Overview

 

The TCRN (TIES Cancer Research Network) is a national network of interconnected tissue archives. Current partners include the University of Pennsylvania, Roswell Park Cancer Institute, Thomas Jefferson University and Augusta University. The funding period is September 25, 2013 – July 31, 2018.

The TCRN, we will use the TIES system to support cross institutional collaboration between collaborating investigators across institutions or to facilitate large scale multi-center programs such as the SPOREs. TCRN is one of the first examples of a functioning federated tissue and data network, and is built on a detailed regulatory and policy framework. The network helps researchers to find rare or limited cancer cases and specific regional or demographic cancer related information. Researchers and node partners can also use the TCRN to collaborate on research studies with individuals from other regions. The TCRN envisions using the TIES system to support more collaboration on cancer research that will hopefully develop at a faster rate to find a cure for cancer.

The underlying system that supports the TCRN is TIES. TIES stands for Text Information Extraction System. TIES provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations.

TIES focuses on two important challenges of bioinformatics:

  • Information extraction (IE) from free text
  • Access to tissue.

Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed.
Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers.
TIES has three goals designed to solve these problems:

  1. Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies.
  2. Provide researchers with the ability to query, browse and request annotated tissue data and physical material across a network of federated sources.
  3. Pioneer research for distributed text information extraction.

TIES provides the functionality required for:

  • organizations to de-identify and concept code a corpus of free-text SPRs and to create a data service which manages this information
  • organizations to provide role-based access to TIES data
  • authorized users to create queries of the TIES datastores and retrieve reports that fit these criteria
  • authorized users to submit requests for tissue (orders) which will be filled by Honest Brokers.

An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time.