is a Data Source.
Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of the molecular-level interactions between genes, gene products, and chemical compounds described in their publications. Author-sourced pathway knowledge is grounded to standard identifiers and made openly available in computable formats for reuse in pathway and network analysis.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| biofactoid.webapp | Biofactoid Web Application | biofactoid.org | GraphicalInterface | http | Web application where authors create ... |
| biofactoid.documents | Biofactoid Pathway Documents | biofactoid.org | Product | json | Openly downloadable author-contribute... |
| biofactoid.api | Biofactoid API | api | ProgrammingInterface | http | Public API (documented via Swagger UI... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| 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... |
Biofactoid is a web-based system that lets authors capture and share machine-readable summaries of the molecular interactions described in their own publications. Authors specify networks of interactions among genes, gene products, and chemical compounds, which Biofactoid grounds to standard identifiers and makes openly available in computable form for downstream pathway and network analysis.
Biofactoid is developed and maintained by the Bader Lab at the University of Toronto as part of the Pathway Commons project.
Wong JV, Franz M, Siper MC, et al. Science Forum: Author-sourced capture of pathway knowledge in computable form using Biofactoid. eLife (2021). doi:10.7554/eLife.68292
Created: June 03, 2026 | Last modified: June 05, 2026