# Presentation: 824111

## Adopting caTissue Core 1.1

***Legacy Data Migration***

- Jack London, Thomas Jefferson University
**February  2007**

## Tissue Bank Environment at KCC

-  As with other cancer centers, KCC has a number of departmental and investigator biospecimen repositories.
-   The long-term goal is to manage the biospecimen characterization data of _all_ these banks with caTissue Suite, to facilitate institutional and caBIGTM research.

## Focus of caTissue Adoption at KCC

- Initially, adoption efforts will focus on only these two repositories:
-   **Pathology Department Research Archive**
-  Primarily frozen tissue and paraffin blocks, all anatomical sites.
-  Not associated with a particular protocol (general tissue consent for             research use of “extra” tissue).
-   Microsoft AccessTM legacy database.
-   **Breast Tissue Bank**
-  Frozen Breast Tissue
-   Microsoft SqlServerTM  legacy database.

## Need for Legacy Data Migration 

-  caTissue Suite can be adopted
-  as a replacement for legacy tumor banking systems
-  need to upload existing data once prior to switching to caTissue Suite for day-to-day tumor bank operations
-   as an institutional front-end for biospecimen data
-  need to upload data at regular intervals to reflect the current legacy system contents
-   A single institutional instance of caTissue Suite can accommodate data from different biospecimen repositories which may or may not be using caTissue Suite for day-to-day tumor bank operations.

## Migration Process

- Legacy Databases

- caTissue
- Core
- (Oracle or
- MySQL)

- Staging Database

- Map data elements and value domain, then load data.

- Migration
- Tool

- caTissue
- Core +
- CSM
- (Oracle or
- MySQL)

- Accessed by
- caTissue Web
- application

## Migration Process

- Legacy Databases

- caTissue
- Core
- (Oracle or
- MySQL)

- Staging Database

- Map data elements and value domain, then load data.

-   The process of populating the Staging Database is a non-trivial task that, because it involves the legacy system, will differ among cancer centers.
-   However, universally applicable  guidelines on loading the target system can be developed, since it will always involve the caTissue object model.

**Migration Process**

## Migration Process

**Migration Process**

- caTissue
- Core
- (Oracle or
- MySQL)

- Staging Database

- Migration
- Tool

- caTissue
- Core +
- CSM
- (Oracle or
- MySQL)

- Accessed by
- caTissue Web
- application

-   While the Staging Database has the same schema as the caTissue Core Database, it alone is not sufficient for the application.
-   The CSM tables are also required.

## CSM ???

- The CSM can be integrated with applications, such as caTissue Core, and provides:
-   Authentication - validating and verifying users’ credentials.
-   Authorization - granting access to data, methods, and objects.
-   User Provisioning - creating/modifying users and their access rights.
-   Audit Logging

**NCICB’s Common Security Module**

## Important Note!

-  To reiterate, simply creating an Oracle or MySQL database using the caTissue schema, and populating it properly will not provide a data store that will work with caTissue.
-   CSM table entries must be properly created for uploaded data.
-   API’s exist to upload data into caTissue with proper CSM recognition.
-   The “Migration Tool,” which assumes that a proper Staging Database has been created, will utilize these API’s and complete the migration process.  This tool is under development.

## Case History:  Legacy Data Migration at KCC

- As a caTissue Adopter, we experimented with a migration process based solely on SQL command structures.
- We mapped the objects and values, and developed a set of SQL commands that loaded data from the Microsoft AccessTM database used for the Pathology Research bank to a caTissue Staging Database.
- We also constructed the SQL commands necessary for the CSM table entries for these uploaded records.
- Using this methodolgy we successfully uploaded 1115 participants, 1176 cases, and 5212 specimens, accessible with the caTissue application.
- We gained an excellent understanding of the caTissue database and the implementation of CSM with caTissue.

## KCC caTissue Adopter project members

-  Devjani Chatterjee
-   Dorothy Glaze
-   Jack London
-   Cheryl Morris
-   Juan Palazzo
-   John  Reber
-   Cinzia Sevignani
-   Karl Smalley
-   Joseph White