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Srikanth_A_caTissueCoreNBN by lanyuehua


									National Cancer Institute


                                        Siteman Cancer Center
                                Washington University School Of Medicine
                                           St. Louis, Missouri
                            21st Century Specimen
National Cancer Institute         Resources
                                                   TBPT – Current Projects
National Cancer Institute

                              caTIES (UPMC) - Text extraction and de-identification of
                              surgical pathology reports.

                              caTISSUE Core (WU) – Core object model and
                              reference inventory system for research biospecimen

                            caTISSUE Clinical Annotation Engine (UPMC) - Mapping
                            of data elements from clinical systems (Tumor Registries,
                            LIMS) to objects in caTISSUE space.
                                            Tissue Banks and Pathology
National Cancer Institute

                            Grid enabling/sharing data
                            Experiment annotation Module
                            Tissue Microarray Module
                            Specimen Shipping / Tracking Module
                            Tissue Imaging Module
                            Billing / Financial Module
                                                         The BIG picture…
National Cancer Institute
                             Tumor Laboratory
                            Registry   IS
                                                           Future Modules

                                                         UPMC         WU

                                                           Annot.     caTISSUE
                                                           Engine       Core


                                                                                 Bank” Data

                                                     Presentation and
                                                      Grid Services
                                                                Functional Outline
National Cancer Institute
                                     Register as a                Log In                 Summary Data
                                      new user

                                 Add / Edit                     Add / Edit                      Search
                               Administrative                  Biospecimen
                                   Data                            Data                      Simple Search
                                                                                             Advanced Search
                            Add / Approve Users              Add / Edit Patient
                                                                                             Query Result
                            Add / Edit Sites                 Add Specimen Collection Group   Export
                            Add / Edit Institutions          Add Specimen                    Shopping Cart
                            Add / Edit Departments           Create Specimen
                            Add / Edit Storage Type
                            Add / Edit Storage Container
                            Add / Edit Collection Protocol
                            Add / Edit Distribution
National Cancer Institute
                       Complete Object Model
                                                                                               cd Logical Model

National Cancer Institute
                                                  cd Logical Model


                            Base object model…

                                                 cd Logical Model                                           0..*

                                                       CollectionProtocol                      ParticipantRegistration

                                                                                    1   0..*





                                                         StorageContainer                            Specimen             1


                                                          SpecimenEv ents
                                                                   Other Objects
National Cancer Institute
                            • SPECIMEN EVENT: An action which is performed on a specimen at a given
                            date/time by a USER, associated with specific attributes.

                            • SITE: A physical location where biospecimens are collected, stored, or shipped.

                            • USER: An individual who participates in biospecimen collection, processing, or
                            utilization events.

                            • COLLECTION PROTOCOL: A set of guidelines that stipulates what, when,
                            and how biospecimens are to be collected and processed.

                            • DISTRIBUTION PROTOCOL: A set of guidelines that stipulates what
                            biospecimens are to be analyzed and for what purpose.

                            • DISTRIBUTION: An event that results in transfer of specimens from one SITE to

                            • STORAGE: A recursive hierarchy where any specimen may have an assigned
                            location within nested storage units at a SITE.

                            • AUDITING: All system transactions recorded with date and actor.
                                                                  Role Based Security
National Cancer Institute

                            Administrator: The ‘super-user’ of the system or “Honest Broker” who has
                            access to all operations on all data.

                            Supervisor: Similar to Administrator but does not have access to administrative
                            functions (i.e. registrations). This is equivalent to a biospecimen bank technician
                            who is granted access to identifiable patient information.

                            Technician: A biospecimen bank technician who can perform operations on
                            biospecimens, but only by using non-identifiable data.

                            Scientist: An authorized researcher who is requesting and utilizing biospecimens
                            and biospecimen data.

                            Public: General audience who can perform limited queries and view aggregated
                            data only.
                                                           Security Requirements
National Cancer Institute
                            Authorization      Description
                            Class Level        Predefined system wide level based on roles.

                            Object Level       This deals with an instance of an object within a class.
                            Proprietary        E.g. PI of a protocol can assign/revoke privileges on
                                               the data (s)he owns.

                            Attribute Level    This level deals with the individual details for an
                            Regulatory/HIPPA   Object. All individual data elements stored within the
                                               system must be secured in order to prevent access to
                                               unauthorized individuals. Due to the initiation of HIPAA
                                               it has become necessary to secure all Participant
                                               identifiers from non-authorized individuals.
National Cancer Institute
                       Administrative Data
National Cancer Institute
                       New Storage Container
National Cancer Institute
                       New Collection Protocol
                            New Distribution Protocol
National Cancer Institute
National Cancer Institute
                       Biospecimen Data
National Cancer Institute
                       Add Participant
National Cancer Institute
                       Register Participant
National Cancer Institute
                       Register Specimen Group
National Cancer Institute
                       Accession Specimen
                            Specimen Event Parameters
National Cancer Institute
                            Specimen Event Parameters
National Cancer Institute
National Cancer Institute
                        Advanced Query
                                                   Advanced Query Example
National Cancer Institute
                            Participant: birth date > 01-01-1940 and race equals White

                               Registered to any protocol

                                   Specimen collection group with “Clinical status”
                               equals “Operative”

                                           Specimen with “Type” Equals “Serum” and
                               “Class” Equals “Fluid”
National Cancer Institute
                       Query Results Browser
National Cancer Institute
                       Query Results Browser
National Cancer Institute
                       Query Results Browser
National Cancer Institute
                       Query Results Browser
National Cancer Institute
                       Query Results Browser

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