biomedical informatics program -- atlanta ctsa (actsi)

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Overview of activities of the Atlanta CTSA (ACTSI) Biomedical Informatics Program


  • 1. Biomedical Informatics Program

2. BIP Team Emory Morehouse Georgia Tech Joel Saltz Elizabeth Ofili Barbara Boyan Tahsin Kurc Alex Quarshie Mary Jean Harrold Tim Morris Adam Davis Alessandro Orso Marc Overcash Doug Blough Andrew Post Karsten Schwan Sanjay Agravat Mustaque Ahamad Circe Tsui Tony Pan Ashish Sharma Fusheng Wang Carlos Moreno 3. BIP ObjectivesThe overarching goal of the ACTSI Biomedical Informatics Program (BIP) is tomaximize the scientific impact of ACTSI investigator proposals and facilitatenovel translational research by 1) enabling management, linkage, analysis andmining of multi-scale, multi-dimensional data across ACTSI institutions and 2)training, consulting, and assisting ACTSI investigators for more effectiveapplication of bioinformatics, biostatistics, and informatics in their projects. 4. BIP Aims Specific Aim 1: Develop a suite of interoperable, linked applications andrepositories for management and integration of clinical, "omics", imaging,laboratory, and tissue data. Specific Aim 2: Engage ACTSI investigators via consultations to maximize theimpact of ACTSI investigator proposals through coordinated use of bioinformatics,biostatistics, and informatics. Specific Aim 3: Educate researchers and others in our academic community on theprinciples and best practices of biomedical informatics and use of biomedicalinformatics applications and tools. Closely coordinated with the ResearchEducation, Training, and Career Development program. Specific Aim 4: Develop novel biomedical informatics techniques and tools for: 1)synthesis of information from very large multi-scale, multi-dimensional data, 2)tools to create patient data registries through a semantic extract-transform-loadprocess, and 3) methods and tools for testing data integrity and maintainingsecurity in federated environments. 5. Aim 1: Develop suite of interoperable, linked applications Develop integrative, federated ACTSI virtualinformation warehouse Integrated clinical/imaging/omic/biomarker/tissue information should always be available A virtually centralized, Atlanta wide information warehouse that has all relevant data Index and federate information generated throughout ACTSI -- information available from patients seen and information gathered at any ACTSI site, specimens sent to any affiliated core, imaging carried out at any affiliated site Governance and technology to manage authentication, authorization 6. Applications and Databases Deployed by BIPApplication DeployedContent and Usage Function and Benefits CR-AssistDec 2005 322 studies since deployment, 126 active Enables researchers to manage studies, 4258 participants, and 439 usersparticipants, schedule and track studyevents (visits, laboratory tests), and printlabels for bio-specimen collection. eBIRTJul 2010 424 services from 57 cores Enables discovery of relevant laboratories,expertise, and services. PAIS DatabaseAug 2010 In silico brain tumor study database ofEnables researches to store, index, and image analysis results from 307 slides explore image markups and annotations onmicro-anatomic structures for correlativestudies.REDCapApr 2010 1057 data instruments created, used by 75Provides support for researchers to easily studiescapture and manage clinical research data. Nautilus LIMSJul 2010421 studies in LIMS and 94 users; numberFacilitates structured and more efficient of aliquots received in LIMS: 754,099management of laboratory workflows andbio-specimens via a commoninfrastructure.AIW Clinical Registry Mar 2011 5 years of data on 4061 Emory patients Provides semantically annotated, easy-to-query databases of clinical data for clinicalresearch.AIW-ReadmissionsMay 2011 5 years of clinical and administrative data on Provides a semantically annotated dataset 149,814 Emory patients for analyzing hospital readmissions. MSM i2b2 Oct 2010 Clinical information from 21,000 patientsEasy to use interfaces for researchers toaccess EHR data for cohort identification. 7. Example Translational Research Projects In silico study of brain tumors Integrative analysis of image, omics, and clinical outcome data Cardiovascular Studies Correlative analyses of integrated data from databases of clinicalinformation as well as genomic and phenotypic information Minority-Health Grid (MH-GRID) Advance genomic science and personalized medicine in minorityhealth research Big Bethel AME Project Uses principles of community engaged research and biomedicalinformatics tools to assist diabetic congregants of the Big Bethel AMEchurch in Atlanta to improve diabetes self management skills. 8. Example Translational Research Projects Glenn Project Increasing rate of consent and research specimen collection at Emory University Hospital, Emory Midtown Hospital and Grady Hospital Early hospital readmission Understand relationship between disease conditions, treatments and environmental factors in predicting hospital readmissions within 30 days. Clinical Interaction Network Search and analysis of de-identified patient data to help investigators plan studies CIN obtains real time notification when study patient is hospitalized and obtains real time EMR data 9. In Silico Brain Tumor Research Center(ISBRTC) A research center of excellence for in silico study of brain tumors Systematically execute in silico analyses (experiments) usingcomplementary data types Collaborative effort among four institutions Emory University Thomas Jefferson University Henry Ford Hospital Stanford University Initial focus on gliomas Better Classification Study Biology of Progression Development of Methods and Workflows Companion National Library of Medicine R01 funded, additionalcompanion proposals in review and preparation7/9/2012 9 10. Minority-Health Grid (MH-GRID) PI: Gary Gibbons, multi-site project involvingMorehouse School of Medicine, Grady, Jackson HindsClinic, and Kaiser Health disparities research focusing on hypertensionin minority populations Integration of de-identified clinical phenotypes,social-environmental data elements, biospecimens,laboratory data, and genomic information Data sharing and federation infrastructure will buildon the BIP Architecture and the Enhanced Registriessystem 11. Big Bethel AME Project PI: Priscilla Igho-Pemu. A Pilot study involving CIN, BIP, and CER programs of theACTSI and Big Bethel AME Church. Hypothesis: Diabetic patients who use ehealthystrides and its social networkingforum will demonstrate better diabetes self management skills. Main outcome variable: attainment of at least 3/7 of the American Association ofDiabetes Educators (AADE7) diabetes self-care behavioral goals. Uses principles of community engaged research and biomedical informatics toolsto assist consented diabetic congregants (Participants) of the Big Bethel AMEchurch in Atlanta under the guidance of a trained coach to improve diabetes selfmanagement skills. Supports consumers as drivers of health transformation. Coaches and participants are trained on the use of the ehealthystridesapplication, personal health record creation, AADE7 goals and use of thestructured behavioral goal setting tools. A community access kiosk with internet access and web portal has beenprovided at the Big Bethel AME church premises to enhance training andutilization of informatics tools by participants. 110 participants have currently been enrolled. 12. GLENN Project POC: Dan Brat, project to define streamlined processes andsystems for Breast Cancer bio-banking at Winship Primary goal: Increasing rate of consent and researchspecimen collection at Emory University Hospital, EmoryMidtown Hospital and Grady Hospital Integration of identified and de-identified clinical phenotypeswith available specimens for use in research Architecture will utilize ACTSI master study participant index,enterprise LIMS implementation and Emory enterprise servicebus Generic architecture for use to support bio-banking acrossEmory/ACTSI 13. LIMS Establish a virtual biobank and specimen trackinginfrastructure across the ACTSI. Labs at many of our Clinical Interaction Networks arein deployment or close to deployment: Emory University, Morehouse School of Medicine, Grady, Midtown, and Childrens In process for next phase laboratories: Hope Clinic Neurology Childrens Research Laboratories 14. Topic-specific Clinical Registries Created using AIW infrastructure Novel semantic extract-transform-load (ETL) tool in AIW to create disease specific, semantically annotated clinical repositories i2b2 is used as user-facing presentation layer Multiple registries are in various stages ofdevelopment for cardiovascular disease, diabetes,oncology, and analyses of re-admissions that drawdata from the Emory Healthcare CDW. 15. eBIRT Integrating Find an Expert functionalitybased off of existing technologies, such as theVIVO project Kicked off the v2, Find a Collaboratorfunctionality and exploring the differentrequirements 16. R-CENTER Web Portal Centralizes access to research resources atMorehouse School of Medicine (MSM)through the internet. Launched in July 2011 Enables discovery of expertise and resourcesfor research at MSM, the ACTSI and RCMITranslational Research Network (RTRN). 17. Aim 2. Engage ACTSI investigators via consultations Goal: Maximize the impact of ACTSI investigatorstudies and proposals through coordinated use ofbioinformatics, biostatistics, and informatics. Carried out in close collaboration with BERD and CIN 18. Aim 2. Engage ACTSI investigators via consultations Ad hoc interactions with investigators and researchgroups by BIP, CIN, and BERD teams Established Studio consultation program Investigators request Studio consultation a coordinated venue for a pre-review and requirements evaluation of proposals/projects by a panel of experts to enhance the impact of ACTSI proposals and projects Requests for BIP assistance are captured through theRAPID system, jointly developed by BIP and th