Knowledgebase and repository · FAIRsharing

PathBank

CatalysisCompounds and reactions

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.

Website
Record in FAIRsharing (doi:10.25504/FAIRsharing.3xwMon)
Subjects: Animal Genetics, Bioinformatics, Biology, Cell Biology, Cheminformatics, Database Management, Drug Metabolism, Endocrinology, Genetics, Human Genetics, Medical Informatics, Metabolomics, Microbiology, Molecular Microbiology, Molecular biology, Plant Genetics, Proteomics, Systems Biology, Transcriptomics

Documentation, events and training

bio.tools API and tool documentation

PathBank (same homepage)

What is known per question

The questions of the decision tree, with what FAIRsharing says about this repository. ✓ supported, ✗ excluded, ? not known.

What kind of data do you want to archive?

? Spectra
? Crystal structures
? Computational chemistry
✓ Catalysis
✓ Compounds and reactions
? Bioassays and chemical biology
? Materials and polymers
? Images and microscopy
? Something else

Subjects: Animal Genetics; Bioinformatics; Biology; Cell Biology; Cheminformatics; Database Management; Drug Metabolism; Endocrinology; Genetics; Human Genetics; Medical Informatics; Metabolomics; Microbiology; Molecular Microbiology; Molecular biology; Plant Genetics; Proteomics; Systems Biology; Transcriptomics

Domains: Drug name; Gene name; Protein interactions; Protein name; Protein structure; Protein-Protein Interaction; Reaction data; Receptor; catalytic activity; disease; drug; drug interaction; enzymatic reaction; enzyme; gene; genetic disorder; glucose metabolic process; metabolite; pathway; polypeptide region; protein; regulation of gene expression; signaling; xenobiotic metabolic process