# Presentation: 871866

## The University of Pittsburgh Cancer InstitutecaBIG Architecture

**Establishing a framework for:**
**	****Creating Products**
** **
**	****Understanding Process **
**	****Producing Value**

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

**Notes:**
I reordered this just to make it flow a little better, but this may require the moving the process slides up before product
Old was:
Creating products, 
Understanding process,
Producing value for patients
VM: I’m not sure what the copyright should read.  We should check with the larger group tomorrow. I’m not sure that I agree with the slogan order change.  I vote for the original order. Depending on the decision, the footers may need to be changes (which I will do). Although one could argue that you should understand process before creating process, I see our process efforts as an evolution of our understanding and sophistication.

## Architectural Goals

- Create a framework for building systems that are widely accessible, modular, interoperable, supportable, locally extensible and future-proof
- Create data storage and communication strategies that are hardware- and software-agnostic
- Support standardization and "convergent evolution" of software tools as they are shared and tested by domain workgroups
***Ca****ncer* **B**iomedical **I**nformatics **G**rid =
*	****C****onvergent ****A****rchitecture* **B**iomedical **I**nformatics **G**rid

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Overview of UPMC/UPCI Architecture

- Message
- Router
- HL7

- Cerner CIS

- Ancillaries

- MARS

- Oracle, Java API, AIX

- Various, Legacy

- Proprietary UPMC, AIX

- C, Python, AIX

*Clinical Users*
- Fat clients, browsers

- Middleware

- Presentation

- Oracle 9i

- CRIS

- Browser, Java applets

- iPlanet, Oracle (PL/SQL), Java,
- Oracle Forms, Cold Fusion, W2K

- Sun Solaris

*Clinical and Research Users*

- HL7 2.x

- HL7 2.x

- UPMC

- UPCI

*Research Users*
- File Transfer

- HTTP, RMI, SSL

- JDBC, Oracle drv

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Overview of UPMC/UPCI Architecture

- Message
- Router
- HL7

- Cerner CIS

- Ancillaries

- MARS

- Oracle, Java API, AIX

- Various, Legacy

- Proprietary UPMC, AIX

- C, Python, AIX

*Clinical Users*
- Fat clients, browsers

- Middleware

- Presentation

- Oracle 9i

- CRIS

- Browser, Java applets

- iPlanet, Oracle (PL/SQL), Java,
- Oracle Forms, Cold Fusion, W2K

- Sun Solaris

*Clinical and Research Users*

- HL7 2.x

- HL7 2.x

- UPMC

- UPCI

- Firewall

- Proxy Server

- VPN

- HTTP, RMI, SSL

- JDBC, Oracle drv

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## OPI Clinical Systems Application Architecture

**Opiunx01**
- UPCI Database
- Production

**1upmc-pci2** intranet.upci.edu

- Database Servers
- Solaris 2.8
- Oracle 9.2.0.1

**1upmc-pci1**
- Java DBServer
- J2EE environment

- Back-end

- 3rd-Tier

**1upmc-opi-cry01**
- Crystal Enterprise Server

- Crystal Reports

- Redo Log Replication

- Client Tier

- Application Servers
- WIN2K OS

- 2nd-Tier

- Web Servers
- WIN2K OS
- Iplanet 6.0
- Cold Fusion

**Opiunx04**
- UPCI Database
- Standby

- Web Browsers

- UPMC Internal Network PC’s (W2K)

- Oracle Forms

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Key caBIG Projects at UPCI

- Mature
- Clinical Trials Management Application
- Tissue Banking System and Organ-Specific Databases
- Currently in development
- SPIN distributed virtual database
- SPIN free text concept extraction

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Clinical Trial Management Application

- Currently deployed at UPCI (since 2000)
- Supports a range of users including
- Nurse Coordinators
- Data Managers
- Clinical Trial Specialists
- Clinicians
- Administrators
- Researchers
- Pharmaceutical representatives
- Houses over 250 active protocols representing in-house, Co-op, NCI and pharmaceutical-sponsored trials
- Contains clinical data for approximately 16,000 patients

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## CTMA Architecture

- Multi-tiered Java implementation
- Java/Swing client applet (pure Java)
- Uses RMI to communicate via SSLava to the middle tier
- Authentication via by iPlanet’s LDAP server and Oracle
- Data access server (DAS) written in Java (Win2K)
- Mediates between RMI client calls and middleware objects or database routines
- Runs on a Windows NT machine designated as intranet host
- Communicates with an Oracle database using JDBC and the Oracle Type 4 Thin SQL driver, with Oracle's RC4_56 encryption algorithms
- Administrative reports via Crystal Reports Enterprise Server
- Database
- Oracle 9i database on SUN Solaris

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Tissue Banking Systemand Organ-Specific Databases

- Inventory, specimen management; organ-specific views of aggregate data
- Consent tracking (universal consent, deceased patients)
- Sample inventory including sample features/quality, bar coding, storage and access tracking
- Manual sample annotation using local data elements

- Organ-specific views provided by form-based applications (Oracle Forms)
- Aggregation and summary based on local data elements
- On-the-fly HIPAA de-identification through local proprietary tools
- In production at UPMC and 15 collaborating institutions.

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Tissue Banking Architecture

- Multi-tiered implementation
- Client display implemented using Oracle Forms
- Middleware layer using Oracle Apache Services
- Data processing and aggregation partially in Java
- Data extraction and processing in PL/SQL
- Database
- Oracle 9i database on SUN Solaris
- Includes primary data and metadata that defines rules for grouping data into specimens, cases, patients, organs, diseases and aggregates of patients

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## SPINShared Pathology Informatics Network

- Distributed virtual database using a peer-to-peer network with query/response communications based on web services

- Query

- Response

- In development at Harvard

- JBoss/servlet middleware
- MySQL back end

- Local databases at
- participating institutions

- SOAP

- Pitt
- Regenstrief
- Harvard
- UCLA

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## SPINShared Pathology Informatics Network

- 2.	Free text UMLS-based concept extraction from pathology reports, in development at Pitt
- De-identification based on local tools
- Processing pipeline includes report section "chunker," tokenizer, and concept tagger including negated concepts, written in Java
- Incorporates Gate, an open source Java framework for language engineering
- Output as XML-structured report with identified subsections (including diagnoses) and embedded code elements
- Modular, will communicate through Java API or web services (automated data extraction from MARS)

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Key Issues/Lessons

- Get software into the hands of users/testers as rapidly as possible.
- Our first generation tools are functional but need to evolve to fully support the ultimate caBIG architecture.
- Iteratively modifying functional tools at implementation sites will be challenging.
- Changes that impact the clinical workflow will be disruptive.
- Developers tend to gravitate to familiar tools. In medical settings, these have not typically included open source.
- Focus when possible on language-agnostic open messaging standards for communication rather than language-specific APIs (consistent with caBIO technical guidelines).

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## UPCI's Role in Realizing the Architecture

- Because the UPCI is involved in several workgroups, it may offer a helpful environment for communication between domain and the cross-cutting workgroups
- Direct communication from the AWG to the project technical staff and direct access to feedback from the projects
- Coordination between the Architecture and the CDE/Vocabulary cross-cutting workgroups.
- Generate integrated feedback to the AWG as policies and recommendations develop.
- Initial implementation and testing of architectural recommendations in several production settings

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Mechanisms for Providing Guidance

- Bi-directional communication between AWG and the domain WGs
- Position statements and guidelines from AWG
- Critiques on guidelines from domain WG
- Documentation from ongoing projects, including early docs such as information models and UML diagrams
- Critique of project plans/designs
- Process and schedule for documenting development (planning and implementation) important
- Communication mechanisms
- Online asynchronous discussion, conference calls sparingly
- Online documents and critiques accessible to all WG
- Periodic meetings of AWG, possibly open source "sprint" style over several days
- Concurrent meetings or representation at domain WG meetings and CDE/Vocab WG
- Explicit connection with other standards organizations (HL7)?

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Development Plan

- Standards-Centered Framework

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics

## Development Plan

- Standards-Centered Framework
*Effectively Communicated*

- caBIG Architecture

- 2004 UPitt Center for Pathology & Oncology Informatics