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Biomedical Informatics Research Network The BIRN Architecture: An Overview Jeffrey S. Grethe, BIRN-CC 10/9/02 BIRN All Hands Meeting 2002.

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Presentation on theme: "Biomedical Informatics Research Network The BIRN Architecture: An Overview Jeffrey S. Grethe, BIRN-CC 10/9/02 BIRN All Hands Meeting 2002."— Presentation transcript:

1 Biomedical Informatics Research Network The BIRN Architecture: An Overview Jeffrey S. Grethe, BIRN-CC 10/9/02 BIRN All Hands Meeting 2002

2 We speak piously of taking measurements and making small studies that will add another brick to the temple of science. Most such bricks just lie around the brickyard. Platt, J.R. (1964) Strong Inference. Science. 146: 347-353.

3 The BIRN Portal

4 BIRN Toolkit Viewing/Visualization Queries/ResultsApplications Data Management Collaboration BIRN Portal Session Mgmt.CustomizationApplication GlueWorkflow Discussion Forum Imaging Whiteboard Active Transcripts Interactive Collaboration Environment SRB Browser gTomo FreeSurfer AFNI LONI Pipeline Volume Renderer Viewing Tools 3D Slicer Conversion APIs Volume Renderer Viewing Tools LONI Pipeline Knowledge Map Browser Smart Atlas SRB Browser Upload Workflow Anonymization Simple Form Complex Query Query Builder Dynamic Reports Smart Atlas Knowledge Map Browser

5

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8 Data Mediation Overview Wrapper User / Client Application Mediator Wrapper External Knowledge Source Integrated View Definitions External Knowledge Source Data Source

9 A “Simple” Use Case User Login & Authentication BIRN Portal Mediation System Data Source External Application Custom Query Form Customize Form

10 Simple Form

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13 Summary Results

14 Domain Map Interface

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16 Coordinates of lines comprising brain regions are stored in an Oracle database Each brain region is linked to a corresponding concept ID in UMLS (Unified Medical Language System) Smart Atlas

17 Registration of Spatial Data Purkinje neuron UMLS ID: C0034143

18 Architecture Workshop Items The BIRN Portal Session 1D. Features & Requirements of the BIRN Portal Develop data sharing framework, incorporating tools from each site Session 2A. Databases and Data Integration - Sharing Design Information, Interfacing to the Mediator, Heterogeneous Database Support Issues Session 2B. Tools for Refinement and Production of Metadata/Visualization &Viewing - 3-D Slicer, FreeSurfer, LONI Tools, APIs etc. Session 1B. Pipelining and Processing - Complex Analysis and Query Processing Develop data access and usage rules Session 1A: BIRN as a Shared Infrastructure: An Overview of Policies and Procedures Session 2D. Data Sharing Guidelines, Anonymization, HIPPA Compliance & IRB Approvals

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