Pathway Interaction Database
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 While the original NCI-hosted PID website is no longer actively maintained and was discontinued, the complete PID dataset has been preserved and remains accessible through Pathway Commons, NDEx Bioscience Network Exchange, and as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.
[{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.cancer.gov/"}], "label": "National Cancer Institute"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.nature.com/"}], "label": "Nature Publishing Group"}]
[{"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "pubmed", "mesh", "pid", "doid", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}]
{"activity_status": "inactive", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.cancer.gov/"}], "label": "National Cancer Institute"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.nature.com/"}], "label": "Nature Publishing Group"}], "creation_date": "2025-01-10T00:00:00Z", "description": "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.", "domains": ["pathways", "biological systems"], "homepage_url": "http://pid.nci.nih.gov/", "id": "pid", "layout": "resource_detail", "name": "Pathway Interaction Database", "products": [{"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "pubmed", "mesh", "pid", "doid", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}], "publications": [{"id": "https://doi.org/10.1093/nar/gkn653", "title": "PID: the Pathway Interaction Database"}], "repository": "https://github.com/NCIP/pathway-interaction-database", "synonyms": ["PID", "Pathway Interaction Database", "NCI-Nature PID"], "taxon": ["NCBITaxon:9606"]}