PathBank

PathBank provides a curated, machine-readable collection of over 110,000 biological pathways across ten model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli, and Pseudomonas aeruginosa) to support analysis in systems biology, proteomics, metabolomics, and transcriptomics.

Key Features:

• Coverage: Contains over 110,000 machine-readable pathways spanning ten specified model organisms.
• Pathway types: Includes metabolic, metabolite signaling, protein signaling, disease, drug, and physiological pathways.
• Diagram annotations: Pathway diagrams include organs, organelles, subcellular compartments, cofactors, molecular locations, chemical structures, and protein quaternary structures.
• Integration with external databases: Small molecules are hyperlinked to HMDB and DrugBank while proteins and enzyme complexes are linked to UniProt.
• File format support: Pathways are available in BioPAX, SBML (Systems Biology Markup Language), PWML (Pathway Markup Language), SBGN (Systems Biology Graphical Notation), RXN, PNG, and SVG formats.
• Curation scope: Curated to provide a pathway for every protein and a map for every metabolite.
• Unique content: Reports that more than 95% of its pathways are not found in other public pathway databases.

Scientific Applications:

• Systems biology: Supports pathway-based modeling and integrative analysis of biological systems.
• Proteomics: Enables mapping of protein data onto curated signaling and metabolic pathways.
• Metabolomics: Facilitates mapping and interpretation of metabolite profiles using metabolite-centric pathway maps and chemical structures.
• Transcriptomics: Supports interpretation of gene expression changes in the context of signaling and metabolic networks.
• Disease and drug research: Provides disease and drug pathway diagrams for mechanistic investigation.

Methodology:

Pathways are curated and represented as hyperlinked diagrams linking small molecules to HMDB and DrugBank and proteins/enzyme complexes to UniProt; pathway files are provided in BioPAX, SBML, PWML, SBGN, RXN, PNG, and SVG formats.