Tissue Banks and Pathology Tools (TBPT) Newcomer Information

Mission and Goals

The TBPT workspace is providing for the integration, development, and implementation of tissue and pathology tools. There is strong interest and investment in this area throughout the cancer center community, and this workspace provides an opportunity to bind systems together into a unified resource through a shared informatics infrastructure. In keeping with the caBIG philosophy of database federation, these systems are being designed or modified to facilitate the integration of, and access to, information from geographically-separate areas. Cancer centers with experience in successfully developing tools in this domain are acting as developers, while other centers are included as testing and validation sites. Centers that have expressed an interest in sharing information regarding specimen repositories and data sets are participating as early test sites, providing an opportunity to demonstrate how the tools perform in real-world practice. This cycle has been successfully conducted for the caTissue Core and caTissue Suite 1.0 applications, with the development / testing & validation cycle currently underway for caTissue Suite 1.1.

Additional overview materials:

• Tissue Banks & Pathology Tools Newcomer Session

You can see who is involved in this workspace on the list of TBPT Participating Organizations.

How It Operates

The TBPT workspace welcomes participation from all individuals interested in the workspace's mission and goals. Participant activities include regular teleconferences and periodic face-to-face meetings in which the progress and status of the workspace are assessed, and requirements are gathered and prioritized for ongoing and future development efforts.

Teleconferences: All individuals interested in learning from and contributing to the TBPT Workspace's activities are welcome to join the workspace teleconferences, held the 3rd Monday of every month from 12 to 1 PM (ET). In addition to the workspace teleconference, there are also weekly meetings for caTissue Suite developers, caTissue Suite developers and adopters, and for the Prostate SPOREs group - a specialized program of research excellence serving as real-world adopters of caTissue. Details for all meetings can be found at the TBPT Schedule Page. Meeting minutes from workspace teleconferences can be found on the Meeting Notes.

Listserv Workspace teleconference information as well as other important workspace wide announcements are communicated over the TBPT Listserv, which serves as the primary means of communication for the workspace. Participants can sign up for the listserv by visiting the NIH TBPT Listserv site, following the "Join or Leave the List" link, and entering the requested information.

Face-to-Face Meetings: In addition to teleconferences, the TBPT workspace periodically gathers for face-to-face meetings. These meetings provide participants the opportunity to receive updates, discuss workspace projects and milestones, collect and prioritize requirements, and help define the workspace's strategic direction via real-time interactions with their TBPT colleagues. These meetings are announced over the TBPT Listserv and in the What's BIG This Week newsletter distributed weekly through the caBIG™ Announce Listserv, and are also listed on the caBIG website under the Events & Calendar section.

What have they done (products)

Tools

Below is a list of the informatics systems and tools produced by the TBPT Workspace that are ready for use by the cancer research community. These systems and tools are interoperable, modular, validated, open source, and freely available. Details about support resources for these tools can be found on the TBPT Tool Support Page.

• caTissue Core
  caTissue Core is caBIG's tissue bank repository tool for biospecimen inventory, tracking, and basic annotation. Version 1.2.1 of caTissue Core permits users to track the collection, storage, quality assurance, and distribution of specimens as well as the derivation and aliquotting of new specimens from an existing one (e.g. for DNA analysis). It also allows users to find and request specimens that may be used in molecular, correlative studies.
• caTissue Suite 1.0
  Like caTissue Core, caTissue Suite 1.0 is a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation. In addition to the functionalities provided by caTissue Core, Suite provides users an enhanced collection protocol definition, facilitated specimen accession, collection protocol consent tracking, pathology annotation, caTIES-like pathology report annotation, custom annotation, an advanced query wizard, and specimen requisition and request tracking.
• cancer Text Information Extraction System (caTIES)
  The cancer Text Information Extraction System (caTIES) is a locator to tissue resources via the extraction of coded information from free text surgical pathology reports (SPRs) that uses controlled terminologies to populate caBIG-compliant data structures. This tool provides researchers the ability to query, browse, and acquire annotated tissue data and physical material across a network.
• caTissue Clinical Annotation Engine (CAE)
  caTissue CAE is a web-based user interface for standards-based manual annotation of biospecimens with clinical information. CAE supports importing structured data from clinical information systems such as anatomic pathology laboratory information systems (APLIS), cancer tumor registries, and clinical pathology laboratory systems. It also allows the integration of annotations from multiple sources within cancer centers, providing a complete picture of a patient’s disease. Potential users of caTissue CAE include researchers, tissue bankers, pathology assistants, pathologists, and registrars. The current version contains only anatomic pathology annotation.

To see a list of all caBIG™ tools, visit the Tools page

Policies, Guidelines and Whitepapers

• Federated Tissue Data Set   A white paper detailing the process for establishing a federated dataset of paraffin embedded tumor tissues across Cancer Centers. [draft v1  9/16/2004]
• Response to OBBR regarding its First Generation Guidelines for NCI-Supported Biorepositories  Response from Data Sharing and Intellectual Capital workspace to the National Cancer Institute Office of Biorepositories and Biospecimen Research. regarding its First Generation Guidelines for NCI-Supported Biorepositories. [v1  6/29/2006]

To see a list of all caBIG™ policies and guidelines, visit the Policies, Guidelines & Whitepapers, section.