# Presentation: 314958

## EDRN & ERNE Tools

- Derek Walker, Fred Hutchinson Cancer Research Center
- caBIG TBPT Workspace F2F Meeting
- November 30, 2004

## ERNE Infrastructure

- EDRN Resource Network Exchange (ERNE) is the informatics infrastructure created to support the Early Detection Research Network (EDRN)
- Consists of several tools:
- Virtual Specimen Repository (*real-time query access to distributed repositories*)
- Common Data Element mapping tools (*local definitions to standard ones*)
- Form generation tools, based on CDEs
- Secure Application Portal
- EDRN Common Data Element (CDE) Repository

**Notes:**
A virtual specimen repository was developed to enable investigators to easily identify the availability of biospecimens and associated epidemiological data needed for their research.

An informatics infrastructure was created for EDRN to support transparent access to existing specimen repositories providing EDRN a virtual knowledge environment despite the distributed nature of the collaboration.

This allows for each institutions specimen databases to be maintained locally.

I will discuss how the project focused on several key aspects including: the EDRN Common Data Elements or CDEs as a common semantic architecture to map to insitutions local data definitions, a distributed informatics technology infrastructure, security and confidentiality and the dynamic portal.

## General Principles

- Technical:
- Location Independence
- Information Hiding
- Model driven architecture
- Scalable, Extensible
- Client APIs for locating and accessing distributed data products
- Common domain information model
- Ontology-driven model
- Common attributes for information model captured as data elements or “CDEs”
- Common meta-models for
- Defining CDEs (based on ISO/IEC 11179 standard for data elements)
- Data interchange (based on a common XML schema)
- Capture and definition of science “products”

## Distributed Query Tools:Virtual Specimen Repository

## Distributed Specimen Query

- Grid of heterogeneous data sources
- Real-time access to distributed specimen repositories

## Distributed Query: Use Cases

**Must support variably-complex queries**
- Find all breast tissue samples for all women that were collected at specified sites
- Find all prostate tissue samples for men ages 70 and older collected before 1980 from all available databases, sorted by grade, age, and site
- Find all available samples for women with breast cancer from whom both diseased and healthy tissue was taken prior to treatment and who have survived at least 5 years post-diagnosis.
**Must return results in a unified set**
- Locally defined data elements and valid values must be mapped to agreed-upon CDEs and values, and the results from all sites should be combined into a single result set for presentation to the user.

## Distributed Query: Technical 

- Virtual Specimen distributed query system is based on OODT (Object Oriented Data Technology), developed for NASA by JPL.
- OODT Framework includes:
- Name Server
- Query Server
- Archive Server
- Profile Server
- Product Server
- Server Manager
- Open source
- Based on open standards: Java, XML, Web Services

## Distributed Query: Component Details

**Profiles** describe and locate items of interest
- Items of interest may be:
- Data Sets, Data Set Browsers, Data Products, Volumes, Websites, Web Applications, etc
- Written as XML documents
- Provide sufficient information to describe and locate resources
- Determine if the resource can resolve a user query
- Profiles may be:
- Static, stored as XML documents
- Dynamic, generated from databases
**Profile Servers** provide access to profiles
- Allow search and retrieval of profiles
- Distributed for local management and scalability

## Product Servers serve Data “Products”
Data Products are served from data repositories
Input: unique product identifiers
Output: products in the requested formats

Middleware
Uses XML documents for communication
Common language and protocols
XML profiles for resource descriptions
XMLQUERY for queries
Implements message passing protocol for distributed processing
Web service encapsulation of existing resources
Product servers for data repositories
Profile servers for catalogs

- Data Products are served from data repositories
- Input: unique product identifiers
- Output: products in the requested formats
**Middleware**
- Uses XML documents for communication
- Common language and protocols
- XML profiles for resource descriptions
- XMLQUERY for queries
- Implements message passing protocol for distributed processing
- Web service encapsulation of existing resources
- Product servers for data repositories
- Profile servers for catalogs

**Dist. Query Component Details (#2)**

## Distributed Query: Component Overview

- Query Server

- Profile Server

- Site 3
- Product Server

- XMLQuery

- XMLQuery

- XMLQuery

- XMLQuery

- XMLQuery

**Profile Server**

- QueryClient

- Web server
- Plugins

- Web Server

- XMLQuery

**Site 1 DB**

**Site 2 DB**

**Site 3 DB**

- Web I/F

- XMLQuery

- XMLQuery

- XMLQuery

- XMLQuery

- Name Server

***Distributed Repositories***

- Site 2
- Product Server

- Site 1
- Product Server

## Example 1 Query: Quick Search

**Example 1 Query: Quick Search**

**Notes:**
The quick search feature sends a limited query to sites and requests a minimum number of data elements to be returned in the summary results. 

## Example 2: Advanced Search Query

**Notes:**
The advanced search allows users to narrow the search further by specifying more detailed criteria such as searching for a specific gender and type of cancer.

## Example 2: Advanced Search Results

**Notes:**
The advanced search returns back both summary and detail results, showing the numbers of queried specimens available at each institution. Users can obatin more details by clicking on the details link. 
As stated earlier for confidentiality reasons, data that identify the specimen donor are not available in any part of the results.

## CDE Repository & Mapping Tools

## CDE Mapping Tool

- EDRN maintains an extensive repository of CDEs for study and specimen data elements, with associated metadata
- The CDE repository provides tools to facilitate the cross-referencing of these local data elements to the core CDEs
- Local sites work with coordinating center to define their data elements, values and metadata, mapping those to agreed-upon CDEs and allowable values
- Export tool generates XML mapping file, which is used by distributed query middleware (OODT) to return result sets in a common format

## CDE Mapping Tools: Technical 

- SQL Server / IIS / ASP 3.0 / XML
- Future Goals:
- Platform agnostic: migrate to Java/J2EE and other RDBMS
- More user friendly, allowing local sites to generate directly
- More flexible and configurable, allowing mapping between any data sources and vocabularies

## Database-Driven Forms Generation:Validation Studies Information Management System (VSIMS)

## VSIMS: Overview

- Created for EDRN to facilitate study management and coordination, and encourage use of standardized CDEs
- Utilizes a centralized repository of CDEs for all studies, linked to separate databases specific to each individual study.
- Provides:
- Flexibility: HTML data entry screens and physical forms are defined by metadata and automatically generated
- Consistency: Common framework results in efficient re-use of CDEs and controlled expansion of CDE repository to meet evolving needs
- Ease of implementation: Data entry screens and physical forms are created by non-technical staff via a user-friendly interface
- Ease of Maintenance: Changes to data elements in the CDE repository automatically result in updates to data entry screens and physical forms
- Traceability: Full audit trail and versioning

## VSIMS: Use Case

- Non-technical study staff must be able to easily generate data entry screens and physical forms via a user-friendly interface using CDEs from the repository.
- Steps to generate study screens/forms:
- Identify existing CDEs in repository
- Create new data elements with metadata in repository
- Select data elements from CDE repository and “link” to data entry screen/physical forms
- Define study-specific details (e.g. question order, skip patterns, # questions per screen, range and logic checks).

## VSIMS: CDE Re-use

## VSIMS: DB-driven screen features

- Data Entry Screens and Physical Form features are defined by user and stored as metadata. These may include:
- The order of questions
- The order of forms (e.g., can require Screening Form be completed first)
- Number of questions on a screen
- Skip patterns of questions
- Format of possible answers (check boxes, radio buttons, or pull-down lists)
- Valid values for a given question (can be added, deleted, or modified)
- Default values can be assigned (e.g. “BLN” can be default value for data element “Visit code” on all forms completed at baseline visit)
- Range and logic checks

## VSIMS: Example CDEs for Specimen DB

- Specimen ID
- Participant ID
- Specimen collection date
- Participant visit code (e.g. baseline, follow-up)
- Specimen source (e.g., blood, urine, bone marrow)
- Specimen stored (e.g., serum, DNA)
- Quantity
- Quantity unit (e.g., mls., mgs.)
- Lab specimen stored
- Building
- Room
- Refrigerator
- Box
- Column
- Row
- Specimen status (e.g., good, used)

## VSIMS: Users & Permissions

## VSIMS: Technical 

- SQL Server / IIS / ASP 3.0 / XML
- Future Goals:
- Platform agnostic: migrate to Java/J2EE and other RDBMS
- Better integration with caBIO and caBIG repositories

## Challenges

- When integrating distributed systems:
- Remote development & support
- Institutional Challenges
- Finicky configurations
- Network bottlenecks
- Political and sociological issues
- IRB concerns
- Local support
- Performance
- Only as fast as the slowest node
- Training

## Discussion

**What could be leveraged for caBIG?**
**Distributed Query with OODT (Object Oriented Data Technology)**
- Framework for distributed query system
- Open Source
- Based on Java, XML, Web Services
**CDE mapping tools**
- XML mapping documents exported from CDE repository and mapping databases
- Enhancements: platform independence, generate XML mapping documents for any source/destination CDEs
**VSIMS - Form generating tools**
- Rapid electronic and paper form development by non-technical users
- Based on CDE repository

## Acknowledgements

- Data Management and Coordinating Center, Fred Hutchinson Cancer Research Center
- H. Lee Moffitt Cancer Center
- University of Texas, San Antonio
- Creighton University
- University of Colorado
- University of Pittsburgh
- University of Michigan/Dartmouth University (Great Lakes New England Consortium)
- Brigham and Womens
- MD Anderson
- New York University
- Cancer Biomarkers Group, NCI
- NCI Center for Bioinformatics
- NASA Jet Propulsion Laboratory