# Presentation: 597890

## caBIG Tissue Banks and Pathology Tools Workspace

- St. Louis, MO
- May 4th and 5th, 2005

**caBIG Tissue Banks and Pathology Tools Workspace**
- Face-to-Face Meeting
**Paraffin-Embedded Tissue Archive**

**University of Pittsburgh (Unfunded Partner)**

## 	 Paraffin-Embedded Tissue Archive 		Background and Significance

- Currently there are vast quantities of paraffin embedded tissue in archives within Surgical Pathology Departments throughout the country. The majority of these archives have little or no associated annotation information that could be used to provide access to the tissue.
- The UPenn Department of Pathology and Laboratory Medicine has approximately 600,000 paraffin-embedded tissue samples that date back to the 1940s.  Each block of tissue has a corresponding microfiche file that contains the information about the tissue and other pathological information.
- The project will use microfiche that will be scanned to create TIFF images of all corresponding pathology reports, extract accession/subject IDs and full text using OCR (optical character recognition).
- caTIES and De-ID will be used to chunk pathology reports and parse specific text strings that describe diagnosis, tissue quality, treatments and phenotype information.  The resulting dataset will be uploaded to the caTIES database, allowing use of the caTIES query interface and data model.
- Conversion of the microfiche information for uploading into the caTIES relational database is required to expose these tissue samples to the caBIG community.

## 	 Paraffin-Embedded Tissue Archive 		Materials and Methods

**	**** **Paraffin-Embedded Tissue Archive** ****	****	****Materials and Methods**

## 	 Paraffin-Embedded Tissue Archive 		Text Extraction

- The Department of Pathology and Laboratory Medicine has stored two forms of pathological data that relates to paraffin-embedded tissues.  The data resides in both formatted index cards and microfiche.
- AIM Document Management is scanning the records and creating text files containing the pathological data for each sample and TIFF image files containing the full pathological report.
- The accession/subject IDs and full text will be extracted using OCR (optical character recognition)

## 	Paraffin-Embedded Tissue Archive 		De-ID Software

- The UPenn developer team will use De-ID to de-identify  all Surgical Pathology Reports prior to future extraction using caTIES creating a searchable de-identified database.
- De-IDTM is a product of De-ID Data Corp.
- De-IDTM meets all HIPAA guidelines.  It scrubs reports of HIPAA identifiers and produces highly readable de-identified text without removing important clinical information.
- The de-identified caTIES-parsed files generated by scanning the pathological data from the paraffin-embedded tissue archive will be loaded into a relational database being used for caTIES at UPenn. The caTIES query interface and data model can then be utilized for the uploaded dataset.

## 	Paraffin-Embedded Tissue Archive 		 caTIES Pipeline

- The text files generated by AIM Document Management will be processed in an automated processing through the caTIES engine.
- The caTIES engine chunks the pathology reports into major sections and allows for parsing of specific text strings that describe diagnosis, tissue quality, treatments and phenotype information.
- To perform this task, the UPenn developer team will work with the University of Pittsburgh caTIES developer team to modify caTIES to store the paraffin-embedded dataset which will include TIFF images of the full Surgical Pathology

## 	Paraffin-Embedded Tissue Archive 		caTIES Pipeline

## 	 Paraffin-Embedded Tissue Archive 		Progress

- Task 1 – Project Management – Cancer Center Project Task Lead will manage Cancer Center level project activities.
- Task 1.1 – The Cancer Center Project Task Lead will track project milestones and deliverables using on-line tools (i.e. cancer Management Portal – caMP) provided by the General Contractor.
- Task 1.2 - The Cancer Center Project Task Lead will plan and document regular (and when needed ad hoc) communications to share project information. Communications may include face-to-face meetings, teleconferences, videoconferences or use of the caBIG website and forums.
- Task 1.3 - The Cancer Center Project Task Lead will generate monthly status reports and submit each one to the General Contractor not later than the 5th working day of each month.
- Task 2 – Text Extraction Training Set Report o Film preparation, Scanning, Full-text OCR (optical character recognition, and indexing of accession/case report.  (Done - low accuracy.  Need hand coding.  Need Business Agreement with Hospitals of the University of Pennsylvania before subcontract to offshore hand coder) - UNDER PROGRESS
- Task 3 – Text Extraction of Pathology Reports: Film preparation, Scanning, Full-text OCR (optical character recognition, and indexing of accession/case report. CD Mastering • Index data for accession or case number• Meta data for full-text capture • TIFF images
- Task 4 – Transmogrify, parse, and de-identify Pathology Report data. o Use caTIES engine, using automated mode for data parsing of text files.
- caTIES-parsed files containing pathological data extracted from paraffin-embedded archives and De-identification of caTIES files
- Task 5 – Uploading of caTIES-De-ID- files to caTIES database o
- Populate the caTIES database with pathology report records
- Utilize caTIES architecture for uploading data
- Develop and implement queries to check quality of data in caTIES database
- Task 6 – Documentation of Lessons Learned

## 	Acknowledgments

- Michael Feldman, MD, PhD
- Tara McSherry
- Vishal Nayak
- Casey Overby
- John Quigley
- Rebecca Crowley, MD
- University of Pittsburgh caTIES team