2012 Summit on CliniCal ReSeaRCh infoRmatiCS · exclusively on cutting-edge innovations, scientific results, and professional networking in the rapidly expanding scope of clinical

AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE

The American Medical Informatics Association designates this educational activity for a maximum of 26.50 AMA PRA Category 1 Credit(s)™. Physicians should only

claim credit commensurate with the extent of their participation in the activity.

March 21-23, 2012 • Parc 55 hotel San FranciSco

2012 Summit on CliniCal ReSeaRCh infoRmatiCS

Flip for TBI! (see reverse side of program)

JOINT SummITS SpONSOrSaMia thankS itS corPorate SPonSorS whoSe

generoSity haS Made the Joint SuMMitS PoSSible

welcome to the third annual aMia clinical research informatics Summit. in a very short three years, the aMia cri Summit has become the premier meeting focused exclusively on cutting-edge innovations, scientific results, and professional networking in the rapidly expanding scope of clinical research informatics. Adjacent to the AMIA translational bioinformatics Summit, these two meetings cover the broad landscape of discovery and translational informatics research, innovations, systems, and results that impact translational science and research.

the 2012 aMia cri Summit call for Participation resulted in the highest number of submissions in all categories: full presentations, podium presentations, panels and posters. the Summit’s four themes were carefully selected to cover the current “hot topics” in cri: research and resource discovery, collaboration and sharing; bedside to base Pairs – from clinical observations to genetic discovery; clinical care and clini-cal research workflow integration; and emerging informatics platforms for integrated translational research. These themes were also chosen to integrate with the four themes in the tbi Summit. as in years past, the two Summits will host a joint plenary session during “bridge day” and the ever-popular “cri year in review” closing session.

As a key scientific and professional networking venue, your participation is critical to the success of the cri Summit. we are honored that you have come to this meeting to engage with leaders and innovators in the field. In addition, we have engaged key ven-dors that provide informatics services and systems to support translational research. Please share your questions, insights, new ideas and concepts with the rest of the CRI community.

the Scientific advisory board members, track chairs and i look forward to a very lively meeting!

Michael kahnchair, cri Summit Scientific Program committee university of colorado

hashtag: #TBICrI12

CrI Summit at a Glance ...................................... 2

Scientific program Committee members ............ 5

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

Keynote presentations......................................... 7

program Chronology

wednesday, March 21 ..................................... 8Thursday, March 22 ........................................ 12Friday, March 23 ............................................. 31

TaBle Of CONTeNTS

2 aMia Joint SuMMitS on tranSlational Science / www.amia.org/jointsummits2012

CrI SummIT aT a GlaNCe

WeDNeSDay, marCh 21

7:30 – 8:30 am coffee and Pastries

7:30 am – 5:00 pm registration open

8:30 – 10:00 am CrI Opening plenary Session and Keynote presentation: Dr. robert m. Califf

10:00 – 10:30 am coffee break

10:30 am – 12:00 pm Scientific Sessions

cri-01: identifying Patients for clinical Studies from electronic health records: the trec Medical Records Track

tbi-17: integrative genomics

tbi-18: crossing the omic chasm: integrating omic data into the ehr

tbi-19: late breaking Session: national center for advancing translational Science

12:15 – 1:15 pm lunch & learn - Velos (new clinical research tools)

1:30 – 3:00 pm Scientific Sessions

cri-02: natural language Processing Methods for cri

tbi-20: big data

tbi-21/cri-03: informatics challenges and Solutions for capturing, taming, and analyzing the data tsunami: report of the acMi 2012 winter Symposium

tbi-22: intellectual Property and entrepreneurship in translational bioinformatics

3:30 – 5:00 pm TBI Closing Session and Translational Bioinformatics year in review: Dr. russ altman

5:00 – 6:00 pm Joint Summits reception, Sponsored by booz allen hamilton

NeW ThIS year! BulleT preSeNTaTIONS! Poster authors will present a five minute “bullet presentation” of their poster to convey their innovative ideas! don’t miss this rare opportunity to learn about cutting edge ideas in the field. bullet presentations will take place after paper and podium abstract presentations sessions.

March 21-23, 2012 • Parc 55 hotel San FranciSco 3

ThurSDay, marCh 22

7:00 – 8:15 am birds of a Feather Session (boF-01): ihe integration


7:00 am – 5:00 pm registration open

8:30 – 10:00 am Scientific Sessions

cri-04: cri tools and Methods

cri-05: infrastructures to support cri

cri-06: natural language Processing for clinical and translational research

cri-07: next-generation distributed research networks



cri-08: cri architectures

cri-09: exploiting ehr data for cri

cri-10: Semantic interoperability for clinical research in europe

cri-11: the chief research information officer (crio): early experiences with a new leadership Role for Academic Health Centers

12:15 – 1:15 pm lunch & learn – recombinant data (clinical and biospecimen data integration)


cri-12: data Sharing

cri-13: ehrs and research

cri-14: academyhealth/electronic data Methods Forum

cri-15: ontologies to drive clinical research: time to get real

3:00 – 3:30 pm coffee break


cri-16: research data

cri-17: ehrs for eligibility

cri-18: Standardizing clinical data elements to Support regulatory review of Marketed Therapeutics

cri-19: Platform demonstrations

5:00 – 6:00 pm poster Session and reception


CrI SummIT aT a GlaNCe

frIDay, marCh 23

7:00 – 8:15 am birds of a Feather Session (boF-02): governance Models for research informatics


7:00 – 11:00 am registration open


cri-20: Papers Vocabularies to support cri

cri-21: Platform demonstrations

cri-22: going beyond cohort discovery: current limitations, advanced Methodologies and Future trends

cri-23: capturing descriptions of human Studies for Federated data Sharing: Frontline experiences from three institutions


10:30 am – 12:00 pm Closing Session and CrI year in review: Dr. peter embi


ChaIrmichael Kahn, university of colorado, Program Committee Chair

TraCK ChaIrStara borlawsky, the ohio State university

chunhua weng, columbia university

bernie laSalle, university of utah

bill barnett, indiana university

SpC memBerSdavid eichmann, university of iowa

Mike conlon, university of Florida

katy borner, university of indiana

charlie barr, roche-genentech

hongfang liu, Mayo clinic

andrew Post, emory university

Joshua denny, Vanderbilt university

Meredith nahm, duke university

anil k. Jain, university of cincinnati

ashish Sharma, emory university

warren kibbe, northwestern university

guoqian Jiang, Mayo clinic

SCIeNTIfIC prOGram COmmITTee

accreditation Statementthe 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 26.5 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 who is 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.


TraCK 1: reSearCh aND reSOurCe DISCOvery, COllaBOraTION aND SharING

The days of the sole investigator are receding quickly as modern science demands access to broad-based teams that apply complimentary knowledge and tools in new and creative ways. but forming a team with access to the right resources, collaborating over large distances and sharing/re-using results by other teams remain daunting challenges. this track will focus on newly emerging semantic-web based search and discovery tools that leverage advances in social networking and distance team collaboration sciences, and new models for data and tool sharing that can help reduce barriers to the next generation of team-based science.

TraCK 2: BeDSIDe TO BaSe paIrS – frOm ClINICal OBServaTIONS TO GeNeTIC DISCOvery

electronic medical records have long held the promise of capturing detailed clinical observations that could be mined for genetic associations. new techniques are required for capturing, storing and analyzing observational eMr data to support complex phenotype detection. This track will focus on advances in data and text mining, data interaction and visualization methods, and data integration tools that unlock the deep potential for phenotype discovery for genetic association studies.

TraCK 3: ClINICal Care aND ClINICal reSearCh WOrK flOW INTeGraTION

To date, clinical care and clinical research have existed as parallel, side-by-side processes. Much work has been done on exploiting eMr capabilities for study subject identification and recruitment. A significant amount of technical standards work has defined methods for integrating clinical care data collection with research data collection. This track will focus on the technical and regulatory barriers that exist in integrating clinical care and clinical research work flows, focusing on data collection, reporting, and adverse event detection.

TraCK 4: emerGING INfOrmaTICS plaTfOrmS fOr INTeGraTeD TraNSlaTIONal reSearCh

Clinical research informatics sits at the nexus of translational bioinformatics, clinical informatics and public health informatics. At its core reside challenges in integrating

complex and heterogeneous data, including biological, clinical and population oriented data that span orders of magnitude in terms of the scale of the presented processes and the size of the involved data sets. Innovation models and technologies

are emerging that attempt to harmonize across biological and clinical observations. this track will focus on emerging integrated informatics platforms that are being developed specifically to incorporate a wide range of highly disparate data into a uniform model, which utilizes ontologies for shared semantics to enable data sharing and analyses across previously siloed translational disciplines.

TraCK DeSCrIpTIONS

learNING OBJeCTIveS• to present the state-of-the-art in biomedical

informatics approaches, theories, and methods relevant to clinical and translational science

• To present the latest research and development findings on using informatics approaches to improve clinical and translational biomedical research

• To demonstrate frameworks for deploying and assessing clinical research informatics initiatives.

• To explore interactions among professionals engaged in clinical and translational science including clinical and translational investigators, computational biologists, genomics researchers, statistical geneticists, clinical informaticians, public health informaticians, and those involved with clinical and research IT policy and regulatory issues.

• To provide a platform to discuss research-related issues among the national and international clinical and translational research informatics initiatives, such as ctSa, cabig, cdiSc, etc.


WeDNeSDay, marCh 21, 2012

8:30 – 10:00 am robert m. Califf, mD room: Cyril magnin I/IIVice chancellor for clinical researchProfessor of Medicine, division of cardiologyduke university’s translational Medicine institute

Vice chancellor for clinical research, director of the duke translational Medicine institute (dtMi), and Professor of Medicine, cardiology, duke university Medical center, dr. robert califf leads a large, multifaceted organization focused on transforming

the path for scientific discoveries into improved medical care. Prior to his role at dtMi, he was the founding director, duke clinical research institute, an academic research organization. he is the editor-in-chief of american heart Journal, and has authored more than 1000 peer-reviewed articles.

he has served on the cardiorenal advisory Panel of the u.S. Food and drug adminnistration and the Pharmaceutical roundtable of the institute of Medicine (ioM). he co-chairs the clinical trials transformation initiative, a public private partnership focused on improving the clinical trials system, as is the director of the clinical research Forum, an organization of academic health and science system leaders working to enhancing the effectiveness of the clinical research enterprise. a member of the drug discovery, development, and translation Forum of the ioM, dr. califf also participates as a member of the national institue of health council on aging, and President obama’s council of advisors on Science and technology.

3:30 – 5:00 pm russ altman, mD, phD room: Cyril magnin I/IIProfessor of bioengineering, genetics, and Medicine(and computer Science, by courtesy)chairman, department of bioengineeringdirector, biomedical informatics training ProgramStanford 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 continued progress in linking clinical data to molecular data, as we usher in a new era of molecular medicine. this session will review notable publications over the past twelve months, highlighting trends and milestones achieved in the past year. this is the fifth installment of this keynote talk by dr. altman.

frIDay, marCh 23, 2012

10:30 am – 12:00 pm peter embi, mD, mS room: Cyril magnin I/IIassociate Professor & Vice chairdepartment of biomedical informatics chief research information officerthe ohio State university Medical center

dr. embi is an internationally recognized researcher and educator in the field of clinical research informatics, with numerous publications and presentations describing his innovations in the field. dr. embi has received numerous awards

for his distinguished work in rheumatology including the 2008 Association of Rheumatology Health Professionals President’s award. he currently serves on the american college of rheumatology’s board of directors. In 2008 he was elected as a fellow in the American College of Physicians.

KeyNOTe SpeaKerS


prOGram ChrONOlOGy

WeDNeSDay, marCh 21, 20127:30 – 8:30 am coffee and Pastries room: cyril Magnin Foyer

7:30 am – 5:00 pm registration open room: cyril Magnin Foyer

8:30 – 10:00 am CrI Opening plenary Session and Keynote presentation room: cyril Magnin i/iidr. robert M. califf duke university See page 7 for more information.

10:00 – 10:30 am coffee break room: cyril Magnin Foyer


CrI-01: panel: Identifying patients for Clinical Studies from electronic health records: The TreC medical records Track track 1 room: cyril Magnin iii

W. Hersh, Oregon Health & Science University; E. Voorhees, NIST; I. Provalov, Cengage Learning; D. Demner-Fushman, NLM

the growing investment in electronic health record (ehr) systems provides an opportunity to augment clinical research by allowing the “secondary use” of clinical data. however, there are a number of challenges to using ehr data, the most significant of which is it being inaccessible and difficult to structure due to it being in mostly free-text form. a related challenge has been a lack of robust collections of such data to facilitate research in this area. this has been addressed by the text retrieval conference (trec), an annual challenge evaluation for information retrieval (ir) researchers. trec is usually organized into 5-6 tracks focused on different ir problems. in 2011, trec instituted a Medical records track, focused on the retrieval of medical records that could enable the selection of patients for possible participation in clinical studies. this panel reports on the development and implementation of the track including presentations by two of the track’s research participants.

TBI-17: papers: Integrative Genomics track 1, 2 room: cyril Magnin iSession chair: Peter tonellato

Integrative analysis of Common Neurodegenerative Diseases using Gene association, Interaction Network, and mrNa expression DataY. Liu, M. Koyut, S. Maxwell, Case Western Reserve University; Z. Zhao, Vanderbilt University; M. Chance, Case Western Reserve University

Identifying Common Genes and Networks in multi-Organ fibrosisK. Wenzke, The Ohio State University College of Medicine; C. Cantemir-Stone, Davis HLRI; J. Zhang, The Ohio State University; C. Marsh, OSU Medical Center; K. Huang, The Ohio State University

Integrating Genome and functional Genomics Data to reveal perturbed Signaling pathways in Ovarian CancersS. Lu, X. Lu, University of Pittsburgh

Coanalysis of GWaS with eQTls reveals Disease-tissue associationsH. Kang, A. Morgan, R. Chen, Stanford University; E. Schadt, Mount Sinai School of Medicine; A. Butte, Stanford University



TBI-18: panel: Crossing the Omic Chasm: Integrating Omic Data into the ehr track 3 room: Mission

J. Starren, Northwestern University; E. Bottinger, Mount Sinai School of Medicine; M. Dente, GE Healthcare; G. Wood, Intermountain Healthcare; J. Hoffman, St. Jude Children’s Research Hospital

implicit in the vision for Personalized genomic Medicine is that genomic and other omic (e.g. proteomic, metabolomics, etc.) data will need to be integrated into the electronic health records (ehrs) of the future. omic data breaks the conventional ehr paradigm in a number of ways. the greatest paradigm shift is that next-generation sequencing allows the collection of large amounts of data about a patient, before the clinical significance of that data is known. another shift is that the raw data are essentially uninterruptable without the aid of computer analysis, even for a domain expert. a number of groups, including the the electronic Medical records and genomics (eMerge) network, the Pharmacogenomics research network (Pgrn) and the hl7 clinical genomics workgroup, as well as individual ehr vendors, are tackling these challenges. The panel will present the perspective and approaches of the various groups.

TBI-19: late Breaking Session - National Center for advancing Translational Sciences track 3 room: cyril Magnin ii

S. Friend, Sage Bionetworks; E. Collier, NCATS; B. Munos, InnoThink Center for Research in Biomedical Innovation; V. Hale, Medicines360/OneWorld Health; J. Tenenbaum, Duke University

with the passage of a fiscal year 2012 spending bill, the national institutes of health created the national center for advancing translational Sciences (ncatS), with the stated mission to catalyze the generation of innovative methods and technologies that will enhance the development, testing, and implementation of diagnostics and therapeutics across a wide range of human diseases and conditions. This panel will address the newly created ncatS from a variety of perspectives including the nih, non-profit research organizations, and pharmaceutical companies. topics for discussion include:

• informatics and ncrr functions beyond diagnostics and therapeutic development• expanding the precompetitive space• rare/neglected diseases• Partnership with industry

Through presentations and discussion, we hope to address what the new center means for the informatics community, and to identify opportunities to contribute to the ncat S mission from the informatics perspective.

12:15 – 1:15 pm lunch & learn room: cyril Magnin iii New Clinical research Tools: Introducing a Solution to your volunteer

recruitment Needs While maintaining Compliance and ethical Standards

Commercial support provided by

WeDNeSDay, marCh 21, 2012 continued



CrI-02: papers and poster Bullets: Natural language processing methods for CrI track 1, 2, 4 room: cyril Magnin iSession chair: hongfang liu

papers

Dependency parser-based Negation Detection in Clinical NarrativesS. Sohn, S. Wu, C. Chute, Mayo Clinic

Semantator: annotating Clinical Narratives with Semantic Web OntologiesD. Song, Lehigh University; C. Chute, C. Tao, Mayo Clinic

feasibility of pooling annotated Corpora for Clinical Concept extractionK. Wagholikar, Mayo Clinic; M. Torii, Georgetown University; S. Jonnalagadda, H. Liu, Mayo Clinic

poster Bullets

an Nlp framework for Classifying Contraception use among uS Women veteransM. Scotch, Arizona State University; J. Womack, VHA Connecticut; S. Leung, VA Palo Alto Healthcare System; C. Brandt, Yale University

an evaluation of the Informativeness of De-identified DocumentsJ. Friedlin, Regenstrief; B. South, VA Salt Lake City Health Care; S. Shen, O. Ferrandez, University of Utah; N. Nokes, M. Maw, VA Salt Lake City Health Care; M. Samore, S. Meystre, University of Utah

prevalence estimates of Clinical epoynyms in De-Identified Clinical DocumentsB. South, S. Shen, M. Maw, VA Salt Lake City Health Care; O. Ferrandez, University of Utah; J. Friedlin, Regenstrief; S. Meystre, University of Utah

modeling uIma Type System using Web Ontology language - towards Interoperability among uIma Nlp ToolsH. Liu, Mayo Clinic College of Medicine; M. Torii, Georgetown University; S. Wu, Mayo Clinic; V. Kaggal, Mayo Clinic College of Medicine; C. Chute, Mayo Clinic

TBI-20: panel: Big Data track 4 room: cyril Magnin iii

L. D’Avolio, VA Boston Healthcare System; P. Tonellato, Harvard Medical School; J. Hammerbacher, Cloudera, Inc.; D. Anderson, OptumInsight; N. Shah, Stanford University

it is well known that we are in the midst of a data deluge. when handling big data, it is necessary to recognize that data can be “big” in terms of size (e.g. next gen sequencing data) or can be big in terms of the number of individuals on which there is some data collected (e.g. administrative and claims data in healthcare). increasingly we are moving towards generating data that is big along both these dimensions. this panel will explore the approaches to store, analyze and interpret big data.




CrI-03/TBI-21: aCmI Bridge Day panel: Informatics Challenges and Solutions for Capturing, Taming, and analyzing the Data Tsunami: report of the aCmI 2012 Winter Symposium

room: cyril Magnin ii

S. Bakken, Columbia University; V. Florance, National Library of Medicine; W. Chapman, USCD

as we move from clinical data warehouses and biobanks to broader conceptualizations of comprehensive health determinants data, numerous challenges arise. to address these challenges, the acMi 2012 winter Symposium focused on relevant topics including: 1) database structures and ontologies that support linkages among disparate data types; 2) de-identification strategies: where and how; query tools for extraction of analytical data sets; 3) visualization tools that provide cognitive support for investigators, and 4) sharing across databanks for discovery and translation. Panelists will provide a summary of the symposium and key recommendations from Symposium participants for solutions that address the informatics challenges related to capturing, taming, and analyzing large volumes of heterogeneous data.

TBI-22: panel: Intellectual property and entrepreneurship in Translational Bioinformatics track 3 room: Mission

A. Butte, Stanford University; W. Hogarth, Sequoia Capital; K. Ku, N. Shah, Stanford University

to realize the full benefit of translational bioinformatics, the scientific breakthroughs made in research laboratories need to be translated into commercially viable ventures. this panel will explore the milestones and challenges on that path as well as point out areas where there is market need but not enough research. the panel will also discuss the key steps in commercializing discoveries by means of discussing use cases from the panelists experience.

3:00 – 3:30 pm coffee break room: cyril Magnin Foyer

3:30 – 5:00 pm TBI Closing Session and Translational Bioinformatics year in review room: cyril Magnin i/ii Dr. russ altman Stanford university See page 7 for more information.

5:00 – 6:00 pm Joint Summits reception room: embarcadero




7:00 – 8:15 am Birds of a feather Session room: cyril Magnin iii

BOf-01: Ihe Integration

L. Bain, CDISC; P. Payne, The Ohio State University; U. Tachinardi, University of Wisconsin-Madison

what is the significance of ihe’s Quality, research, and Public health (QrPh) domain to aMia’s clinical research informatics (cri) efforts? ihe’s QrPh domain, in collaboration with cdiSc, have developed a number of integration profiles that enable clinical study execution through ehrs. these profiles leverage core standards from cdiSc and hl7. the approach has received encouragement from representatives of Fda. the session will describe the basic approach, and solicit participation from aMia and its members to bring the approach to a higher level of attainment.

7:00 – 8:30 am coffee and Pastries room: cyril Magnin Foyer

7:00 am – 5:00 pm registration open room: cyril Magnin Foyer


CrI-04: papers and poster Bullets: CrI Tools and methods track 1, 3, 4 room: cyril Magnin iSession chair: chunhua weng

papers

I-spline Smoothing for Calibrating predictive modelsY. Wu, X. Jiang, J. Kim, L. Ohno-Machado, University of California San Diego

Integrating Diabetes Data for analysis, Sharing, and DiscoveryN. Heintzman, UC San Diego; B. Chen, UCLA; T. Dave, San Diego State University; L. Ohno-Machado, UC San Diego

Named entity recognition in the meDlINe affiliation field: a Step towards enhanced maintenance of researcher profile SystemsM. Torii, Georgetown University Medical Center; K. Wagholikar, H. Liu, Mayo Clinic College of Medicine

poster Bullets

Bridging the Data-Terminology-researcher Gap: user Interface Design for the Terminology Browsing in the NIh’s Biomedical Translational research Information SystemJ. Cimino, E. Ayres, S. Rath, NIH

a hybrid System using CaISIS and reDCap for Comprehensive management of longitudinal follow-up and patient-reported OutcomesP. Fearn, J. Gore, University of Washington; C. Higano, Seattle Cancer Care Alliance

Improving Workflow and Security: The marshfield Data Submission Tracking SystemT. Nguyen, P. Peissig, L. Verhagen, Marshfield Clinic Research Foundation; L. Rasmussen, J. Starren, Northwestern University

evolution of electronic Data Capture at academic health Centers: Tools, accessibility, and WorkflowsR. Rice, T. Borlawsky, H. Lansky, The Ohio State University

ThurSDay, marCh 22



CrI-05: podium abstracts and four poster Bullets: Infrastructures to support CrItrack 1, 3, 4 room: cyril Magnin iiSession chair: bernie laSalle

podium abstracts

Specification of a Cardiovascular metadata model: a Consensus StandardR. Wilgus, Duke Clinical Research Institute; D. Pinchotti, American College of Cardiology Foundation; S. Mungal, Duke Cancer Institute; D. Kong, J. Tcheng, B. McCourt, Duke Clinical Research Institute

an Initial log-based usage analysis of research Networking SystemsM. Boland, Columbia University; S. Johnson, Weill Cornell Medical College; S. Trembowelski, Columbia University; D. Dine, Columbia University; R. Steinman, Columbia University; S. Bakken, Columbia University; C. Weng, Columbia University

piloting a research permissions management System on a portable DeviceR. Alexander, J. Obeid, I. Sanderson, Medical University of South Carolina

electronic Capture and management of Informed Consent for researchA. Boxwala, UCSD; J. Barker, Barker Health Communications; A. Gupta X. Qian, M. Wong, L. Ohno-Machado, UCSD

poster Bullets

full-genome analysis and prediction of Causal regulatory variationsV. Bernard, P. Tan, D. Arenillas, W. Wasserman, Centre for Molecular Medicine and Therapeutics (CMMT)

Surface-shape Characterization of pulmonary hypertensionS. Hon, Duke University; H. Berty, University of Pittsburgh; B. Chapman, University of California, San Diego

Characterizing populations of vascular Structures with GraphsA. Sullivan, University of California, San Diego; H. Berty, University of Pittsburgh; B. Chapman, University of California, San Diego

rlab: a lightweight freezer management System for Small laboratoriesX. Hertzenberg, R. Shaker, J. Brinkley, University of Washington

ThurSDay, marCh 22, 2012 continued



CrI-06: panel and four poster Bullets: Natural language processing for Clinical and Translational research track 4 room: cyril Magnin iiiSession chair: hongfang liu

panel

Natural language processing for Clinical and Translational researchH. Liu, Mayo Clinic College of Medicine; C. Chute, Mayo Clinic; W. Chapman, UCSD; N. Shah, Stanford University; H. Xu, Vanderbilt University

over the last few decades, growing deployments of electronic health records (ehrs) systems have established large practice-based longitudinal datasets, which have become enabling resources for clinical and translational research. however, much of detailed patient information in ehrs is embedded in narrative clinical text and cannot be directly used for clinical studies. therefore, natural language Processing (nlP), which can extract structured information from narrative text, has received great attention and has played a critical role in enabling secondary use of ehrs for clinical and translational research. Various clinical nlP systems have been developed at different institutions and have been successfully applied to a broad range of clinical studies, such as identifying patient safety occurrences, detecting new adverse events of drugs from ehr, and facilitating genomic research including gene-disease association analysis and pharmacogenomic studies. currently, clinical nlP systems developed at different institutions often generate different types of output, which make it difficult to exchange data across institutions. Additionally, semantic interoperability between nlP results and structured data is also critical since clinical information can be recorded in either structured or free text format. this panel will discuss utilities of nlP in clinical and translational research and efforts in tackling nlP interoperability issues.

poster Bullets

ancillary Study management Systems: What Do We Need?E. Nelson, B. Piehler, A. Rauch, LabKey Software; S. Ramsay, D. Holman, Statistical Center for HIV/AIDS Research & Prevention, Fred Hutchinson Cancer Research Center; S. Asare, A. Asare, Immune Tolerance Network; M. Igra, LabKey Software

using electronic Community Care Data to enrich Translational health researchB. Westra, C. Delaney, G. Melton, K. Monsen, University of Minnesota

errors, Biases, and Concerns in Secondary use of ehr Data: Soliciting Community KnowledgeH. Lehmann, Johns Hopkins; W. Hersh, Oregon Health & Science University; T. Hartzog, Medical University of South Carolina; P. Embi, The Ohio State University

Inter-annotator reliability of medical events in Clinical Narratives by annotators with varying levels of Clinical expertiseA. Lai, P. Raghavan, The Ohio State University




CrI-07: panel: Next-generation Distributed research Networks track 4 room: MissionSession chair: Michael kahn

J. Speakman, NCI/CBIIT; C. Kesselman, Information Sciences Institute

the use of distributed computing services has been adopted widely by the physical sciences community but has been much less successfully deployed in the biomedical sciences. cabig, funded by the national cancer institute, and birn, funded by national center for research resources, are two contemporary grid-based distributed data and service oriented architectures that have similar high level goals but markedly different use cases, user communities, and implementation approaches. both cabig and birn have also undergone continuous evolution as new challenges have emerged that have impeded adoption. in this panel, the leaders from cabig and birn will reflect on the lessons learned from “Phase 1” of each network’s existence and look forward to the future “Phase 2” as both networks continue to push distributed services-oriented architectures forward.



CrI-08: podium abstracts and four poster Bullets: CrI architectures track 1, 2, 3, 4 room: cyril Magnin iSession chair: david eichmann

podium abstracts

enabling Clinical research in rare Diseases: linking Distributed research Data using a lightweight Service Oriented architectureP. Payne, S. James, D. Ervin, J. Pierce, T. Borlawsky, The Ohio State University

Designing an Open architecture for mobile healthI. Sim, UCSF; D. Estrin, J. Selsky, UCLA; D. Haddad, openmHealth.org

Supporting multisite Clinical Trials with Software and policy in i2b2S. Murphy, M. Mendis, N. Wattanasin, Partners Healthcare; W. Simons, Childrens Hospital; I. Kohane, Harvard University; S. Churchill, Partners Healthcare

poster Bullets

The vIvO Ontology: enabling Networking of ScientistsJ. Corson-Rikert, S. Mitchell, B. Lowe, Cornell University; Y. Ding, Indiana University

embedding research Networking Data and access points Where users Will actually See ThemA. Chatterjee, L. Yuan, UCSF

Classification of emergency Department CT Imaging reports using Natural language processing and machine learningE. Sarioglu, K. Yadav, H. Choi, The George Washington University

Introduction to Genomic medicine: Informatics Instruction through an Interdisciplinary Seminar SeriesK. Holmes, T. Druley, S. Dutcher, R. Govindan, Washington University School of Medicine




CrI-09: papers and poster Bullets: exploiting ehr data for CrI track 1, 2, 3, 4 room: cyril Magnin iiSession chair: andrew Post

papers

analyzing patterns of Drug use in Clinical Notes for patient SafetyP. LePendu, Y. Liu, S. Iyer, M. Udell, N. Shah, Stanford University

using Temporal patterns in medical records to Discern adverse Drug events from IndicationsY. Liu, P. LePendu, S. Iyer, N. Shah, Stanford University

a patient-Driven adaptive prediction Technique (aDapT) to Improve personalized risk estimation for Clinical Decision SupportX. Jiang, A. Boxwala, R. El-Kareh, J. Kim, L. Ohno-Machado, University of California, San Diego

poster Bullets

Systematizing Colonoscopy follow-up recommendationsS. Wu, S. Sohn, K. Wagholikar, S. Buehler, L. Boardman, Mayo Clinic

point of Care resources Comparison Chart: Which point of Care Decision Support Tool Best meets the Needs of NIh Clinical Staff?J. Welsh, NIH

Comparison of health Behavior-related Data in Survey and ehrS. Yoon, Columbia University; M. Patrao, New York Presbyterian Hospital; A. Wilcox, S. Bakken, Columbia University

Information Quality in healthcare: Where to start?M. Nahm, E. Hammond, Duke University




CrI-10: platform Demonstrations and four poster Bullets track 1 room: cyril Magnin iiiSession chair: ashish Sharma

platform Demonstrations

physiomImI: a light-Weight, Domain Ontology-Driven environment for Integrating and exploring Disparate Data SourcesG-Q. Zhang, S. Sahoo, Case Western Reserve University; S. Redline, R. Mueller, Harvard University

we present a demo of an ontology-driven data integration environment called PhysioMiMi (Multi-modality, Multi-resource information integration environment for Physiological and clinical research) (http://physiomimi.case.edu) and illustrate a variety of deployment scenarios of this environment. PhysioMiMi uses a federated data management approach with a domain ontology as the semantic infrastructure driving data integration, query interface design, and data harmonization across studies. the front-end of PhysioMiMi is a reusable and user-friendly query interface called Visage (Visual aggregator and explorer). the backend of PhysioMiMi uses an ontology-driven Map and connect approach, in contrast to the traditional etl (extract, transform and load) process used in a data warehouse approach. the Map and connect paradigm embodies flexibility for accommodating data quality improvements in source data by pushing data curation tasks upstream in a source-specific, decentralized way, so that updates can be managed distributively throughout the data reuse life-cycle.

poster Bullets

automated Cancer Data extraction and rapid Case ascertainment from Text Based electronic pathology reportsG. Cernile, Artificial Intelligence in Medicine, Inc.; K. Ward, Rollins School of Public Health; M. Goodman, Emory University School of Public Health

Overcoming Technical and Behavioral Barriers to adopting a Shared eDC and Clinical registryJ. DeShazo, T. Aro, Virginia Commonwealth University

Dynamic Integration of Clinical research Data: Schema mapping by analysts using the analyst DashboardJ. Logan, Oregon Health & Science University; S. Britell, L. Delcambre, Portland State University

uCSf profiles as a Web platform for Integration and CollaborationE. Meeks, L. Yuan, A. Chatterjee, M. Kahlon, University of California, San Francisco




CrI-11: panel and poster Bullets track 3 room: MissionSession chair: Peter embi

panel

The Chief research Information Officer (CrIO): early experiences with a New leadership role for academic health CentersP. Embi, The Ohio State University; Y. Lussier, The University of Illinois at Chicago; U. Tachinardi, University of Wisconsin-Madison

the conduct of research is critical to the tri-partite mission of academic health centers (ahc). Increasingly, clinical and research information systems have the potential to accelerate research and enable quality improvement. given the challenges inherent in doing so, dedicated leadership and expertise is needed to optimally design, deploy and leverage various information resources to advance research activities at ahcs. Some institutions have created a new leadership position to oversee such activities, the chief research information officer (crio). Panelists will provide an overview of their respective crio positions within their ahcs, discuss their early experiences, and share lessons learned for this emerging leadership role in clinical and translational research informatics.

poster Bullets

lightweight Data Integration frameworks for Clinical researchR. Shaker, X. Hertzenberg, J. Brinkley, University of Washington

The NeuroDevNet Neuroinformatics CoreE. Portales-Casamar, University of British Columbia; A. Evans, McGill University; W. Wasserman, Centre for Molecular Medicine and Therapeutics (CMMT); P. Pavlidis, University of British Columbia

exploration of Two approaches for Determination of recipients of Targeted Communication in a Scientific Collaborative NetworkS. Bakken, Columbia University; Y. Senathirajah, D. Dine, Irving Institute for Clinical and Translational Research; S. Johnson, C. Weng, Irving Institute for Clinical and Translational Research

Toward Computable mappings of Normalized ehr Data To Input Specifications for phenotyping algorithmsC. Tao, Mayo Clinic; S. Rea, Intermountain Healthcare; J. Pathak, Mayo Clinic; T. Oniki; C. Parker; S. Huff, Intermountain Healthcare; C. Chute, Mayo Clinic

12:15 – 1:15 pm lunch & learn room: cyril Magnin iiipanel: Clinical and Biospecimen Data Integration





CrI-12: papers and poster Bullets: Tools and Techniques for Data Sharing track 1, 2, 3, 4 room: cyril Magnin iSession chair: bernie laSalle

papers

lC Data QueST: a Technical architecture for Community federated Clinical Data SharingK. Stephens, C. Lin, L. Baldwin, A. Echo-Hawk, G. Keppel, D. Buchwald, R. Whitener, D. Korngiebel, A. Berg, R. Black, P. Tarczy-Hornoch, University of Washington

Cohort Identification for Clinical research: Querying federated electronic healthcare records using Controlled vocabularies and Semantic TypesS. Lim Choi Keung, L. Zhao, E. Tyler, University of Birmingham; A. Taweel, B. Delaney, Kings College London; S. Speedie, University of Minnesota; R. Hobbs, University of Oxford; T. Arvanitis, The University of Birmingham

poster Bullets

Wisconsin Genomics Initiative Collaborative Web portalL. Verhagen, P. Peissig, T. Nguyen, Marshfield Clinic Research Foundation; L. Rasmussen, J. Starren, Northwestern University

harvard Catalyst profiles: research Networking, Bibliometric analysis, and Social Network analysis based on linked Open Data and vIvO OntologyG. Weber, Harvard Medical School

adding value to research Networking Sites through OpenSocial to Increase adoption and usageA. Bowline, Wake Forest School of Medicine

enhanced Collaboration and research Discovery through vIvOM. Conlon, University of Florida; K. Holmes, Washington University School of Medicine; Y. Ding, Indiana University




CrI-13: podium abstracts and poster Bullets: enabling ehrs for Clinical research track 2, 3, 4 room: cyril Magnin iiSession chair: andrew Post

podium abstracts

an ehr middleware for Coordinating patient Care and research visitsS. Berhe, L. Busacca, M. Florenz, L. Carlos, R. Steinman, T. Bigger, C. Weng, Columbia University

Towards Quality assessment of ehr Data in the Context of Clinical researchN. Weiskopf, C. Weng, Columbia University

Clinical research alerting for early Septic Shock DetectionS. Weber, H. Lowe, S. Malunjkar, V. Ojha, R. Pearl, J. Quinn, Stanford University

using Natural language processing to Identify lines and Devices in portable Chest X-ray reports: evaluation of 500 reportsD. Wang, VA Palo Alto Health Care System; D. Rubin, Stanford University; D. Chambers, VAPAHCS; J. Chambers, VA Palo Alto Health Care System; B. South, Salt Lake City VA Medical Center; T. Hwang, M. Goldstein, VA Palo Alto Health Care System

poster Bullets

pilot Study: Information extraction from Semi-structured pathology reportY. Lyu, S. Shin, J. Lee, Asan Medical Center

Discovering the Semantics of ehr Data elements Through Bayesian Networks and recursive Tree partitioningB. Ray, H. Lehmann, J. Aaronson, Johns Hopkins University, School of Medicine

Suitability of lOINC Document Ontology as a reference Terminology for Clinical Document Types: a Case report of a research-oriented ehrV. Huser, National Institutes of Health, Clinical Center; L. Taft, NIH NLM; J. Cimino, NIH Clinical Center

Comparing methods for left ventricular ejection fraction Clinical Information extraction (Board 30)S. Meystre, Y. Kim, University of Utah; J. Garvin, Salt Lake City VA Medical Center




CrI-14: academyhealth/electronic Data methods forum and poster Bullets track 1, 3, 4 room: cyril Magnin iiiSession chair: Judith logan

academyhealth/electronic Data methods forumE. Holve, AcademyHealth; W. Hersh, Oregon Health & Science University; R. Stubbs-Dame, New York City Primary Care Information Project

in 2010 the agency for healthcare research and Quality (ahrQ) funded a series of twelve projects to advance the use of biomedical informatics for quality improvement (Qi), comparative effectiveness research (cer) and patient centered outcomes research (Pcor). in total the projects represent an investment of approximately $100 million over three years and will address several timely challenges, including: interoperability between healthcare delivery sites and databases; collection of patient-reported outcomes; and the development of sound, sustainable infrastructure to protect patient privacy and ensure data quality. concurrently, the clinical translation Science award program has developed a new taskforce to discuss common challenges for informatics and cer, and the office of the national coordinator has been engaged in a variety of projects to advance the use of electronic clinical data for public health improvement and evaluation. the goal of this panel is to discuss implications of these significant investments to advance Qi, research, and clinical decision support. Panelists will reflect on lessons learned over the course of several efforts to assess the challenges and opportunities of using electronic clinical data. The panel will inform participants of the scope of these projects and ways for the aMia community to provide input and feedback on innovations as well as information and resource needs that may be addressed by the projects. opportunities to leverage the methods, tools, and findings being produced by these projects to accelerate local efforts to use electronic clinical data for Qi, research, and clinical decision support will also be discussed.

poster Bullets

SparC: a multi-institutional Integrated Web Based research management SystemR. Sampson, J. Glenn, M. Gunnels, A. Cates, M. Scott, J. Schneider, G. Fredericks, J. Obeid, Medical University of SC

Cooperative review of research protocols using an electronic IrB System across multiple Institutions at the Statewide Scale in South CarolinaR. Shelley, J. Manfredi, T. Coggins, J. Obeid, I. Sanderson, Medical University of South Carolina

meaningfully engaging Consumers and patients within Cer using electronic Clinical DataM. Hamilton Lopez, E. Holve, A. Rein, R. Sabharwal, AcademyHealth

automating alerts for Changes in vital Status to ensure Timely Submission of regulatory and protocol DataJ. Niland, G. Peterson, A. Chuang, L. Chen, S. Hmwe, S. Pannoni, City of Hope




CrI-15: panel and poster Bullets track 4 room: MissionSession chair: Mark Musen

panel

using Ontologies to Drive Clinical research: Time to Get realM. Musen, Stanford University; S. Murphy, Partners Healthcare; R. Wynden, UCSF; P. Mirhaji, The University of Alabama at Birmingham; N. Shah, Stanford University

The advent of technologies that make explicit the knowledge needed to drive software systems have the potential to make clinical research more agile, more productive, and more informative. They can facilitate data integration and analysis, and help investigators to identify relationships in the data that would be otherwise elusive. the use of semantic technologies—and in particular, ontologies—historically has been viewed as difficult, however, due to the arcane form in which many ontologies are represented and the lack of ease with which ontologies are accessed in many software systems. newer technologies, such as those under development by the national center for biomedical ontology, offer the possibility to make ontologies more accessible. indeed, semantic technologies are already having a measurable effect on the way in which we conduct research and derive new knowledge from data about individuals and populations. this panel brings together investigators who have been successful in putting ontologies to work to enhance the clinical research enterprise. the panelists will discuss the ways in which ontological resources have been important in their work, the benefits and limitations of their respective approaches, and the ways in which clinical organizations need to evolve to make maximal use of these new technologies.

poster Bullets

efficient & effective post hoc error Detection methods for eCrfsC. McDonald, The University of Tennessee Health Science Center

Implementation of the aTheNa-hTN Clinical Decision Support SystemL. Shluzas, Stanford University; R. Cronkite, D. Chambers, VA Palo Alto Health Care System; D. Owens, Stanford University; M. Goldstein, VA Palo Alto Health Care System

Standardization of Data Dictionaries: a Case Study from the pharmacogenomics research NetworkQ. Zhu, R. Freimuth, M. Durski, J. Pathak, C. Chute, Mayo Clinic

Surgical risk predictive modeling in large Clinical Databases: Next Generation Clinical Decision Support and hypothesis GenerationA. AbuSalah, G. Melton, T. Adam, University of Minnesota

3:00 – 3:30 pm coffee break room: cyril Magnin Foyer




CrI-16: podium abstracts and poster Bullets: research Data methods track 1, 2, 3, 4 room: cyril Magnin iSession chair: david eichmann

podium abstracts

Clinical research modeling: a Three level Source Data Based approachW. Kuchinke, T. Karakoyun, C. Ohmann, Heinrich-Heine University Duesseldorf; B. Delaney, A. Taweel, King’s College London; R. Verheij, NIVEL; A. Nixon Andreasson, L. Agreus, Karolinska Institutet; S. Speedie, University of Minnesota

The SmarT emr view in the Informatics for Integrating Biology and the Bedside (i2b2) platformN. Wattanasin, A. Porter, S. Ubaha, Partners Healthcare; G. Weber, Harvard Medical School; J. Mandel, Children’s Hospital Boston; R. Ramoni, Harvard School of Dental Medicine; K. Mandl, Harvard Medical School; I. Kohane, Harvard University; S. Murphy, Partners Healthcare

TraW: a Workflow approach to Transform Data into InformationX. Wang, University of Chicago and Argonne National Laboratory; L. Liu, K. Chard, J. Fackenthal, O. Olopade, University of Chicago

Striving for Optimal Sensitivity to De-identify Clinical DocumentsO. Ferrandez, University of Utah; B. South, VA Salt Lake City Health Care; S. Shen, University of Utah; M. Maw, N. Nokes, VA Salt Lake City Health Care; J. Friedlin, Regenstrief; S. Meystre, University of Utah

poster Bullets

ClObjects - a Novel methodology for electronic phenotypingO. Gottesman, S. Ellis, V. Lotay, R. Nadukuru, I. Huopaniemi, E. Bottinger, Mount Sinai School of Medicine

every Needle in a haystack: finding fingerprints in a Safe harbor Dataset using a Single Common lab TestD. Fort, Columbia University; J. Cimino, NIH; A. Wilcox, Columbia University

The pharmacogenomics Knowledge Base (pharmGKB): Bridging the Gap Between accumulation of Gene-Drug Knowledge and application in the ClinicE. McDonagh, T. Klein, Stanford University

researchIQ (research Integrative Query) preliminary Needs assessmentP. Yen, O. Lele, T. Borlawsky, P. Payne, The Ohio State University




CrI-17: papers and poster Bullets: using ehrs for eligibility track 3, 4 room: cyril Magnin iiSession chair: bernie laSalle

papers

evaluating alert fatigue and response patterns to ehr-based Clinical Trial alerts: findings from a randomized, Controlled StudyP. Embi, The Ohio State University; A. Leonard, University of Cincinnati

eliXr-TIme: a Temporal Knowledge representation for Clinical research eligibility CriteriaM. Boland, Columbia University; S. Tu, Stanford University; S. Carini, I. Sim, University of California, San Francisco; C. Weng, Columbia University

using Semantic Web Technologies for Cohort Identification from electronic health records for Clinical researchJ. Pathak, R. Kiefer, C. Chute, Mayo Clinic

poster Bullets

using Clinical Data mining to Improve Completion of Clinical TrialsJ. London, D. Chatterjee, Thomas Jefferson University

enhancing the Informed Consent process using video and New electronic mediaJ. Obeid, K. Magruder, S. Sonne, S. Gentilin, J. Andrews, I. Sanderson, Medical University of South Carolina

Developing a Tool to predict 30-Day readmission to acute Care hospitalsJ. Talbert, T. Johnson, A. Stromberg, University of Kentucky

research registry Team approach to research productivityJ. Sharp, Cleveland Clinic




CrI-18: panel and poster Bullets track 3 room: cyril Magnin iiiSession chair: rachel richesson

panel

Standardizing Clinical Data elements to Support regulatory review of marketed TherapeuticsM. Nahm, Duke University; r. kush, cdiSc; r. richesson, university of South Florida college of Medicine

in the last decade, large-scale clinical data element standardization efforts have become increasingly common. often, such efforts focus on a clinical specialty or disease domain of interest. relevant standards development methodologies are discussed according to representation formalism(s), artifacts produced, standardization mechanism, and stewardship model. we report the rationale, progress, and current efforts toward standardization of clinical data elements in specialty and disease domains in support of regulatory review of therapeutic products.

poster Bullets

using electronic Community Care Data to enrich Translational health researchB. Westra, G. Melton, K. Monsen, C. Delaney, University of Minnesota

Classification of emergency Department CT Imaging reports using Natural language processing and machine learningE. Sarioglu, K. Yadav, H. Choi, The George Washington University

Integration of Clinical Data for the medical Intelligence and Clinical Outcomes registryJ. Sharp, J. Guzman, M. Sasidhar, Cleveland Clinic

Supporting Investigators Needs in Comparative effectiveness research: Defining a population in an emerging fieldA. Wilcox, Columbia University




CrI-19: platform Demonstrations and poster Bullets Track 4 room: Mission Session chair: nigam Shah

platform Demonstration

using Ontology Web Services for Clinical and Translational research

N. Shah, P. Whetzel, Stanford University

the national center for biomedical ontology (ncbo) offers a range of web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. this platform presentation will demonstrate the use of ncbo resources to facilitate tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management for Clinical and Translational Research.

poster Bullets

Informatics Support for Data Integrity Testing in heterogeneous and Dynamic Database environmentsK. Tahsin, Emory University; M. Kim, Georgia Institute of Technology; J. Cobb, A. Orso, M. Harrold, College of Computing; A. Post, J. Saltz, A. Sharma, Emory University

using Coronal Depth maps to Detect Identifiable Surface features on Structural head ImagingK. Sideris, UCLA; L. Leong, UCSD; B. Chapman, UCSD

Diverse Clinical research Data Needs at university of Illinois at ChicagoA. Boyd, M. Liang, G. Stevenson, T. Johnson, A. Valenta, University of Illinois at Chicago

Informatics Solutions for managing the financial aspects of Clinical research at an academic health CenterU. Topaloglu, J. Bian, W. Hogan, C. Lane, T. Wells, L. Hutchins, University of Arkansas for Medical Sciences

5:00 – 6:00 pm poster Session and reception room: cyril Magnin Foyer

Surgical risk predictive modeling in large Clinical Databases: Next Generation Clinical Decision Support and hypothesis Generation (Board 1)A. AbuSalah, G. Melton, T. Adam, University of Minnesota

exploration of Two approaches for Determination of recipients of Targeted Communication in a Scientific Collaborative Network (Board 2)S. Bakken, Columbia University; Y. Senathirajah, D. Dine, S. Johnson, C. Weng, Irving Institute for Clinical and Translational Research

full-genome analysis and prediction of Causal regulatory variations (Board 3)V. Bernard, P. Tan, D. Arenillas, W. Wasserman, Centre for Molecular Medicine and Therapeutics (CMMT)

adding value to research Networking Sites through OpenSocial to Increase adoption and usage (Board 4)A. Bowline, Wake Forest School of Medicine

Diverse Clinical research Data Needs at university of Illinois at Chicago (Board 5)A. Boyd, M. Liang, G. Stevenson, T. Johnson, A. Valenta, University of Illinois at Chicago



automated Cancer Data extraction and rapid Case ascertainment from Text Based electronic pathology reports (Board 6)G. Cernile, Artificial Intelligence in Medicine, Inc.; K. Ward, Rollins School of Public Health; M. Goodman, Emory University School of Public Health

embedding research Networking Data and access points Where users Will actually See Them (Board 7)A. Chatterjee, L. Yuan, UCSF

Bridging the Data-Terminology-researcher Gap: user Interface Design for the Terminology Brows-ing in the NIh’s Biomedical Translational research Information System (Board 8)J. Cimino, E. Ayres, S. Rath, NIH

enhanced Collaboration and research Discovery through vIvO (Board 9)M. Conlon, University of Florida; K. Holmes, Washington University School of Medicine; Y. Ding, Indiana University

The vIvO Ontology: enabling Networking of Scientists (Board 10)J. Corson-Rikert, S. Mitchell, B. Lowe, Cornell University; Y. Ding, Indiana University

Overcoming Technical and Behavioral Barriers to adopting a Shared eDC and Clinical registry (Board 11)J. DeShazo, T. Aro, Virginia Commonwealth University

a hybrid System using CaISIS and reDCap for Comprehensive management of longitudinal follow-up and patient-reported Outcomes (Board 12)P. Fearn, J. Gore, University of Washington; C. Higano, Seattle Cancer Care Alliance

every Needle in a haystack: finding fingerprints in a Safe harbor Dataset using a Single Common lab Test (Board 13)D. Fort, Columbia University; J. Cimino, NIH; A. Wilcox, Columbia University

an evaluation of the Informativeness of De-identified Documents (Board 14)J. Friedlin, Regenstrief; B. South, VA Salt Lake City Health Care; S. Shen, O. Ferrandez, University of Utah; N. Nokes, M. Maw, VA Salt Lake City Health Care; M. Samore, University of Utah; S. Meystre, University of Utah

ClObjects - a Novel methodology for electronic phenotyping (Board 15)O. Gottesman, S. Ellis, V. Lotay, R. Nadukuru, I. Huopaniemi, E. Bottinger, Mount Sinai School of Medicine

meaningfully engaging Consumers and patients within Cer using electronic Clinical Data (Board 16)M. Hamilton Lopez, E. Holve, A. Rein, R. Sabharwal, AcademyHealth

rlab: a lightweight freezer management System for Small laboratories (Board 17)X. Hertzenberg, R. Shaker, J. Brinkley, University of Washington

Introduction to Genomic medicine: Informatics Instruction through an Interdisciplinary Seminar Series (Board 18)K. Holmes, T. Druley, S. Dutcher, R. Govindan, Washington University School of Medicine

Surface-shape Characterization of pulmonary hypertension (Board 19)S. Hon, Duke University; H. Berty, University of Pittsburgh; B. Chapman, University of California, San Diego

Suitability of lOINC Document Ontology as a reference Terminology for Clinical Document Types: a Case report of a research-oriented ehr (Board 20)V. Huser, National Institutes of Health, Clinical Center; L. Taft, NIH NLM; J. Cimino, NIH Clinical Center




Inter-annotator reliability of medical events in Clinical Narratives by annotators with varying levels of Clinical expertise (Board 21)A. Lai, P. Raghavan, The Ohio State University

errors, Biases, and Concerns in Secondary use of ehr Data: Soliciting Community Knowledge (Board 22)H. Lehmann, Johns Hopkins; W. Hersh, Oregon Health & Science University; T. Hartzog, Medical University of South Carolina; P. Embi, The Ohio State University

modeling uIma Type System using Web Ontology language - towards Interoperability among uIma Nlp Tools (Board 23)H. Liu, Mayo Clinic College of Medicine; M. Torii, Georgetown University; S. Wu, Mayo Clinic; V. Kaggal, Mayo Clinic College of Medicine; C. Chute, Mayo Clinic

Dynamic Integration of Clinical research Data: Schema mapping by analysts using the analyst Dashboard (Board 24)J. Logan, Oregon Health & Science University; S. Britell, L. Delcambre, Portland State University

using Clinical Data mining to Improve Completion of Clinical Trials (Board 25)J. London, D. Chatterjee, Thomas Jefferson University

pilot Study: Information extraction from Semi-structured pathology report (Board 26)Y. Lyu, S. Shin, J. Lee, Asan Medical Center

The pharmacogenomics Knowledge Base (pharmGKB): Bridging the Gap Between accumulation of Gene-drug Knowledge and application in the Clinic (Board 27)E. McDonagh, T. Klein, Stanford University

efficient & effective post hoc error Detection methods for eCrfs (Board 28)C. McDonald, The University of Tennessee Health Science Center

uCSf profiles as a Web platform for Integration and Collaboration (Board 29)E. Meeks, L. Yuan, A. Chatterjee, M. Kahlon, University of California, San Francisco

Comparing methods for left ventricular ejection fraction Clinical Information extraction (Board 30)S. Meystre, Y. Kim, University of Utah; J. Garvin, Salt Lake City VA Medical Center

Information Quality in healthcare: Where to start? (Board 31)M. Nahm, E. Hammond, Duke University

ancillary Study management Systems: What Do We Need? (Board 32)E. Nelson, B. Piehler, A. Rauch, LabKey Software; S. Ramsay, D. Holman, Statistical Center for HIV/AIDS Research & Prevention, Fred Hutchinson Cancer Research Center; S. Asare, A. Asare, Immune Tolerance Network; M. Igra, LabKey Software

Improving Workflow and Security: the marshfield Data Submission Tracking System (Board 33)T. Nguyen, P. Peissig, L. Verhagen, Marshfield Clinic Research Foundation; L. Rasmussen, J. Starren, Northwestern University

automating alerts for Changes in vital Status to ensure Timely Submission of regulatory and protocol Data (Board 34)J. Niland, G. Peterson, A. Chuang, L. Chen, S. Hmwe, S. Pannoni, City of Hope

enhancing the Informed Consent process using video and New electronic media (Board 35)J. Obeid, K. Magruder, S. Sonne, S. Gentilin, J. Andrews, I. Sanderson, Medical University of South Carolina




The NeuroDevNet Neuroinformatics Core (Board 36)E. Portales-Casamar, University of British Columbia; A. Evans, McGill University; W. Wasserman, Centre for Molecular Medicine and Therapeutics (CMMT); P. Pavlidis, University of British Columbia

Discovering the Semantics of ehr Data elements through Bayesian Networks and recursive Tree partitioning (Board 37)B. Ray, H. Lehmann, J. Aaronson, Johns Hopkins University School of Medicine

evolution of electronic Data Capture at academic health Centers: Tools, accessibility and Work-flows (Board 38)R. Rice, T. Borlawsky, H. Lansky, The Ohio State University

SparC: a multi-institutional Integrated Web Based research management System (Board 39)R. Sampson, J. Glenn, M. Gunnels, A. Cates, M. Scott, J. Schneider, G. Fredericks, J. Obeid, Medical Uni-versity of South Carolina

Classification of emergency Department CT Imaging reports using Natural language processing and machine learning (Board 40)E. Sarioglu, K. Yadav, H. Choi, The George Washington University

an Nlp framework for Classifying Contraception use among uS Women veterans (Board 41)M. Scotch, Arizona State University; J. Womack, VHA Connecticut; S. Leung, VA Palo Alto Healthcare System; C. Brandt, Yale University

lightweight Data Integration frameworks for Clinical research (Board 42)R. Shaker, X. Hertzenberg, J. Brinkley, University of Washington

research registry Team approach to research productivity (Board 43)J. Sharp, Cleveland Clinic

Integration of Clinical Data for the medical Intelligence and Clinical Outcomes registry (Board 44)J. Sharp, J. Guzman, M. Sasidhar, Cleveland Clinic

Cooperative review of research protocols using an electronic IrB System across multiple Institu-tions at the Statewide Scale in South Carolina (Board 45)R. Shelley, J. Manfredi, T. Coggins, J. Obeid, I. Sanderson, Medical University of South Carolina

Implementation of the aTheNa-hTN Clinical Decision Support System (Board 46)L. Shluzas, Stanford University; R. Cronkite, D. Chambers, VA Palo Alto Health Care System; D. Owens, Stanford University; M. Goldstein, VA Palo Alto Health Care System

using Coronal Depth maps to Detect Identifiable Surface features on Structural head Imaging (Board 47)K. Sideris, UCLA; L. Leong, B. Chapman, UCSD

prevalence estimates of Clinical epoynyms in De-Identified Clinical Documents (Board 48)B. South, VA Salt Lake City Health Care; S. Shen, University of Utah; M. Maw, VA Salt Lake City Health Care; O. Ferrandez, University of Utah; J. Friedlin, Regenstrief; S. Meystre, University of Utah

Characterizing populations of vascular Structures with Graphs (Board 49)A. Sullivan, University of California, San Diego; H. Berty, University of Pittsburgh; B. Chapman, University of California, San Diego




Informatics Support for Data Integrity Testing in heterogeneous and Dynamic Database environ-ments (Board 50)K. Tahsin, Emory University; M. Kim, Georgia Institute of Technology; J. Cobb, A. Orso, M. Harrold, College of Computing; A. Post, J. Saltz, A. Sharma, Emory University

Developing a Tool to predict 30-Day readmission to acute Care hospitals (Board 51)J. Talbert, T. Johnson, A. Stromberg, University of Kentucky

Toward Computable mappings of Normalized ehr Data To Input Specifications for phenotyping algorithms (Board 52)C. Tao, Mayo Clinic; S. Rea, Intermountain Healthcare; J. Pathak, Mayo Clinic; T. Oniki; C. Parker; S. Huff, Intermountain Healthcare; C. Chute, Mayo Clinic

Informatics Solutions for managing the financial aspects of Clinical research at an academic health Center (Board 53)U. Topaloglu, J. Bian, W. Hogan, C. Lane, T. Wells, L. Hutchins, University of Arkansas for Medical Sciences

Wisconsin Genomics Initiative Collaborative Web portal (Board 54)L. Verhagen, P. Peissig, T. Nguyen, Marshfield Clinic Research Foundation; L. Rasmussen, J. Starren, Northwestern University

harvard Catalyst profiles: research Networking, Bibliometric analysis, and Social Network analy-sis based on linked Open Data and vIvO Ontology (Board 55)G. Weber, Harvard Medical School

point of Care resources Comparison Chart: Which point of Care Decision Support Tool Best meets the Needs of NIh Clinical Staff (Board 56)J. Welsh, NIH

using electronic Community Care Data to enrich Translational health research (Board 57)B. Westra, G. Melton, K. Monsen, C. Delaney, University of Minnesota

Supporting Investigators Needs in Comparative effectiveness research: Defining a population in an emerging field (Board 58)A. Wilcox, Columbia University

Systematizing Colonoscopy follow-up recommendations (Board 59)S. Wu, S. Sohn, K. Wagholikar, S. Buehler, L. Boardman, Mayo Clinic

researchIQ (research Integrative Query) preliminary Needs assessment (Board 60)P. Yen, O. Lele, T. Borlawsky, P. Payne, The Ohio State University

Comparison of health Behavior-related Data in Survey and ehr (Board 61)S. Yoon, Columbia University; M. Patrao, New York Presbyterian Hosptial; A. Wilcox, S. Bakken, Columbia University

Standardization of Data Dictionaries: a Case Study from the pharmacogenomics research Net-work (Board 62)Q. Zhu, R. Freimuth, M. Durski, J. Pathak, C. Chute, Mayo Clinic




frIDay, marCh 23, 20127:00 – 8:15 am Birds of a feather Session room: cyril Magnin iii

BOf-02: Governance models for research InformaticsP. Embi, The Ohio State University; M. Weiner, University of Pennsylvania

this session will bring together those interested in discussing institutional governance models and resource requirements at the intersection of IT, informatics, and the research community and clinical operations. the goal is to share prevailing and emerging models and best practices for applying research informatics methods, streamlining the introduction of informatics findings into practical use, creating sustainable governance and funding models within and across institutions, and all with the goal of improving the efficiency, safety and generalizability of clinical research and its impact on clinical care. Anticipated areas of focus may include overarching governance models, creating strategic alignment of research information needs with clinical operations, and models to support shared data-intensive efforts at the intersection with research such as Qi, and medical home initiatives.

7:00 – 8:30 am coffee and Pastries room: cyril Magnin Foyer

7:00 – 11:00 am registration open room: cyril Magnin Foyer


CrI-20: papers: vocabularies to Support CrI track 4 room: cyril Magnin iSession chair: hongfang liu

using SNOmeD-CT to encode summary level data - a corpus analysisH. Liu, K. Wagholikar, Mayo Clinic College of Medicine; S. Wu, Mayo Clinic

Quality evaluation of value Sets from Cancer Study Common Data elements using the umlS Semantic GroupsG. Jiang, H. Solbrig, Mayo Clinic College of Medicine; C. Chute, Mayo Clinic

umlS Term Occurrences in Clinical Notes: a large-scale Corpus analysisS. Wu, H. Liu, D. Li, C. Tao, Mayo Clinic; M. Musen, Stanford University; C. Chute, Mayo Clinic; N. Shah, Stanford University


frIDay, marCh 23, 2012 continued


CrI-21: panel: Semantic Interoperability for Clinical research in europe track 3 room: cyril Magnin ii

C. Daniel, INSERM-Paris Descartes University; B. Delaney, Kings College London; M. Jaulent, INSERM; P. Massonet, Cetic

the development and integration of advanced electronic health record systems (ehrs) for medical research can provide to patients more rapid access to innovative medicines and improved health outcomes. This panel will explore four european research projects proposing innovative semantic interoperability solutions or policies for the re-use of primary health in clinical research. the underlying concept of tranSForm is to develop an advanced computational infrastructure that can improve both patient safety and the conduct and volume of clinical research in europe. the ehrcr project is one of the largest public-private partnerships aiming at providing adaptable, reusable and scalable tools and services for reusing data from ehrs for clinical research. Ponte aims at providing a platform offering intelligent automatic identification of individuals eligible to participate in clinical trials. the Semantic health net is a european network of excellence developing a scalable and sustainable pan-european organizational and governance process for semantic interoperability across healthcare systems and institutions in europe. the panel participants will present their technical implementation approaches for integrating ehrs to clinical research. overall, an understanding of the key steps towards realizing semantic interoperability across europe, focusing on the re-use of primary health data for clinical research, will be discussed.

CrI-22: panel: Going Beyond Cohort Discovery: Current limitations, advanced methodologies and future Trends track 3 room: cyril Magnin iii

V. Huser, National Institutes of Health, Clinical Center; V. Deshmukh, U of Utah; A. Wilcox, Columbia Univer-sity; H. Lowe, Stanford University

the objective of this panel is to provide the current status of research, methods and uses of self service query tools facilitating cohort discovery and human-expert-mediated advanced data querying. an interdisciplinary group of panelists will present four perspectives representing a broad spectrum of healthcare institutions. General discussion will include overview of current query tools and their limitations, institutional lessons learned and policies governing different data querying options. The panel will present existing informatics approaches as well as challenges for future research which go beyond simple cohort discovery and providing count data. examples of transition from (1) self-service retrospective cohort estimation to (2) query problems not covered by self service tools and even to (3) prospective, computer-assisted cohort recruitment will be discussed.



CrI-23: panel: Capturing Descriptions of human Studies for federated Data Sharing: frontline experiences from Three Institutions track 1 room: Mission

I. Sim, UCSF; S. Chakraborty, Duke University; H. Lehmann, Johns Hopkins; S. Mollah, The Rockefeller University

interventional and observational human studies are the most important source of evidence for advancing our understanding of health, disease, and treatment options. To promote discovery, the design and results of these studies should be made machine-readable for large-scale data mining, synthesis, and re-analysis. the human Studies database (hSdb) Project aims to define and implement a semantic web-based infrastructure for research institutions to share the design of their human studies using the ontology of clinical research (ocre) as the reference semantics. in our data sharing architecture, the ocre owl model is automatically transformed into an XMl Schema in which entities are indexed back to ocre using the Semantic annotations for Swdl (SaSwdl) technology; individual study protocols are instantiated as XMl instances; instances are made available on the internet from the institutions’ web servers; the Query integrator from the university of washington is used to query the instances as well as ocre and clinical terminologies (e.g., SnoMed) through subsumption and other queries to bioPortal. in this panel, rockefeller university, Johns hopkins university, and duke university will discuss their sociotechnical experiences as they implement the hSdb vision. they will discuss the alignment of hSdb with their broader institutional goals, their processes for human studies data acquisition and curation, and the key success factors and challenges they have faced so far. All presentations will identify and draw out crosscutting themes and lessons for discussion on data sharing of human studies descriptions in particular, and for data sharing in clinical and translational research in general.


10:30 am – 12:00 pm Closing Session and CrI year in review room: cyril Magnin i/ii Dr. peter embi

the ohio State universitySee page 7 for more information.

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