University of Pennsylvania

1
University of Pennsylvania

• Abramson Cancer Center
• Michael Feldman, MD, PhD
• Director, Tumor/Tissue Bank

2
Workspace

• Tissue Banking and Pathology Tools

3
Data Availability

• Data from disease - specific tumor tissue banks
• de-identified
• Cancer Center Database based on Oracle/Sun
  platform ported from Vanderbilt University

4
Tools needed

• Common data standard for Tissue Banking (XML/DTD)
  for interoperability
• Pathology nomenclature standards
• SNOMED RT Coding of pathology and clinical data
• Shared search engine across all NCI caBIG tissue
  banks
• TMA (tissue microarrays) tools
• Database (TMA creation, management and scoring)
• Image processing assist in automated scoring
  TMAs
• Data analysis tools for data analysis of TMAs

5
Resources for Evaluation

• Production environment with
• Central Cancer Center Tissue Bank staff
• End user multidisciplinary research groups in all
  major organ systems
• Development of new TMA core at Cancer Center
• Whole slide digitization (Aperio and Bliss) for
  image processing needs

6
System Integration

• Biomedical Informatics Facility
• Systems analysis, database administration,
  Programming support

7
End User Testing

• Server
• Available to load and run software locally
• Web-based portal for workspace adopters to share
  testing functionality and ideas
• Identified user base in all major organ
  specialties
• Bug reporting and tracking into searchable
  database

8
Software Validation

• Again, rely on Biomedical Informatics Facility

9
Interaction with Workspace Developers

• Web-based portal for idea exchange
• Teleconferencing
• caBIG workspace meetings