Transmissible Spongiform Encephalopathy(TSE) Risk Project

Background

This project is the first real-world, large-scale effort to annotate a web-site with SHOE. It will demonstrate the capabilities of SHOE and validate the concepts. Hopefully, this will serve as an example for future efforts. As progress is made on the project, we will periodically add or update the material here.

The Joint Institute for Food Safety and Applied Nutrition (JIFSAN) is working to expand the knowledge and resources available to support risk analysis in the food safety area. JIFSAN is a partnership between the Food and Drug Administration (FDA) and the University of Maryland. One of the responsibilities of JIFSAN is to develop a clearinghouse on food safety risks. This web site demonstrates some of the research being done to create a food safety resource that will serve both the general public and individuals who assess risk.

TSEs are brain diseases that cause sponge-like abnormalities in brain cells. "Mad Cow Disease", technically known as Bovine Spongiform Encephalopathy (BSE), is a TSE that affects the central nervous system of cattle. Other TSE diseases, such as Creutzfeldt-Jakob Disease (CJD), affect humans.

Concept

The TSE Risk Website will focus on three main areas: Source Material, Processing, and End-Product Use. Each source, process, and product has its own web page. The links between these pages are provided by annotating SHOE relationships. The primary means of accessing information will be a graphical display which allows the user to view one of the following:

The processes are invoked on a chosen source material, and the resulting products
The inputs and outputs of a chosen process
The processes that can be used to create a product, and the source materials that were inputs to these processes

This display will be created dynamically based on SHOE relationships. As such, it will be automatically updated as new information becomes available, including information that has been made available elsewhere on the web. Other query methods will also be available, including the Parka Browser, a graphical tool to query the knowledge base.

How Will it Work?

Authors who wish to make material available to the TSE Risk Website will use the Knowledge Annotator to mark-up their pages with SHOE, using the TSE Ontology.
Exposé, a SHOE robot, will crawl along the web, searching for more SHOE annotated pages with relevant TSE information. It will also look for updates to pages.
New SHOE knowledge will be loaded into a Parka knowledge base.
Java applets on the TSE Risk Website will access the knowledge base to dynamically change the page or respond to users' queries. These applets include the TSE Path Analyzer, SHOE Search and PIQ (see below).

Applications

The Knowledge Annotator: A tool for adding SHOE Knowledge to a web page. In case Java is not properly enabled in your browser, here's a screen shot.
PIQ (Parka Interface for Queries): A tool for issuing complex queries to the knowledge base consisting of all TSE knowledge currently collected from the web (this KB is very small right now). Here's a screen shot.
SHOE Search: A tool for issuing queries against the knowledge base by selecting a category and filling in values for desired properties of instances of the category. As such, this tool is more suitable for casual users than the PIQ.
TSE Path Analyzer: A tool that uses the current knowledge collected from the web to show all paths associated with a Source, Process or End Product. Here's a screen shot.

Resources

TSE Ontology
Summaries of other TSE-Related Web Sites
- BSE Information
- TSE Scientific Abstracts
Sample Annotations for Pathways
- Sources
  - Bovine
  - Human
  - Mammal
  - Mouse
  - Ovine
  - Porcine
  - Ruminant
  - Bones
  - Carcasses, slaughtered
  - Gelatin
  - Meat and Bone Meal
  - Offal
  - Tallow
  - Trimmings
- Processes
- End Products
- Routes of Exposure

Web Accessibility