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Architecture of HSDB (caGrid Human Studies Database Service)


Mission and Vision

Human studies, encompassing interventional and observational studies, are the most important source of evidence for advancing our understanding of health, disease, and treatment options. To accelerate the discovery of findings from human studies, study designs and results should be available for large-scale data mining, synthesis, analysis, and reuse.

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. Our broad long term vision is:

  • 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

A national or even international human studies database will be an incomparably rich resource for clinical and translational research. An overview of HSDB is available Image:Pdf.pnghere.


Contents

Project Goals

  • Enhance national clinical and translational research capability: As a computable database with detailed scientific information about past and ongoing human studies, HSDB will be a critical infrastructure for large-scale analysis and reuse of human studies data. Together with other clinical research databases (e.g., ClinicalTrials.gov, recruitment databases), HSDB will also support scientific portfolio and other clinical research management.
  • Ensure standardized computable descriptions of human studies through use of ontologies and controlled clinical vocabularies The semantic foundation for HSDB is the Ontology of Clinical Research, with mappings to and integration with other relevant models and vocabularies (e.g., BRIDG, SNOMED). This semantic foundation is independent of the particular technology or architecture used for implementing data sharing.
  • Provide a set of tools for institutions to contribute their human studies data to HSDB and to share this data over caGrid The value of HSDB will increase exponentially as more institutions contribute more studies. We are defining a scalable approach to HSDB data acquisition and sharing using a combination of i2b2 and caGrid technology. We are focusing first on federating descriptions of study designs before federating study results.


People and Participating Institutions

Project members

While current project members are predominantly from Clinical and Translational Science Award (CTSA) institutions, the HSDB project is open to all interested parties.

UCSF (Leader): Ida Sim (Project Leader), Simona Carini, Rob Wynden

Duke University: Meredith Nahm, Swati Chakraborty

Columbia University: Suzanne Bakken

Johns Hopkins: Harold P. Lehmann

Mayo Clinic: Chris Chute

The Rockefeller University: Ed Barbour, Shamim A. Mollah, Knut M. Wittkowski

Stanford: Samson Tu

UC Davis: Davera Gabriel, Hien Nguyen

University of Colorado: Jessica Bondy

University of Manchester, UK: Alan Rector

UT Health Science Center San Antonio: Brad H. Pollock

UT Southwestern: Herbert K. Hagler, Richard H. Scheuermann

University of Washington: Jim Brinkley, Todd Detweiller

Washington University St. Louis: Rakesh Nagarajan, Jahangheer Shaik

Work Plan Overview

Center

Modeling and Modeling Evaluation

  • Domain modeling in Ontology of Clinical Research, on Google Code [1] and on BioPortal [2].
    • Evaluate with domain-limited studies (assemble and instantiate test studies)
    • Evaluate with random sets of studies
  • Typology of study designs (see pilot evaluation)
    • Evaluate with more studies [in progress]

Architecture and Methods for Data Federation

  • Define core HSDB data elements for data federation
  • Generate view of HSDB Core in OCRe
  • Curate CDEs (e.g., into CSHARE) and expose on a DSR (e.g., into openMDR)

Data Sharing from Multiple Institutions

  • Curate Administrative Core Data Elements
    • Compile a master list of common administrative data elements and definitions of variables used across various institutional Clinical Trial Management Systems
  • Acquire data using HSDB Entry tool with deep navigation links or through direct harvesting from electronic sources (e.g., eIRBs)
  • Generate local databases: for local databases based on i2b2 or caGrid technology
  • Map instances of local data into HSDB format [Health Ontology Mapper (HOM)]
  • Expose instance mapped data over the HSDB caGRID network: see OSU Introduce

Data Query and Visualization Interfaces

  • New supplement just funded to build data entry interface
  • Query interfaces to build on caB2B, CTSearch, and CTeXplorer

News and Updates

All the publications referenced in this section are available under Articles and Reference Materials

  • March, 2011 One HSDB-related panel and two posters were presented at the AMIA Clinical Research Informatics Summit.
  • March, 2010 Two HSDB-related papers received the Distinguished Paper awards at the AMIA Clinical Research Informatics Summit.
    • Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann RH, Lehmann HP, Wittkowski KM, Nahm M, Bakken S. The Human Studies Database Project: Federating Human Studies Design Data Using the Ontology of Clinical Research. AMIA CRI Summit 2010.
    • Wynden R, Weiner MG, Sim I, Gabriel D, Casale M, Carini S, Hastings S, Ervin D, Mobed K, Cucina RJ. Ontology Mapping and Data Discovery for the Translational Investigator. AMIA CRI Summit 2010.
  • February, 2010 Awarded supplement to NCRR R01, for developing a data entry interface (R01-RR026040-01S1)
  • November, 2009 HSDB paper awarded Distinguished Paper at 2009 AMIA Symposium in San Francisco!
    • Simona Carini, Bradley H. Pollock, Harold Lehmann, Meredith Nahm, Davera Gabriel, Suzanne Bakken, Ed Barbour, Herb Hagler, Shamim Mollah, Richard Scheuermann, Ida Sim Development and Evaluation of a Study Design Typology for Human Subjects Research
  • September, 2009 Awarded R01 from NCRR, "Ontology-Based Integration of Human Studies Data" (R01-RR026040)

Becoming a Collaborator

To join HSDB, please register as a collaborator at the Registration Process for Collaborators page (under construction).

Subscribing to Our Listserv You can subscribe to our HSDB-public listserv and receive project announcements changes to the wiki, and other newsworthy items. To subscribe, please contact Ida Sim to be added to the project mailing list.

Members Only


Resources

Useful Links

Articles and Reference Materials

Image:Pdf.png Sim I, Chakraborty S, Lehmann H, Mollah S, for the Human Studies Database Project. Capturing Descriptions of Human Studies for Federated Data Sharing: Frontline Experiences from Three Institutions AMIA CRI Summit 2012 [abstract]
Slides from the panel presentation:
Image:Pdf.png Ida Sim (UCSF)
Image:Pdf.png Harold Lehmann (Johns Hopkins)
Image:Pdf.png Swati Chakraborty (Duke)
Image:Pdf.png Shamim Mollah (Rockefeller)

Image:Pdf.png CTSA Human Studies Database Project Classifying Human Studies into Design Types Using Factors [Version of the Study Typology as of December 19, 2011]

Image:Pdf.png 2011 Project Abstract CTSA Informatics All Hands Meeting (Oct 2011)
2011 Project Demo CTSA Informatics All Hands Meeting (Oct 2011)
XSD file referenced in the slides CTSA Informatics All Hands Meeting (Oct 2011) [Be advised that this file is subject to changes as the project progresses]
One of the XML files referenced in the slides CTSA Informatics All Hands Meeting (Oct 2011) [Be advised that this file is not complete with respect to the relevant study]

Image:Pdf.png Wynden R, Solbrig H, Tu S, Brinkely J. The Value of Value Sets AMIA CRI Summit 2011 [abstract]
Slides from the panel presentation:
Image:Pdf.png Rob Wynden (UCSF)
Image:Pdf.png Harold Solbrig (Mayo)
Image:Pdf.png Samson Tu (Stanford)
Image:Pdf.png Jim Brinkley (U of Washington)
Sim I, for the Human Studies Database Project. An Approach to Practical Applications of An OWL Ontology for Clinical Research. AMIA CRI Summit 2011 Image:Pdf.png poster abstract
Detweiler L, Brinkley J. Value Sets via Ontology Views. AMIA CRI Summit 2011 Image:Pdf.png poster abstract
Video of a Grand Rounds Harold Lehmann (Johns Hopkins) gave on HSDB on February 18, 2011
Image:Pdf.png 2010 Project Abstract CTSA Informatics All Hands Meeting (Oct 2010)
Image:Pdf.png 2010 Project Presentation CTSA Informatics All Hands Meeting (Oct 2010)
Image:Pdf.png Sim I, et al. The Human Studies Database Project: Federating Human Studies Design Data Using the Ontology of Clinical Research. AMIA CRI Summit 2010. [AMIA Distinguished Paper Award]
Image:Pdf.png Wynden R, et al. Ontology Mapping and Data Discovery for the Translational Investigator. AMIA CRI Summit 2010. [AMIA Distinguished Paper Award]
Image:Pdf.png CTSA Human Studies Database Project Classifying Human Studies into Design Types Using Factors [Version of the Study Typology as of February 14, 2011]
Image:Pdf.png CTSA Human Studies Database Project Classifying Human Studies into Design Types Using Factors [September 3, 2010 version superseded by the February 14, 2011 version ]
Image:Pdf.png Carini S, et al. Development and Evaluation of a Study Design Typology for Human Subjects Research. AMIA Annu Symp Proc., 2009 [AMIA Distinguished Paper Award]
Image:Pdf.png 2009 Project Abstract CTSA Informatics All Hands Meeting (Oct 2009)
Image:Pdf.png 2009 Project Presentation CTSA Informatics All Hands Meeting (Oct 2009)
Image:Pdf.png Project Report To CTSA Informatics Key Function Committee (Aug 2009)
Image:Pdf.png 2008 Project Abstract CTSA Informatics All Hands Meeting (Oct 2008)
Image:Pdf.png 2008 Project Presentation CTSA Informatics All Hands Meeting (Oct 2008)
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