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Human Studies Database (HSDB)

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)

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  1. 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

  2. Participants

  3. Outline Purpose(s) The Ontology of Clinical Research (OCRe) Differences from similar efforts Ontogeny

  4. Purposes

  5. Above and Below the Line What How 5

  6. Cartoon Research Workflow

  7. Focus on the Abstract Protocol Protocol

  8. Protocol Information

  9. Hopkins’ IRB eFormA: Free Text

  10. 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

  11. More Use Cases Systematic reviews: Reduce searching and extractions by months to years Methodological decision support: Depends on understanding study intent and design

  12. 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

  13. 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

  14. 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

  15. RU Clinical and Research Systems<Shamim Mollah/Rockefeller>

  16. Swati Chakraborti, Duke

  17. Johns Hopkins

  18. The Ontology of Clinical Research (OCRe)

  19. ?

  20. OCRe Family

  21. 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

  22. Modeling Study Outcomes and Analyses

  23. HSDB-OCRe Components (v258, 21 Feb 2012) http://bioportal.bioontology.org/ontologies/2100

  24. OCRe: Ontology of Clinical Research OBO Basis

  25. Study

  26. Study Design

  27. Outcomes

  28. Sources

  29. Differences from Similar Efforts

  30. CRMS Protocol Schema Builder

  31. CDISC BRIDG v3.0.3 (Dec, 2010)Data Model

  32. 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

  33. Other Differences • Limited to trials • And their analyses • Granularity regarding outcomes • Single vs joint • E.g., Death or stroke • What instrument • “Basic results”

  34. 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

  35. Developments

  36. 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> …..

  37. RU <Shamim Mollah>

  38. Data mapping @ RU

  39. Hopkins Study in Oxygen

  40. OCRe XSD in Oxygen

  41. CTSA All-Hands Demo Oct 2011

  42. 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

  43. “Data” Collection XSLT Mapper CT.gov

  44. XSLT Mapper

  45. 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?

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

  47. Querying & Performance: U Washington • Put HSDB’ized protocols online • Put MANY protocols online

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