Biomedical Informatics Program -- Atlanta CTSA (ACTSI)
Biomedical Informatics Program
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
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.
BIP Aims Specific Aim 1: Develop a suite of interoperable, linked applications and repositories for management and integration of clinical, "omics", imaging, laboratory, and tissue data. Specific Aim 2: Engage ACTSI investigators via consultations to maximize the impact of ACTSI investigator proposals through coordinated use of bioinformatics, biostatistics, and informatics. Specific Aim 3: Educate researchers and others in our academic community on the principles and best practices of biomedical informatics and use of biomedical informatics applications and tools. Closely coordinated with the Research Education, 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-load process, and 3) methods and tools for testing data integrity and maintaining security in federated environments.
Aim 1: Develop suite of interoperable, linked applications Develop integrative, federated ACTSI virtual information 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
Applications and Databases Deployed by BIP Application Deployed Content and Usage Function and Benefits CR-Assist Dec 2005 322 studies since deployment, 126 active Enables researchers to manage studies, 4258 participants, and 439 users participants, schedule and track study events (visits, laboratory tests), and print labels for bio-specimen collection. eBIRT Jul 2010 424 services from 57 cores Enables discovery of relevant laboratories, expertise, and services. PAIS Database Aug 2010 In silico brain tumor study database of Enables researches to store, index, and image analysis results from 307 slides explore image markups and annotations on micro-anatomic structures for correlative studies. REDCap Apr 2010 1057 data instruments created, used by 75 Provides support for researchers to easily studies capture and manage clinical research data. Nautilus LIMS Jul 2010 421 studies in LIMS and 94 users; number Facilitates structured and more efficient of aliquots received in LIMS: 754,099 management of laboratory workflows and bio-specimens via a common infrastructure.AIW Clinical Registry Mar 2011 5 years of data on 4061 Emory patients Provides semantically annotated, easy-to- query databases of clinical data for clinical research.AIW-Readmissions May 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 patients Easy to use interfaces for researchers to access EHR data for cohort identification.
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 clinical information as well as genomic and phenotypic information Minority-Health Grid (MH-GRID) Advance genomic science and personalized medicine in minority health research Big Bethel AME Project Uses principles of community engaged research and biomedical informatics tools to assist diabetic congregants of the Big Bethel AME church in Atlanta to improve diabetes self management skills.
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
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) using complementary 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, additional companion proposals in review and preparation 7/9/2012 9
Minority-Health Grid (MH-GRID) PI: Gary Gibbons, multi-site project involving Morehouse School of Medicine, Grady, Jackson Hinds Clinic, and Kaiser Health disparities research focusing on hypertension in minority populations Integration of de-identified clinical phenotypes, social-environmental data elements, biospecimens, laboratory data, and genomic information Data sharing and federation infrastructure will build on the BIP Architecture and the Enhanced Registries system
Big Bethel AME Project PI: Priscilla Igho-Pemu. A Pilot study involving CIN, BIP, and CER programs of the ACTSI and Big Bethel AME Church. Hypothesis: Diabetic patients who use ehealthystrides and its social networking forum will demonstrate better diabetes self management skills. Main outcome variable: attainment of at least 3/7 of the American Association of Diabetes Educators (AADE7) diabetes self-care behavioral goals. Uses principles of community engaged research and biomedical informatics tools to assist consented diabetic congregants (Participants) of the Big Bethel AME church in Atlanta under the guidance of a trained coach to improve diabetes self management skills. Supports consumers as drivers of health transformation. Coaches and participants are trained on the use of the ehealthystrides application, personal health record creation, AADE7 goals and use of the structured behavioral goal setting tools. A community access “kiosk” with internet access and web portal has been provided at the Big Bethel AME church premises to enhance training and utilization of informatics tools by participants. 110 participants have currently been enrolled.
GLENN Project POC: Dan Brat, project to define streamlined processes and systems for Breast Cancer bio-banking at Winship Primary goal: Increasing rate of consent and research specimen collection at Emory University Hospital, Emory Midtown Hospital and Grady Hospital Integration of identified and de-identified clinical phenotypes with available specimens for use in research Architecture will utilize ACTSI master study participant index, enterprise LIMS implementation and Emory enterprise service bus Generic architecture for use to support bio-banking across Emory/ACTSI
LIMS Establish a ‘virtual’ biobank and specimen tracking infrastructure across the ACTSI. Labs at many of our Clinical Interaction Networks are in deployment or close to deployment: Emory University, Morehouse School of Medicine, Grady, Midtown, and Children’s In process for next phase laboratories: Hope Clinic Neurology Children’s Research Laboratories
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 of development for cardiovascular disease, diabetes, oncology, and analyses of re-admissions that draw data from the Emory Healthcare CDW.
eBIRT Integrating “Find an Expert” functionality based off of existing technologies, such as the VIVO project Kicked off the v2, “Find a Collaborator” functionality and exploring the different requirements
R-CENTER Web Portal Centralizes access to research resources at Morehouse School of Medicine (MSM) through the internet. Launched in July 2011 Enables discovery of expertise and resources for research at MSM, the ACTSI and RCMI Translational Research Network (RTRN).
Aim 2. Engage ACTSI investigators via consultations Goal: Maximize the impact of ACTSI investigator studies and proposals through coordinated use of bioinformatics, biostatistics, and informatics. Carried out in close collaboration with BERD and CIN
Aim 2. Engage ACTSI investigators via consultations Ad hoc interactions with investigators and research groups 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 the RAPID system, jointly developed by BIP and the ACTSI Tracking & Evaluation program
Investigator Studios (a joint operation with BERD, BIP, and CIN) Studios started in July of 2010, designed to provide “one-stop shopping” for pre-submission consultations In 2011 there were nine Studios conducted involving the full complement of BERD, BIP, and CIN faculty Ongoing 2012 schedule slots for the first Friday of each month Investigators are requested to submit research plans and goals in advance of the Studio session Junior researchers can include their senior faculty mentors in any session Advertising on ACTSI web site and in Weekly Roundup has been beneficial
Aim 3: Informatics Training Program Closely coordinated with RETCD Clinical Informatics Academy. This Continuing Medical Education (CME) activity is targeted at clinical researchers, clinicians, public health researchers, physicians, nurses, and medical technologists with computer science, engineering, or biomedical background. It focuses on practical aspects of employing biomedical informatics in research projects and patient care. The course consists of 14 hours of lecture and breakout sessions. The first session was held on June 1-2, 2011 with 42 participants enrolled. The next course is scheduled for March 2012.
Aim 3: Informatics Training Program Biomedical informatics (BMI) track in MSCR. A biomedical informatics track with one student currently enrolled and another two students to be added in Fall 2011. Introduction to Biomedical Informatics is a required course and will provide an introduction to clinical information systems, bioinformatics, medical imaging, and computational tools. Students will carry out a required translational research rotation and will take Ethics as another required course. Two student slots in the MSCR BMI track will be sponsored with GT ACTSI BIP matching funds.
Aim 3: Informatics Training Program Biomedical Informatics PhD Program. In Fall 2010, Emory obtained approval for a new BMI PhD program that is jointly administered by Emory’s Departments of Biomedical Informatics, Math & CS, Biostatistics and Bioinformatics, and CCI. It will engage students with computational and biomedical training within teams of software system researchers and scientific investigators, addressing translational bioinformatics and clinical research informatics focus areas. Certificate Program in Biomedical Informatics. This program is targeted at researchers and clinical professionals who would like to take a set of short courses on the basics and principles of biomedical informatics.
Aim 3: Informatics Training Program Clinical and Translational Informatics Rounds (CTIR). CTIR is a monthly meeting targeted at clinical and translational researchers, clinicians, pharmacists, nurses and information services support staff. It provides a venue for participants to critically discuss a diverse set of landmark and current informatics papers, present their work before or after presentation at national meetings, and brainstorm about current or planned informatics projects, databases, decision support systems in patient-related research areas. One of the objectives is to form a group of informaticians across the institution in preparation for the American Medical Informatics Association efforts to implement subspecialty board certification in Clinical Informatics.
Aim 4. Develop novel biomedical informatics techniques and tools for Next Generation Integrative Methods in Medicine. Develop high-performance computing and data management tools that will make it feasible to systematically carry out large-scale comparative analyses using high-resolution, high-throughput datasets. Semantic Extract-Transform-Load (ETL) for Data Registries. Develop a semantic ETL tool that will support temporal concepts and data mappings to semantic terms. Integrity Testing: Biomedical Data Sources and Data Federation. Develop, in a collaborative effort between GT and Emory, a framework of tools and techniques designed to detect errors by combining domain knowledge, modeling, and software testing techniques Authentication and Access Control in Federated Environments. Develop a standards-based security framework in a collaborative effort between GT and Emory to enhance security capabilities in federated environments.
Next Generation Integrative Methods (in collaboration with Georgia Tech) Large volumes of data generated by state-of-the-art next generation sequencing instruments and image scanners Integration of these data types is limited in research and healthcare delivery because of challenges with large scale data management and analysis Development of fast methods and tools that take advantage of Large scale storage environments and deep memory hierarchies Clusters of CPU-GPU nodes
Semantic ETL Tools and Enhanced Registries Linked Databases for Research Leverages common data elements and models and existing standards. Initially for cardiovascular disease, diabetes and co-morbidities. Derived data elements represent categories of data and temporal patterns of interest. Linked to source data – initially, the Emory Healthcare Clinical Data Warehouse and the Grady Health System Diabetes Patient Tracking System. Supports end-user researcher query and analysis.
Federated Security (in collaboration with Georgia Tech) Allow federated management of accounts across institutional boundaries Policy-driven, dynamic authorization based on attributes. Selection of applicable policies and conflict resolution algorithm occurs in a dynamic fashion. Standards based and leverage existing tools: XACML, SAML, Shibboleth based standards A paper at BIBM 2011 conference
Testing of ACTSI Federated Environment (in collaboration with Georgia Tech) Studies involve multiple databases and (complex) data gathering and management processes How to assess the integrity of the federated environment when Data sources are added, updated, deleted A framework to Define rules that describe constraints, dependencies, relationships, and business protocols Compose and execute offline and online tests based on rules and federated databases A paper and a poster in AMIA Joint Summit. Another paper submitted to a software engineering conference
Next Generation Exome Sequencing (in collaboration with MSM) Motivated by Minority Health GRID project Exome sequencing of specimens from 2400 patients Analysis and integration of genomic data with EHR and observational data Development of infrastructure for storage and management High performance computing support through use of compute clusters
Interactions with other Institutions The Southeast CTSA Consortium of eight CTSA projects in the southeastern United States including ACTSI. ACTSI BIP leads the informatics group. a clinical data sharing initiative to study and develop regulatory policies, governance and informatics infrastructure surrounding inter- CTSA clinical and translational research Collaboration with the Ohio State University (OSU) CTSA in the development of a common middleware toolkit to support data integration and resource federation part of OSU-led CTSA Service Oriented Architecture affinity group efforts BIP is pursuing collaborative work with NCBO to integrate their tools for semantic data modeling into the clinical registry capability.
Interactions with other Institutions Institution Collaborative Activities Development of standards-based data sharing framework (initially driven byUniversity of North Carolina cardiovascular disease research) as part of the Southeast CTSA consortium and use of BIP’s Analytical Information Warehouse and semantic ETL tools for EHR-linked bioinformatics and bio-repository infrastructure. Deployment of Emory eCOI system at University of Florida CTSA. Collaboration onUniversity of Florida interfacing of eBIRT and VIVO systems. Collaborations through CTSA Imaging Informatics Working Group and caBIG® ImagingMayo Clinic Workspace on informatics tools for secure image data sharing in translational research and in defining the image data sharing infrastructure in the RSAN image sharing project. Collaboration through CTSA Imaging Informatics Working Group (IWG) to create commonDuke University Medical Center infrastructure and data models for management and sharing of biomedical image data and quantitative imaging biomarkers. Joint design and development of LIMS Study Design Module that has been deployed inChildrens Hospital of Philadelphia both institutions. Shared implementation strategies.
Interactions with other Institutions Institution Collaborative Activities Collaboration in the CTSA Service Oriented Architecture Affinity Group for development ofUniversity of Michigan interoperable translational research informatics systems. Joint development of integrative cardiovascular and cancer related research projects. Dr. Saltz serves as Chair of Michigan CTSA Biomedical Informatics Core external advisory committee. Collaborations in the Service Oriented Architecture Affinity Group for CTSA, the caGridOhio State University infrastructure development, and the caGrid Knowledge Center -- Emory and Ohio State co-lead the caGrid Knowledge Center effort. Development of interoperable translational research informatics infrastructure. Development of standards-based, federated informatics infrastructure and clinical dataJohns Hopkins University management systems for the CardioVascular Research Grid (CVRG) and application of these systems in the driving biomedical projects of the CVRG consortium. Deployment at Emory of REDCap and ResearchMatch systems. Active participation inVanderbilt consortium, shared deployment strategies, and extension of REDCap code.