CauseWay

CauseWay is a Macos application providing a graphical interface to construct and visualize functional (vs mechanistic) pathways, based on MacOS SpriteKit with tight integration with a full ISO Prolog system. Although motivated by biological pathways, CauseWay is suitable for construction, visualization, and interogation of any sort of causal network. It couples the ease of use of a full-fledged GUI app with the power and flecibility of a programmable Prolog database and engine to allow quick and intuitive pathway analysis.

Causeway imports pathway ontologies and knowledge bases from eg. KEGG pathways or Gene Ontology, and stores the functional relationships (represented as edges) between consitituent compounds and gene products (represented as nodes or atoms) in a Prolog knowledgebase. The app provides both interactive (point and click) as well as command-line REPL manipulation of the resulting network graph, and the construction of new pathways. Graph queries (e.g. upstream activators, or downstream targets, of selected nodes) can be invoked directly on selected elements in the pathway, and are passed to a backend Prolog engine (ALSProlog from Applied Logic Systems). Query solutions are displayed by selective highlighting of graph elements, as well as recorded in a query history. A number of library functions are avaible, and new user-defined Prolog functions can be easily added and integrated with the user interface.