About PathCase System

PathCase is an integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined as well as ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. PathCase has multiple levels, with multiple tools at each level.

The PathCase web client is a web-based interface to the PathCase Database, and provides a web-based toolset via a Java applet loaded within a browser window. It is designed as an intuitive and easy-to-use tool, with no need to study user manuals.

The PathCase Desktop Client is a desktop application for browsing and interacting with the PathCase database. The desktop client is discontinued, and the latest version can be found under the "Legacy Software" link on the left.

PathCase Data and Visualization Model

Living organisms behave as complex systems that are flexible and adaptive to their surroundings. At the molecular level, organisms consist of intricate networks of molecular reactions, which are often called "biochemical pathways." In order to maintain, visualize, and ultimately, analyze organism functions that result from biochemical pathways, the PathCase Pathways Database System was developed and populated. Presently, the system contains a pathways database and the associated tools to store, compare, query, and visualize metabolic pathways. Signaling pathways and Gene Ontology (GO)-based metabolic pathway functional templates will be added into the PathCase system in the near future. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. The ultimate goal of the system is to describe, utilize, and predict systems functions and behaviors of living organisms.

Pathways are the sequential and cumulative action of genetically distinct, but functionally related molecules. Each reaction in a pathway is a biochemical step from specific substrates (input molecules) to products (output molecules) that are chemically modified substrates. Each step may also use various combinations of molecules as cofactors, activators, inhibitors, and regulators, and usually involves at least one genetically unique gene product that catalyzes the reaction step.

Pathways, in general, illustrate the functional relations between molecules. Presently in PathCase, the available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products. Other possible information to be included into PathCase are RNA and protein expression patterns, reaction kinetics, and associated phenotypic variation and diseases. Ultimately, many other kinds of information (or knowledge) can be incorporated. Such information forms a rich research resource that integrates genomic and biological information which can be managed, analyzed, queried and displayed in dynamic ways at various levels of biological and genetic detail to provide insight into diverse biological processes in health and disease. For more details about the PathCase system, please see the associated publications.