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Human Studies Database (HSDB). Harold P Lehmann MD PhD Johns Hopkins Division of Health Sciences Informatics http://bioportal.bioontology.org/ontologies/2100 NCBO Ontology Workshop April 2012. Participants. Outline. Purpose(s) The Ontology of Clinical Research (OCRe)
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Human Studies Database(HSDB) Harold P Lehmann MD PhD Johns Hopkins Division of Health Sciences Informatics http://bioportal.bioontology.org/ontologies/2100 NCBO Ontology Workshop April 2012
Outline Purpose(s) The Ontology of Clinical Research (OCRe) Differences from similar efforts Ontogeny
Above and Below the Line What How 5
Focus on the Abstract Protocol Protocol
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
More Use Cases Systematic reviews: Reduce searching and extractions by months to years Methodological decision support: Depends on understanding study intent and design
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 Wikihttp://hsdbwiki.org/index.php/HSDB_Collaborative_Wiki
HSDB Vision • A virtualcomputable 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 captureHSDB 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
RU Clinical and Research Systems<Shamim Mollah/Rockefeller> OutpatientScheduling System Visual Cactus Medical Staff credential Visits iMedRIS IRB management Study management MRN demographic ADT KIOSK Patients self register Inpatient HL7Admission, Discharge and Transfer OutpatientHL7 visits McKesson Pharmacy
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 • Scope • All clinical domains, all variable types (quant, qual, imaging, genomics, etc) • Sim I, et al., AMIA CRI Summit 2010
HSDB-OCRe Components (v258, 21 Feb 2012) http://bioportal.bioontology.org/ontologies/2100
OCRe: Ontology of Clinical Research OBO Basis
ClinicalTrials.gov • “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 Design Treatment..Diagnostic… Intervention model Number of arms Masking..Allocation Study classification Study model Time perspecteive Biospecimen Retention Enrollment Arm info Intervention type Eligibility
Other Differences • Limited to trials • And their analyses • Granularity regarding outcomes • Single vs joint • E.g., Death or stroke • What instrument • “Basic results”
Non-Ontology Work Hartling 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 • EBM guidances • Alberta Toolkit • JAMA Guide • Methodology Checklists • Systematic reviews • Classification • Hartling, et al. 2011
OCRe-XSD <?xml version="1.0" encoding="UTF-8"?><Rootxmlns: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> …..
RU <Shamim Mollah>
Translate from CT.gov tags to HSDB tags Simona Carini (UCSF), Karl Burke (JH) XSLT transform Pull all of CT.gov down Getting More Data
“Data” Collection XSLT Mapper CT.gov
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?
Semantic Validation • Get protocols • Get experts to “type” the design • Get others to use the HSDB typology • Calculate agreement
Querying & Performance: U Washington • Put HSDB’ized protocols online • Put MANY protocols online