# Presentation: 605601

## CaTISSUE Core Update 

- CaTISSUE Core Update
- October 2005

**Rakesh Nagarajan, M.D., Ph.D.**
**Mark A. Watson, M.D., Ph.D.**
**Washington Univ. / Siteman Cancer Center**

- http://caBIG.nci.nih.gov

**Srikanth Adiga**
**Kapil Kaveeshwar**
**Aarti Sharma**
**Gautam Shetty**
**Mandar Deshmukh**
**Aniruddha Phadnis**
**Poornima Govindrao**

## caTISSUE Core:  Rationale

-  Many specimen resource centers have little, inadequate, and/or **closed source** specimen banking / tracking informatics systems.
-  Many tissue resource centers have large, sophisticated legacy systems that still must be mapped to a ‘caBIG-compliant’ object model and data elements to make them ‘grid-enabled.’
-  Most existing informatics systems are **not modular** and can not easily accommodate the expanding functionality of specimen resource centers.

## caTISSUE Core:  Guiding Principles

-  Develop Use Cases from existing systems to build the caTISSUE object model - ***Don’t reinvent the wheel****.*
-  Create an **open source** object model, data elements, and vocabularies for biospecimen informatics management that are “caBIG Gold Compliant.”
-  Utilize best practices for data sharing, confidentiality, and patient consent tracking.
-  Develop a **modular architecture** that allows the addition of other functionality in the future.

## caTISSUE Core:  Project Scope

-  Core biospecimen object model
-  Data elements for specimen tracking, inventory, distribution, and QA.
-  Use cases for specimen accessioning, data update, and querying based on core specimen data elements.
-  ***Not*** pathology annotation (will use caTIES / CAE).
-  ***Not*** clinical annotation (will use CAE).
-  ***Not ***biological annotation (yet).
-  ***Not *** financial / ***Not*** shipping / ***Not ***automated request.

## caTISSUE Core Base Object Model

- Unique Participant Identifier (UPI)
*Patient Demographic Data*

- Link to Clinical Trials Data
- Link to Hospital / Medical Systems
**CT WS**

**Protocol Collection Event**
- Unique Event Identifier (UEI)
*Event Data*

- Link to Pathology Report / Data
**CaTIES PROJECT**

**Specimen**
- Unique Specimen Identifier (USI)
*Specimen Data*
**Fluid Specimen**
**Tissue Specimen**
**Cell Specimen**
**Molecular Specimen**

- Link to Specimen-Based Research Data
**ICR WS**

## caTISSUE Core Logical Object Model

## caTISSUE Core:  Other Objects

-  **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 another.
-  **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.

## caTISSUE Core:  Role Based Security

**Clinician:**  A physician, nurse, CRA, or other allied health worker who is interacting with a PARTICIPANT, has access to identified clinical data, and is performing read/write/edit operations based on select identified or non-identifiable data.
**Scientist:**  An authorized researcher who is requesting and utilizing biospecimens and biospecimen data, but who has no access to and no need of identifiable patient data.
**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.
**Public:**  General audience who can perform limited queries and view aggregated data only.
**Custom:  **Administrative configurable.

## caTISSUE Core:  Security Requirements

-   The system must constrain at the object (e.g. PATIENT), record (e.g. PatientID=1234), and attribute (e.g. LastName) level which users (by administrator-defined user roles) may perform what operations (add, edit, view)

-   Proprietary concerns must be addressed.  For example, an actor (*clinician*)* *registers a PROTOCOL.  View privileges for that PROTOCOL and all children objects (PARTICIPANTPROTOCOL, COLLECTIONEVENT, SPECIMEN) can be restricted to specific actors (*clinicians, scientists*).  The exception is the *administrator* actor and other actors defined as *technicians/supervisors*.

-   Regulatory concerns must be addressed.  For example, an actor (*clinician*) enters a PARTICIPANT onto a PROTOCOL.  The clinician has access to all identified information for that PARTICIPANT, but does not have access to identified information for other PARTICIPANTs _***or***_ to identified information for that same PARTICIPANT with respect to a different PROTOCOL

## caTISSUE Core:  Functional Outline

**Register as a new user**

**Log In**

**Add / Edit Administrative Data**

**Add / Edit Biospecimen Data**

**Search**

**Summary Data**

- Add / Approve Users
- Add / Edit Sites
- Add / Edit Institutions
- Add / Edit Departments
- Add / Edit Storage Type
- Add / Edit Storage Container
- Add / Edit Collection Protocol
- Add / Edit Distribution Protocol

- Add / Edit Patient
- Add Specimen Collection Group
- Add Specimen
- Create Specimen

- Simple Search
- Advanced Search
- Query Result Export
- Shopping Cart

## Design Deliverables

- Draft Design Document - Done
- Finalize the UML Model - Done
- Evaluate EVS for required concepts (EVS Report) - Done
- Creation of CDEs (Loading to caDSR Server) – In progress
- CDE Curation (Value Domain)

## Completed Deliverables

- Creation of Business Classes & Objects
- OR Mapping of Object Model
- Final DB Schema Creation
- Alpha Release
- Login Module
- Administrative Module
- Biospecimen Module
- Distribution Module
- Audit Module

## Deliverables In Progress

- Query Module
- Simple : Nov 2nd week
- Advanced : Nov 3rd week
- CSM Module : Nov 3rd week
- HTTP-based API: Nov 3rd week
- Beta release: Nov 4th week
- Performance tuning: Dec 1st week
- Final Release : Dec 2nd week

## caTISSUE Core:  Home

## caTISSUE Core:  Log On

## caTISSUE Core:  Administrative Data

## caTISSUE Core:  New Storage Container

## caTISSUE Core:  New Collection Protocol

## caTISSUE Core:  New Distribution Protocol

## caTISSUE Core:  Biospecimen Data

## caTISSUE Core:  Add Participant

## caTISSUE Core:  Register Participant

## caTISSUE Core:  Register Specimen Group

## caTISSUE Core:  Accession Specimen

## caTISSUE Core:  Specimen Event Parameters

## caTISSUE Core:  Specimen Event Parameters

## caTISSUE Core:  Query Results Browser

## caTISSUE Core:  Query Results Browser

## caTISSUE Core:  Query Results Browser

## caTISSUE Core:  Query Results Browser

## caTISSUE Core:  Query Results Browser

## caTISSUE Core:  Project Timeline

**PHASE I – YEAR ONE**
- Deploy majority of basic specimen tracking functions to seven adopter institutions
_**Phase Ia & Ib - 2005 Oct**_
- Working prototype with all basic functionality
_**Phase Ic – 2006 Feb**_
- Stable version with caBIG security model and feedback from adopters on prototype.

**PHASE II – YEAR TWO**
- Integration with other TBPT tools and full Grid enablement / Gold level compliance
_**Phase IIa: 2006 Aug**_
- caTIES, CAM
_**Phase IIb: 2007 Feb**_
- caTISSUE EAM

**PHASE III – YEAR THREE**
_**Phase III – 2007 Aug**_
- Future modules including
- automated distribution request and billing / financial.

**2005 - 06**

**2006 - 07**

**2007 - 08**