PathwayMatrix presents novel methods to visualize and interact with representations of signaling pathways. It provides visual anayltics tools that allow systems biologists and cancer researchers to find patterns in the relationships and reactions between proteins and protein complexes.
ReactionFlow is a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway
BioPAX (Biological Pathway Exchange) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
PathNER (Pathway Named Entity Recognition) is a tool for the identification of specific pathway mentions from biomedical literature.It’s implemented under the GATE framework, including two major components: rule-based detection and dictionary matching.