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Informatics for Clinical Research

Informatics for Clinical Research. Ida Sim, MD, PhD January 23, 2001 Division of General Internal Medicine, and the Graduate Group in Medical Informatics, UC San Francisco. Outline. Introductions Course Goals and Overview The Web and Clinical Research

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Informatics for Clinical Research

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  1. Informatics for Clinical Research Ida Sim, MD, PhD January 23, 2001 Division of General Internal Medicine, and the Graduate Group in Medical Informatics, UC San Francisco Overview Informatics for Clinical Research

  2. Outline • Introductions • Course Goals and Overview • The Web and Clinical Research • understanding the web and basic computer terms • clinical trial resources on the web • introduction to clinical research informatics Overview Informatics for Clinical Research

  3. Introductions • Ida Sim, MD, PhD • Asst. Professor General Internal Medicine • PhD in Medical Informatics, Stanford • Interests: computer-assisted clinical decision-making, electronic knowledge publication, meta-analysis, economics of health information technology • Mike Kohn, MD, MPP • Asst. Clinical Professor of Medicine and Surgery • Attending Emergency Physician, UCSF • Interests: clinical epidemiology, data management for clinical research Overview Informatics for Clinical Research

  4. Informatics in Clinical Research • My data’s in the computer but it’s a mess and I can’t analyze what I want to analyze • The programmer’s left and now I’m in a real pickle • I know I should give more detail about my data management plans in my grant proposal but I’m not sure how to do so • Why can’t I merge my database with Jane’s? It’d be so great to have all the data in one place! • I’d like to use the web for forms and data sharing but I don’t even know where to start with this • The electronic medical record is really going to help us do clinical research... Overview Informatics for Clinical Research

  5. Patient Database Working Group • UCSF group convened late 1999 • Problems • multiple poorly designed databases (DBs), some antiquated, that can’t inter-communicate • parallel DB development and perpetuation of common problems • lack of DB design standards and guidelines • lack of project and campus DB management expertise • Result is disjointed, suboptimal clinical research foundation at UCSF Overview Informatics for Clinical Research

  6. Informatics and Future of Research • Computers needed to increase research efficiency • Human genome findings will need to be linked to population and clinical medicine • Computers needed to help translate research results to practice • over 10,000 RCTs indexed in 1999 Medline • Medicine and medical research is information intensive yet health sector underinvests in information technologies (2% revenue vs. ~10%) • both opportunities and shortcomings exist Overview Informatics for Clinical Research

  7. Course Goals • Know how to plan for, budget, and supervise data management for a research project • Be able to use Access, Excel, and STATA to store, manage, analyze and display your data • Understand how the web can be used to conduct and support clinical research • Understand the basics of how computers are used to manage information in health care • electronic medical records, data warehouses, etc. • Be familiar with electronic privacy legislation Overview Informatics for Clinical Research

  8. Base Assumptions • Data management cannot be an afterthought • you plan your statistics carefully before your study; plan your data management too • A basic understanding of how computers can be used will give you the power to exploit them appropriately • course will be case based • no programming Overview Informatics for Clinical Research

  9. Course Overview • 5 Lectures (Sim) • case based discussions, class participation expected • 1 Lecture and 3 Labs (Kohn) [and 2 optional labs] • hands-on 1 hr. sessions (split up by alphabet) • Assignments • 4 homeworks, due in the following class • final due 3/20/00: write up data management personnel, budget, and methods for your own study; an Access exercise • Office “hours”: sim@medicine.ucsf.edu, mkohn@itsa.ucsf.edu http://chanane.ucsf.edu/epidem/courses/schedule/med_informatics.html Overview Informatics for Clinical Research

  10. Lectures • Jan. 23 Overview: the web and clinical research, basic networking and security • Jan. 30 Computers for Data Management: data models, database systems, • Feb. 13 Data Management for Clinical Research: relational database example, normalization, basic tables for clinical research • Feb. 27 Using the Electronic Medical Record for Clinical Research: electronic medical records, coding systems, data warehouses, electronic data privacy • Mar. 6 Advanced Computation for Clinical Research: automated eligibility determination, web-based trial recruitment, decision support, data mining, open discussion • Mar. 13 Budgeting, Hiring, Supervising: what goes into grant application • Labs • Feb. 20 AM Introduction to MS Access: setting up a database • Feb 20 PM Access Tables and Queries: querying a database • Feb. 27 PM Access Forms and Reports: generating data entry forms and reports, exporting to Excel and STATA • Mar 6 PM [Optional] Access consultation

  11. Application to Your Own Studies • Will be using a running example through lectures and lab • infant jaundice study • As class progresses, you’ll have more questions about how this applies to your own study plans • will have increasing amounts of open discussion time in class • ask questions so you’ll be prepared for your final! Overview Informatics for Clinical Research

  12. Glossary • Available at course home page, under continous development • In syllabus materials, italicized terms are defined in the glossary • Please give us feedback on how to improve the glossary • No question is too stupid... Overview Informatics for Clinical Research

  13. Informatics for Clinical Research • Introductions • Course Goals and Overview • The Web and Clinical Research • understanding the web and basic computer terms • clinical trial resources on the web • introduction to clinical research informatics Overview Informatics for Clinical Research

  14. Case: Web for Clinical Research • You are planning on study on ... • What relevant RCTs • have been completed on this topic? • are ongoing? • You’re interested in running your study over the web as much as possible. • what types of clinical research activities can be done over the web? • how good is the technology for these activities? Overview Informatics for Clinical Research

  15. Relevant Trials: Completed • Medline • Cochrane Controlled Trials Register • 290,000+ Medline records of all controlled trials • manual logging of CCTs by hand searching journals • accessible from UCSF machine (IP address) only • can set up proxy access • metaRegister of Controlled Trials • 6350 commercial and ongoing trials Overview Informatics for Clinical Research

  16. Internet = Network of Networks myhome.com nci.nih.gov cochrane.uk amazon.com Main Trunk Cables aol.com local trunk cable through Berkeley pacbell.net medicine or use a commercial Internet Service Provider (ISP) via dial--up or DSL ucsf.edu itsa LAN dial-in to itsa.ucsf.edu via modem at home Overview Informatics for Clinical Research

  17. Clients Web Server Client/Server Model • Computers can be servers and/or clients • Web server “serves” web pages to “clients,” who view these pages using a browser • MS Internet Explorer or Netscape Communicator Overview Informatics for Clinical Research

  18. What’s a Platform? • Computers are physical; software is abstract • operating systems allow software to make physical things happen • write to a disk, display a window, make a phone call • certain operating systems (OSs) are designed to work better with certain processors • e.g., WindowsOS on Intel Pentium chips • “Platform” usually refers to the operating system Overview Informatics for Clinical Research

  19. Common Platforms and OSs Overview Informatics for Clinical Research

  20. Is the Web a Platform? • Not really... • the web is a network of networks that shuttle information around • it does not affect any physical objects directly • it does not have its own operating system • BUT • it is a suite of communication standards that most computers can interpret and can use their own OSs to do physical things • so the Web looks and feels like a “platform” that runs over many types of machines Overview Informatics for Clinical Research

  21. What Happens over Network Cables? myhome.com nci.nih.gov cochrane.uk amazon.com Main Trunk Cables aol.com pacbell.net medicine ucsf.edu itsa LAN at home Overview Informatics for Clinical Research

  22. Networking Protocols • Protocol = grammar for machines talking to each other • Protocol for the WWW = http • WWW vs. Internet vs. Intranet vs. VPN • WWW = http-based communication on Internet • Intranet = network of networks restricted to within an organization (usually implies only http-based communication) • Virtual Private Network is an Intranet that physically uses part of the Internet Overview Informatics for Clinical Research

  23. Networking Bandwidth Overview Informatics for Clinical Research

  24. Networking Media • Copper wire (twisted pair) • generally not well suited to high bandwith transmission • Coaxial cable • can carry high frequencies without leak • cable industry has “more bandwidth by accident than the telephone people have on purpose” • Fiber optic • highest bandwidth, but expensive and de novo • Curb-to-home problem • only phone and coax cables now run from curb to home • hybrid fiber/coax cables and approaches coming Overview Informatics for Clinical Research

  25. Relevant Trials: Completed • Medline • Cochrane Controlled Trials Register • 290,000+ Medline records of all controlled trials • manual logging of CCTs by hand searching journals • accessible from UCSF machine (IP address) only • can set up proxy access • metaRegister of Controlled Trials • 6350 commercial and ongoing trials Overview Informatics for Clinical Research

  26. galen.ucsf.edu ucsf.edu itsa LAN Proxy Gateways and Firewalls • To access UCSF-restriced resources from outside UCSF • configure your browser to route requests to the proxy machine rather than directly to the server • Firewalls • physical and software mechanisms for protecting a group of machines Internet proxy gateway Firewall Overview Informatics for Clinical Research

  27. Relevant Trials: Ongoing • Non-profit/government • www.clinicaltrials.gov • 5000 trials, 2900 open • NIH-supported and some commercial cancer and AIDS trials • cancertrials.nci.nih.gov • www.actis.org • AIDS Clinical Trials Information Service • www.trialscentral.org (from Cochrane people) • pointers to hundreds of clinical trial registries, by disease Overview Informatics for Clinical Research

  28. Relevant Trials: Ongoing • Commercial: mostly for patient recruitment • www.centerwatch.com • www.ClinicalTrialFinder.com • www.controlled-trials.com • www.clinicaltrials.com • etc., etc., etc. • How to get better web searching results • check out Web Search 101 • http://websearch.about.com/internet/websearch/library/weekly/aa011599.htm Overview Informatics for Clinical Research

  29. Case: Web for Clinical Research • You are planning on an RCT on ... • What relevant RCTs have been completed on this topic? • What ongoing trials should you know about? • You’re interested in running your trial over the web as much as possible. • what types of RCT activities can be done over the web? • how good is the technology for these activities? Overview Informatics for Clinical Research

  30. Industry is the Innovator • RCTs now a $3.6 billion business (C. Scott, 7/00) • in 1988, 95% of RCTs conducted by academics • now, over 80% conducted by industry • Ergo, much of the technology innovation in clinical research execution is going on in industry • Applied Clinical Trials software directory • http://www.pharmaportal.com/itsol/index.cfm • What’s the global picture for research informatics technologies? Overview Informatics for Clinical Research

  31. Infant Jaundice Study • Nested case control study • Do infants with neonatal jaundice differ from normal infants on neuropsychiatric exams at age 5 • Cases: infants born between 2005 and 2006 at Kaiser, hospitalized for neonatal jaundice • Controls: Randomly selected from birth cohort • Outcome is a single neuropsychiatric exam score Overview Informatics for Clinical Research

  32. Web Functions Desired • Want an Infant Jaundice website • contact information, status of study, etc. • Want master forms to be kept at one place only • case report forms • neuropsych exam forms • Want local investigators at Bay Area Kaisers to fill out these forms online over the web • versus printing them out and faxing back • Expect that birth cohort data will be separately collected directly from Kaiser Overview Informatics for Clinical Research

  33. Infant Jaundice Client/Server Model Kaiser Oakland Kaiser Santa Clara Kaiser San Diego Internet • The “jaundice.ucsf.edu” computer has • web server software. It “serves” web pages • in response to http commands such as • http://jaundice.ucsf.edu/project-home.html aol.com pacbell.net jaundice ucsf.edu itsa LAN dial-in to itsa.ucsf.edu via modem at home Overview Informatics for Clinical Research

  34. Project Website • Project website • GISSI website has summaries of trial protocols, results, references • Requirements • web server computer • use a web hosting service (see http://www.cnet.com) • or have a web server program (e.g., Apache) • pages of material • produce these using Word (save as HTML file) • or use a web editor (FrontPage, Dreamweaver) Overview Informatics for Clinical Research

  35. Project Website (cont.) • Personnel • webmaster:handles the machine stuff • web designer: produces text & graphical content • Status: easily doable today Overview Informatics for Clinical Research

  36. Protocol and Forms Distribution • Allows for centralized forms management and storage through a project website • If expecting users to download, print, fill out and fax form back • need protocol and forms in electronic format (e.g.,Word or PDF) • scan it using a scanner ($100-$4000) • makes an image of the page (e.g., .gif or .jpeg) • optical character recognition (OCR) scanning • convert scanned text into an editable document (e.g., Word) • Status: easily doable today Overview Informatics for Clinical Research

  37. Infant Jaundice Forms Download Kaiser Oakland Kaiser Santa Clara Kaiser San Diego Internet • “jaundice.ucsf.edu” “serves” forms such as • http://jaundice.ucsf.edu/case-form.pdf for • printing out aol.com pacbell.net jaundice ucsf.edu itsa LAN dial-in to itsa.ucsf.edu via modem at home Overview Informatics for Clinical Research

  38. Protocol and Forms Distribution • If expecting users to enter data online over the web • need someone to design the forms and build them to be served over the web • e.g., using Access Visual Basic • need security mechanisms (e.g., user login) • need data validation checks built into forms entry • data forms must send data to a database • Status: doable with some programming Overview Informatics for Clinical Research

  39. Infant Jaundice Online Forms Kaiser Oakland Kaiser Santa Clara Kaiser San Diego Internet • “jaundice.ucsf.edu” “serves” online entry forms • such as http://jaundice.ucsf.edu/case-form.asp. • Users enter data, which get checked at the client • side, and data is sent back to “jaundice.ucsf.edu.” aol.com pacbell.net jaundice ucsf.edu itsa LAN dial-in to itsa.ucsf.edu via modem at home Overview Informatics for Clinical Research

  40. Other Internet-Based Research Activities • Randomization • 24 hour automated services • Electronic Data collection • fax, voice, electronic handheld • Data repository • HERS main results revised tables from JAMA report Overview Informatics for Clinical Research

  41. Web-based Randomization • Requirements • a web-based data collection form to collect patient information • programs to verify eligibility and randomize patient • program to generate a response to the enroller • security, privacy, and backup provisions • Some commercial systems do this for you • Status: doable with some programming patient info randomization results Enroller Project Central Overview Informatics for Clinical Research

  42. Electronic Data Capture • Fax • Voice • most systems about 95-99% accurate for restricted domains • can speak normally, but may need to train computer to your voice • Handheld Electronic • your favorite PDA and docking station for downloading to a database (over the web) • wireless PDAs can’t be far from a receiver node • radiofrequency: slow, prone to interference • infrared: requires line of sight between PDA and node Overview Informatics for Clinical Research

  43. Issues in Remote Data Capture • Managing copies (local and central copies?) • Concurrent updates • what if 2 people want to update same record? • Merging data • Security and privacy • System downtime • System response time • Workflow issues Overview Informatics for Clinical Research

  44. Data Repository • Requirements • a project website (server and content pages) • electronic files for clients to download • Word, PDF, ASCII text, Excel, etc. • Real-time searching of your data over the web • some databases (e.g., FilemakerPro, Access) can be exported to the web, but usually this involves moderate programming • Must devise and enforce an access control and privacy policy • Status: very doable today Overview Informatics for Clinical Research

  45. jaundice ucsf.edu itsa LAN Network Security • Physical security • firewalls • Encryption • public/private keys • People security • authority • authentication • access • audit Internet Firewall Overview Informatics for Clinical Research

  46. People Security • Authentication • are you who you say you are? • use passwords, biometrics (e.g., retinal scan), smartcards • Authority • do you have a need to know? • different levels of data access for different users • Access • how to allow only authenticated users to perform authorized activities on authorized data? • Audit • who actually got into what? Overview Informatics for Clinical Research

  47. Audit • A post-hoc monitoring approach • If announced clearly, can deter unauthorized use • Examples • Beth Israel (Boston) EMR • audit trail of all who’ve examined a patient’s psychiatric evaluation notes • audit trail periodically sent to psychiatrist • why to the psychiatrist and not to the patient? • Veteran’s Administration Hospitals (DHCP system) Overview Informatics for Clinical Research

  48. Summary of Internet Research Informatics • Project website • easily doable today • Protocol and forms distribution • easily doable today • Randomization • doable with some programming • Data collection • fax • voice • electronic handheld • Data repository • very doable Overview Informatics for Clinical Research

  49. Deferred Topics • Integrating data collection systems with • research databases • real-time clinical care systems • Electronic data privacy Overview Informatics for Clinical Research

  50. Teaching Points • Data management skills are central to effective clinical research • “Servers” serve data to a network; “clients” retrieve and submit data to “servers” • Many clinical trial registries and resources on the web • Internet and clinical research • project website, forms distribution, data repositories easily doable • electronic data capture variably ready for prime time • Security is as much a people as a technical issue Overview Informatics for Clinical Research

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