Docstoc

caTISSUE devel meeting JGIPresentation caBIG

Document Sample
caTISSUE devel meeting JGIPresentation caBIG Powered By Docstoc
					The Isolated Tissue Bank


                        •    Tissue banks exist outside the core
                             informatics (and operational, financial &
                             legal) infrastructure of the medical
                             center.




    UPMC Pathology and Oncology Informatics
The Isolated Tissue Bank

                        •    Manual Re-entry of clinical information
                             into non-standard data elements in
                             stand-alone databases and spread-
                             sheets
                        •    Variable IT architecture and support
                        •    Existence depends of research grants
                             and powerful Principle Investigators
                        •    Local IRB, Consent and Permission
                             Procedures, HIPAA and security issues,
                             TUC, etc.
                        •    Limited access from the general
                             research community
                        •    Extreme inefficiencies and costs




    UPMC Pathology and Oncology Informatics
… Adenocarcinoma of the prostate from
patients less than 60 years old at
diagnosis…High Grade, organ confined,
Five year follow up with no chemical or
anatomic recurrences, No hormonal
Rx prior to resection…




 UPMC Pathology and Oncology Informatics
                                           The Other Problem

                                                                        •    Medical Centers support multiple
                             Patient                                         tissue banks

                                                                        •    Samples from a single patient (or a
Accession                                               Accession            single operation) are stored in
                                                                             multiple tissue banks

                                                                        •    Each bank operates and annotates
   Collection

                Collection

                              Collection

                                           Collection

                                                          Collection



                                                                             differently

                                                                        •    And there is chaos…




                                                    UPMC Pathology and Oncology Informatics
Visions and Goals

                    •    Bring tissue management into the
                         mainstream operations of medical center

                    •    Not a single central tissue bank, but
                         central operations for core annotation,
                         consent, security, query, display, etc.

                    •    Place existing, funded, mandated hospital
                         systems (AP LIS, Registry, etc) at the
                         pleasure of the tissue bankers

                    •    Take advantage of ongoing initiatives
                         such as CAP, LOINC, Cancer Registries,
                         etc



UPMC Pathology and Oncology Informatics
caTISSUE, SPIN and TIES

                        •    The caTISSUE accepted SPIN/TIES as
                             our first major initiative because it
                             represents these concepts on a grand
                             scale

                        •    TIES takes two major (and despised)
                             components of every medical center’s
                             infrastructure – the Paraffin Archive and
                             the Free Text Pathology Report - and
                             allows them to serve tissue banking




    UPMC Pathology and Oncology Informatics
The Archive and the Bank Interact

                                                   •    The Banked and Archived Tissue are
                                                        related through the tissue donor
  Pre Diagnostic Biopsy

        Diagnostic Biopsy                          •    The Archive contains
                 Resection – Clinical Discards           – Diagnostic & Pre Diagnostic Biopsies
                            Progression Bx
                                                         – Diagnostic Tissue Samples
                                  Protocol Bx
                                                   •    The Bank tends to have frozen tissue -
                                                        protocol samples and clinical discards
             Time

                                                   •    One needs both the Archive and the
                                                        Bank to get a complete view




                               UPMC Pathology and Oncology Informatics
                              caTISSUE
                        A Tissue Bank Centric Model

 caTISSUE Lite                                              Annotation Services


                                                                            Lab Data


Tissue Processing and
       Storage

                                     Standards Based                      Pathology Data
                                  Tissue Bank Database

 Clients and Projects


                                                                         Outcomes and Rx



                                   Tissue Bank Viewer
                                      On the caBIG




 Core Bank Activities                                    Enterprise Activities
 Washington University                                   University of Pittsburgh

                        UPMC Pathology and Oncology Informatics
                                            Annotation Services Model
                                                                                                         Enterprise Activities
     Tissue Processing and




                                       Clients and Projects




                                                                                                                                            Outcomes and Rx
                                                                                                                           Pathology Data
                                                                                                           Lab Data
            Storage




                                                              Standard Data
                                                                                                                         Data
                         Tissue Bank                                                 Data Mapping
                                                                                                                      Aggregation
                                                              For Annotation

                                                                     Request for Information


Tissue Bank Activities
                                                               UPMC Pathology and Oncology Informatics
Enterprise View of Tissue




                                                                                                                       Outcomes and Rx
                                                                                         Pathology Data
                                                                         Lab Data
              Standard Tissue Processing Data



                      Tissue Processing,
Tissue Bank
                   Inventory and Availability

                                                                                                          Enterprise Annotation Services

                      Tissue Processing,
Tissue Bank
                   Inventory and Availability



                      Tissue Processing,                                            Aggregator
Tissue Bank
                   Inventory and Availability



                      Tissue Processing,
Tissue Bank
                   Inventory and Availability



                                                                       Enterprise Tissue Dataset
                            Extend Local Dataset


                                                              Enterprise wide Patient/Specimen centric view of tissue


                             UPMC Pathology and Oncology Informatics
                                      UPMC System

                                Identified “Clinical” Data in Silos


           Clinical        Anatomic                Cancer               Tissue              Clinical
             LIS             LIS                   Registry             Banks                Trials
                                              Outcomes                         Permission        Status in trials
         Tumor            Synoptic
                                              Progression & Rx                 Procession
         Markers          Reports

                                              Datawarehouse
Merging Data Mapping to disease                                         Mapping to Canonical Elements

Error Correction         De-identification

                                                                                  Mapping to Client Elements
                                Data           Data         Data       Data
                                Mart           Mart         Mart       Mart


                   Integrated, Standard De-identified Data for Researchers




                                     UPMC Pathology and Oncology Informatics
                           Enterprise Tissue Management

                                                                                                                                    •   Standard Clinical Annotation provided
                                                                                                                                        centrally

Enterprise View of Tissue




                                                                                                                Outcomes and Rx
                                                                                                                                    •



                                                                                  Pathology Data
                                                                                                                                        A small number of processing data
                                                          Lab Data
              Standard Processing Data
                                                                                                                                        elements are provided from each bank
                  Tissue Processing,
Tissue Bank

                                                                                                                                    •
               Inventory and Availability

                                                                                                   Enterprise Annotation Services       One can provide a standard, enterprise
Tissue Bank
                  Tissue Processing,
               Inventory and Availability
                                                                                                                                        view of all tissue samples
                  Tissue Processing,                                        Aggregator
Tissue Bank

                                                                                                                                    •
               Inventory and Availability
                                                                                                                                        The enterprise view can be mapped to
Tissue Bank
                  Tissue Processing,
               Inventory and Availability
                                                                                                                                        standard national data elements and
                                                                     Enterprise Tissue Dataset
                                                                                                                                        published to the caBIG
                        Extend Local Dataset




                                                                                                                                    •
                                               Enterprise wide Patient/Specimen centric view of tissue

                                                                                                                                        Any local bank can extend the central
                                                                                                                                        annotation



                                                    UPMC Pathology and Oncology Informatics
                           Enterprise Tissue Management

                                                                                                                                    •   Standard Clinical Annotation provided
                                                                                                                                        centrally

Enterprise View of Tissue




                                                                                                                Outcomes and Rx
                                                                                                                                    •



                                                                                  Pathology Data
                                                                                                                                        A small number of processing data
                                                          Lab Data
              Standard Processing Data
                                                                                                                                        elements are provided from each bank
                  Tissue Processing,
Tissue Bank

                                                                                                                                    •
               Inventory and Availability

                                                                                                   Enterprise Annotation Services       One can provide a standard, enterprise
Tissue Bank
                  Tissue Processing,
               Inventory and Availability
                                                                                                                                        view of all tissue samples
                  Tissue Processing,                                        Aggregator
Tissue Bank

                                                                                                                                    •
               Inventory and Availability
                                                                                                                                        The enterprise view can be mapped to
Tissue Bank
                  Tissue Processing,
               Inventory and Availability
                                                                                                                                        standard national data elements and
                                                                     Enterprise Tissue Dataset
                                                                                                                                        published to the caBIG
                        Extend Local Dataset




                                                                                                                                    •
                                               Enterprise wide Patient/Specimen centric view of tissue

                                                                                                                                        Any local bank can extend the central
                                                                                                                                        annotation



                                                    UPMC Pathology and Oncology Informatics
                                                          Institution is a RIM entity that
                                                          Represents the medical or research
                                                          Institute responsible of the TCE
      A person is a RIM entity
                                                                                                                                                                 A Collection Authority is a RIM
                                                                           Institution                                                                           Entity. It has the power to allow
              Person                                                                                         The Tissue Collector is a Surgeon-like              A project to collect and store tissue
                                                                                 1                           Role. There may be more than one                    Samples for research. There are
                                                                                                             “collector” for each TCE.                           usually two authorities, the IRB
                                                                                 0..*                                                                            (representing the patient) and
                                                                                                                                                                 The Institution (representing the
                                                 1      0..*                                          0..*          1..*                                         institution
                                 Tissue Donor                   Tissue Collection Event                                    Tissue Collector
                                                                                                                                                                                Collection Authority
A Tissue Donor is a Patient-like
Role. Note however, that a Tissue                                             1 1
                                                                                                                                                                                           1..*
Donor may or may not be ill or                                                           Collected and Labeled Specimen
Receiving care. Further, a donor may
Or may not have given consent                                                                                                                                        Authority
                                    0..*                                                                            1..*
For banking.                                                                                                                                                         Document
                                                               May be associated with
                                                                                                           Clinical
                              Pathology Report/Part
                                                                                                          Specimen                    0..*                               0..*
                                                                                1..*                                                            Sponsoring Project
                                                                                                      1             1
                                                                                                                                                             1
                                                  A specimen can be clinical or research                      1
                                                  Across its lifetime.
                                                                                                          Research
                                                A sample can be split or                                  Specimen                   0..*
                                                Converted to another type                                                                             All research specimens have a sponsoring
                                                                               1..*                                                                   Project that has the authority to “bank” tissue
                                                                                                  1                 0..*
                                                                                                                                                      For research, and is responsible for the
                                                                                                             0..*
                                                                                                                                                      Appropriate use of that specimen.
                                           A research project uses the tissue (or data)
                                           It requires IRB authority and permission from              Research Project
                                           The Sponsoring Project(s)
                                                                                                             0..*
                                                                                1..*
                                                      Research Authority
                                                                                          Authority
                                                                                          Document




                                                                             Draft
                                                         Center for Pathology & Oncology Informatics

                                                      UPMC Pathology and Oncology Informatics
    Data Dictionaries


            Source              AP LIS           Registry            CP LIS                 TIES                      CTMA
            Applications


             API or Reports                                                                                                           Application Adapters

          Tissue Bank
          Applications
                                                                                                                                          Consent
                                                                     Aggregator                                                            Data
          Tissue Bank                            [identify patients/samples data across sources]

                                                                                      Mapping


          Tissue Bank                                 Patient       Accession       Sample

                                                       Merged Annotation in “Containers”


          Tissue Bank
                                                                                                                                   Download
                                    API/XLM                                                                                                    Canonical




                                                                                                       Dictionary
                                                     Containers in Canonical Object Model




                                                                                                       Metadata
                                                                                                                                                 DE
                                                                                  Mapping
Consent                                                                                                                            Download
 Data
                                                                                                                                                 caDRS
                                                            Data Mapped to “caBIG CDE”

                                                    Published Data              De-identification
                 API/XLM                                                                                                       Institutional Firewall
                              API




                                 Tissue                                                  Enterprise
                                                Q/A Data             SPORE                                             CaBIG                     caBIG
                                  Bank                                                  Presentation
                                               Presentation        Presentation                                     Presentation                 GRID
                              Presentation                                              Tissue Res.


                                              UPMC Pathology and Oncology Informatics
         Data Dictionaries


                  Source             AP LIS           Registry           CP LIS             TIES               CTMA
                  Applications




Data Containers                                                                                                                                     Identification
                                                                                                                                                      Metadata
           Donor ID               Rx History       Tumor Marker Hx        Pathology Hx           Progression




                                                                                                                      Mapping and Transformations
            Disease
                                                      Business Rules                                                                                Local Systems
                                                                                                                                                      Metadata
                                                         Mapping



                                               Clean Canonical Patient Model                                                                          Canonical
                                                                                                                                                      Metadata
                                                                           Mapping and Transformation



                                                                                                                                                       CaBIG
                             Tissue Bank                Enterprise                  CaBIG                                                             Metadata
                             Presentations             Presentation               Presentation




                                                UPMC Pathology and Oncology Informatics

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:3
posted:5/30/2012
language:
pages:16