# Presentation: 831902

## Informatics Tools for Biospecimen Banks and Pathologists

- Mark A. Watson, M.D., Ph.D.
- Washington University / Siteman Cancer Center

## 20th Century Biospecimen Resources

**?**

## 21st Century Biospecimen Resources

## 21st Century Biospecimen Resources

## caTISSUE Project Rationale

** **Many specimen resource centers have little, inadequate, and/or **closed source** specimen banking / tracking informatics systems.
-  Many tissue resource centers have large, sophisticated 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 Project Approach

** **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 Project Security

-   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, Dr. X initiates a specimen collection PROTOCOL.  View privileges for that PROTOCOL and all related objects (PARTICIPANTS, COLLECTIONEVENTS, SPECIMENS) can be restricted to specific clinicians and scientists.

-   Regulatory concerns must be addressed.  For example, Dr. X enters a PARTICIPANT onto a PROTOCOL.  Dr. X 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

## Tissue Bank and Pathology Tools Applications

## Tissue Bank and Pathology Tools Applications

## Tissue Bank and Pathology Tools Applications

** ****Planned Modules**
**Tissue Microarray Module**
**Specimen Shipping / Tracking Module**
**Tissue Imaging Module**
**Billing / Financial Module**

## caTISSUE Core Model

**Participant**
- 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 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 Functionality

**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

## caTISSUE Core Demo

**http://catissuecore.wustl.edu/demo**
** **
**Login Name: admin@admin.com**
**Password: Login123**

## caTIES Process Flow

**Pathology Report Text**

**De-Identification Algorithm**

**Investigator Queries**

## caTIES Pathology Text Coding

## caTIES Pathology Report Query

## caTISSUE Clinical Annotations Engine

## caTISSUE Project Integration

**Existing “Specimen Bank”  Data**

**Surgical Pathology Reports**

**Tumor Registry**

**Laboratory IS**

**Presentation and Grid Services**

**Future Modules**

**Clinical Annot. Engine**

**UPMC**

**WU**

**caTIES**

## caTISSUE 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, CAE
_**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**

**PHASE I – YEAR TWO**
**Adopters**

**PHASE I – YEAR ONE**
**Prototype System**