challenges in Personal Genomics


10:30 am – 12:00 pm Scientific Sessions TBI-09: Leveraging Clinical Phenotypes for Translational Bioinformatics TBI-10: Semantic Approaches for Linking and Managing Clinical and Biological Knowledge TBI-11: Practical Implications of Translational Bioinformatics Knowledge TBI-12: Associating Semantic and Genomic Information

12:15 – 1:15 pm TransMed Lunch-and-Learn: Realizing Translational Medicine – A Success Story

1:30 – 3:00 pm Scientific Sessions TBI-13: Discovering and Tracking Genomic Variants TBI-14: Community Approaches to Advancing Translational Bioinformatics

TBI SuMMIT aT a GLaNCe

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TueSDay, MaRCh 8 continued

TBI-15: Service-oriented Architecture in Clinical and Translational Science Awards Applications TBI-16: Resources for Pharmacogenomics: Current and Future


3:30 – 5:00 pm Keynote Presentation: Carl Zimmer, lecturer, journalist, and author

5:00 – 6:30 pm Poster Session 2 and Reception

WeDNeSDay, MaRCh 9 ‘BRIDGe Day’



8:30 – 10:00 am CRI opening Session and Keynote Presentation: Kenneth H. Buetow, Director, NCI Center for Bioinformatics and Information Technology, Laboratory Chief, Laboratory of Population Genetics, National Cancer Institute


10:30 am – 12:00 pm Scientific Sessions TBI-17: Exploring Clinical Phenotypes to Enable Translational Bioinformatics TBI-18: Case Studies Demonstrating the use of Interoperable caBIG® Tools in Support of Integrative Translational Research TBI-19/CRI-01: ACMI Bridge Panel: Integrating Genomic and Clinical Data in Electronic Health Records and Biomedical Repositories: Challenges, Solutions and opportunities CRI-02: Semantic Web and Knowledge Acquisition

12:15 – 1:15 pm forte Lunch-and-Learn: Creating Communities of Practice — Beyond Technology

1:30 – 3:00 pm Scientific Sessions TBI-20/CRI-03: Translational Science Job Fair tBi-21: ViVo: enabling national networking of Scientists CRI-04: Personalized Medicine Requires Personalized Clinical Decision Support CRI-05: Data Synthesis and Novel Analyses


3:30 – 5:00 pm TBI Closing Session: Translational Bioinformatics year in Review Russ Altman, Professor of Bioengineering, Genetics, and Medicine, Stanford University

5:00 – 6:-00 pm Bridge Day Reception

TBI SuMMIT aT a GLaNCe


ChaIR Nancy M. Lorenzi Vanderbilt University Medical Center ChaIR-eLeCT Gilad J. Kuperman New York Presbyterian Hospital

PReSIDeNT aND Ceo edward h. Shortliffe AMIA

SeCReTaRy Christoph u. Lehmann Johns Hopkins Children’s Medical and Surgical Center Johns Hopkins University School of Medicine

TReaSuReR R. Scott evans LDS Hospital Intermountain Health Care

DIReCToRSDominik aronsky Vanderbilt University

eta S. Berner University of Alabama at Birmingham

atul J. Butte Stanford University School of Medicine

helen Burstin National Quality Forum

Connie J. Delaney University of Minnesota School of Nursing

John h. holmes University of Pennsylvania

Rita Kukafka Columbia University

eneida Mendonca University of Chicago

Blackford Middleton Partners HealthCare Harvard Medical School

Thomas Payne University of Washington

Justin B. Starren Marshfield Clinic Research Foundation

Bonnie L. Westra University of Minnesota School of Nursing ex-offICIo BoaRD MeMBeRS

american College of Medical Informatics President James Cimino NIH Clinical Center

Student WG Representative David C. Kaelber Case Western Reserve University

aMIa BoaRD of DIReCToRS

aCCReDITaTIoN STaTeMeNT The American Medical Informatics Association is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.

DeSIGNaTIoN STaTeMeNTThe American Medical Informatics Association designates this educational activity for a maximum of 30 AMA PRA Category 1 Credit(s)™. Physicians should only claim credit commensurate with the extent of their participation in the activity.

DISCLoSuRe of fINaNCIaL ReLaTIoNShIPS WITh aNy CoMMeRCIaL INTeReSTAs a sponsor accredited by the ACCME, the American Medical Informatics Association requires that everyone in a position to control the content of an educational activity disclose all relevant financial relationships with any commercial interest prior to the educational activity.

The ACCME considers relationships of the person involved in the CME activity to include financial relationships of a spouse or partner.

Faculty and planners who refuse to disclose relevant financial relationships will be disqualified from participating in the CME activity. For an individual with no relevant financial relationship(s), the participants must be informed that no conflicts of interest or financial relationship(s) exist.

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PRoGRaM CoMMITTee ChaIR

Indra Neil Sarkar, University of Vermont

TRaCK ChaIRS

Lewis frey, University of UtahMaricel Kann, University of Maryland- Baltimore CountyNigam Shah, Stanford UniversityJessica Tenenbaum, Duke University SPC MeMBeRS

Gil alterovitz, Massachusetts Institute of Technologyolivier Bodenreider, National Library of MedicineMichael Cantor, Pfizer, Inc.Jake y. Chen, Indiana University-Purdue University IndianapolisJulio facelli, University of UtahKaren eilbech, University of UtahRobert freimuth, Mayo Clinichannah Tipney, University of ColoradoBenjamin Keller, Eastern Michigan UniversityJason Moore, Dartmouth Medical SchoolRaul Rabadan, Columbia UniversitySoumya Raychaudhuri, Broad InstituteThomas Rindflesch, National Library of MedicineShyam Visweswaran, University of Pittsburghhua xu, Vanderbilt University aDVISoRy CoMMITTee

atul Butte, Stanford University, 2008 TBI Chair yves Lussier, University of Chicago, 2009 TBI ChairPeter Tarczy-hornoch, University of Washington, 2010 TBI ChairGilad Kuperman, Columbia University, AMIA 2010 SPC Chairolga Troyanskaya, Princeton University, 2010 ISMB SPC ChairRuss altman, Stanford UniversityJudith Blake, The Jackson LaboratoryLarry hunter, University of ColoradoIsaac Kohane, Harvard UniversityDaniel Masys, Vanderbilt University

SCIeNTIfIC PRoGRaM CoMMITTee


TRaCK 1 INfoRMaTICS CoNCePTS, TooLS aND TeChNIqueS To eNaBLe INTeGRaTIVe TRaNSLaTIoNaL BIoINfoRMaTICS ReSeaRCh

Integrative translational research projects make coordinated use of molecular (genomic, epigenetic, proteomic, etc.) as well as clinical information (imaging, EMR, etc.) to understand pathophysiology and to understand and predict responses to therapeutic interventions. Studies of this kind are core components of many NIH Roadmap projects and aim to relate molecular and imaging parameters to the pathophysiology and clinical parameters. This interdisciplinary track addresses the development of informatics tools in the semantic modeling, grid, natural language processing, information integration and information warehouse areas that have to potential for facilitating integrative translational bioinformatics research.

TRaCK 2 INfoRMaTICS MeThoDS foR The INTeGRaTIVe aNaLySIS of MoLeCuLaR aND CLINICaL MeaSuReMeNTS

Novel modalities for molecular measurements, including those for epigenetics, interactions, and proteins, continue to be introduced each year. This track addresses the development of novel analytic methods for these molecular measurements as applied to disease, how molecular measurements can be stored and retrieved in electronic health records, and how existing analytic methods can now be applied to clinical measurements. DNA sequencing, gene expression micro-arrays and other tools measuring outputs of the genome have been forecast to enable the discovery of biomarkers for disease and novel types of therapeutics. In particular, this track will focus on how data-driven, knowledge-driven, and physics-driven approaches can be applied to facilitate drug and biomarker discovery.

TRaCK 3 ReLaTING aND RePReSeNTING PheNoTyPeS aND DISeaSe foR TRaNSLaTIoNaL BIoINfoRMaTICS ReSeaRCh

Phenotypes broadly describe the unique traits of an organism, some of which are related to disease. Improved measurement technologies and ontologies have enabled investigators to obtain and represent large collections of phenotypes, but relating these to clinical research and human health remains a challenge. Though electronic health records are being increasingly adopted, much of the useful phenotypic and clinical descriptors remain in free-text limiting their use for translational research. This track addresses all of these challenges, with presentations geared towards enabling novel prognostic, diagnostic, and therapeutic applications.

TRaCK 4 INfoRMaTICS MeThoDS BRIDGING BaSIC SCIeNCe DISCoVeRIeS aND CLINICaL PRaCTICe

In recent years, over 250 disease genes have been discovered from genetic studies, the majority of which are associated with complex diseases such as diabetes, hypertension, cancer, etc. Consequently, molecular bioinformatics methods are increasingly considered for the identification of additional disease gene candidates. Further, with the reducing cost of genome-wide sequencing or assaying, new opportunities are emerging to provide personalized genome maps and their interpretation. This track focuses on the development of bioinformatics methods to enable discovery of disease genes and processes, the integration of genetic data and knowledge in decision-making and support, electronic records, and other genetic applications to clinical practice and personal health management.

TRaCK DeSCRIPTIoNS

four tracks focus on methodological innovations from bench to bedside, with a particular emphasis on clinical implications based on the latest in molecular and cellular biology innovations:

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MoNDay, MaRCh 7

1:30 – 3:30 pm Room: Cyril Magnin I/IILincoln Steinontario Institute for Cancer Research

The technology required for cancer research has become increasingly more complex over the past several years. Accordingly, the development of innovative solutions to handle the large and complicated datasets these new technologies generate has become an essential part of the cancer research process. oicr’s informatics and Bio-computing Platform, led by Dr. Lincoln Stein, integrates and interprets this data, developing visualization tools to turn raw data into meaningful information for biologists, clinicians, and trainees.

TueSDay, MaRCh 8

3:30 – 5:00 pm Room: Cyril Magnin I/IICarl ZimmerLecturer at yale university, journalist, author

This year the scientific community is celebrating the ten-year anniversary of the sequencing of the human genome. Yet scientists are also well aware that this achievement has not yet led to many medical applications. Human biology is too complex for that. In fact, human biology is not exclusively human. We are home to thousands of species of bacteria, viruses and other microbes, upon which our very survival depends. only recently has our inner jungle become the subject of intense genome-sequencing. The preliminary results are exciting and provocative, potentially helping us understand human metabolism, immunity, and even behavior.

Carl Zimmer is the author of nine books, including Parasite Rex, Microcosm: E. coli and the New Science of Life, and the forthcoming A Planet of Viruses. He regularly contributes articles to The New York Times, National Geographic, Scientific American, and Discover, where he is a contributing editor and writes a column about neuroscience. Zimmer has won the National Academies Communication Award for his journalism, and he is a two-time winner of the American Association for the Advancement of Science Journalism. He teaches science writing at Yale.

KeyNoTe PReSeNTaTIoNS


WeDNeSDay, MaRCh 9

8:30 – 10:00 am Room: Cyril Magnin I/IIKenneth h. Buetowassociate Director, Bioinformatics and Information TechnologyDirector, Center for Biomedical Informatics and Information Technology National Cancer Institute

The CRI Summit Opening Plenary and Keynote Address are supported by Velos

Dr. Ken Buetow’s scientific career has focused for more than 20 years on understand-ing the role of genetics in complex human diseases such as cancer, and the application of sophisticated informatics technologies to solve major biomedical challenges. In his current role as National Cancer Institute Associate Director, responsible for Bioinformat-ics and Information Technology, he oversees the caBIG® (cancer Biomedical Informatics Grid®) program, a groundbreaking initiative to speed developments in cancer research by facilitating interoperability in order to create a “World Wide Web” of biomedical re-search to connect the entire cancer community. caBIG® offers a revolutionary interoper-able infrastructure, unifying standards, and a variety of services to enable organizations and individual researchers to securely share biomedical data, and its capabilities serve as a demonstration of the connectivity required for Personalized Medicine.

Dr. Buetow also serves as the Director of the NCI Center for Bioinformatics and Infor-mation Technology (NCI CBIIT), which is responsible for interoperability and integra-tion of NCI research. He is also the Chief of the Laboratory of Population Genetics (LPG), where his group applies genomics to increase our understanding of the genetics of complex phenotypes. In addition to serving on the governing and advisory boards for numerous government organizations, academic institutions, and scientific and medi-cal societies, Dr. Buetow has published more than 160 scientific papers. Most recently, Dr. Buetow has been elected as a Fellow by the American College of Medical Informat-ics, a distinguished honor given to those who have demonstrated major contributions in biomedical Informatics. Additional honors and awards include The Editor’s Choice Award from Bio-IT World (2008), The Federal 100 Award (2005), The NIH Award of Merit (2004) and the NCI Director’s Gold Star Award (2004). Dr. Buetow received a B.A. in biology from Indiana University in 1980 and a Ph.D. in human genetics from the University of Pittsburgh in 1985.

3:30 – 5:00 pm Room: Cyril Magnin I/IIRuss altmanStanford university

The importance of Translational Bioinformatics continues to grow in biomedical research, genetics, education, and diagnostic and therapeutic discovery. In the past year, we have seen the public-release of the first human diploid genome, as well as tens of thousands of individuals participating in genome-wide association studies. This session will review a sample of notable events that have occurred in the past twelve months. Included will be new findings from the published literature, achievements in the application of bioinformatics, changes in public policy and government, and emerging new methodologies. The implications of these events for the future of Translational Bioinformatics and clinical practice will be addressed.

KeyNoTe PReSeNTaTIoNS

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MoNDay, MaRCh 7

7:30 – 8:30 am Coffee & Pastries Room: Cyril Magnin Foyer

7:30 am – 5:30 pm Registration open Room: Cyril Magnin Foyer

8:30 am – 12:00 pm Tutorials

T01: Introduction to Translational Bioinformatics Atul Butte, Stanford University Room: Stockton

In 2005, Dr. Elias Zerhouni, Director of the National Institutes of Health (NIH), wrote “It is the responsibility of those of us involved in today’s biomedical research enterprise to translate the remarkable scientific innovations we are witnessing into health gains for the nation... At no other time has the need for a robust, bidirectional information flow between basic and translational scientists been so necessary.” Clearly evident in Dr. Zerhouni’s quote is the role biomedical informatics needs to play in facilitating translational medicine. American Medical Informatics Association (AMIA) now hosts the Joint Summits on Translational Science of which the Summit on Translational Bioinformatics is one of the two components. This tutorial is designed around the successful curriculum used in Stanford’s course in Translational Bioinformatics, one of the first courses to be offered in this field. This tutorial is designed to teach the basics of the various types of molecular data and methodologies currently used in bioinformatics and genomics research, and how these can interface with clinical data. This tutorial will address the hypotheses one can start with by integrating molecular biological data with clinical data, and will show how to implement systems to address these hypotheses. The tutorial will cover real-world case-studies of how genetic, genomics, and proteomic data has been integrated with clinical data. T02: ontology Services for Translational Research in the i2b2 Workbench Room: Mission IShawn Murphy, Massachusetts General Hospital (i2b2) and Nigam H Shah, Stanford University (NCBO)

The i2b2 platform uses vocabularies extensively in the querying and manipulation of patient data for translational and clinical research. The National Center for Biomedical ontology offers an extensive range of Web services for accessing ontologies, generating value sets and lexicons, annotating data, and performing information retrieval that form key elements of software systems in informatics. Given the importance of the use of ontologies for data integration, ncBo and i2b2 have initiated a collaboration to provide access to cutting edge ontology services from within the i2b2 workbench to enable cross institution data transformation. This tutorial will review the drivers of this collaboration, provide experience in using the ncBo’s resources, and will offer participants in-depth understanding of how ontologies and terminologies are used in biomedical informatics. This tutorial will review the use of ontologies in i2b2 and discuss their integration with the ncBo’s ontology Web Services infrastructure.

T03: Statistics Concepts for Translational Researchers Michael G. Walker, Stanford University Room: Mission II

In this tutorial we will introduce key statistics concepts for biomedical researchers. These include understanding how t-tests work, how to interpret a p-value, power and sample size, Design of experiments (Doe) and how Doe can increase your research productivity. The emphasis is on concepts and applications, not theory or proofs. Explanations will be intuitive, understandable, and memorable.

PRoGRaM ChRoNoLoGy


10:00 – 10:30 am Coffee Break Room: Cyril Magnin Foyer

12:15 – 1:15 pm IDBS Lunch-and-Learn Room: Cyril Magnin III Lung Genomics Research Consortium: Building a Translational Research Portal to Improve the Molecular understanding of Lung Disease Mick Correll, Associate Director, Center for Cancer Computational Biology, Dana-Farber Cancer Institute The LGRC portal represents a revolutionary new way to support collaborative research in the genetics of chronic lung disease. The portal addresses many needs, from supporting uploading of large experimental data sets, assessment of available samples and their characteristics, sample and data tracking capabilities across a distributed consortium, and the availability of sophisticated, automated analytical tools. Learn about the project requirements, solution design, and commercial and open-source tools that were utilized to construct the system.

1:30 – 3:00 pm TBI opening Plenary Session and Keynote address: Room: Cyril Magnin I/II Lincoln Stein ontario institute for cancer research See page 8 for more information.

3:00 – 3:30 pm Coffee Break Room: Cyril Magnin Foyer

3:30 – 5:00 pm Scientific Sessions

TBI-01: Paper: Text Mining and Pharmacogenomics Track 1, 2, 3 Room: Mission

Comparison of automated and human assignment of MeSh Terms on Publicly-available Molecular DatasetsD. Ruau, Stanford University; M. Bagwu, The Ohio State University College of Medicine; J. Dudley, V. Krishnan, A. Butte, Stanford University

Mining the Scientific Literature to Build a Rich Semantic Network for Pharmacogenomics Knowledge aggregation and Discovery using Natural Language Processing and ontology-based TechniquesY. Garten, Stanford University; A. Coulet, University of Nancy; N. Shah, M. Musen, R. Altman, Stanford University

Selective Polypharmacology towards Drug Repositioning Based on Cancer Related Signaling PathwaysX. Peng, Regenstrief Institute; L. Li, B. Wang, S. Meroueh, Center for Computational Biology and Bioinformatics

facilitating electronic health Records-based Pharmacogenetic Studies using Natural Language Processing: a Case Study of WarfarinH. Xu, M. Jiang, M. Oetjens, E. Bowton, A. Ramirez, J. Jeff, M. Basford, J. Pulley; J. Cowan, M. Ritchie, D. Masys, D. Roden, D. Crawford, Vanderbilt University; J. Denny, Vanderbilt School of Medicine

PRoGRaM ChRoNoLoGy

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MoNDay, MaRCh 7 continued

TBI-02 Paper: analysis of Complex Disorders Track 1, 2, 3, 4 Room: Cyril Magnin I

Genomic Variation in autism PathwaysD. Wall, M. Banos, Harvard University

autism Candidate Genes via Mouse PhenomicsT. Meehan, The Jackson Laboratory; C. Carr, North Caroline State University; C. Bult, E. Chesler, J. Blake, The Jackson Laboratory

Cross-disease analysis Between autism and autoimmune DiseasesJ. Jung, D. Wall, Harvard Medical School

The application of Naive Bayes Model averaging to Predict alzheimer’s Disease from Genome-wide DataW. Wei, G. Cooper, S. Visweswaran, University of Pittsburgh

TBI-03: Paper: Bioinformatic Knowledge Clustering Track 1, 2, 4 Room: Cyril Magnin II

Clustering Disease Connections Revealed by DMDM: Domain Mapping of Disease MutationsN. Nehrt, T. Peterson, A. Adadey, M. Kann, University of Maryland, Baltimore County

analysis of the WTCCC Dataset using a Novel Gene-based Method for Ranking Candidate GenesH. Sagreiya, R. Daneshjou, N. Tatonetti, R. Altman, Stanford University

hierarchical Naïve Bayes Classifiers for Genetic association StudiesA. Malovini, N. Barbarini, R. Bellazzi, Università di Pavia

Converting Pathogen Whole Genome Sequencing into Clinically actionable DataV. Sintchenko, University of Sydney; S. Anthony; E. Coiera, University of New South Wales


MoNDay, MaRCh 7 continued

TBI-04: Panel: Therapy-relevant Stratification of Breast Cancer: Integrating Pathology and quantitative Biomarker analyses Track 4 Room: Cyril Magnin III

H. Hu, Windber Research Institute; H. Rui, Thomas Jefferson University; A. Kovatich, MDR Global, LLC; T. Hyslop, Thomas Jefferson University; J. Eberhardt, DecisionQ, Corp.

This panel will address several important bioinformatics and biomedical informatics topics in translational research. We will discuss our multidisciplinary collaboration to improve personalized care for breast cancer patients, by collecting, generating, warehousing, and interrogating clinicopathologic and molecular data with a unique combination of state-of-the-art methods. Breast cancer is a heterogeneous disease and there is a great need to improve personalized therapy using molecular profiling. our consortium is quantifying levels of a carefully selected panel of 250 therapy-relevant proteins across 5,000 invasive breast cancer specimens in order to stratify breast cancer according to predicted responsiveness to emerging and existing drugs. The goal is to accelerate rational recruitment of patients into cost-effective clinical trials of limited size by identifying subgroups of patients most likely to respond based on protein biomarkers. Cost-effective analyses are made possible by our novel high density tissue microarray platform that is combined with quantitative multi-color immunodetection. In this panel, domain experts will discuss the selection and collection of cancer cases and clinicopathologic data, the creation of high density tissue arrays and the generation of molecular data, the management and integration of the data, the analysis and mining of the integrated data, and the presentation of the derived knowledge.

5:00 – 6:30 pm Poster Session 1 and Reception Room: Cyril Magnin Foyer See page 24 for Posters.

TueSDay, MaRCh 8



8:30 – 10:00 am Scientific Sessions

TBI-05: Paper: Complex analytics of Bioinformatics Data Track 2, 3, 4 Room: Cyril Magnin I

Testing all SNP Pairs for Joint association with DiseaseR. Schuyler, L. Hunter, University of Colorado School of Medicine

a New Computational Pipeline for miRNa enrichment analysesA. Nuzzo, F. Mulas, University of Pavia; B. Zupan, University of Ljubljana; R. Bellazzi, Università di Pavia

how Cytokines Co-occur across asthma Patients: from Bipartite Network analysis to a Molecular-based ClassificationS. Bhavnani, University of Texas; S. Victor, W. Calhoun, University of Texas Medical Branch; W. Busse, University of Wisconsin School of Medicine and Public Health; E. Bleecker, Wake Forest University Baptist Medical Center; M. Castro, Washington University School of Medicine; H. Ju, A. Brasier, University of Texas Medical Branch

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assessing Stem Cells Developmental Stage from Genome-wide expression DataF. Mulas, University of Pavia; L. Zagar, University of Ljubljana; L. Sacchi, S. Garagna, University of Pavia; G. Shaulsky, Baylor College of Medicine, Houston; M. Zuccotti, University of Parma; B. Zupan, University of Ljubljana; R. Bellazzi, Università di Pavia

TBI-06: Paper: Knowledge Representation and Mining of Primary Biological Data Track 1, 3, 4 Room: Cyril Magnin II

Towards Structuring unstructured GenBank Metadata for enhancing Comparative Biological StudiesE. Chen, N. Sarkar, University of Vermont

enhancing Phylogeography by Improving Geographical Information from GenBankM. Scotch, Arizona State University; N. Sarkar, University of Vermont; C. Mei, Yale University; R. Leaman, Arizona State University; K. Cheung, Yale University; P. Ortiz, A. Singh, G. Gonzalez, Arizona State University

Mining Gene ontology annotations from hyperlinks in the Gene WikiB. Good, A. Su, GNF

Go-Module: functional Synthesis and Improved Interpretation of Biologically or Clinically Prioritized Gene ontology TermsJ. Li, The University of Chicago; X. Yang, Y. Lee, Section of Genetic Medicine and Center for Biomedical Informatics; Y. Lussier, The University of Chicago

TBI-07: Paper: Insights to Disease etiology using Gene expression Track 1, 2, 3, 4 Room: Mission

Mining Microarray Data to Predict the histological Grade of a Breast CancerM. Fabregue, LIRMM UM2 CNRS; S. Bringay, LIRMM UMR 5506; P. Poncelet, LIRMM UM2 CNRS; M. Teisseire, CEMAGREF; B. Orsetti, INSERM U896, UM1, CRLC

utility of Gene-specific algorithms for Predicting Pathogenicity of Gene VariantsD. Crockett, University of Utah; E. Lyon, ARUP Laboratories; M. Williams, Intermountain Healthcare; S. Narus, J. Facelli, J. Mitchell, University of Utah

expression Profiling Discovers Diverging Signatures of aging in Disease and CancerR. Tirrell, A. Morgan, J. Dudley, A. Butte, Stanford University

Novel Genome-wide array for Conducting Species-Specific expression of human Cancer Cell and Mouse Stroma in xenograft modelsX. Yang, Y. Huang, Y. Lee, Q. Zhang, J. Shen, R. Xing, Section of Genetic Medicine and Center for Biomedical Informatics; Y. Lussier, The University of Chicago



TBI-08: Panel: Current Challenges in Personal Genomics Track 2 Room: Cyril Magnin IIIY. Lussier, The University of Chicago; A. Butte, R. Altman, Stanford University; M. Kann, University of Maryland, Baltimore County

Post genomics technologies are rapidly revealing different molecular facets of individuality. High throughput mass spectrometry and microarrays have been followed by an increase in affordable and paradigm shifting next generation and whole genome sequencing. The molecular architecture of disease predisposition and response to therapy are thus increasingly accessible to scientific and clinical inquiry. In the interim, corporations have been providing direct-to-customer services, which range from conventional and established practices to those incorporating debatable methods. This panel will address the technical, analytical, and economical challenges associated with these technologies focusing on pharmacogenomics, next generation sequencing, gene expression/transcription, and post-translational dimensions of personal genomics. The risks, benefits and tradeoffs of different screening and analytical technologies will also be contrasted in the context of clinical care.


10:30 am – 12:00 pm Scientific Sessions

TBI-09: Paper: Leveraging Clinical Phenotypes for Translational Bioinformatics Track 2, 3 Room: Cyril Magnin I

using Clinical Trial Data to Identify Candidates for Drug Re-PurposingM. Sorani, J. Arron, J. Haris, J. Monroe, Genentech, Inc.

a Computational analysis Pipeline for Determining Nut allergy In VitroN. Zimmerman, Y. Gernez, A. Das, L. Herzenberg, G. Walther, Stanford University

an environment-wide association Study (eWaS) on Serum Lipid LevelsC. Patel, M. Cullen, J. Ioannidis, A. Butte, Stanford University

Whole exome Sequencing Study Incidentally Reveals Genetic Cause of one Case of Idiopathic hemolytic anemiaR. Robison, University of Utah; G. Lyon, Children’s Hospital of Philadelphia; T. Jiang, Beijing Genomics Institute; R. Van Wijk, University Medical Center; L. Yang, P. Zhang, R. Wu, Y. Liu, X. Yang, Beijing Genomics Institute; J. Xing, B. Moore, University of Utah; J. Glessner, Children’s Hospital of Philadelphia; L. Sugerman, F. Reimherr, University of Utah; W. van Solinge, University Medical Center; J. Elia, Children’s Hospital of Philadelphia; M. Yandell, W. McMahon, University of Utah; W. Johnson,; M. Clement, Brigham Young University; H. Hakonarson, Children’s Hospital of Philadelphia; J. Wang, Beijing Genomics Institute; K. Wang, Zilkha Neurogenetic Institute

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TBI-10: Paper: Semantic approaches for Linking and Managing Clinical and Biological Knowledge Track 1 Room: Cyril Magnin II

Developing a Semantic framework for Clinical and Translational ResearchS. Matney, R. Bradshaw, O. Livne, B. Bray, J. Mitchell, S. Narus, University of Utah

The Translational Medicine ontology and Knowledge Base: using Semantic Web Technology in Personalized Medicine for Data IntegrationJ. Luciano, Rensselaer Polytechnic Institute; B. Andersson, AstraZeneca; C. Batchelor, Royal Society of Chemistry; T. Clark, Harvard Medical School; C. Domarew, Albany Medical Center; T. Gambet, W3C; A. Jentzsch, Freie Universität Berlin; V. Kashyap, CIGNA; P. Kos, Harvard Medical School; J. Kozlovsky, AstraZeneca; M. Marshall, Leiden University Medical Center; J. McCusker, D. McGuinness, T. Lebo, Rensselaer Polytechnic Institute; C. Ogbuji, Cleveland Clinic; E. Pichler, W3C; R. Powers, Predictive Medicine, Inc.; E. Prud’hommeaux, W3C; M. Samwald, IRF Society Office; L. Schriml, University of Maryland; P. Tonellato, Harvard Medical School; P. Whetzel, Stanford University; J. Zhao, Oxford University; M. Dumontier, Carleton University; S. Stephens, Johnson & Johnson Pharmaceutical Research and Development

assessing the Complexity of Clinical Data RequestsD. Capurro, P. Tarczy-Hornoch, University of Washington

onWaRD: ontology-driven Web-based framework for Multi-center Clinical StudiesV. Tran, N. Johnson, Case Western Reserve University; S. Redline, Harvard Medical School; G. Zhang, Case Western Reserve University

TBI-11: Paper: Practical Implications of Translational Bioinformatics Knowledge Track 1, 2 Room: Mission

Knowledge-based analysis Implicates hypoxia in Beta-blocker ResponseH. Tipney, D. Kao, M. Bristow, L. Hunter, B. Lowes, University of Colorado Denver

finding Cellular Response to Varying Doses of Cancer TherapeuticsT. Chen, M. Clutter, N. Kotecha, G. Nolan, S. Batzoglou, Stanford University

a Novel Signal Detection algorithm to Identify hidden Drug-drug Interactions in the fDa adverse event Reporting SystemN. Tatonetti, G. Fernald, R. Altman, Stanford University

PaPaya: applications in oncology Decision SupportA. Janevski, N. Banerjee, S. Kamalakaran, V. Varadan, N. Dimitrova, Philips Research North America


TueSDay, MaRCh 8 CoNTINueD

TBI-12: Panel: associating Semantic and Genomic Information Track 1 Room: Cyril Magnin IIIL. Frey, K. Eilbeck, University of Utah; R. Freimuth, Mayo Clinic; M. Krauthammer, Yale University; N. Shah, Stanford University

This panel will examine methods and implications of associating semantic and genomic information. The focus will be on the following areas: (1) annotation of sequence data, (2) community collection and maintenance of semantic information, (3) reasoning over large data sets and (4) hypothesis generation from semantics data. With the growth of whole genome sequencing, there is an acute need to associate semantic information with genetic information, because by itself, a genomic sequence is only a string of letters. The addition of semantic knowledge to the genetic information is paramount. Coupling this information has already started to take place. How this semantic information is collected and maintained in a community informed and curated approach is important to the overall effort. To ensure quality of the semantic information, it needs to be validated by experts and tools are needed to support this effort. If implemented well, such work opens up the possibility of using the semantic technology to reason over multi-modal omics data. In addition to omics analysis, there is reasoning over the semantic information itself. Here, there are questions of how to generate and test hypotheses from such semantic information.

12:15 – 1:15 pm TransMed Lunch-and-Learn Room: Cyril Magnin III Realizing Translational Medicine — a Success Story Jeremy Miller, PhD, Director of Scientific Engineering; Frank DuPont, Vice President, Field Services TransMed will demo three key capabilities their customers have implemented to achieve translational medicine. First, they will show how Cohort Explorer enables investigators to identify and group cohorts of patients with similar characteristics or outcomes; next, will be how BioClinical Analyzer helps investigators analyze retrospective data in order to discover markers; followed by showing how to codify and apply the marker on new patients.


TBI-13: Paper: Discovering and Tracking Genomic Variants Track 1, 2, 3 Room: Cyril Magnin I

Rapid Development of Viral human Interactome Prediction System for New VirusesH. Osmanbeyoglu, M. Ganapathiraju, University of Pittsburgh

use of Genomic Variants in Informatics for Integrating Biology and the Bedside (i2b2)L. Phillips, Partners HealthCare; S. Minovitsky, I. Ratnere, DOE Joint Genome Institute; I. Dubchak, Lawrence Berkeley National Laboratory; I. Kohane, Children’s Hospital; S. Murphy, Massachusetts General Hospital

Non-synonymous and Synonymous Coding SNPs Show Similar Likelihood and effect-Size of human Disease associationR. Chen, E. Davydov, M. Sirota, A. Butte, Stanford University

Transfer Rule Learning for Biomarker Discovery and Verification from Molecular Profiling StudiesP. Ganchev, D. Malehorn, W. Bigbee, V. Gopalakrishnan, University of Pittsburgh

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TBI-14: Paper: Community approaches to advancing Translational Bioinformatics Track 1 Room: Cyril Magnin II

CaGI: The Critical assessment of Genome Interpretation, a Community experiment to evaluate Phenotype PredictionS. Repo, University of California, Berkeley; J. Moult, University of Maryland; S. Brenner, University of California, Berkeley

Distributed Interoperable Research experts Collaboration Tool (DIReCT)G. Weber, Harvard Medical School; M. Conlon, University of Florida; D. Eichmann, University of Iowa; H. Falk-Krzesinski, Northwestern University; M. Halaas, Stanford School of Medicine; L. Johnson; E. Meeks, UCSF; D. Mitchell, Stanford University School of Medicine; T. Schleyer, University of Pittsburgh, School of Dental Medicine; S. Stallings, University of Colorado Denver; M. Kahlon, University of California, San Francisco

a Linked open Data approach to Interoperability Between Biomedical Resource InventoriesC. Borromeo, University of Pittsburgh; P. Whetzel, Stanford University; M. Haendel,; C. Torniai, Oregon Health & Sciences University; A. Bandrowski, UCSD

The CardioVascular Research Grid (CVRG) ProjectR. Winslow, The Johns Hopkins University; J. Saltz, Emory University; I. Foster, The University of Chicago; J. Carr, Y. Ge, Wake Forest University Health Sciences; M. Miller, L. Younes, D. Geman, S. Granite, The Johns Hopkins University; K. Tahsin, A. Post, Emory University; R. Madduri, The University of Chicago; T. Ratnanather, The Johns Hopkins University; J. Larkin, National Heart, Lung, and Blood Institute, NIH; S. Ardekani, T. Brown, A. Kolasny, K. Reynolds, M. Shipway, The Johns Hopkins University

TBI-15: Panel: Service-oriented architecture in Clinical and Translational Science awards applications Track 1 Room: Cyril Magnin IIID. Ervin, The Ohio State University; J. Osborne, University of Alabama at Birmingham; R. Wynden, UCSF; K. Tahsin, Emory University

The Clinical and Translational Science Awards (CTSA) is an NCRR sponsored initiative focused on supporting translational research, and accelerating basic and clinical science, and ultimately to improve patient care. Various institutions are granted CTSA awards to create programs within their institution aimed at these goals, as well as collaboration and outreach with other CTSA institutions. Within the CTSA, groups of like minded institutions and individuals are encouraged to establish affinity groups which lead to greater collaboration and innovation in focused areas of interest. Numerous CTSA institutions have realized a need for a service oriented architecture which can realize the common business and research needs faced by CTSAs as they take on the challenges and meet the needs of their researchers and customers. Such an architecture is necessary to facilitate intra-institutional collaboration, facilitate interoperability, and accelerate the pace of team science. This panel aims to introduce the motivating factors and current state of progress within CTSA institutions which necessitate the common informatics platform.



TBI-16: Panel: Resources for Pharmacogenomics: Current and future Track 1 Room: Mission

D. Demner-Fushman, US National Library of Medicine; N. Shah, Stanford University; A. Aronson, M. Fiszman, O. Bodenreider, National Library of Medicine; R. Altman, Stanford University

Pharmacogenomics is on the verge of delivering on the promise of truly personalized medicine, as exemplified in recently announced stage III clinical trials of afatinib for HER2-positive breast cancer patients. This panel will present the current state of information management in support of pharmacogenomics by summarizing research presented at the PSB 2010 session on mining the pharmacogenomics literature and discussing resources provided by nlM, national center for Biomedical ontology and PharmGKB, as well as data processing methods developed by these institutions. The panel hopes to encourage a lively discussion of: 1) existing and needed new resources and tools for pharmacogenomics; 2) future directions in the development of information management resources and infrastructure for pharmacogenomics; 3) community-wide involvement and collaboration in creating common resources.


3:30 – 5:00 pm Keynote Presentation Room: Cyril Magnin I/II Carl Zimmer “The Inner Jungle: The Natural History of the Human Microbiome” See page 8 for more information.

5:00 – 6:30 pm TBI Poster Session 2 and Reception Room: Cyril Magnin Foyer See Posters on page 24.

WeDNeSDay, MaRCh 9

‘BRIDGe Day’



8:30 – 10:00 am CRI opening Plenary Session and Keynote Presentation Room: Cyril Magnin I/II Kenneth Buetow See page 9 for more information.


10:30 am – 12:00 pm Scientific Sessions

TBI-17: Paper: exploring Clinical Phenotypes to enable Translational Bioinformatics Track 1, 2, 3, 4 Room: Cyril Magnin I

enabling enrichment analysis with the human Disease ontologyP. LePendu, M. Musen, N. Shah, Stanford University

Sex Differences in Pain across 386 Diseases in electronic Medical RecordsD. Ruau, L. Liu, D. Clark; M. Angst, Stanford University School of Medicine; A. Butte, Stanford University

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WeDNeSDay, MaRCh 9 continued

using Lagged Linear Correlation to find Relationships between Laboratory Values and Clinician ConceptsG. Hripcsak, D. Albers, A. Perotte, Columbia University

Population Physiology: Conjoining ehR Dynamics with Physiological ModelingD. Albers, M. Schmidt, G. Hripcsak, Columbia University TBI-18: Panel: Case Studies Demonstrating the use of Interoperable caBIG tools® in Support of Integrative Translational Research Track 1 Room: Mission

C. Schaefer, M. Heiskanen, Center for Biomedical Informatics and Information Technology/NCI; E. Siegel, Baltimore Veterans Affairs Medical Center Radiology/University of Maryland Medical Center

The cancer Biomedical Informatics Grid® (caBIG®) is a collaborative network designed to accelerate the translation of discoveries from research to clinical care. This extensible informatics platform integrates diverse data types and supports interoperable software tools in the areas of clinical sciences, biospecimen management, imaging, and basic research. The panel will be discussing translational research projects including The Cancer Genome Atlas (TCGA) that are supported by the caBIG® informatics tools. TCGA data are currently available through the TCGA data portal, and Cancer Genome Workbench (CGWB) and caIntegrator data warehouses. In addition to browsing data from public studies, researchers can setup custom, caBIG®-compatible web portals to conduct integrative research, without requiring programming experience. These tools also allow researchers and oncologists to assess how radiology data can be used in conjunction with genetic and other molecular data to predict outcome and treatment response. The TCGA Radiology Project is an excellent example of how existing caBIG® resources can be linked together to enable researchers to aggregate and analyze clinical, imaging and molecular data in an integrated manner.



TBI-19/CRI-01: Panel: aCMI Sponsored Bridge Day Panel: Integrating Genomic and Clinical Data in electronic health Records and Biomedical Repositories: Challenges, Solutions, and opportunities Track 1 Room: Cyril Magnin III

J. Cimino, National Institutes of Health Clinical Center; S. Murphy, Massachusetts General Hospital, Harvard Medical School, and Partners HealthCare; H. Lowe, Stanford University; L. Ohno-Machado, University of California at San Diego; E. Bernstam, University of Texas at Houston; P. Tarczy-Hornoch, University of Washington; R. Bellazzi, Università di Pavia

The integration of genomic data into the more traditional phenomic databases, such as electronic health records and biomedical data warehouses, offers great potential for the advancement of biomedical research and patient care. However, there are a number of challenges to accomplishing this integration in a seamless manner, including the consistent, standardized representation and coding of the data, coping with the shear volume of information, and proper indexing of important genomic features to facilitate retrieval. The panelists, all Fellows of the American College of Medical Informatics, each a leader in their own institutions and in the field of biomedical informatics, will describe their work on addressing the challenges of genomic-phenomic integration, with working solutions and examples of how such integration can be brought to bear on tasks such as helping clinicians understand their patients’ genetic data, using genetic data to support clinical decision making, and advancing biomedical research. The panel will also discuss implications for national standards on representation and data sharing. The session will include time for audience participants to share the solutions from their own institutions.

CRI-02: Paper: Semantic Web and Knowledge acquisition CRI Track 2 Room: Cyril Magnin II

Towards Semantic-Web Based Representation and harmonization of Standard Meta-data Models for Clinical StudiesC. Tao, G. Jiang, Mayo Clinic; W. Wei, University of Minnesota Twin Cities & Mayo Clinic; H. Solbrig, C. Chute, Mayo Clinic

using Statistical Text Mining to Supplement the Development of an ontologyS. Luther, James A. Haley VMAC; D. Berndt, University of South Florida; D. Finch, E. Hickling, James A. Haley Veterans Hospital; M. Richardson; D. Hickam, Portland VA Medical Center

CNTRo 2.0: a harmonized Semantic Web ontology for Temporal Relation Inferencing in Clinical Narratives

C. Tao, H. Solbrig, C. Chute, Mayo Clinic Semantic Web-based annotation and Reasoning for Temporal Information in Clinical Narratives C. Tao, Mayo Clinic; G. Savova, Children’s Hospital Boston and Harvard Medical School; H. Solbrig, P. de Groen, Mayo College of Medicine/Mayo Clinic; C. Chute, Mayo Clinic

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12:15 – 1:15 pm forte Lunch-and-Learn Room: Cyril Magnin III Creating Communities of Practice — Beyond Technology Panelists will discuss considerations for accommodating people and processes when integrating systems. Moderator: Tony O’Hare, PhD, co-founder and Chief Scientific Officer, Forte Research Systems, Inc. Tahsin Kurc, Emory University (focus: Grid-based data federation) Rob Wynden, UCSF (focus: Linking multiple SOA and data warehousing platforms) Griffin Weber, Harvard University (focus: semantic Web technologies and research networking)


TBI-20/CRI-03: Translational Science Job fair Track 1, 2, 3, 4 Room: Divisadero

The Joint Summits Job Fair, open and free to all registrants, provides graduate trainees opportunity to meet investigators—and organizations—who can meet their training needs. This event will pair together young professionals with faculty members looking for postdoctoral fellows. Particularly useful for students in their final year and faculty members looking for informatics-savvy postdoctoral fellows.

TBI-21: Panel: VIVo: enabling National Networking of Scientists

Track 1 Room: Cyril Magnin III

VIVo: enabling National Networking of ScientistsK. Holmes, Washington University School of Medicine; M. Conlon, C. Barnes, University of Florida; Y. Ding, Indiana University; V. Davis, University of Florida

ViVo is an open-source semantic Web application that enables the discovery of research and scholarship across disciplinary and administrative boundaries through interlinked profiles of people and other research-related information. ViVo, originally developed at Cornell University, is being expanded through a $12.2 million stimulus grant from the National Center for Research Resources (NCRR) of the National Institutes of Health (NIH) to the University of Florida and six partner institutions. ViVo uses data ingested from institutional sources of record and external sources, supplemented with manual entry to populate detailed profiles of researchers with information related to publications, grants, educational background, research interests, teaching, awards, professional affiliations, community services, and more. Data in ViVo conform to a public ontology of types and relationships that can be extended for local needs via the ontology editor included with the ViVo application. ViVo’s ontology supports faceted searching for quick retrieval of people, organizations, events, and research-related information. institutional ViVos and other compatible profiling applications are producing data to form a rich network of information that can be searched to foster collaboration across institutions and enable open sharing of research discovery. ViVo project members will discuss major project efforts and platform features during the presentation.



CRI-04: Panel: Personalized Medicine Requires Personalized Clinical Decision Support Track 2 Room: Mission

E. Bernstam, The University of Texas Health Science Center at Houston; T. Johnson, University of Kentucky; H. Strasberg, Wolters Kluwer Health; W. Hersh, Oregon Health & Science University

We discuss personalized medicine from an informatics perspective. Personalized medicine is fundamentally a process of dividing patient populations into smaller sub-populations and eventually individuals. Although nearly universally accepted as a worthy goal, personalized medicine presents multiple informatics challenges. First, we consider the problem from a clinical viewpoint. What does it mean for a clinician to practice personalized medicine? Second, we discuss personalized medicine from a cognitive perspective. Clinical practice already strains or even exceeds human cognitive capacity. Thus, even small increases in cognitive load are problematic. The massive amount of molecular “-omics” information associated with personalized medicine is clearly beyond our cognitive abilities. Thus, to practice personalized medicine, we must also develop and implement personalized decision support. We explore what vendors and academia are doing in this area. We conclude by discussing the fundamental problems underlying the challenges and solutions presented by the first three speakers.

CRI-05: Paper: Data Synthesis and Novel analyses CRI Track 1, 2 Room: Cyril Magnin II

Modeling Complex Warfarin Pharmacogenetic Protocols in Clinical Trial SimulationsV. Fusaro, P. Patil, C. Chi, C. Contant, P. Tonellato, Harvard Medical School

Spatio-temporal Structure of the uS Critical Care Transfer NetworkK. Unnikrishnan, University of Michigan Medical School; D. Patnaik, Virginia Tech; T. Iwashyna, University of Michigan Medical School

Smooth Isotonic Regression - a New Method to Calibrate Predictive Models X. Jiang, M. Osl, J. Kim, L. Ohno-Machado, University of California, San Diego

Simulating Clinical Trials with observational Data M. Weiner, R. Tannen, University of Pennsylvania


3:30 – 5:00 pm TBI Closing Session: Translational Bioinformatics year in Review Russ Altman, Stanford University Room: Cyril Magnin I/II See page 9 for more information.

5:00 – 6:00 pm Bridge Day Reception Room: Embarcadero Join your colleagues at the Bridge Day Reception. Mix and mingle with SPC members of both Summits. Sponsored by Booz Allen Hamilton Booz Allen Hamilton has been at the forefront of strategy and technology consulting for nearly a century, providing a broad range of services in strategy and organization, technology, operations, and analytics. BAH helps health leaders and practitioners facilitate biomedical and translational research, accelerate scientific discovery, and enable effective clinical care delivery across the ‘bench to bedside’ continuum. From biomedical data management to biomedical informatics and advanced analytics, BAH capabilities span the spectrum of client needs in data collection, predictive modeling and simulation, or anything in between. Count on Booz Allen to help deliver results that endure. Learn more at www.boozallen.com.

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TBI PoSTeR SeSSIoN 1Monday, March 7 • 5-6:30 pm

Pharmacy fill Data as an Indicator of Patient adherence BoaRD 1 R. Belew, UC San Diego; D. Looney, VA San Diego Healthcare System

Network Visualization and analysis of Pregnant uterine Contractions BoaRD 2 S. Bhavnani, S. Victor, University of Texas Medical Branch; H. Eswaran, G. Rathinaswamy, UAMS

Predicting Colorectal Cancer Patients’ Survivability: The Comparison of using Three Data Mining Methods - artificial Neural Network, Logistic Regression and Decision Tree BoaRD 3 C. Chang, Y. Shih, H. Liu, Y. Chang, C. Chu, National Defense Medical Center

Genome-wide Methylation analysis of CpG Island Methylator Phenotype Cancers BoaRD 4 M. Choong, Centre for Health Informatics; M. Hitchins, Prince of Wales Clinical School; G. Tsafnat, Centre for Health Informatics

Modeling the expansion of Cancer Registry Services across Distributed Grid Computer Systems using a Sampling Based approach BoaRD 5 M. Cryer, A. Stroup, L. Frey, University of Utah

Toward an automatic Method for extracting Cancer and other Disease-related Point Mutations from The Biomedical Literature BoaRD 6 E. Doughty, University of Maryland, Baltimore County; O. Bodenreider, U.S. National Library of Medicine; G. Thompson, A. Adadey, T. Peterson, M. Kann, University of Maryland, Baltimore County

Discovering Biomedical Research Resources in Text: an ontology-driven approach using Curated Data for Incremental Retraining BoaRD 7 H. Frost, L. Hadden, D. Bourges-Waldegg, Harvard Medical School; M. Haendel, C. Torniai, N. Vasilevsky, M. Wilson, Oregon Health & Sciences University; P. Thompson, Dartmouth Medical School; D. MacFadden, Harvard Medical School

Managing Variability in Co-expression Network Construction BoaRD 8 D. Gibbs, A. Bankhead III, OHSU

a Metamodel for Collaborative Sharing of Biomedical Research experiments BoaRD 9 J. Gunnels, J. Schwacke, J. Zheng, L. Cowart, J. Obeid, Medical University of South Carolina

Differential expression analysis for Pathways BoaRD 10 W. Haynes, Hendrix College

Mining and Visualization of Pain Descriptors from Clinical Records — a Pilot Study BoaRD 11 N. Heintzelman, D. Anderko, L. Childs, Lockheed Martin, Co; R. Taylor, L. Simonsen, R. Lustig, Sage Analytica; J. Haythornthwaite, G. Bova, Johns Hopkins University, School of Medicine

PoSTeRS


TBI PoSTeR SeSSIoN 1 continued

Monday, March 7 • 5-6:30 pm

Discovering Disease associations by Integrating electronic health Records and Medical Literature BoaRD 12 A. Holmes, H. Khiabanian, Columbia University; A. Hawson, C. Friedman, Columbia University Medical Center; R. Rabadan, Columbia University

using Circulating Plasma Protein Biomarkers of Inflammation and Vascular Modeling to Detect abdominal aortic aneurysm BoaRD 13 H. Itakura, M. Ahmed, J. Dyer, R. Olshen, P. Tsao, Stanford University

oaMiner: an application of hypothesis Discovery within the osteoarthritis Domain BoaRD 14 S. James, The Ohio State University

annotation of Disease-associated SNPs with eqTLs to elucidate mechanisms of Disease BoaRD 15 H. Kang, R. Chen, A. Butte, Stanford University

Semantic Web Methodologies Provide access to fLu Data without Getting you Sick of Searching BoaRD 16 T. Lebo, J. Luciano, Rensselaer Polytechnic Institute

Capturing Structured Gene Variant Data using GVf, xML and hL7 BoaRD 17 S. Lee, D. Crockett, University of Utah; G. Wood, Intermountain Healthcare; C. Jung, B. Bray, J. Mitchell, K. Eilbeck, University of Utah

uncovering Genes associated with human Infections in Pathogenic Bacteria: a Novel Integrative analysis Linking Genome, Bibliome, and Diseasome BoaRD 18 F. Lin, University of New South Wales

funDo: a Web Tool exploring Genes using functional Disease ontology annotations BoaRD 19 S. Lin, W. Kibbe, Northwestern University

Stratification of osteoarthritis Patients by Molecular Profiling analysis of Synovium Tissue BoaRD 20 H. Liu, R. Dryer-Minnerly, T. Ort, Centocor Research & Development, Inc; P. Marsters, Johnson & Johnson Pharmaceutical Research & Development, L.L.C; C. Huang, K. Picha, M. Curran, Centocor Research & Development, Inc; W. Marshall, University of Toronto; H. Fan, P. Branigan, S. Stephens, F. Baribaud, Centocor Research & Development, Inc.

The university of California at Santa Cruz - university of California at San francisco Prostate Cancer Genomics Browser BoaRD 21 J. Long, S. Nadaf, J. Zhu, D. Haussler, University of California at Santa Cruz

PoSTeRS

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Translational Informatics to Link Gene activity to ontologies with and without Context BoaRD 22 K. Marwah, Harvard Medical School; N. Noy, Stanford University; G. Alterovitz, M. Ramoni, Harvard Medical School

Conceptual Models for Interoperability in caBIG using the Semantic Web BoaRD 23 J. McCusker, D. McGuinness, Rensselaer Polytechnic Institute

using openSocial to Build a Shareable Library of Research applications BoaRD 24 E. Meeks, L. Yuan, M. Kahlon, University of California, San Francisco; G. Weber, Harvard Medical School

Imaging Genetics: Replication of aPoe, PICaLM, and BIN1 associations with alzheimer Disease BoaRD 25 K. Nho, Regenstrief Institute

Supporting Disease ontology Refinement and query accuracy through a Cohort Identification Interface BoaRD 26 J. Osborne, D. Dempsey, M. Wyatt, University of Alabama at Birmingham

use of Supervised and unsupervised Machine Learning algorithms to Identify Subtypes in Subjects with Post Traumatic Stress Disorder BoaRD 27 J. Ross, B. Apfel, T. Neylan, San Francisco Veteran’s Administration Health Center; A. Das, Stanford University; I. Sim, UCSF

Sigmoid Weighted Relieff (SWRf) for Ranking SNPs BoaRD 28 M. Stokes, S. Visweswaran, University of Pittsburgh

Genome-wide association Study of Personality Disorder in adults with attention Deficit hyperactivity Disorder BoaRD 29 L. Sugerman, B. Marchant, P. Wilson, F. Reimherr, E. Williams, C. Halls, C. Pommerville, R. Strong, University of Utah; G. Lyon, Children’s Hospital of Philadelphia, Center for Applied Genomics; R. Robison, University of Utah

aCCf/aha Key Data elements and Definitions of a Base Cardiovascular Vocabulary for electronic health Records BoaRD 30 J. Tcheng, Duke University Medical Center; R. Hendel, University of Miami; M. Isler, American College of Cardiology; R. Karlsberg, UCLA; D. Roman, American College of Cardiology; W. Weintraub, Christiana Health System

VIVo: Support for Translational Research BoaRD 31 M. Tennant, University of Florida; K. Holmes, Washington University in St. Louis School of Medicine; C. Barnes, V. Davis, S. Gonzalez, University of Florida; L. McIntosh, Washington University in St. Louis School of Medicine; S. Mitchell, Cornell University; M. Conlon, University of Florida

PoSTeRS




The Regulation of Smoking on airway epithelial Gene expression and a Detection Model for Smoking history BoaRD 32 C. Tseng, Y. Shih, Y. Chang, C. Chang, H. Liu, C. Chu, National Defense Medical Center

Distributed Infrastructure for Biomolecular Simulation-derived Data Sharing and analysis BoaRD 33 J. Thibault, T. Cheatham, J. Facelli, University of Utah

Integrative analysis Identifies a Novel Regulator of Colorectal Cancer Invasion BoaRD 34 B. Zhang, Z. Shi, N. Prodduturi, N. Deane, D. Beauchamp, Vanderbilt University

Genetic Risk-variants Target foxa1 Genomic activity BoaRD 35 X. Zhang, Dartmouth Medical School

TBI PoSTeR SeSSIoN 2Tuesday, March 8 • 5-6:30 pm

how Circos Ideograms Complement Networks: a Case Study in asthma BoaRD 1 S. Bhavnani, R. Pillai, W. Calhoun, A. Brasier, University of Texas Medical Branch

Linking Genotype to Phenotype: a Pilot Project to Create a Research Data Warehouse of Biospecimen and “omic” Information BoaRD 2 X. Bi, C. Wu, University of Delaware; P. McGarvey, Georgetown University; J. London, Thomas Jefferson University; E. Ewen, Christiana Care Health System; T. Bunnell, University of Delaware

Developing an ontology-driven Data Collection application BoaRD 3 D. Bourges-Waldegg, Harvard Medical School; T. Bashor, Wonder Lake Software, LLC; H. Frost, L. Hadden, Harvard Medical School; M. Haendel, C. Torniai, Oregon Health & Sciences University; D. MacFadden, Harvard Medical School

Cancer Informatics Services: an Infrastructure for Translational Cancer Biomarker Studies BoaRD 4 U. Chandran, S. Winters, L. Schmandt, M. Becich, University of Pittsburgh

a Novel Bioinformatics framework to explore the existing Possibility of New Drug Target Proteins in the human Malaria Parasite BoaRD 5 Y. Chang, C. Chu, Y. Shih, C. Chang, H. Liu, National Defense Medical Center

Protein-network Modeling of Prostate Cancer Gene Signatures Reveals essential Pathways in Disease Recurrence BoaRD 6 J. Chen, J. Li, W. Stadler, Y. Lussier, The University of Chicago

PoSTeRS

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Tuesday, March 8 • 5-6:30 pm

Proposed agent-directed Composition of Biomedical and Simulation ontologies: facilitating Dynamic hypothesis Instantiation BoaRD 7 S. Christley, G. An, University of Chicago

Drug-gene Retriever: an unsupervised System to Identify Drug-gene Relationships BoaRD 8 D. Dempsey, C. Crasto, University of Alabama at Birmingham

MouSeR: an online Mouse Registry for Biomedical Researchers BoaRD 9 D. Dempsey, M. Wyatt, R. Hendrickson, University of Alabama at Birmingham

Designing effective Clinical Trials using Simulations BoaRD 10 V. Fusaro, P. Patil, Harvard Medical School; C. Contant, Beth Israel Deaconess Medical Center; P. Tonellato, Harvard Medical School

Paradigm Integrated Pathway analysis of Drug Subtype Sensitivity (DSS) BoaRD 11 T. Goldstein, J. Stuart, S. Benz, S. Ng, D. Haussler, University of California at Santa Cruz

finding Text in Scientific Publications Relevant to Phenotypic Concepts BoaRD 12 S. Hassanpour, A. Das, Stanford University

PheGenI: an Integrated Resource for Browsing Genetic association Data BoaRD 13 L. Hindorff, NHGRI, NIH; D. Hoffman, NCBI, NIH; H. Junkins, National Human Genome Research Institute; B. Kattman, D. Maglott, R. Maiti, J. Mehta, J. Paschall, L. Phan, NCBI, NIH; E. Ramos, National Human Genome Research Institute; S. Sherry, NCBI, NIH; T. Manolio, NHGRI, NIH; M. Feolo, NCBI, NIH

The faceBase Management and Coordination hub: Development and Design Principles for a Translational BioInformatics Data Portal BoaRD 14 H. Hochheiser, C. Borromeo, L. Schmandt, K. Desai, M. Stefanko, M. Becich, University of Pittsburgh; J. Murray, University of Iowa; M. Marazita, University of Pittsburgh

Gene Signature Identified by Tissue-decomposition Predicts Response to Preoperative Chemotherapy BoaRD 15 Y. Huang, Section of Genetic Medicine and Center for Biomedical Informatics; Y. Lussier, University of Chicago; S. Gutkind, V. Patel, NIH/NIDCR; R. Xing, University of Chicago

The Phenx Toolkit: Toward Data Interoperability for Genome Wide association Studies BoaRD 16 W. Huggins, H. Pan, V. Bakalov, J. Levy, Y. Qin, N. Whitehead, L. Strader, RTI International; E. Ramos, H. Junkins, National Human Genome Research Institute; C. Hamilton, RTI International

PoSTeRS




The human Variome Project: a Network of Scientists and Tools Constructed with the Goal of understanding and Treating Genetic Diseases BoaRD 17 T. Kalbfleisch, University of Louisville; R. Cotton, Howard Florey Institute

Clustering of human Diseases and Genetic and environmental factors BoaRD 18 C. Kimmel, University of Pittsburgh; J. Lustgarten, University of Pennsylvania School of Veterinary Medicine; I. Wong, S. Visweswaran, S. Handler, University of Pittsburgh

understanding Variable Representation for Causal Inference in ehRs BoaRD 19 S. Kleinberg, G. Hripcsak, Columbia University

International, Interoperable, harmonized Systems for Integrating Multi-omic Data Sources to Characterize and quantify Metabolic and Nutritional Phenotypes BoaRD 20 M. Lange, J. Kaput, FDA

Novel Method for Identification of Chromosomal Gain Loci from Conventional Gene expression arrays BoaRD 21 Y. Lee, Section of Genetic Medicine and Center for Biomedical Informatics; Y. Lussier, The University of Chicago

Revealing Signaling Modules in Cancers by Mining TCGa Data With Integrated Data-mining and Knowledge-mining BoaRD 22 S. Lu, X. Lu, University of Pittsburgh

Institutional architecture for Secondary Data use BoaRD 23 A. Lynn, Duke University; H. Shang, Duke University Health System; S. Chakraborty, Duke University; B. McCourt, Duke Clinical Research Institute; M. Nahm, Duke University; J. Ferranti, Duke University Health System; J. Tenenbaum, Duke University

a Practical approach to automated oWL annotation BoaRD 24 S. Mollah, A. Mauer, M. Wrobel, E. Barbour, The Rockefeller University

Linking Model organisms and Resources to human Diseases using an ontology-based approach BoaRD 25 C. Mungall, Lawrence Berkeley National Laboratory; A. Bandrowski, University of California San Diego; C. Torniai, Oregon Health & Science University; M. Martone, University of California San Diego; J. Turner, TCG; D. Anderson, University of Washington; M. Haendel, Oregon Health & Sciences University

PoSTeRS

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acquiring Biomedical ontologies from Spreadsheets BoaRD 26 M. O’Connor, A. Das, Stanford University

extending i2b2 for Cancer Research: adding episode and Somatic Mutations BoaRD 27 J. Orechia, M. Ullman-Cullere, A. Pathak, J. Mathew, Dana-Farber Cancer Institute

using Density estimates to aggregate Patients and Summarize Disease evolution BoaRD 28 A. Perotte, Columbia University

Informatics System with Imaging and Touchscreen Devices for Duchenne Muscular Dystrophy Multicenter Clinical Trial BoaRD 29 N. Raum, C. Barnes, Y. Li, S. Williams, University of Florida

PoSTeRS


Best Wishes to the First Recipient of the Marco Ramoni Distinguished Paper Award!

Established to honor the memory of Dr. Marco Ramoni, 1963-2010, accomplished scientist, educator, author, and entrepreneur, who advanced and influenced the field of biomedical informatics, and who authored more than 100 publications in genetics, biomedical informatics, statistics, and artificial intelligence, the Marco Ramoni Distinguished Paper Award for Translational Bioinformatics will be presented for the first time at the 2011 AMIA Summit on Translational Bioinformatics.

The recipient will be the author of the paper that best exemplifies the spirit and scholarship of Marco Ramoni; applying informatics methods to the elucidation of basic molecular biology processes relevant to the conquest of human disease.

The Marco Ramoni Distinguished Paper will be recommended for journal publication with other top contributions from the meeting.

Thanks to the generosity of scores of individual donors and a matching corporate gift from Microsoft, the Award recipient will receive a certificate accompanied by a monetary prize. If you would like to contribute to the Marco Ramoni fund in support of future awards to distinguished authors, please contact Jonathan Grau: [email protected].

The Marco Ramoni Distinguished Paper award will be presented at the closing session of the Summit on TBI on ‘Bridge Day’, Wednesday, March 9.

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Come to the Job Fair on Bridge day!it’s not too late to sign up and meet,

mingle, and network your way to a new position while at the Joint Summits!

employers and Principal investigators will be there, too!rSVP online at http://jointsummits2011.amia.org

Make new connections on Bridge day

wednesday, March 9!1:30 – 3 pm, DivisaDero room

Dear Colleagues and Friends,

On behalf of AMIA, I would like to welcome you to the Second Annual Summit on Clinical Research Informatics (CRI). Thank you for attending this dynamic gathering of CRI thought leaders and innovators. I hope you find the scientific sessions, panels, and networking events to be exciting and productive.

Given the dramatic trajectory of research, training, and practice in the CRI domain over the last several years, this Summit represents an unparalleled opportunity for individuals and organizations at all levels to develop and enhance a comprehensive understanding of the CRI landscape. By gathering such an outstanding cross-section of CRI leaders, this Summit provides a catalyst for new, high-impact collaborations. The CRI Summit represents a unique opportunity not only to learn about the latest advances in our field, but also to engage in dialogue that shapes the future of CRI science and practice.

I’d like to take a moment to draw your attention to ‘Bridge Day’ which joins the TBI and CRI Summits together and provides an outstanding opportunity for our two communities to translate and exchange critical innovations and knowledge existing at the intersection of our two complementary disciplines.

Finally, I would like to take this opportunity to thank the Scientific Program Committee members, our Advisory Committee, and the AMIA staff for their diligent and continuous efforts throughout the planning and scientific programming process that has led to the creation of this year’s Summit. It is only through their dedication and hard work that a meeting such as this is possible; we owe all of these individuals our gratitude for their commitment to the advancement of CRI.

Philip R.O. Payne, PhDChair, 2011 Scientific Program Committee

Philip R.O. Payne, PhD

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Bio-repository and Correlative Data ManagementStandards and Knowledge Representation














Bio-repository and Correlative Data ManagementBio-repository and Correlative Data Management










Standards and Knowledge RepresentationData Coordinating Centers


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CRI Summit at a Glance ................................................................................................... 3

Scientific Program Committee ............................................................................................ 5

Track Descriptions ............................................................................................................. 6

Keynote Presentations ....................................................................................................... 7

Program Chronology

Wednesday, March 9—‘Bridge Day’ ....................................................................... 9

Thursday, March 10 .............................................................................................. 14

Friday, March 11 .................................................................................................. 24

Posters ............................................................................................................................ 27

TaBle Of COnTenTs


WeDnesDay, MaRCh 9 ‘BRIDge Day’


7:30 am – 5:00 pm Registration Open

8:30 – 10:00 am CRI Opening Plenary and Keynote: Kenneth h. Buetow, Director, nci center for Bioinformatics and information technology, laboratory chief, laboratory of Population Genetics, national cancer institute


10:30 am – 12:00 pm scientific sessions tBi-17: exploring clincial Phenotypes to enable translational Bioinformatics TBI-18: Case Studies Demonstrating the use of Interoperable caBIG® Tools in Support of Integrative Translational Research TBI-19/CRI-01: ACMI Bridge Panel: Integrating Genomic and Clinical Data in electronic health records and Biomedical repositories: challenges, Solutions and Opportunities CRI-02: Semantic Web and Knowledge Acquisition

12:15 – 1:15 pm forte lunch-and-learn: Creating Communities of Practice — Beyond Technology

1:30 – 3:00 pm scientific sessions TBI-20/CRI-03: Translational Science Job Fair tBi-21: ViVo: enabling national networking of Scientists CRI-04: Personalized Medicine Requires Personalized Clinical Decision Support cri-05: Data Synthesis and novel analyses


3:30 – 5:00 pm TBI Closing session: Translational Bioinformatics Year in Review: Russ Altman, Stanford University

5:00 – 6:00 pm Bridge Day Reception

ThuRsDay, MaRCh 10


7:00 – 8:30 am Birds-of-a-feather (BOf) sessions BOF-01: Workflow Modeling and Analysis BOF-02: Multi-center Research Programs and Data Coordinating Centers BOF-03: Data Warehousing and Secondary Use BOF-04: Data in the electronic Medical record (eMr): a Discussion of Potential issues

7:00 am – 5:00 pm Registration Open

8:30 – 10:00 am scientific sessions cri-06: Perspectives on cri education CRI-07: Semantically Aware, Service-oriented Clinical Trial Applications to Promote Interoperability and Improved Data Quality CRI-08: Bridging Research, Clinical Practice, and Community CRI-09: Cross Institutional Systems to Support Phenotyping in Biomedical Research cri-10: research networking and Socio-cultural Factors


CRI suMMIT aT a glanCe

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ThuRsDay, MaRCh 10 continued

10:30 am – 12:00 pm scientific sessions cri-11: evidence Generating Medicine: integrating research and Practice to Accelerate Clinical and Translational Science CRI-12: Synthetic Patients Use in Clinical Research CRI-13: Study Planning CRI-14: Case Studies in Clinical Research Informatics 1 cri-15: challenges and emerging Solutions for Securing Medical Data and Applications

12:15 – 1:15 pm Recombinant Data lunch-and-learn: Innovation in Research Informatics—Making an Impact

1:30 – 3:00 pm scientific sessions cri-16: Building clinical research capacity in Developing nations; can emerging information technologies reduce Barriers of entry cri-17: challenges and lessons learned with i2b2 Deployment CRI-18: Data, Information, and Knowledge Management 1 CRI-19: Data Integration and Security CRI- 20: Clinical Research Informatics Town Hall


3:30 – 5:00 pm scientific sessions CRI-21: Participant Recruitment cri-22: library-based Support for clinical and translational research: the Informationist CRI-23: Data, Information, and Knowledge Management 2 CRI-24: Data Warehousing and Research Registries CRI-25: Case Studies in Clinical Research Informatics 2

5:00 – 6:30 pm CRI Poster session and Reception

fRIDay, MaRCh 11


7:30 – 10:30 am Registration Open

8:30 – 10:00 am scientific sessions cri-26: Meaningful Use and Personalized Patient education CRI-27: Developing Governance Approaches to Clinically Derived Research Resources CRI-28: Clinical Research Tools and Standards CRI-29: The Value of Value Sets


10:30 am – 12:00 pm CRI Closing session: clinical informatics Year in review, Peter embi, the ohio State University

CRI suMMIT aT a glanCe


sPC ChaIRPhilip R.O. Payne, The Ohio State University TRaCK ChaIRs

Rachel Richesson, University of South FloridaJaved Mostafa, University of north carolina – Chapel HillChunhua Weng, Columbia Universityeta Berner, UAB

sPC MeMBeRselmer Bernstam, University of Texas, Houstonelizabeth Chen, University of VermontPaul harris, Vanderbilt UniversityTodd Johnson, University of Texas, Houstonalbert lai, The Ohio State Universityhenry lowe, Stanford Universitygenevieve B. Melton-Meaux, University of Minnesotashawn Murphy, Partners HealthcareMark Weiner, University of Pennsylvaniaadam Wright, Partners Healthcareg.Q. Zhang, Case Western Reserve University

aDvIsORy COMMITTeePeter embi, University of Cincinnati, Immediate Past ChairMichael Kahn, University of Colorado – DenverJoyce niland, city of hope national Medical Center

sCIenTIfIC PROgRaM COMMITTee

aCCReDITaTIOn sTaTeMenT The American Medical Informatics Association is accredited by the Accreditation Council for Continuing Medical education to provide continuing medical education for physicians.

DesIgnaTIOn sTaTeMenTThe American Medical Informatics Association designates this educational activity for a maximum of 30 AMA PRA Category 1 Credit(s)™. Physicians should only claim credit commensurate with the extent of their participation in the activity.

DIsClOsuRe Of fInanCIal RelaTIOnshIPs WITh any COMMeRCIal InTeResTas a sponsor accredited by the accMe, the american Medical Informatics Association requires that everyone in a position to control the content of an educational activity disclose all relevant financial relationships with any commercial interest prior to the educational activity.

the accMe considers relationships of the person involved in the cMe activity to include financial relationships of a spouse or partner.

Faculty and planners who refuse to disclose relevant financial relationships will be disqualified from participating in the cMe activity. For an individual with no relevant financial relationship(s), the participants must be informed that no conflicts of interest or financial relationship(s) exist.

6

TRaCK 1 ReseaRCh PlannIng anD PaRTICIPanT ReCRuITMenT

With the increasing complexity of clinical study de-signs, and challenges surrounding the recruitment of targeted participants for such research programs, the informatics community has and continues to develop a broad variety of clinical research planning and par-ticipant recruitment tools. This track focuses on the design, evaluation, and use cases for such systems.

TRaCK 2 DaTa ManageMenT, shaRIng, anD RePResenTaTIOn

Clinical research is an inherently information-intensive endeavor, involving the collection, storage, manage-ment, query, integration, analysis, and dissemination of heterogeneous and multi-dimensional data sets. This track focuses on the theoretical and technical frameworks intended to address such needs, as well as evaluation studies examining their efficacy and impact on clinical research workflow and outcomes.

TRaCK 3 PeOPle, ORganIZaTIOnal, anD POlICy Issues

The development and use of informatics-based tools and methods in the clinical research domain introduces or influences a broad variety of people, organization-al, and policy issues. This track focuses on the explo-rations of such issues and socio-technical factors, using a variety of methods and evaluation techniques.

TRaCK 4 eDuCaTIOnal anD COMMunITy DevelOPMenT

Significant challenges surrounding the delivery of appropriate training curricula and the satisfaction of critical knowledge and skills competencies for individu-als involved in the CRI community have been regularly reported. Similarly, the need to create collaborative frameworks in which members of the CRI community can interact in productive and high-impact ways have been called for in numerous settings, while the methods and mechanisms for doing so remain largely unde-veloped. This track focuses on novel and evolving ap-proaches to address these two complementary issues.

TRaCK DesCRIPTIOns

four tracks focus on methodological innovations from bench to bedside, with a particular emphasis on clinical implications based on the latest in molecular and cellular biology innovations:


WeDnesDay, MaRCh 9

8:30 – 10:00 am Room: Cyril Magnin I/IIKenneth h. Buetowassociate Director, Bioinformatics and Information TechnologyDirector, Center for Biomedical Informatics and Information Technology national Cancer Institute

The CRI Summit Opening Plenary and Keynote Address are supported by Velos

Dr. Ken Buetow’s scientific career has focused for more than 20 years on understand-ing the role of genetics in complex human diseases such as cancer, and the application of sophisticated informatics technologies to solve major biomedical challenges. In his current role as national cancer institute associate Director, responsible for Bioinformat-ics and Information Technology, he oversees the caBIG® (cancer Biomedical Informatics Grid®) program, a groundbreaking initiative to speed developments in cancer research by facilitating interoperability in order to create a “World Wide Web” of biomedical re-search to connect the entire cancer community. caBIG® offers a revolutionary interoper-able infrastructure, unifying standards, and a variety of services to enable organizations and individual researchers to securely share biomedical data, and its capabilities serve as a demonstration of the connectivity required for Personalized Medicine.

Dr. Buetow also serves as the Director of the nci center for Bioinformatics and infor-mation technology (nci cBiit), which is responsible for interoperability and integra-tion of nci research. he is also the chief of the laboratory of Population Genetics (lPG), where his group applies genomics to increase our understanding of the genetics of complex phenotypes. In addition to serving on the governing and advisory boards for numerous government organizations, academic institutions, and scientific and medi-cal societies, Dr. Buetow has published more than 160 scientific papers. Most recently, Dr. Buetow has been elected as a Fellow by the American College of Medical Informat-ics, a distinguished honor given to those who have demonstrated major contributions in biomedical informatics. additional honors and awards include the editor’s choice award from Bio-it World (2008), the Federal 100 award (2005), the nih award of Merit (2004) and the nci Director’s Gold Star award (2004). Dr. Buetow received a B.A. in biology from Indiana University in 1980 and a Ph.D. in human genetics from the University of Pittsburgh in 1985.

3:30 – 5:00 pm Room: Cyril Magnin I/IIRuss altmanstanford university

The importance of Translational Bioinformatics continues to grow in biomedical research, genetics, education, and diagnostic and therapeutic discovery. In the past year, we have seen the public-release of the first human diploid genome, as well as tens of thousands of individuals participating in genome-wide association studies. This session will review a sample of notable events that have occurred in the past twelve months. Included will be new findings from the published literature, achievements in the application of bioinformatics, changes in public policy and government, and emerg-ing new methodologies. The implications of these events for the future of Translational Bioinformatics and clinical practice will be addressed.

KeynOTe PResenTaTIOns

8

fRIDay, MaRCh 11

10:30 am – 12:00 pm Room: Cyril Magnin IPeter embi The Ohio state university

Clinical Research Informatics has emerged as an important sub-domain of biomedical informatics. Major efforts in CRI have led to significant advances in clinical and trans-lational science through improved, informatics-enabled research processes, efficiency, and effectiveness. Major funding efforts from the nih as well as other agencies, orga-nizations and institutions have spurred advances in CRI in recent years. This session will be the first such ‘year-in-review’ of the CRI domain. We will cover major findings from the published literature, achievements in CRI, and developing efforts over the past year. As the first such review for CRI, we will also reach back to major accomplish-ments from the past that put these more recent ones in context, and lay the foundation for this and future year’s updates of CRI accomplishments and their implications.

KeynOTe PResenTaTIOns continued


WeDnesDay, MaRCh 9 — ‘BRIDge Day’


7:30 am – 5:30 pm Registration Open Room: Cyril Magnin Foyer

8:30 – 10:00 am CRI Opening Plenary session and Keynote address: Room: Cyril Magnin I/II Kenneth Buetow For more information go to page 7.


10:30 am – 12:00 pm scientific sessions

TBI-17: Paper: exploring Clinical Phenotypes to enable Translational Bioinformatics Room: Cyril Magnin I TBI Track 1, 2, 3, 4

enabling enrichment analysis with the human Disease OntologyP. LePendu, M. Musen, N. Shah, Stanford University

sex Differences in Pain across 386 Diseases in electronic Medical RecordsD. Ruau, L. Liu, D. Clark,; M. Angst, Stanford University School of Medicine; A. Butte, Stanford Univeristy

using lagged linear Correlation to find Relationships between laboratory values and Clinician ConceptsG. Hripcsak, D. Albers, A. Perotte, Columbia University

Population Physiology: Conjoining ehR Dynamics with Physiological ModelingD. Albers, M. Schmidt, G. Hripcsak, Columbia University

PROgRaM ChROnOlOgy

10

WeDnesDay, MaRCh 9 continued

TBI-18: Panel: Case studies Demonstrating the use of Interoperable caBIg tools® in support of Integrative Translational Research TBI Track 1 Room: Mission

C. Schaefer, M. Heiskanen, Center for Biomedical Informatics and Information Technology/NCI; E. Siegel, Baltimore Veterans Affairs Medical Center Radiology/University of Maryland Medical Center

The cancer Biomedical Informatics Grid® (caBIG®) is a collaborative network designed to accelerate the translation of discoveries from research to clinical care. This extensible informatics platform integrates diverse data types and supports interoperable software tools in the areas of clinical sciences, biospecimen management, imaging, and basic research. The panel will be discussing translational research projects including The Cancer Genome Atlas (TCGA) that are supported by the caBIG® informatics tools. TCGA data are currently available through the TCGA data portal, and Cancer Genome Workbench (CGWB) and caIntegrator data warehouses. In addition to browsing data from public studies, researchers can setup custom, caBIG®-compatible web portals to conduct integrative research, without requiring programming experience. These tools also allow researchers and oncologists to assess how radiology data can be used in conjunction with genetic and other molecular data to predict outcome and treatment response. The TCGA Radiology Project is an excellent example of how existing caBIG® resources can be linked together to enable researchers to aggregate and analyze clinical, imaging and molecular data in an integrated manner.

TBI-19/CRI-01: Panel: aCMI sponsored Bridge Day Panel: Integrating genomic and Clinical Data in electronic health Records and Biomedical Repositories: Challenges, solutions, and Opportunities Track 1 Room: Cyril Magnin III

J. Cimino, National Institutes of Health Clinical Center; S. Murphy, Massachusetts General Hospital, Harvard Medical School, and Partners HealthCare; H. Lowe, Stanford University; L. Ohno-Machado, University of California at San Diego; E. Bernstam, University of Texas at Houston; P. Tarczy-Hornoch, University of Washington; R. Bellazzi, Università di Pavia

The integration of genomic data into the more traditional phenomic databases, such as electronic health records and biomedical data warehouses, offers great potential for the advancement of biomedical research and patient care. However, there are a number of challenges to accomplishing this integration in a seamless manner, including the consistent, standardized representation and coding of the data, coping with the shear volume of information, and proper indexing of important genomic features to facilitate retrieval. The panelists, all Fellows of the American College of Medical Informatics, and each a leader in their respective institutions and in the field of biomedical informatics, will describe their work addressing the challenges of genomic-phenomic integration, with working solutions and examples of how such integration can be brought to bear on tasks such as helping clinicians understand their patients’ genetic data, using genetic data to support clinical decision-making and advancing biomedical research. The panel also will discuss implications for national standards on representation and data-sharing. The session will include time for audience participants to share solutions from their own institutions.



CRI-02: Paper: semantic Web and Knowledge acquisition Track 2 Room: Cyril Magnin II

Towards semantic Web-based Representation and harmonization of standard Meta-data Models for Clinical studiesC. Tao, G. Jiang, Mayo Clinic; W. Wei, University of Minnesota Twin Cities & Mayo Clinic; H. Solbrig, C. Chute, Mayo Clinic

using statistical Text Mining to supplement the Development of an OntologyS. Luther, James A. Haley VMAC; D. Berndt, University of South Florida; D. Finch, E. Hickling, James A. Haley Veterans Hospital; M. Richardson; D. Hickam, Portland VA Medical Center

CnTRO 2.0: a harmonized semantic Web Ontology for Temporal Relation Inferencing in Clinical narratives

C. Tao, H. Solbrig, C. Chute, Mayo Clinic semantic Web-based annotation and Reasoning for Temporal Information in Clinical narratives C. Tao, Mayo Clinic; G. Savova, Children’s Hospital Boston and Harvard Medical School; H. Solbrig, P. de Groen, Mayo College of Medicine/Mayo Clinic; C. Chute, Mayo Clinic

12:15 – 1:15 pm forte lunch-and-learn Room: Cyril Magnin III Creating Communities of Practice — Beyond Technology Panelists will discuss considerations for accommodating people and processes when integrating systems. Moderator: Tony O’Hare, PhD, co-founder and Chief Scientific Officer, Forte Research Systems, Inc. Tahsin Kurc , Emory University (focus: Grid-based data federation) Rob Wynden, UCSF (focus: Linking multiple SOA and data warehousing platforms) Griffin Weber, Harvard University (focus: Semantic Web technologies and research networking)

1:30 – 3:00 pm scientific sessions

TBI-20/CRI-03: Translational science Job fair Track 1, 2, 3, 4 Room: Divisadero

The Joint Summits Job Fair, open and free to all Summit registrants, provides graduate trainees seeking advanced training in TBI and CRI opportunity to meet investigators—and organizations-—who can meet their training needs. This event will pair together young professionals with faculty members looking for postdoctoral fellows. Students in their final year are encouraged to participate as are faculty members looking for informatics-savvy postdoctoral fellows.

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TBI-21: Panel: vIvO: enabling national networking of scientists Track 1 Room: Cyril Magnin III

vIvO: enabling national networking of scientistsK. Holmes, Washington University School of Medicine; M. Conlon, C. Barnes, University of Florida; Y. Ding, Indiana University; V. Davis, University of Florida

VIVO is an open source Semantic Web application that enables the discovery of research and scholarship across disciplinary and administrative boundaries through interlinked profiles of people and other research-related information. VIVO, originally developed at Cornell University, is being expanded through a $12.2 million stimulus grant from the national center for research resources (ncrr) of the national institutes of health (nih) to the University of Florida and six partner institutions. VIVO uses data ingested from institutional sources of record and external sources, supplemented with manual entry to populate detailed profiles of researchers with information related to publications, grants, educational background, research interests, teaching, awards, professional affiliations, and community services, and more. Data in VIVO conform to a public ontology of types and relationships that can be extended for local needs via the ontology editor included with the VIVO application. VIVO’s ontology supports faceted searching for quick retrieval of people, organizations, events, and research-related information. Institutional VIVOs and other compatible profiling applications are producing data to form a rich network of information that can be searched to foster collaboration across institutions and enable open sharing of research discovery. VIVO project members will discuss major project efforts and platform features during the presentation. CRI-04: Panel: Personalized Medicine Requires Personalized Clinical Decision support Track 2 Room: Mission

E. Bernstam, The University of Texas Health Science Center at Houston; T. Johnson, University of Kentucky; H. Strasberg, Wolters Kluwer Health; W. Hersh, Oregon Health & Science University

We discuss personalized medicine from an informatics perspective. Personalized medicine is fundamentally a process of dividing patient populations into smaller sub-populations and eventually individuals. Although nearly universally accepted as a worthy goal, personalized medicine presents multiple informatics challenges. First, we consider the problem from a clinical viewpoint. What does it mean for a clinician to practice personalized medicine? Second, we discuss personalized medicine from a cognitive perspective. Clinical practice already strains or even exceeds human cognitive capacity. Thus, even small increases in cognitive load are problematic. The massive amount of molecular “-omics” information associated with personalized medicine is clearly beyond our cognitive abilities. Thus, to practice personalized medicine, we must also develop and implement personalized decision support. We explore what vendors and academia are doing in this area. We conclude by discussing the fundamental problems underlying the challenges and solutions presented by the first three speakers.



CRI-05: Paper: Data synthesis and novel analyses Track 1, 2 Room: Cyril Magnin II

Modeling Complex Warfarin Pharmacogenetic Protocols in Clinical Trial simulationsV. Fusaro, P. Patil, C. Chi, C. Contant, P. Tonellato, Harvard Medical School

spatio-temporal structure of the us Critical Care Transfer networkK. Unnikrishnan, University of Michigan Medical School; D. Patnaik, Virginia Tech; T. Iwashyna, University of Michigan Medical School

smooth Isotonic Regression - a new Method to Calibrate Predictive Models

X. Jiang, M. Osl, J. Kim, L. Ohno-Machado, University of California, San Diego simulating Clinical Trials with Observational Data M. Weiner, R. Tannen, University of Pennsylvania


3:30 – 5:00 pm TBI Closing session: Translational Bioinformatics year in Review Room: Cyril Magnin I/II Russ Altman, Stanford University For more information go to page 7.

5:00 – 6:00 pm Bridge Day Reception room: embarcadero Join your colleagues at the Bridge Day Reception. Mix and mingle with SPC members of both Summits. Sponsored by Booz Allen Hamilton

Booz Allen Hamilton has been at the forefront of strategy and technology consulting for nearly a century, providing a broad range of services in strategy and organization, technology, operations, and analytics. BAH helps health leaders and practitioners facilitate biomedical and translational research, accelerate scientific discovery, and enable effective clinical care delivery across the ‘bench to bedside’ continuum. From biomedical data management to biomedical informatics and advanced analytics, BAH capabilities span the spectrum of client needs in data collection, predictive modeling and simulation, or anything in between. Count on Booz allen to help deliver results that endure. learn more at www.boozallen.com.

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ThuRsDay, MaRCh 10


7:00 – 8:30 am Birds-of-a-feather (BOf) sessions These sessions are informal discussions, free of formal presentations, where people with common interests meet for in-depth conversation on specific topics recommended by prospective conference attendees.

BOf-01: Data Warehousing Room: Cyril Magnin I The use of data warehousing platforms is a common feature of both prospective and retrospective clinical studies. numerous challenges and opportunities exist relative to the use of data warehouses in this capacity, including the design of appropriate data structures, the implementation of data exchange and transformation platforms, and the provision of data query and analysis tools. This birds-of-a-feather session will bring together thought-leaders in the data warehousing domain to explore and discuss such issues. BOf-02: Workflow Modeling and analysis Room: Cyril Magnin II The effective implementation of clinical research informatics interventions requires a systems-level understanding of “real world” workflows in which such technologies are to be deployed. A growing body of work is beginning to develop surrounding best practices and methodological approaches to workflow modeling and analysis in this capacity. This birds-of-a-feather session will bring together innovators in the workflow modeling and analysis domains to explore and discuss such issues.

BOf-03: Multi-Center Research Program and Data Coordinating Centers Room: Cyril Magnin IIIIncreasingly, clinical research is being conducted in multi-site settings, often with the assistance of data coordinating centers. The role of informatics in supporting such multi-site research paradigms is significant, spanning a spectrum from data collection and management best practices to the design and implementation of integrative data analysis and quality assurance tools. This birds-of-a-feather session will bring together individuals with experience and interests in such areas to explore and discuss the state-of-the-art in informatics as applied to such scenarios.

BOf-04: Research Data in the electronic Medical Record (eMR): a Discussion of Potential Issues Room: Mission

Whether it is by design, or because of enterprise business rules, collecting and storing research data in hospital electronic medical records presents problems with security, confidentiality and privacy while excluding the same data may adversely impact patient care. The objective of this meeting is to get input from the stakeholders of leading national research institutions to frame these issues and act as a catalyst to form working groups to propose solutions.

7:00 am – 5:00 pm Registration Open Room: Cyril Magnin Foyer



8:30 – 10:00 am scientific sessions

CRI-06: Panel: Perspectives on CRI education Track 4 Room: Cyril Magnin III

E. Berner, University of Alabama at Birmingham; A. Boyd, University of Illinois at Chicago; J. Mostafa, University of North Carolina at Chapel Hill; W. Hersh, Oregon Health and Science University; P. Embi, The Ohio State University

As the development of informatics approaches for clinical research matures, there is also a need to educate clinical researchers and informaticians on the appropriate use of these tools and methodologies. To date, little attention has been given nationally to the content of this education. This panel will identify key educational topics, challenges and strategies for addressing them. eta Berner will provide context for the key issues and topics for CRI education that the panel will address. Her presentation will be informed by survey work conducted through the CTSA consortium’s Informatics Key Function Committee. The first panelist (Andrew Boyd) will present an overview of the formal CRI educational program conducted at the University of Illinois at Chicago (UIC). The second panelist (Javed Mostafa) will address key educational issues related to information security, the third panelist (William Hersh) will address CRI education as it relates to ongoing onchit funded Workforce Development curriculum efforts, and the final panelist (Peter embi) will share his perspective on the differences between educating informaticians and clinical researchers in CRI through the AMIA 10x10 program. At the end of this panel presentation the audience will be able to identify key challenges for CRI education and will be able to describe some of the approaches for addressing them.

CRI-07: Panel: semantically aware, service-oriented Clinical Trial applications to Promote Interoperability and Improved Data Quality Track 2 Room: Mission

E. Helton, Center for Biomedical Informatics and Information Technology/NCI; U. Topaloglu, University of Arkansas for Medical Sciences; S. Nadaf, UCSF Helen Diller Family Comprehensive Cancer Center

The cancer Biomedical Informatics Grid® (caBIG®) is a collaborative network designed to accelerate the translation of discoveries from research to clinical care. This extensible informatics platform integrates diverse data types and supports interoperable software tools in the areas of clinical sciences, biospecimen management, imaging, and basic research. the panel will introduce participants to the caBiG® nci enterprise Services (neS) and the Suite of caBIG® Clinical Trials applications that have been developed to utilize these services; and will feature case studies by two universities to discuss their implementation of caBIG® Clinical Trials tools, and how it has benefitted their organization.

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CRI-08: Paper: Bridging Research, Clinical Practice, and Community Track 2 Room: Cyril Magnin I

a Process approach to linking Research systems and eMRsL. Bain, R. Kush, CDISC; M. Arratoon, GE Healthcare

Clinical Trials – Challenges in Data Capture – a ReviewA. Chahal, S. Abrol, H. Chahal, Velos, Inc.

efficient Research Data Capture in Clinical OperationsG. Gordon, M. Wyatt, K. McDonald, H. Gazzalla, E. Berner, University of Alabama at Birmingham

Beyond framingham: Creating an Informatics Infrastructure for Patient-centered Outcomes Research in an at-risk PopulationA. Wilcox, Columbia University CRI-09: Panel: Cross Institutional systems to support Phenotyping in Biomedical Research: experiences from the eMeRge network Track 2 Room: Cyril Magnin II

L. Rasmussen, Marshfield Clinic Research Foundation; D. Carrell, Group Health Research Institute; J. Pathak, Mayo Clinic; W. Thompson, Northwestern University; H. Xu, Vanderbilt University

the electronic Medical records & Genomics network (eMerGe) is comprised of five institutions engaged in the use of electronic medical records and biobanks to facilitate genome-wide association studies (GWAS). In the course of the project, each institution has worked not only on the development of electronic phenotyping algorithms to support intra- and inter-institutional GWAS, but also the development and dissemination of software tools and methods to facilitate and support such research. a unique aspect of the eMerGe network is the potential to rapidly share these tools and methods to others within the network and receive feedback from actual usage scenarios, demonstrating real-world, cross-site use of these systems and methods in the course of translational research. The focus of this panel is to describe the software tools and methods that have been created or enhanced within the context of the eMerGe network and the experiences of each site with their use. Particular focus will be paid to the benefits of developing tools in the context of a collaborative network, as well as the applicability of these tools to the broader research community.



CRI-10: Paper: Research networking and socio-cultural factors Track 2, 3, 4 Room: Divisadero

harvard Catalyst Profiles: next steps in Research networkingG. Weber, Harvard Medical School

Digital vita: a Qualitative evaluationT. Schleyer, H. Spallek, University of Pittsburgh, School of Dental Medicine; B. Butler, University of Pittsburgh, Joseph M. Katz Graduate School Of Business & College of Business Administration; M. Song, M. Dziabiak, University of Pittsburgh, School of Dental Medicine; W. Shirey, J. Milnes, University of Pittsburgh, School of Medicine

Management of the Clinical Research Coordinator Pool: an essential Component of Clinical Trial logistics

G. Fromell, M. Warner, M. Weiner, University of Pennsylvania School of Medicine


10:30 am – 12:00 pm scientific sessions

CRI-11: Panel: evidence generating Medicine: Integrating Research andPractice to accelerate Clinical and Translational scienceTrack 2 Room: Cyril Magnin III

P. embi, P. Payne, the ohio State University; M. Weiner, University of Pennsylvania;W. Hersh, Oregon Health & Science University

Advances in health information technology and biomedical informatics have laid the groundwork for significant improvements in healthcare and clinical research. electronic health records (ehr ) in particular can help improve the delivery of evidence-based medicine (eBM). additionally, research has revealed ways to leverage our increasingly interconnected Health IT-equipped environments to accelerate clinical and translational research and facilitate the generation of evidence needed to inform eBM. Despite these advances, challenges limit our ability to leverage resources and methods to drive discovery and improvements from and to the point-of-care. These limitations stem from a fundamentally flawed research-practice paradigm that fails to recognize the fact that research and practice are not entirely distinct activities. a new paradigm is needed. the evidence Generating Medicine (eGM) paradigm enables advances in discovery driven healthcare by addressing the fundamental problems that keep us from leveraging our pointof- care systems, resources, and personnel for the generation of evidence. this panel will discuss the eGM concept from an informatics perspective, and specifically cover a range of key informatics elements and issues required to operationalize the adoption of eGM.

ThuRsDay, MaRCh 10 continuedCRI-12: Panel: synthetic Patients use in Clinical Research Track 2 Room: Mission

P. Tonellato, Harvard Medical School; P. Payne, The Ohio State University; M. Gastonguay, Metrum Research Group

The objective of this panel is to provide the current status of research, methods and uses of synthetic patient data sets. An interdisciplinary group of panelists will present three areas of synthetic patient population use, supporting techniques and methods and will provide general discussion of the current and future uses of synthetic patient datasets, methods to create the synthetic data sets and the future objectives and problems that may be addressed if the methods, analysis and tools existed to produce unbiased synthetic patient data.

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CRI-13: Paper: study Planning Track 1 Room: Cyril Magnin I

Probabilistic Databases for estimating Patient Counts in Clinical Data WarehousesR. Myers, Rice University; J. Herskovic, UTHSC-H

an unsupervised learning Method to Improve Cohort Identification using structured DataS. Kandula, Q. Zeng-Treitler, University of Utah; L. Chen, Scientific Systems Company, Inc.; W. Salomon, Clinical Metrics LLC; B. Bray, University of Utah

use Case and application Requirements for a Protocol lifecycle Tracking Tool, with a focus on the Trial Initiation PhaseJ. London, Thomas Jefferson University; S. Elcombe, Mayo Clinic; A. Villasin, C. Sagenich, Thomas Jefferson University; P. Davis, Essex Management Protecting Count Queries in Cohort IdentificationS. Vinterbo, A. Sarwate, A. Boxwala, University of California San Diego CRI-14: Paper: Case studies in Clinical Research Informatics 1 Track 2 Room: Divisadero

TRansfoRm: Requirements analysis for the learning healthcare systemB. Delaney, Kings College London; P. Van Royen, Universiteit Antwerpe; A. Taweel, Kings College London; L. Agreus, Karolinska Institutet; M. McGilchrist, University of Dundee; R. Verheij, NIVEL; W. Kuchinke, Heinrich-Heine University Duesseldorf; T. Arvanitis, The University of Birmingham

TRansfoRm: a flexible Zone Model of a Data Privacy framework for Primary Care ResearchW. Kuchinke, Heinrich-Heine University Duesseldorf; E. van Veen, MedLawConsult; B. Delaney, King’s College; R. Verheij, NIVEL; A. Taweel, King’s College; C. Ohmann, Heinrich-Heine-University

a framework to Determine Patient Drug exposure from eMR: an application to WarfarinM. Liu, V. Kawai, C. Stein, D. Roden, H. Xu, Vanderbilt University

The national Cardiovascular Research Infrastructure: year One Progress ReportR. Wilgus, B. Barham, Duke Clinical Research Institute; D. Pinchotti, A. Khalid, American College of Cardiology Foundation; C. Kluchar, J. Huvane, Duke Clinical Research Institute; S. Mungal, Duke Comprehensive Cancer Center; B. McCourt, Duke Clinical Research Institute; D. Kong, Duke University Medical Center



CRI-15: Panel: Challenges and emerging solutions for securing Medical Data and applications Track 2 Room: Cyril Magnin IIM. Kamerick, University of California, San Francisco; J. Mostafa, University of North Carolina; D. Ervin, The Ohio State University

The panel will discuss data security in the context of medical data provisioning, particularly focused on long-term storage, manipulation, generation of derivative data, collaborations among team members, and keeping pace with changing policies, rules, and regulations.

12:15 – 1:15 pm Recombinant Data lunch-and-learn Room: Cyril Magnin III Innovation in Research Informatics — Making an Impact Moderator: Michael Kamerick, Senior Director, Health Systems Solutions, Recombinant Data Corp.

“Translating Strategic Initiatives into Informatics Tools — Building Administration and User Buy-In’, Connie White Delaney, PhD, RN, FAAN, FACMI, University of Minnesota School of Nursing Professor & Dean, University of Minnesota Academic Health Center Director, Biomedical Health Informatics (BMHI), Associate Director CTSI-BMI, and Acting Director of the Institute for Health Informatics (IHI)

“Research Permissions Management System (RPMS) — Capturing and Managing Patient Content Data”, Iain Sanderson, MSc, FRCA, Chief Medical Information Officer, Health Sciences South Carolina


CRI-16: Panel: Building Clinical Research Capacity in Developing nations: Can emerging Information Technologies Reduce Barriers of entry? Track 3 Room: Mission

D. Parrish, Digital Infuzion; V. Pillai, Oracle; J. Kagan, National Institute of Allergy & Infectious Diseases; B. Mayes, AMIA

The goals of worldwide improvement of health, reduction of health disparities, and protection from bioterrorism are key components of global health strategies and highlight the vital importance of international collaboration and cooperation in biomedical research to limit the spread and reduce the impact of global health threats. However, in many developing countries, insufficient clinical research infrastructure limits the ability to develop country research agendas, train future researchers and participate in multinational clinical research. This panel will explore the use of information technologies to overcome some of the impediments and also provide a base for addressing issues such as ownership, sustainability, and development of national research capacity in the developing world. This session will be structured around a case study approach, discussing the potential impact of technologies such as service oriented architectures, distributed computing and the emergence (or re-emergence) of cloud computing on specific clinical research capacity issues identified by the panelists, based on their experiences, including serious adverse event reporting, ethical review, quality assurance monitoring, etc. each panelist will describe an application or infrastructure solution, framed in the context of establishing sustainable capabilities that will increase national research capacity, while also supporting conduct of a distributed clinical trial.

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CRI-17: Panel: Challenges and lessons learned with i2b2 Deployment Track 2 Room: Cyril Magnin III

J. Niland, K. Dawson, City of Hope, J. London, Kimmel Cancer Center at Jefferson, K. Anderson, University of California at Davis

informatics for integrating Biology & the Bedside (i2b2) is a scalable open-source informatics framework to leverage existing clinical, genomics, and other research data to new discovery research1-3. Adopted by over 60 organizations to date, i2b2 is in use for cohort/ biospecimen selection and hypothesis generation in translational and clinical research. Variability exists among organizations in how they have adopted and deployed i2b2, driven by business goals and data sources, and diverse regulatory, governance, and human subject protection landscapes. Cultural differences also exist in information sharing, governance, and protection of proprietary data. The panelists will discuss challenges and lessons learned from i2b2 adoption and deployment at three academic healthcare organizations--City of Hope Cancer Center, Kimmel Cancer Center, and the University of California at Davis Health System, selected to represent three different phases of i2b2 deployment. While City of Hope just completed its i2b2 pilot deployment, Kimmel Cancer Center is expanding its pilot to prepare for production, and UC Davis, an advanced adopter, already operates multiple i2b2 instances. each presenter will highlight their strategies to prepare for implementation, sources of data, use cases, and regulatory approaches. The continuum from pilot to full production will be described, followed by interactive audience discussion.

CRI-18: Paper: Data, Information, and Knowledge Management 1 Track 2 Room: Divisaderoa Partnership approach for electronic Data Capture in small-scale Clinical TrialsJ. Franklin, A. Guidry, J. Brinkley, University of Washington

a framework and standardized Methodology for Developing Minimum Clinical DatasetsP. Svensson-Ranallo, T. Adam, F. Sainfort, University of Minnesota

an Informatics framework for Testing Data Integrity and Correctness of federated Biomedical DatabasesK. Tahsin, Emory University; M. Kim, A. Orso, J. Cobb, M. Harrold, College of Computing; A. Post, J. Saltz, D. Gutman, Emory University hash-based algorithmic linkage of Patient Records in De-identified Multi-site Patient Research RegistriesS. Weber, H. Lowe, A. Das, T. Ferris, Stanford University



CRI-19: Paper: Data Integration and security Track2 Room: Cyril Magnin I

evaluating Phenotypic Data elements for genetics and epidemiological Research: experiences from the eMeRge and PhenX network ProjectsJ. Pathak, Mayo Clinic; H. Pan, Research Triangle Institute; J. Wang, S. Kashyap, Vanderbilt University Medical Center; P. Schad, C. Hamilton, Research Triangle Institute; D. Masys, Vanderbilt University Medical Center; C. Chute, Mayo Clinic

Integrating Clinical Research to the healthcare enterprise: the Re-use projectA. Elfadly, B. Rance, N. Lucas, AP-HP; P. Lastic, Sanofi-aventis; G. Chatellier, C. Daniel, AP-HP

MyResearch: using security to speed the adoption of the IDRR. Wynden, M. Kamerick, UCSF

an abstraction-based extract, Transform and load Process for Creating Registry Databases for ResearchA. Post, T. Kurc, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory University Center for Comprehensive Informatics; M. Overcash, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory University Research and Health Sciences IT; D. Cantrell, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/ Emory University Center for Comprehensive Informatics/Emory Healthcare Information Services Department; T. Morris, K. Eckerson, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory University Research and Health Sciences IT; C. Tsui, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory University Research and Health Sciences IT/Grady Health System; T. Willey, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory Healthcare Information Services Department; A. Quyyumi, D. Eapen, G. Umpierrez, Emory Healthcare Dept.; D. Ziemer, Emory Healthcare Dept. of Medicine/Grady Health System; J. Saltz, Atlanta Clinical and Translational Science Institute Biomedical Informatics Program/Emory University Center for Comprehensive Informatics

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CRI-20: Panel: Clinical Research Town hall Track 1, 2, 3, 4 Room: Cyril Magnin II

achieving better access to authentic personal health information for biomedical, health services, and public health research while improving safety, data security, and privacy. Moderated by Don E. Detmer, AMIA and University of Virginia. Additional participants to be announced.

This town hall will provide a forum to discuss policies for access to personal health information for the purposes of research and discovery and safer care. Scientists and clinicians agree that availability of authentic longitudinal personal health data will be essential to bridging the gap between genomics and clinical relevance. Moderator Don Detmer has called for legislation to support sharing personal health data without anonymization for IRB-approved research, including use of an associated unique personal health identifier for research and care purposes. Citizens who are not interested in participating for whatever reason may opt-out of participation in the program. Dr. Detmer will introduce the session with an overview of his current thinking on this topic as a provocateur for dialogue with the audience. numerous organizations point out that current policy is going to make it even more difficult and expensive to conduct research in the future. The goal of this session is to surface new ideas, refine current proposals, and examine positions in the CRI community through a town hall style discussion. A summary of the discussion may be prepared for publication and AMIA may choose to advocate formally for some version of such a policy in the future.



CRI-21: Paper: Participant Recruitment Track 2 Room: Cyril Magnin I

eliXR: an approach to eligibility Criteria extraction and RepresentationC. Weng, Z. Luo, S. Johnson, Columbia University

Real-time Identification and Recruitment of eligible Patients for Clinical TrialsA. Taweel, G. Tyson, King’s College London; T. Van Staa, GPRD/MHRA; B. Delaney, Kings College London

Model Representation of eligibility Criteria for Primary Care Clinical TrialsS. Smith, A. Taweel, S. Speedie, B. Delaney, Kings College London

Physician Response Patterns to ehR-based, Clinical Trial alerts: findings from a Randomized Controlled studyP. Embi, The Ohio State University; A. Leonard, University of Cincinnati



CRI-22: Panel: library-based support for Clinical and Translational Research: The Informationist Track 4 Room: Cyril Magnin III

M. Tennant, University of Florida; K. Holmes, Washington University School of Medicine; L. Johnson, University of Minnesota; J. Lyon, University of Florida

The emergence of translational research has made apparent the critical need for information dissemination and collaboration across disciplines. Biomedical libraries and the information professionals they employ provide resources, technology and services in support of research and clinical care. In recent years, biomedical libraries have enhanced traditional services with those provided by “informationists” or “information specialists in context” - information professionals with academic degrees and/or advanced training in biomedically-related disciplines. These informationists are well-positioned to support the varied information needs of the translational research community. The four participants in this panel - the assistant director of a biomedical and health information services department, a bioinformaticist, a clinical research librarian, and an informatioinst supporting community engagement - will highlight the varied roles that informationists play in the library-based support for translational research. They will describe the services they perform and compare and contrast some of the successful strategies they have employed to build services and create collaborations. Panelists will discuss specific details about their unique and varied roles, including bioinformatics instruction and consultation, evaluating the impact of the institution’s research, embedding within research teams, and facilitating collaboration and community engagement.

CRI-23: Paper: Data, Information, and Knowledge Management 2 Track 2 Room: Cyril Magnin II

Integrating Patient-reported symptoms in the arthritis Care RecordH. Zheng, D. Ayers, J. Milner, W. Yang, P. Franklin, University of Massachusetts Medical School

Quality evaluation of Cancer study Common Data elements using the uMls semantic networkG. Jiang, H. Solbrig, C. Chute, Mayo Clinic

Providing Domain analysts with natural schemas to enable Clinical ResearchS. Britell, Portland State University; J. Buckmaster, J. Logan, Oregon Health & Science University; L. Delcambre, Portland State University; V. Kapoor, Oregon Health & Science University

Creation of a Repository of automatically De-Identified Clinical Reports: Processes, People, and PermissionW. Chapman, University of California San Diego; M. Saul, J. Houston, J. Irwin, D. Mowery, H. Harkema, M. Becich, University of Pittsburgh

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CRI-24: Paper: Data Warehousing and Research Registries Track 1, 2, 3 Room: Mission

a Model for efficient Review of Clinical Data by Researchers within the sTRIDe Clinical Data WarehouseH. Lowe, S. Weber, Stanford University; T. Ferris, Stanford University School of Medicine; P. Hernandez, N. Ramamoorthy, Stanford University

Complying with Patient expectations for Data De-identification in i2b2S. Murphy, M. Mendis, Partners Healthcare; S. Churchill, I. Kohane, Harvard University

Development and sustainability of an ehR-based Chronic Kidney Disease RegistryJ. Sharp, S. Arrigain, J. Nally, W. Saupe, A. Jain, Cleveland Clinic

Managing and Computing Quality Measures across the enterpriseK. Marsolo, J. Napora, Y. Bracha, J. Mirus, B. Mehta, Cincinnati Children’s Hospital Medical Center CRI-25: Case studies in Clinical Research Informatics 2 Track 2 Room: Divisadero

using ConText to Identify Candidate Pulmonary embolism subjects Based on Dictated Radiology ReportsB. Chapman, UCSD; S. Lee, University of Pittsburgh; H. Kang, Stanford University; W. Chapman, University of California San Diego

visualizing hIv Treatment Patterns with network ModelsW. Bridewell, W. Lee, A. Das, Stanford University

The semantic foundation to Interoperable Clinical and Research Information systems in CardiologyB. McCourt, Duke Clinical Research Institute; J. Tcheng, D. Kong, Duke University Medical Center; B. Kisler, Clinical Data Interchange Standards Consortium

enabling Distributed electronic Research Data Collection for a Rural appalachian Tobacco Cessation study

T. Borlawsky, O. Lele, The Ohio State University; D. Jensen, The Ohio State University Medical Center; N. Hood, The Ohio State University

5:00 – 6:30 pm CRI Poster session and Reception See page 27 for Posters.


fRIDay, MaRCh 11


7:30 – 10:30 am Registration Open Room: Cyril Magnin Foyer

8:30 – 10:00 am scientific sessions

CRI-26: Panel: Meaningful use and Personalized Patient education Room: Track 2 Room: Cyril Magnin III

J. Mostafa, University of North Carolina; G. Del Fiol, Duke University; L. Kelly Hall, Healthwise/Northwest Nazarene University for Health Information; J. Cimino, National Institutes of Health

limited health literacy affects a large portion of the US population, compromising patient engagement in the health care decision-making process and self-care. In order to help patients become better informed about their health and health care options, the Meaningful Use regulation for electronic health records includes a number of measures to stimulate patient engagement, including delivery of patient-specific education resources into ehr systems. in this panel, experts in information retrieval, patient education, and context-specific knowledge integration into ehr systems will discuss state-of-the-art advances in consumer health education, including personalized consumer information retrieval methods, consumer health knowledge resources with ehr integration capabilities, knowledge integration architectures, and a set of international standards to facilitate this kind of integration. The panelists will present a series of large-scale implementation examples, discuss challenges and limitations of the proposed approach, and talk about potential future directions.

CRI-27: Panel: Developing governance approaches to Clinically Derived Research ResourcesTrack 2 Room: Mission

N. Anderson, University of Washington; M. Kamerick, University of San Francisco, California; A. Post, Emory University; K. Marsolo, Cincinnati Children’s Hospital Medical Center

Significant national infrastructure investment from the Clinical Translational Scienceawards (ct Sa), office of the national coordinator for health information technology(onc -hit ), the american recovery and reinvestment act (arra ) and others arecollectively stimulating a common level of technical expertise, evolving resourceinfrastructure and motivations to discover, request, share, and analyze clinical andclinically acquired data for secondary research. However, despite these commonevolving competencies, opportunities and engaged stakeholders, there remains alack of best practices of how to establish effective data sharing policies and practicesthat balance assurance of protection to patients, institutions and researchers againstresearch utility and obligation to research and patient communities. This panel willexplore four network-scale data integration and delivery projects that span a spectrumof end-user delivery modalities and infrastructure topologies, but share commonchallenges in establishing technically leveraged governance processes to ensure highvalue use for end-users. The panel participants will each discuss how the motivatingproject research questions and target users are defining their technical implementationapproaches to data access and delivery. Overall, an understanding of the possiblepaths to providing clinically derived data for secondary research will be discussed.

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fRIDay, MaRCh 11 continued

CRI-28: Paper: Clinical Research Tools and standards Track 2 Room: Cyril Magnin I

Mapping Multi-institution Data sources to Domain Ontology for Data federation: the PhysioMIMI approachR. Mueller, S. Sahoo, X. Dong, S. Redline, S. Arabandi, L. Luo, G. Zhang, Case Western Reserve University

an Ontology for Transformation and visualization of longitudinal DataS. Tu, M. O’Connor, A. Richards, A. Das, Stanford University

Online exploration of Case-control study Designs in vIsageG. Zhang, R. Mueller, N. Johnson, L. Luo, X. Dong, Case Western Reserve University; S. Redline, Harvard University; S. Sahoo, Case Western Reserve University

ReDCap - Characterizing the Rapid adoption at a large academic health CenterJ. Sharp, C. Trunick, A. Jain, Cleveland Clinic

CRI-29: Panel: The value of value sets Track 2 Room: Cyril Magnin II

R. Wynden, UCSF; H. Solbrig, Mayo Clinic; S. Tu, Stanford University; J. Brinkley, University of Washington

A common definition of value set will be provided and fully characterized relative to its proposed uses. We will describe, compare, and contrast several approaches to specifying and referencing value sets in a stable manner over time. The term “value set”, although ubiquitous within biomedical informatics has no common definition and has yet to be fully described in a formal manner. It is essential for the design and launch of new ontologies, biomedical informatics applications and data sharing environments that a common and well-understood definition of “value set” is provided. It is also essential that options and trade-offs be understood for what type of technology is appropriate for the implementation and usage of particular types of value set for particular use cases.


10:30 am – 12:00 pm CRI Closing session: Clinical Research Informatics year in Review Room: Cyril Magnin I Peter Embi, The Ohio State University For more information go to page 8.


POsTeRs

CRI POsTeR sessIOn Thursday, March 10, 5-6:30 pm

framing the Clinical Question: a Collaboration to enhance Data Warehouse user education BOaRD 1 E. Anderson, T. O’Grady, Mount Sinai School of Medicine

automatically grouping Individuals with Medical Measures BOaRD 2 L. Berman, George Washington University

linking genotype to Phenotype: a Pilot Project to Create a Research Data Warehouse of Biospecimen and “Omic” Information BOaRD 3 X. Bi, University of Delaware; P. McGarvey, Georgetown University; J. London, Thomas Jefferson University; E. Ewen, Christiana Care Health System; T. Bunnell, C. Wu, University of Delaware

understanding Data and Query Requirements for Cohort Identification in Clinical Research studies BOaRD 4 A. Boxwala, H. Kim, UCSD; J. Choi, Spaulding Rehabilitation Hospital; L. Ohno-Machado, UCSD

fostering Interdisciplinary Research in Informatics BOaRD 5 A. Boyd, A. Valenta, University of Illinois at Chicago

The Dynamic edges of the evolving social network: new Collaborations Predicted with Information Theory BOaRD 6 M. Burton, D. Saner, University of Chicago; X. Yang, Section of Genetic Medicine; H. Li, J. Solway, Y. Lussier, The University of Chicago

studysearch: a Tool for Connecting Potential Participants with locally Recruiting studies BOaRD 7 D. Carpenter, B. Kelsey, R. Rice, C. Reider, T. Borlawsky, The Ohio State University

Reusable Tool to Dynamically Build Data Dictionary and study Database - Meta-Metadata approach BOaRD 8 S. Chakraborty, Duke University; B. McCourt, C. Hill, Duke Clinical Research Institute

veterans health administration stakeholders’ Input on Implementation of aThena-Opioid Therapy (OT) Clinical Decision support (CDs) system BOaRD 9 R. Cronkite, J. Trafton, D. Chambers, E. Lewis, A. Midboe, VA Palo Alto Health Care System; R. Kerns, VA Connecticut Healthcare System; S. Martins, VA Palo Alto Health Care System; D. Wang, Medcisive LLC; S. Ghaus, M. Goldstein, VA Palo Alto Health Care System

value sets via Ontology views BOaRD 10 L. Detwiler, J. Brinkley, University of Washington

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CRI POsTeR sessIOn continued

Thursday, March 10, 5-6:30 pm

Improving Investigator adherence to Best Practice guidelines in electronic Data Capture using an automated Tool (CheckMate) BOaRD 11 S. Ellert, L. Carlin, U. Kaya, J. Bondy, M. Kahn, University of Colorado Denver

Delivering Informatics services with a Cloud-based Commercial CRM BOaRD 12 T. Ferris, S. Weber, A. Martin, H. Lowe, Stanford University

establishing an International network for using health Information Technology in hIv/TB Medication Management Research BOaRD 13 S. Gavi, T. Mudzviti, University of Zimbabwe; F. Sayidine, Q. Ma, K. Tooley, R. Difrancesco, NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; R. Bessette, SUNY at Buffalo; G. Morse, NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; C. Maponga, University of Zimbabwe

Rapid Development of Research Databases with Web access, flexible schemas, and linkage to local Data Resources BOaRD 14 J. Harrison, Jr., J. Roberts, K. Scully, J. Lyman, University of Virginia

a Practical MetaData Dictionary based on “Observed Ontologies” to Improve usability of a self-service aggregate Cohort estimator BOaRD 15 R. Hendrickson, J. Osborne, H. Taneja, M. Wyatt, University of Alabama at Birmingham

use of Rxnorm and snOMeT-CT® to support the use of Medication Information in Research Patient Cohort searching BOaRD 16 P. Hernandez, T. Podchiyska, Stanford University; T. Ferris, Stanford University School of Medicine; S. Weber, H. Lowe, Stanford University

versatile, Portable and secure - a Robust, Institutional Data Management system enhances Clinical and Translational Research BOaRD 17 E. Huang, University of Tennessee; I. Brooks, University of Tennessee Health Science Center; C. Russell, C. McDonald, University of Tennessee

longitudinal Curves of the Different generations Derived from the Quasi-healthy Patients’ laboratory Data accumulated at Kochi university hospital BOaRD 18 Y. Kurihara, Kochi Medical School

evaluating Ontology Based semantic similarity Measures for Treatment Comparison BOaRD 19 W. Lee, A. Das, Stanford University

Complex Disease network of Trait-associated snPs unveiled by Information Theory BOaRD 20 H. Li, Y. Lee, J. Li, J. Chen, E. Rebman, Y. Lussier, University of Chicago

POsTeRs




heterogeneity and accuracy Issues in federated Patient Data Repositories BOaRD 21 S. Lim Choi Keung, E. Tyler, University of Birmingham; A. Taweel, King’s College London; T. Arvanitis, The University of Birmingham; B. Delaney, Kings College London; R. Hobbs, University of Birmingham

Pedigree explorer - advanced Query Interface for large Pedigree Databases BOaRD 22 E. Manilich, Cleveland Clinic; M. Ozsoyoglu, Case Western Reserve University; J. Church, Cleveland Clinic

Open source and Community ventures in the i2b2 architecture BOaRD 23 M. Mendis, N. Wattanasin, L. Phillips, R. Kuttan, J. Donahoe, Partners HealthCare; I. Kohane, C. McGow, Harvard University; S. Churchill; G. Weber; S. Murphy, Partners Healthcare

Distributed Queries for Quality Control Checks in Clinical Trials BOaRD 24 N. Nichols, L. Detwiler, J. Franklin, J. Brinkley, University of Washington

automatic BI-RaDs Classification of Mammography Reports BOaRD 25 B. Percha, D. Rubin, Stanford University

Research Recruitment in anesthesia using eMR Data BOaRD 26 M. Pickett, J. Sharp, Cleveland Clinic

Managing Medical vocabulary updates in a Clinical Data Warehouse: a CPT Case study BOaRD 27 T. Podchiyska, P. Hernandez, T. Ferris, Stanford University School of Medicine; H. Lowe, Stanford University

lessons learned in evaluating vIvO BOaRD 28 L. Sanders McIntosh, Washington University School of Medicine; E. Cramer, Cornell University

Design of a Registry Management Tool for eMR Data BOaRD 29 J. Sharp, M. Pickett, Cleveland Clinic

an approach to Practical applications of an OWl Ontology for Clinical Research BOaRD 30 I. Sim, UCSF

Disambiguation of Data for the semantic Web BOaRD 31 N. Skaggs, University of Florida

Developing and Deploying Clinical Models for the early Detection of Clinical Complications in neurological Intensive Care units BOaRD 32 D. Sow, IBM Research; M. Schmidt, Columbia University College of Physicians and Surgeons; D. Alberts, Columbia University Medical Center; A. Beygelzimer, A. Biem, G. Luo, D. Turaga, IBM Research

POsTeRs

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Implementation of a Medicare Budgeting Tool for Researchers BOaRD 33 J. Sposato, R. Tiwari, C. Barnes, N. Raum, University of Florida

annotation of Discharge summaries Based on selection Criteria BOaRD 34 A. Stubbs, J. Pustejovsky, Brandeis University

extending the cagrid federated Query Capability BOaRD 35 H. Taneja, N. Thota, R. Hendrickson, M. Wyatt, J. Osborne, University of Alabama at Birmingham

substitutable health applications in the i2b2 “sMart enabled” Platform BOaRD 36 N. Wattanasin, M. Mendis, Partners Healthcare; G. Weber, Harvard Medical School; J. Mandel, B. Adida, Children’s Hospital Boston; R. Ramoni, Harvard School of Dental Medicine; K. Mandl, Harvard Medical School; I. Kohane, Harvard University; S. Murphy, Partners Healthcare

Comparing Research Productivity using the h-index: should the h-index be used as a Benchmark for Research Productivity by nIh ICs? BOaRD 37 J. Welsh, NIH

vIvO harvester: aggregation of scholarly Data into a semantic Data store for use in a national network of scientists BOaRD 38 S. Williams, C. Barnes, N. Skaggs, N. Raum, University of Florida

extending CQl with uRI’s for i2b2 and value sets BOaRD 39 R. Wynden, UCSF; R. Hendrickson, University of Alabama at Birmingham; D. Ervin, The Ohio State University; J. Robinson, UAB

automated Construction of a Medical Image Knowledge Base from WWW (Preliminary Report) BOaRD 40 R. Xu, Y. Chen, G. Zhang, Case Western Reserve University

vInsIa: visual navigator for surgical Information access BOaRD 41 G. Zhang, L. Luo, R. Xu, Case Western Reserve University

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Velos is proud to sponsor the Opening Plenary Session and Keynote Address

for the second annual AMIA Summit on Clinical Research Informatics

Welcome scientists, Investigators, and Innovators!

Documents

Hashtag: #TBICRI11 - AMIA | Informatics Professionals. · PDF file · 2016-04-18Distributed Electronic Data Interchange and ... Chen, Indiana University-Purdue University Indianapolis