is a Data Source.
PathBank is an interactive, visual pathway database that provides more than 600,000 machine-readable pathways across 10 model organisms. It supports metabolomics, transcriptomics, proteomics, and systems biology workflows through searchable pathway diagrams, pathway analysis tools, and downloads in tabular, image, sequence, and pathway-exchange formats.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pathbank.portal | PathBank Portal | pathbank.org | GraphicalInterface | http | Interactive web portal for browsing, ... |
| pathbank.downloads | PathBank Downloads | downloads | Product | http | Download catalog for PathBank tabular... |
| pathbank.pathways.csv | PathBank Pathways CSV | downloads | Product | csv | CSV download of PathBank pathway subj... |
| pathbank.biopax | PathBank BioPAX Archive | downloads | GraphProduct | biopax | BioPAX archive of PathBank pathway da... |
| pathbank.sbml | PathBank SBML Archive | downloads | GraphProduct | sbml | SBML archive of PathBank pathway mode... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| obo-db-ingest.pathbank.tsv | pathbank Nodes TSV | pathbank.tsv (710.6 KB) | Product | tsv | had primary source | pathbank Nodes TSV |
| translator.pathbank.graph | Translator PathBank KGX Graph | latest | GraphProduct | kgx-jsonl | had primary source | KGX JSONL graph package for Pathbank ... |
| translator.translator_kg.graph | Translator Aggregate KGX Graph | latest | GraphProduct | kgx-jsonl | had primary source | Aggregated KGX JSONL graph package co... |
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| pathwhiz.pathways | PathWhiz Pathway Library | pathways | GraphicalInterface | http | was informed by | Public library of pathway diagrams th... |
| pathwaycommons.downloads | Pathway Commons Data Downloads | v14 | Product | mixed | was derived from | Download directory for Pathway Common... |
| pathwaycommons.sif | SIF Network Format | pc-hgnc.sif.gz (9.4 MB) | Product | sif | was derived from | PC v14 Simple Interaction Format netw... |
| pathwaycommons.gmt | GMT Gene Set Format | pc-hgnc.gmt.gz (256.4 KB) | Product | ❔ | was derived from | PC v14 Gene Matrix Transposed gene se... |
| pathwaycommons.txt | Extended SIF TXT Format | pc-hgnc.txt.gz (110.3 MB) | Product | txt | was derived from | PC v14 tab-delimited extended SIF nod... |
PathBank is a curated pathway database focused on model-organism biology and metabolomics. According to the PathBank site, the current release contains more than 600,000 machine-readable pathways and provides browsing, search, pathway enrichment, and download workflows for pathway, compound, and protein data.
Official downloads include pathway tables plus BioPAX, SBGN, SBML, PWML, image, and sequence exports. The 2024 PathBank 2.0 update in Nucleic Acids Research reports expansion from 110,234 to 605,359 total pathways and from 1,720 to 6,951 primary pathways.
Created: February 26, 2026 | Last modified: April 02, 2026