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caTIES adoption at UAMS. Umit Topaloglu, Ph.D. Agenda. Introduction UAMS Platform , Version, and Database Interface Engine Which component of caTIES are we using? HL7 Pipeline. De-ID Pipeline. Tie Pipeline. Current workflow. UAMS Research Portal

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caTIES adoption at UAMS

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caTIESadoption at UAMS

Umit Topaloglu, Ph.D.

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  • Introduction

    • UAMS

    • Platform, Version, and Database

    • Interface Engine

  • Which component of caTIES are we using?

    • HL7 Pipeline.

    • De-ID Pipeline.

    • Tie Pipeline.

  • Current workflow.

    • UAMS Research Portal

    • UAMS Tissue Bank

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UAMS: Vision

  • Implement an interoperable basic and clinical research solution across the enterprise utilizing NCI’s caBIG® and other open source tools

  • This vision is being championed by the Cancer Institute administration and the Informatics Team

    • UAMS is willing to share experiences gained and code developed

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The Winthrop P. Rockefeller Cancer Institute’s involvement in caBIG®

Established a caBIG project team

Evaluated numerous caBIG tools

Early adopter of caBIG C3D

First adopter of caXchange and CCTS (C3PR, PSC, Labviewer)

Developed the portal and SSO LDAP integration

OpenClinica Integration and caXchange Connector Development

Switched to caTissue Suite as biospecimen banking solution

caArray is in use

caTIES is being used by the Tissue Bank and other researchers

UAMS: caBIG Involvement

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UAMS’ Process Flow

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caTies instance at UAMS

  • caTIES Version

    • 3.6

  • Platform

    • Windows Server 2003.

    • Windows Services - Java Service Wrapper (JSW).

  • Database

    • MySQL (single server: public + private).

  • Interface Engines

    • Java Composite Application Platform Suite (JCAPS).

    • Mirth Connect.

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Which component of caTIES do we use?

  • HL7 Pipeline

    • Picking up HL7 reports from a centralized report folder.

  • De-id Pipeline

    • Harvard Scrubber (HS)

    • De-identification with pattern matching (Customized Regex Rules).

    • Challenge

      • The pipeline currently does not support de-identification based on HL7 header information (e.g. patient name, patient MRN, etc).

      • Solutions

        • Creating makers for patient information. E.g. [[ Jason ]]

        • De-identifying makers with customized regex rules.

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Which component of caTIES do we use?

  • Tie Pipeline

    • Concept coding the de-identified reports.

    • Pathology Reports, Radiology, Reports and Transcripts.

  • Index Pipeline

    • De-activated.

    • We are using our own GUI interface.

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Current workflow


- Transformation

- Creating Makers

  • - Concept Indexing

  • Demographic Retrieving

UAMS Research Portal

  • Storing reports

  • Assigning identifiers

- Concepts Decoding

- Identified Reports Retrieving

- De-identified Reports Retrieving


- HL7 pipe

- De-id pipe

- Tie pipe

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Research Portal

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Research Portal

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Research Portal

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Research Portal

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Use in caTissue

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Contact information:

Umit Topaloglu Ph.D.

501- 686 - 7238

Thanks for listening

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