Human Studies Database(HSDB)

Harold P Lehmann MD PhDJohns Hopkins

Division of Health Sciences Informatics

http://bioportal.bioontology.org/ontologies/2100

NCBO Ontology Workshop April 2012

http://hsdbwiki.org/

Participants

http://hsdbwiki.org/

Outline

• Purpose(s)• The Ontology of Clinical Research (OCRe)• Differences from similar efforts• Ontogeny

Purposes

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Above and Below the Line

5

What

How

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Hypothesis

Generation

Protocol Design

Ethics Approval

Study Executio

nData

AnalysisDissemi-nation

Cartoon Research Workflow

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Hypothesis

Generation

Protocol Design

Ethics Approval

Study Executio

nData

AnalysisDissemi-nation

Focus on the Abstract Protocol

Protocol

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Protocol Information

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Hopkins’ IRB eFormA: Free Text

http://hsdbwiki.org/

Use Cases• Institutional portfolio view of ongoing

research Improvement of measurement and data

collection methods Inform process improvement initiatives Cross-institutional view: “big data” benefits

for science in general For research networking, research design,

enrollment• Process improvement

Protocol document/e-protocol authoring Collect complete and useful data up front

at the earliest opportunity Enter study description once and reuse for

IRB, CRMS, ClinicalTrials.gov, populating recruitment registries, scientific computation, etc.

• New IRB sharability Characterizing racial/SES Disparities in

research CT.gov management

http://hsdbwiki.org/

More Use Cases• Systematic reviews:

Reduce searching and extractions by months to years

• Methodological decision support: Depends on understanding study intent and design

http://hsdbwiki.org/

HSDB Goals/Architecture• “The Human Studies Database (HSDB) is a federated,

computable database of the design and results of human studies from multiple institutions. HSDB uses the Ontology of Clinical Research and common clinical vocabularies to standardize the storage of this information, so that researchers can precisely search and analyze across studies even if they come from different sources and address different clinical domains.

• “It is especially important that HSDB contain rich detail about study designs, because the use and interpretation of study data depends critically on the context in which those data were collected.”

• HSDB Wiki http://hsdbwiki.org/index.php/HSDB_Collaborative_Wiki

http://hsdbwiki.org/

•A virtual computable scientific database of the design and results of all human studies in any clinical domain, involving any kind of data (e.g., quantitative, qualitative, imaging, genomic, etc)•Tools for investigators, comparative effectiveness researchers, policy makers and others to search and compare, visualize, analyze, and synthesize studies and study results•Data entry and data acquisition tools that allow institutions to capture HSDB data as part of their research workflows (e.g., IRB approval, clinical trial registration), so that multiple institutions can contribute HSDB data while maintaining local control and ownership of the data

HSDB Vision

http://hsdbwiki.org/

RU Clinical and Research Systems<Shamim Mollah/Rockefeller>

OutpatientScheduling System

iMedRISIRB management

Study management

Visual CactusMedical Staff credential

ADT

KIOSK Patients self register

McKesson Pharmacy

Visits

OutpatientHL7 visits

Inpatient HL7Admission, Discharge and Transfer

MRN demographic

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RU Clinical and Research Systems<Shamim Mollah/Rockefeller>

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Swati

Cha

krab

orti,

Duk

e

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Johns Hopkins

The Ontology of Clinical Research (OCRe)

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?

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OCRe Family

http://hsdbwiki.org/

OCRe• OWL 2.0 at HSDBwiki.org, NCBO BioPortal• Models human studies for scientific query and

analysis• Domain

All studies in which humans, parts of humans, or groups of humans are enrolled, exposed, or observed

• ScopeAll clinical domains, all variable types (quant, qual,

imaging, genomics, etc)• Sim I, et al., AMIA CRI Summit 2010

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Modeling Study Outcomes and Analyses

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HSDB-OCRe Components (v258, 21 Feb 2012)

http://bioportal.bioontology.org/ontologies/2100

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OCRe: Ontology of Clinical Research

OBO Basis

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Study

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Study Design

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Outcomes

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Sources

Differences from Similar Efforts

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CRMS Protocol Schema Builder

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CDISC BRIDG v3.0.3 (Dec, 2010)

Data Model

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•“ClinicalTrials.gov is a registry of federally and privately supported clinical trials conducted in the United States and around the world. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care

professionals.” •Study Type

Interventional.. Observational..Expanded Acess

•FDA info

Study status (why stopped...)Study DesignTreatment..Diagnostic…Intervention modelNumber of armsMasking..AllocationStudy classificationStudy modelTime perspecteiveBiospecimen RetentionEnrollmentArm infoIntervention typeEligibility

ClinicalTrials.gov

http://hsdbwiki.org/

Other Differences

• Limited to trialsAnd their analyses

• Granularity regarding outcomes• Single vs joint

E.g., Death or stroke• What instrument• “Basic results”

http://hsdbwiki.org/

Non-Ontology Work• EBM guidances

Alberta ToolkitJAMA Guide

• Methodology ChecklistsSystematic reviews

• ClassificationHartling, et al.

2011Hartling L, et al. Testing a tool for the classification of study

designs in systematic reviews of interventions and exposures showed moderate reliability and low accuracy. J Clin Epidemiol.

2011 Aug;64(8):861-71

Developments

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<?xml version="1.0" encoding="UTF-8"?><Root xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation ="HSDB_xsd_V11_a9.xsd" xmlns:sawsdl="http://purl.org/net/OCRe" > <Study> <RecruitmentSite> <Name>Heng County Health and Epidemic Prevention Station</Name> <Address> <PostalAddress> <Zip>532002I</Zip> <Country>China</Country> </PostalAddress> <AddressString> Hengzhou Town, Guangxi</AddressString> </Address> </RecruitmentSite> <RecruitmentSite> <Name>Guangxi Centers for Disease Control, China</Name> <Address> <PostalAddress> <Zip>532002I</Zip> <Country>China</Country> </PostalAddress> <AddressString> Guangxi, Nanning</AddressString> </Address> </RecruitmentSite> <RecruitmentSite> <Name>Xinjiang Uygar Autonomous Region Ctr. for Disease Control and Prevention, HPTN Project Office </Name> <Address> <PostalAddress> <Zip>830011</Zip> <Country>China</Country> </PostalAddress> <AddressString> Urumqi, Xinjiang</AddressString> </Address> </RecruitmentSite> <RecruitmentSite> <Name>Research Institute for Health Sciences (RIHES) </Name> <Address> <PostalAddress> <Country>Thailand</Country> </PostalAddress> <AddressString> Chaing Mai</AddressString> </Address> </RecruitmentSite>…..

OCRe-XSD

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RU<Shamim Mollah>

http://hsdbwiki.org/

Data mapping @ RU

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Hopkins Study in Oxygen

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OCRe XSD in Oxygen

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CTSA All-Hands Demo Oct 2011

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Getting More Data

• Translate from CT.gov tags to HSDB tagsSimona Carini (UCSF), Karl Burke (JH)XSLT transform

• Pull all of CT.gov down

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“Data” Collection

CT.govXSLT

Mapper

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XSLT Mapper

http://hsdbwiki.org/

Direction 1: Validations

• Semantic: Does the ontology capture the meanings we need? Is the typology correct?

• Querying: Can we query across corpora/institutions?

• Performance: Can we query fast enough?

http://hsdbwiki.org/

Semantic Validation

• Get protocols• Get experts to “type” the design• Get others to use the HSDB typology• Calculate agreement

http://hsdbwiki.org/

Querying & Performance: U Washington

• Put HSDB’ized protocols online

• Put MANY protocols online

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<!-- StudyDesignType="Case-crossover study design" - when ct.gov study_design has Observational Model: Case-Crossover

|"Parallel group study design"- when ct.gov study_design has Intervention Model: Parallel Assignment |"Crossover study design" - when ct.gov study_design has Intervention Model: Crossover Assignment |"Single group study design" - when ct.gov study_design has Intervention Model: Single Group Assignment |"Cohort study design" - when ct.gov study_design has Observational Model: Cohort |"Case-control study design" - when ct.gov study_design has Observational Model: Case Control |"Cross-sectional study design" - when ct.gov study_design has Time Perspective: Cross-Sectional |"N-of-1 crossover study design" - never from ct.gov clinical_study |"Quantitative study design" - never from ct.gov clinical_study |"Qualitative study design" - never from ct.gov clinical_study |"Observational study design"- when none of above, and ct.gov study_type is Observational |"Interventional study design" - when none of above, and ct.gov study_type is Interventional

Direction 2: CT.gov vs OCRe

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Where Are We Now?

• Listening for pain points• Articulating what HSDB can

do that others cannot• Prototype applications• Improving data quality in

CT.gov