is an Aggregator.
Pathway Commons is a centralized web resource that aggregates biological pathway and molecular interaction data from pathway, interaction, protein, chemical, and identifier-mapping sources into BioPAX and related network formats. Its PC v14 metadata lists 26 datasource rows, 6,692 pathways, 3,579,336 molecular interactions, and 4,168,535 physical entities.
infores:pathway-commons
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pathwaycommons.api | Pathway Commons REST API | pc2 | ProgrammingInterface | http | RESTful web service API for programma... |
| pathwaycommons.web | Pathway Commons Web Interface | www.pathwaycommons.org | GraphicalInterface | http | Interactive Pathway Commons web inter... |
| pathwaycommons.downloads | Pathway Commons Data Downloads | v14 | Product | mixed | Download directory for Pathway Common... |
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | PC v14 integrated BioPAX Level 3 unif... |
| pathwaycommons.sif | SIF Network Format | pc-hgnc.sif.gz (9.4 MB) | Product | sif | PC v14 Simple Interaction Format netw... |
| pathwaycommons.gmt | GMT Gene Set Format | pc-hgnc.gmt.gz (256.4 KB) | Product | ❔ | PC v14 Gene Matrix Transposed gene se... |
| pathwaycommons.txt | Extended SIF TXT Format | pc-hgnc.txt.gz (110.3 MB) | Product | txt | PC v14 tab-delimited extended SIF nod... |
| pathwaycommons.documentation | Pathway Commons Documentation | swagger-ui.html | DocumentationProduct | http | Comprehensive API documentation, data... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| pharmebinet.json | PharMeBINet JSON Release | content (1.8 GB) | GraphProduct | json | was derived from | PharMeBINet V2 JSON release published... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (1.8 GB) | GraphProduct | tsv | was derived from | PharMeBINet V2 TSV release published ... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (1.9 GB) | GraphProduct | mixed | was derived from | PharMeBINet V2 GraphML release publis... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (3.6 GB) | GraphProduct | neo4j | was derived from | PharMeBINet V2 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (3.4 GB) | GraphProduct | neo4j | was derived from | PharMeBINet V2 Neo4j dump release pub... |
| genemania.networks | GeneMANIA Interaction Network Archive | current | GraphProduct | txt | was derived from | Downloadable GeneMANIA interaction ne... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | GraphProduct | neo4j | was derived from | Neo4j knowledge graph serialization o... |
Pathway Commons aggregates biological pathway and molecular interaction data for
systems biology reuse. The canonical KG-Registry identifier for this resource is
pathwaycommons; the previous alternate entry has been merged into this page.
The PC v14 metadata describes 26 datasource rows, including ChEBI, UniProt, UniChem, Reactome, PID, PhosphoSitePlus, HumanCyc, HPRD, PANTHER, DIP, BioGRID, IntAct, BIND, CORUM, MSigDB, miRTarBase, DrugBank, Recon X, CTD, KEGG, INOH, NetPath, PathBank, InnateDB, and Biofactoid. These upstream sources are recorded as provenance for the integrated Pathway Commons download products.
Created: June 02, 2026 | Last modified: June 03, 2026