The Biomedical Translational Research Information System BTRIS

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The Biomedical Translational Research Information
System (BTRIS)

• James J. Cimino
• Chief, Laboratory for Informatics Development
• National Institutes of Health Clinical Center
• Senior Scientist, Lister Hill Center for
  Biomedical Communications
• National Library of Medicine
• Adjunct Professor, Department of Biomedical
  Informatics
• Columbia University College of Physicians and
  Surgeons
• September 12, 2008

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Learning Objectives

• An introduction to the compilation and
  integration of clinical and research data from
  multiple disparate sources
• Understanding the authorization issues related to
  reuse of patient clinical data
• Understanding the terminology issues related to
  the reuse of coded clinical and research data
• Familiarity with the approach being taken at the
  National Institutes of Health to collect,
  integrate, and code clinical and research data
  into a single repository, for authorized resuse
  in biomedical research.

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No Relevant Financial Relationships with
Commercial Interests
Disclosures
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The Clinical Center, 1981
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What Was the Problem?

• Patients in the NIH Clinical Center were on
  research protocols, but
• their data were in a clinical information system
• Needed to extract individual data for analysis
• Needed cross-patient queries for additional
  analysis

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Patient Information Graphics System (PIGS)

• Integration of a desktop computer (pre-PC) to
  mainframe clinical information system (TDS)
• Download vital sign and drug administration data
• Various graphical displays
• SCAMC, 1981

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The Columbia University Medical Center Clinical
Data Warehouse

• Clinical data repository to collect data from
  ancillary systems
• Coded with the Medical Entities Dictionary

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MED Structure
Medical Entity
CHEM-7
Plasma Glucose Test
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Using the MED for Summary Reporting
Lab Display
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
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The Columbia University Medical Center Clinical
Data Warehouse

• Clinical data repository to collect data from
  ancillary systems
• Coded with the Medical Entities Dictionary

• Back end for clinical information systems (CIS,
  WebCIS, PatCIS, PalmCIS, QingCIS, MendonÇIS)
• Reorganized for use as Clinical Data Warehouse

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How often are patient with the diagnosis of
myocardial infarction started on beta blockers?
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How often are patient with the diagnosis of
myocardial infarction started on beta blockers?
Find all patients with Diagnosis in class
MYOCARDIAL INFARCTION
Find all patients with Diagnosis in class
MYOCARDIAL INFARCTION AND with Medication in
class BETA BLOCKER
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The Clinical Center, 2008
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The Clinical Center, 2008

• Patient data stored in EHR (Eclipsys)
• Need to extract individual data for analysis
• Need cross-patient queries for additional
  analysis
• Data may require transformation
• De-identification and Re-identification
• Indexing
• Aggregation by time
• Abstraction by classification
• Conversion to relevant concepts

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What is BTRIS?

• Biomedical data
• Research data collected using clinical
  information systems
• Clinical data collected using clinical
  information systems
• Research data from research information systems
• Non-human data
• Reuse of data to support translational research
• Hence Biomedical Translational Research
  Information System

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The NIH, 2008
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What is BTRIS?
BTRIS
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What is BTRIS?
BTRIS
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What is BTRIS?
O n t o l o g
y
Data Retrieval Functions Authorization
Subject-Oriented Cross-Subject
Re-Identification NLP
Data Repository
BTRIS
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BTRIS Issues

• Data sources
• Data model integration
• Research Entities Dictionary
• Access policies
• User requirements
• User access and user Interface
• Terminology-based queries

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Data Sources

• Order entry system
• Ancillary systems
• Institute and Center (IC) systems
• Individual researchers systems
• Notebooks

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Data Model Integration

• Events and details
• Entity-relation vs entity-attribute-value
• Denormalization

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Research Entities Dictionary

• Apelons Terminology Development Editor
• NCI/caBIG Thesaurus

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Research Entities Dictionary (RED)
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Research Entities Dictionary

• Apelons Terminology Development Editor
• NCI/caBIG Thesaurus

• Content
• Organization

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Access Policies

• Privacy Act, not HIPAA
• Policy Working Group
• Intellectual property vs. public domain
• Identifiers
• Unlinked, coded data

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BTRIS Data Storage Policy
1. All clinical and research data, whether from
active or inactive protocols, are stored in BTRIS
in a timely manner.
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BTRIS Data Use Policy
Active Protocols
Inactive Protocols
2. PIs can see data collected on their patients
as part of their active protocols
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BTRIS Data Use Policy
Blocked By PI
Active Protocols
Inactive Protocols
3. PIs may indicate that some of their data
should be blocked to avoid unmasking their study
subject assignment.
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BTRIS Data Use Policy
Identifiers
Coded Data
Blocked By PI
Active Protocols
Inactive Protocols
4. It is helpful to consider data to consist of
identifiers vs. other (coded) data linked to
those identifiers. PIs can get to coded data in
their own active protocols, but not those in
inactive protocols.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Active Protocols
Inactive Protocols
5. It is also helpful to consider that coded data
can be further divided into recorded events (such
as a medication order or a lab result report) and
results (such as the medication ordered or the
value of the test result).
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
Inactive Protocols
6. Identifiers in active protocols are restricted
to PIs but other data are generally be sharable
with some PI control.
The PI may designate some
events, and perhaps their data, as completely
restricted while the protocol is active.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
Unencumbered By PI
No Access
Inactive Protocols
7. When a protocol becomes inactive, the
identifying information is inaccessible, but the
other (coded) data (events and results) become
generally available.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
Unencumbered By PI
No Access
Inactive Protocols
Collaborative with PI
8. A PI may restrict use of some data from
inactive protocols, for example requiring other
users of the data to work in collaboration with
the PI.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
Unencumbered By PI
No Access
Inactive Protocols
Collaborative with PI
9. Data may move back to be considered active if
a PI (not necessarily the original PI), gets
approval to use the data, including (as per the
IRB), identifying information.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
Unencumbered By PI
No Access
Inactive Protocols
Collaborative with PI
10. To summarize, PIs have access to data in
their own active protocols, subject to any
blocking that may be required.
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BTRIS Data Use Policy
Coded Events
Identifiers
Coded Results
Restricted By PI
PI Only
Active Protocols
Sharable Through PI
PI Only
NIH Community
Unencumbered By PI
No Access
Inactive Protocols
Collaborative with PI
11. The NIH community will have access to all
data, except identifiers, with restrictions on
data (active or inactive) by PIs. Restrictions
may differ for events versus results.
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User Requirements

• 2006 study of user requirements

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User Requirements

• Provide Medication lists at time of patient
  encounters. Include drug diaries for inpatient,
  outpatient and in-between encounters in the
  patient medical record. Include all chemo and
  non-chemo drugs from CRIS and IC systems
• Provide Medication administration documentation
  (drug diaries) with times as part of patient
  record
• Provide ability to compare patient results,
  Medication Administration Records between dates
  and/or encounters
• Provide drug randomization info, compliance
  records and drug accountability info for all
  investigational, study and prescription drugs
• Provide all Clinical Center lab results with
  times of specimen draws
• Provide external lab results
• Provide archival images
• Provide demographics data including age, BMI,
  race, gender, contact info, etc
• Provide access to genomics and bio-markers data
• Provide cumulative blood volumes, research drugs
  and radiation for subject over a given period
• Provide ability for ICs to feed expanded
  diagnosis/problem lists
• Provide searching and filtering patients' data by
  all diagnosis, tests, procedures, protocol
  protocol classifications

• Standardize medication and lab test codes.
• Provide integration of adverse events data in the
  data warehouse,
• Provide integration of protocol census, status
  and subject accrual tracking data from Protrak in
  the data warehouse
• Provide ability to attribute different events to
  protocols, viz., consent signed, protocol
  activated, orders, observations, adverse events,
  etc
• Provide integration of staff, patient and user
  index data across source systems in data
  warehouse.
• Provide original informed consent, and updated
  consents for re-contact of patients for research
  for all protocols. Provide searchable consents
  and image of consents in database. Provide
  answers to
• Can tissues be used for cancer/genetic research,
  other research, germ line testing
• Can patient be re-contacted for questions?
• Provide single patient amendments
• Provide access and track biological specimen data
  
• Provide access to Appointment Data
• Provide Review of Systems info for each patient
  visit.
• Provide patient de-identification services
• Standardize Units Of Measure

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User Requirements

• 2006 study of user requirements

• Investigator User Group
• Demos
• To user group
• One-on-One
• Town hall meeting

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User Access/User Interface

• Canned reports (e.g., recruitment for IRB)
• Reports with prompts (e.g., sets of lab results)
• Ad hoc queries (whatever you want!)
• Selected Business Objects

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Terminology-Based Queries

• Hripcsak G, Allen B, Cimino JJ, Lee R. Access to
  Data Comparing AccessMed to Query by Review.
  Journal of the American Medical Informatics
  Association 19963(4)288-299.

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Terminology-Based Queries

• Hripcsak G, Allen B, Cimino JJ, Lee R. Access to
  Data Comparing AccessMed to Query by Review.
  Journal of the American Medical Informatics
  Association 19963(4)288-299

• Business Objects prompt with hierarchy

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Terminology-Based Queries

• Hripcsak G, Allen B, Cimino JJ, Lee R. Access to
  Data Comparing AccessMed to Query by Review.
  Journal of the American Medical Informatics
  Association 19963(4)288-299.
• Business Objects prompt with hierarchy

• Ancestor-descendant join with filtering

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Ancestor-Descendant Joinwith Filtering

• Start with parent-child table
• Transitive closure produces ancestor-descendant
  table
• Designate subset of searchable classes
  (ancestors)
• Display flat list (no tree walk)
• Let user select desired classes
• Query selects ancestor-descendant rows and joins
  data tables based on descendants

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Status

• Modeling source data
• Clinical Research Information System
• Clinical Data Repository
• Crimson (NIAID)

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Status

• Modeling source data
• Clinical Research Information System
• Clinical Data Repository
• Crimson (NIAID)

• Unified BTRIS data model

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Status

• Modeling source data
• Clinical Research Information System
• Clinical Data Repository
• Crimson (NIAID)
• Unified BTRIS data model

• Database versions
• Specific for principal investigator
• Scrambled data for general use
• Business Objects demonstration

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BTRIS in the Research Process
Scientific Review
Analysis of Resources Required
Write Protocol
IRB Approval
Hypothesis Generation
Recruitment
Publications
Patient Accrual
Data Gathering And Analysis
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Next Steps

• Rebuild database in Oracle
• Total historical data sets from CDR, CRIS,
  CRIMSON
• Live interfaces with Lab, Radiology, CRIS and
  CRIMSON
• Continue to collect user feedback
• Develop report sets
• BTRIS 1.0 - July 2009

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More Issues

• Patient ownership of de-identified data
• If genomic data are included, can we truly
  de-identify?
• Is protocol number a patient identifier?
• How important is protocol attribution?
• What data should not be shown to PIs?
• What is the extent of data control by PIs?

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Moving Forward

• Despite centuries of clinical research, data are
  still fragmented
• Sophisticated terminology is the key to reuse of
  disparate data
• Policy issues are bigger than technical issues

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BTRIS Will

• Be the preferred system to analyze NIH clinical
  and non-clinical data
• Aggregate and standardize disparate and isolated
  data sets
• Automate and streamline processes that are
  traditionally manual and cumbersome
• Prioritize data sources and functionality based
  on needs of user community
• Future of BTRIS today the NIH, tomorrow the
  world?

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btris.nih.gov