Paley S.M., Green M.L., Krummenacker M., Karp P.D. Creating Fungal Pathway/Genome Databases Using Pathway Toolsin Applied Mycology and Biotechnology, Elsevier, 2006.
The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism. Such a knowledge resource will minimize duplication of experimental effort, ensure that all relevant knowledge will be brought to bear on interpreting new experimental resulte, and permit system-level computational analyses. Creation of a new Pathway/Genome Database (PGDB) by Pathway Tools includes inference of fungal metabolic pathways and pathway hole fillers (genes that code for enzymes missing from predicted pathways). Pathway Tools also infers the transport reactions present in an organism. A collection of interactive editing tools allows refinement of a PGDB by adding or modifying gene functions or pathways to capture knowledge from the biomedical literature. Pathway Tools provides a variety of query and visualization capabilities including a genome browser, displays of biochemical pathways, and a visualization of the cellular biochemical network. The Omics Viewer paints multiple types of functional genomics data onto that cellular network diagram. Comparative genomics capabilities allow comparison with other fungal Pathway/Genome Databases.