is a Data Source.
The Pathway Interaction Database (PID) was a highly curated collection of human molecular signaling, regulatory pathways, and key cellular processes developed through a collaboration between the US National Cancer Institute and Nature Publishing Group. The database focused specifically on cancer-relevant signaling and regulatory pathways rather than metabolic processes, providing detailed network-level representations of molecular interactions with comprehensive literature citations and evidence codes for each event. PID contained three main data collections the NCI-Nature Curated pathways representing expert-curated cancer signaling networks, imported Reactome pathways in BioPAX format, and BioCarta pathway data, together comprising 77 expert-reviewed pathways with over 4,300 manually curated interactions involving more than 2,600 proteins annotated with detailed posttranslational modifications including 7,400+ phosphorylation events. Each interaction in the NCI-Nature curated collection was associated with specific literature references from over 3,100 distinct PubMed citations and annotated with evidence codes indicating the type of experimental support. The database employed a sophisticated data model distinguishing five types of molecular events including transcription, translocation, biochemical reactions, protein modifications, and macroprocesses, with molecules characterized by posttranslational modifications, cellular locations, and activity states. PID provided powerful query capabilities enabling users to search by molecule names, construct dynamic interaction networks connecting specified molecules, overlay experimental data from gene expression studies onto pathways using batch query tools with statistical enrichment analysis, and visualize both predefined expert-curated pathways and novel networks generated computationally from the interaction database. The resource was particularly valuable for cancer research, allowing identification of parallel signaling paths, elucidation of therapy resistance mechanisms, and integration of genomic abnormalities with pathway contexts. While the original NCI-hosted PID website is no longer actively maintained and was discontinued, the complete PID dataset has been preserved and remains accessible through Pathway Commons, NDEx Bioscience Network Exchange, and as BioPAX Level 2 format exports, ensuring continued availability of this valuable curated knowledge for the research community.
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| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| spoke.graph | SPOKE Graph | data-tools | GraphProduct | http | had primary source | The SPOKE knowledge graph containing ... |
| alzkb.browser | AlzKB Graph Database Browser | login | GraphicalInterface | http | had primary source | A browser interface for a knowledge g... |
| alzkb.data | AlzKB Data Release (Version 2.0.0) | v2.0.0 | GraphProduct | ❔ | had primary source | Memgraph data release for AlzKB. |
| obo-db-ingest.pid.pathway.tsv | pid.pathway Nodes TSV | pid.pathway.tsv (3.8 KB) | Product | tsv | had primary source | pid.pathway Nodes TSV |
| hetionet.neo4j | Hetionet v1.0 Neo4j Database | browser | GraphicalInterface | http | had primary source | Browser for complete Hetionet v1.0 gr... |
| hetionet.data.json | Hetionet v1.0 JSON | hetionet-v1.0.json.bz2 (131 B) | GraphProduct | json | had primary source | Hetionet v1.0 in JSON format |
| hetionet.data.neo4j | Hetionet v1.0 Neo4j | hetionet-v1.0.db.tar.bz2 (132 B) | GraphProduct | ❔ | had primary source | Hetionet v1.0 as a Neo4j database |
| hetionet.data.edges | Hetionet v1.0 edges (SIF) | hetionet-v1.0-edges.sif.gz (131 B) | GraphProduct | sif | had primary source | Hetionet v1.0 as SIF edges |
| hetionet.data.nodes | Hetionet v1.0 nodes (TSV) | hetionet-v1.0-nodes.tsv (417.1 KB) | GraphProduct | tsv | had primary source | Hetionet v1.0 as TSV nodes |
| hetnetpy | hetnetpy | hetnetpy | ProcessProduct | ❔ | had primary source | Python package for creating, querying... |
| hetionet.search | Hetnet Connectivity Search | search | GraphicalInterface | http | had primary source | Web application to search and explore... |
| msigdb.downloads.human ⚠ | MSigDB Human Gene Sets Downloads | downloads.jsp#msigdb | Product | mixed | used | Downloadable gene set files in GMT, X... |
| msigdb.downloads.mouse ⚠ | MSigDB Mouse Gene Sets Downloads | downloads.jsp#msigdb | Product | mixed | used | Downloadable gene set files for mouse... |
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| 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... |
| 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... |
The Pathway Interaction Database (PID) was a highly curated collection of human signaling and regulatory pathways focused on cancer biology, developed by the National Cancer Institute and Nature Publishing Group. Though no longer actively maintained at its original NCI site, PID data remains accessible through Pathway Commons and NDEx.
Created: January 10, 2025 | Last modified: December 13, 2025