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February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Case Studies in Clinical Research Informatics
Ida Sim, MD, PhD
February 26, 2008
Division of General Internal Medicine, andCenter for Clinical and Translational Informatics
UCSF
Copyright Ida Sim, 2008. All federal and state rights reserved for all original material presented in this course through any medium, including lecture or print.
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Outline
• Recap
• Clinical Research Informatics Overview
• Case studies– Integrated Data Repository– CTSA Human Studies Metadata
Repository
• Summary
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Major Informatics Issues
• Naming data
• Exchanging data
• Reasoning with data and information to generate knowledge
• Secondary issues– user-centered design, organizational
change/QI, cost-benefits of health IT
Clinical Informatics Today
Clinic 2008
FrontDesk
Radiology
Claims
MedicalInformationBureau
Archive
Walgreens
Prescribing
Pharm BenefitManager
Benefits Check(RxHub)
HealthNetFormulary Check
B&TEligibility Authorization
Personal HealthRecord (PHR)
UCare
Electronic HealthRecord (EHR)
Specialist
Referral
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7)
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Challenge of Naming Data • The more coded your data, the more
expressive the vocabulary, the more computing you can do with the data– because the computer can “understand” more
• But coding costs time and effort– e.g., selecting billing codes
• And coding systems are hard to design, especially for changing fields like medical research
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Outline
• Recap
• Clinical Research Informatics Overview
• Case studies– Integrated Data Repository– CTSA Human Studies Metadata
Repository
• Summary
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Clinical Research Informatics• Systems needed to support clinical research, just
like EHR supporting clinical care– study design and initiation
• protocol simulation, IRB submission, trial registration, etc.
– clinical trial management systems (CTMS)• case report forms, remote data capture, web-based surveys,
GCP compliance, study site management, etc.
– data management and discovery• analytic algorithms, visualization, modeling, etc.
– collaboration: wikis and beyond– reporting and data sharing
• publishing, trial results reporting, data repositories, etc.
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Catch-up To Clinical Informatics• >80% of clinical research still using paper charts and forms
– $12 billion for paper-based trials vs. $2 b/yr for electronic trials industry
– transactional systems• enroll a patient, fill out case report form, report Adverse Event• NOT why this primary outcome, what is the design and why
• Naming data– beyond ICD-9...beyond even SNOMED...
• Exchanging data– clinical research is as fragmented as clinical care– need an “HL7” for exchanging research protocol and results
information
• Reasoning from data and information to knowledge
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Health Informatics Big Picture
• Puts care and research together
• Separates data from the transactional systems used to collect that data– no hostage data!
• Shows need to capture computable knowledge, not just data
• Clear place for decision support
• Emphasizes user-centered design as glue
VirtualPatient
Transactions
Raw data
Medicalknowledge
Clinicalresearch
transactions
Rawresearch
data
DecisionsupportMedical logic
PATIENT CARE /WELLNES RESEARCH
Workflow modeling and support, usability, cognitive support,computer-supported cooperative work (CSCW), etc.
Where clinicianswant to stay
EHRs
CTMSs
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Lecture Progression
• Case studies in clinical research informatics
• EHRs• Clinical research IT
systems• Decision support• Translational
eScience/The Knowledge Layer
VirtualPatient
Transactions
Raw data
Medicalknowledge
Clinicalresearch
transactions
Rawresearch
data
DecisionsupportMedical logic
PATIENT CARE /WELLNES RESEARCH
Workflow modeling and support, usability, cognitive support,computer-supported cooperative work (CSCW), etc.
Where clinicianswant to stay
EHRs
CTMSs
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Outline
• Recap
• Clinical Research Informatics Overview
• Case studies– Integrated Data Repository– CTSA Human Studies Metadata
Repository
• Summary
Data Spread out All Over
Clinic 2008
FrontDesk
Radiology
Claims
MedicalInformationBureau
Archive
Walgreens
Prescribing
Pharm BenefitManager
Benefits Check(RxHub)
HealthNetFormulary Check
B&TEligibility Authorization
Personal HealthRecord (PHR)
UCare
Electronic HealthRecord (EHR)
Specialist
Referral
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7)
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
MICU
FinanceResearch
QA
Integrated Data Repository
Internet
ADT Chem EHR XRay PBM Claims
• Integrated historical data common to entire enterprise
Bring It All Together?
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
EHR vs. Clinical DR Queries
• EHR Queries
• What was Mr. Smith’s last potassium?
• Does he have an old CXR for comparison?
• What antihypertensives has he been on before?
• What did the neurology consult say about his epilepsy?
• Clinical Data Repository Queries
• What proportion of diabetics with AMI admissions were discharged on -blockers?
• What was the average Medicine length of stay in 2000 compared to 1995?
• What is the trend in use of head CTs in patients with migraine?
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
EHR/Data Repository Comparison
• Enterprise viewpoint more appropriate for QI and research
• Data repository cleans and aggregates data from multiple sources
Viewpoint Time Queries
EHR Patient Real-Time ClinicalData Repository Enterprise Historical Ad Hoc
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
IDR Informatics, etc. Challenges• Naming data: homework exercise using ICD-9 for
pneumonia• Exchanging data• Mapping similar data across different sources
– reconciling ICD-9, SNOMED, free text, etc. • Running huge databases (petabyte scale)• Data ownership, access rights, obligations
– governance agreements with data sources (e.g., hospital)– intellectual property protection (e.g., for star faculty)
• Privacy– patient opt-in vs. opt-out for being contacted for research
purposes
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
MICU
FinanceResearch
QA
IntegratedData Repository
Internet
ADT Chem EHR XRay PBM Claims
• How do the machines “talk” to each other?
Networking Basics
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Internet = Network of Networks
itsa
medicine
ucsf.edu
nci.nih.gov cochrane.uk myhome.com
Main Trunk Cables
local trunk cablethrough Berkeley
amazon.com
at homedial-in to itsa.ucsf.edu via modem
pacbell.net
aol.com
Internet Service Provider (ISP)via DSLor cable
LAN
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
• Protocol = grammar for machines talking to each other– e.g., hypertext transfer protocol http for web
• http://www.epibiostat.ucsf.edu/courses/schedule/med_informatics.html
– e.g., ftp file transfer protocol– all sit on top of basic networking protocol TCP/IP
• Health-specific protocols needed “on top of” http or TCP/IP– a “grammar” for how to exchange health-related data
What Happens Over the Cables
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Health Data Interchange Protocols• HL7, “containers” for data packages, e.g., lab
• DICOM, “containers” for radiology studies– machine used, type of study, # of images, etc.
• CCD (Continuity of Care Document) for chart– e.g., SOAP, problem list, allergies, family history– not widely used, still controversial
MSH|…message header
PID|…patient identifier
<!-OBX…observation result>
OBX|1|ST|84295^NA||150|mmol/l|136-148|H||A|F|19850301<CR>
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Data Interchange Challenges• Lots of complex data need to be sent to many
different groups for many different uses
• HL7 and DICOM widely used, but don’t address– the data naming issue (e.g., Na, sodium, serum
sodium)– exchange of other data, e.g.,
• clinical chart notes (CCD)
• microarray and gene expression data (MAGE/MIAMI)
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
MICU
FinanceResearch
QA
IntegratedData Repository
Internet
UCare PICIS Flowcast STOR IDXRad TSI
Where to Start?
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Use Cases
• Technique in software and systems engineering to tease out functional requirements of a computer system– define user needs/requests– define what the system response should
be
• don’t worry about how the system works
• Includes goals, scenarios, actors, preconditions, exceptions, etc.
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
IDR Use Cases?
• Cohort identification– find all diabetics discharged in 2007 with
acute MI (who opt-in to research contact)• Geno-pheno correlation• Data mining across all clinical data for
– new associations to explore– quality improvement
• Identification of available biospecimens
IDR Source Systems Prioritization
UCareSTOR
LPPIEMR
PICIS
Worx CNeXT
FlowcastValue/Utility
Feasibility (based on availability, which can be influenced by either organizational or technical barriers or both)
TSI
CoPath
Misys
IDXradKaiserVA/
VistaSFGH/LCR
ED Apollo
Data in UCare:
All data
Some data
No data
axiUm
Jan. 2009Jan. 2010
Jan. 2011
Jan. 2012
IDR Phases and Target Systems
Phase IJan. 2009
UCarePICIS
Inpatient EMR and future outpatient EMRPeri-operative System
Phase IIJan. 2010
STOR WORX CoPath IDXRadApollo CNeXT Flowcast TSIED
Outpatient EMR and historic inpatient EMRCurrent pharmacy systemPathology RadiologyCardiology SystemUCSF Cancer RegistryScheduling and demographicsBilling systemEmergency Department System
Phase IIIJan. 2011
Langley-Porter Breast Care Center Urology Velos axiUmLCRMisysStudent Health
Separate outpatient EMRPatient/tumor tracking dbPatient tracking dbCTMS for Cancer CenterDentistry EMRSFGH EMR – Lifetime Clinical RecordClinical Labs systemSeparate EMR
Phase IVJan. 2012
VAMCKaiser
Vista EMREpic EMR
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Implications of Use Cases
• Which data sources are important to capture? How clean must the data be?
• How far back should data be collected? How often must data be refreshed?
• How robust must the controlled vocabular(ies) be? What data interchange standard(s) should be used?
• Who owns the data? Who decides access? What can be done with the data? Who adjudicates disputes?
• How are experimental conditions described? (trials, observational studies, microarray experiments, etc)
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Outline
• Recap
• Clinical Research Informatics Overview
• Case studies– Integrated Data Repository– CTSA Human Studies Metadata
Repository
• Summary
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Human Studies• One of most valuable sources of research data
– how many clinical studies are active at UCSF? how many are in pediatrics? in prevention?
– what are most common study outcomes in alcoholism trials? what are common eligibility criteria in asthma studies?
– how many Phase III trials does NHLBI fund in CTSA institutions? what’s being studied? what’s not?
• New requirement in FDA Amendments Act 2007 that all clinical trials phase II and above be registered in ClinicalTrials.gov– 20+ data about the trials (metadata=data about data) must
be reported, in text– to uniquely identify trials at inception to guard against
reporting bias / hiding of negative studies
Ida Sim, WHO, 2006
WHO Registration Data Set (1)WHO Registration Data Set (1)
1.1. Primary Register and Trial ID# (e.g., NCT)Primary Register and Trial ID# (e.g., NCT)
2.2. Date of Registration in Primary RegisterDate of Registration in Primary Register
3.3. Secondary ID#sSecondary ID#s
4.4. Source(s) of Monetary or Material SupportSource(s) of Monetary or Material Support
5.5. Primary SponsorPrimary Sponsor
6.6. Secondary Sponsor(s)Secondary Sponsor(s)
7.7. Contact for Public QueriesContact for Public Queries
8.8. Contact for Scientific QueriesContact for Scientific Queries
9.9. Public TitlePublic Title
10.10. Scientific TitleScientific Title
Ida Sim, WHO, 2006
WHO Registration Data Set (2)WHO Registration Data Set (2)
11.11. Countries of RecruitmentCountries of Recruitment
12.12. Health Condition(s) or Problem(s) StudiedHealth Condition(s) or Problem(s) Studied
13.13. Intervention(s)Intervention(s)
14.14. Key Inclusion & Exclusion CriteriaKey Inclusion & Exclusion Criteria
15.15. Study TypeStudy Type
16.16. Date of First EnrollmentDate of First Enrollment
17.17. Target Sample SizeTarget Sample Size
18.18. Recruitment StatusRecruitment Status
19.19. Primary Outcome(s)Primary Outcome(s)
20.20. Key Secondary Outcome(s)Key Secondary Outcome(s)
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Beyond ClinicalTrials.gov• ClinicalTrials.gov extends WHO 20 metadata items. e.g.,
– study type => study design: Phase, randomization, etc.– satisfies FDA law, US Congress, public demand for
pharmaceutical sector accountability
• Is text reporting in ClinicalTrials.gov sufficient for CTSA use cases for clinical and translational research?– research characterization
• e.g., research purpose, clinical aims, enrolled population, research design, etc.
– research operations• e.g., facilitating IRB approval and trial registration, portfolio
management
– cross institutional• e.g., research inventory, benchmarking across CTSAs
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
GenomicsProteomicsPharmacogenomicsMetabolomics, etc.
Clinical trialsEpidemiologyMolecular Epi
Evidence-based practicePatient safetyQuality of care
Human Studies Metadata Repository
• ...to enable the “translation” in translational research
Basic Discovery
Clinical Research
Clinical Care
T1
Translation
T2
Translation
Bioinformatics
Medical Informatics
Human Studies
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Human Studies Metadata
• Build a standardized repository of key descriptors (metadata) of all human studies conducted at CTSA institutions for CTSA priority use cases– Administrative data
• NCT number, primary sponsor, funder, public contact, PI,
public title, scientific title, date of first enrollment,
recruitment status
– Scientific data• health condition, key eligibility criteria, study type/study
design, sample size, interventions, primary outcomes,
key secondary outcomes, biospecimens collected
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Standardizing Metadata Items
• Interventions, what are subfields?– intervention name (MeSH? CPT? SNOMED?)
– what else?• Difficult items
– eligibility criteria– study type / study design– interventions– outcomes– biospecimens collected
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Current Status• CTSA Informatics national consortium project,
strong interest from NCRR, CTSA PIs, 12 participating CTSA institutions– define priority use cases– define metadata items and subfields based on use
cases– test and evaluate vocabulary and ontology
standards for representing items• e.g., SNOMED, RxNORM, Ontology of Clinical Research
(defn. of “study outcome”, allocation concealment), models of time, quantities, dates, etc.
• Get buy-in across all CTSA institutions, roll out
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Outline
• Recap
• Clinical Research Informatics Overview
• Case studies– Integrated Data Repository– CTSA Human Studies Metadata
Repository
• Summary
February 26, 2008: I. Sim Clinical Research Informatics Case StudiesMedical Informatics
Summary• Clinical research informatics parallels, but is behind,
clinical care informatics• Research repository challenges discussed
– use cases to drive specification of functional requirements– naming data...and defining subfields
• “Garbage in garbage out” or “where is the information we have lost in data” – if raw data is wrong, incompatible, not computable– if information is not all right (e.g., out of context, incomplete)– if can’t get data out of source systems (technical, privacy,
intellectual property reasons)