is a Data Source.
It is part of the Ber collection.
Reactome is a comprehensive, curated, and peer-reviewed pathway database representing human biological processes. It integrates information on biological molecules including proteins, small molecules, and RNA, organizing them into networks of functional interactions organized as pathways. With sophisticated graph database backend and multiple data access formats, Reactome is an essential resource for systems biology, functional genomics, drug discovery, and biomedical research, providing insights into gene function in the context of cellular and organismal processes.
biological systems, pathways, systems biology, biomedical
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infores:reactome
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| reactome.data.human | Reactome Human from BioPAX, sqlite | reactome-hs.db.gz (169.8 MB) | Product | ❔ | Conversion from BioPAX, human subset |
| reactome.biopax | Reactome BioPAX Format | download-data | GraphProduct | owl | Complete Reactome pathway data in Bio... |
| reactome.sbml | Reactome SBML Format | download-data | GraphProduct | sbml | Reactome pathway data in SBML (System... |
| reactome.rdf | Reactome RDF/XML Format | download-data | GraphProduct | rdfxml | Reactome data in RDF/XML format for s... |
| reactome.neo4j | Reactome Neo4j Graph Database | download-data | GraphProduct | neo4j | Complete Reactome pathway database in... |
| reactome.flat | Reactome Flat Files | download-data | GraphProduct | tsv | Reactome pathway and interaction data... |
| reactome.api | Reactome REST API | ContentService | ProgrammingInterface | http | RESTful web service API for programma... |
| reactome.browser | Reactome Pathway Browser | PathwayBrowser | GraphicalInterface | http | Interactive pathway browser providing... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| obo-db-ingest.rhea.sssom.tsv | Rhea SSSOM | rhea.sssom.tsv (150.6 KB) | MappingProduct | sssom | Rhea SSSOM |
| obo-db-ingest.bigg.metabolite.sssom.tsv | bigg.metabolite SSSOM | bigg.metabolite.sssom.tsv (391.1 KB) | MappingProduct | sssom | bigg.metabolite SSSOM |
| spoke.graph | SPOKE Graph | ❔ | GraphProduct | ❔ | The SPOKE knowledge graph containing ... |
| ubkg.neo4j | UBKG Neo4j Docker Distribution | ubkg-downloads.xconsortia.org | GraphProduct | ❔ | Turnkey neo4j distributions that depl... |
| ubkg.csv | UBKG Ontology CSV Files | ubkg-downloads.xconsortia.org | GraphProduct | csv | Ontology CSV files that can be import... |
| rtx-kg2.graph.nodes | RTX-KG2.10.1c KGX JSONL Nodes | kg2c-2.10.1-v1.0-nodes.jsonl.gz (359.1 MB) | GraphProduct | kgx-jsonl | Nodes for KGX distribution of the RTX... |
| rtx-kg2.graph.edges | RTX-KG2.10.1c KGX JSONL Edges | kg2c-2.10.1-v1.0-edges.jsonl.gz (1.7 GB) | GraphProduct | kgx-jsonl | Edges for KGX distribution of the RTX... |
| rtx-kg2.neo4j | RTX-KG2 Neo4j | arax.ncats.io | ProgrammingInterface | ❔ | Neo4j distribution of the RTX-KG2 as ... |
| alzkb.browser | AlzKB Graph Database Browser | login | GraphicalInterface | http | A browser interface for a knowledge g... |
| alzkb.data | AlzKB Data Release (Version 2.0.0) | v2.0.0 | GraphProduct | ❔ | Memgraph data release for AlzKB. |
| bioteque.embeddings | Bioteque Embeddings | embeddings | Product | ❔ | Network embeddings of the Bioteque gr... |
| mechreponet.kg | MechRepoNet Knowledge Graph | publication | ❔ | The MechRepoNet knowledge graph in it... | |
| indra.cogex.code | INDRA CoGEx Build Code | indra_cogex | ProcessProduct | ❔ | INDRA CoGEx is a graph database integ... |
| clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | Neo4j database dump of the Clinical K... |
| drugmechdb.graph | DrugMechDB Graph Dataset | zenodo.8139357 | GraphProduct | mixed | Curated mechanistic drug–disease path... |
| kg-monarch.graph | KGX Distribution of KG-Monarch | monarch-kg.tar.gz (220.2 MB) | GraphProduct | kgx | KGX Distribution of KG-Monarch |
| kg-monarch.graph.jsonl | KGX JSON-L Distribution of KG-Monarch | monarch-kg.jsonl.tar.gz (301.0 MB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.rdf | RDF Distribution of KG-Monarch | monarch-kg.nt.gz (838.5 MB) | GraphProduct | rdfxml | RDF Distribution of KG-Monarch |
| kg-monarch.graph.neo4j | Neo4j Dump of KG-Monarch | monarch-kg.neo4j.dump (1.3 GB) | GraphProduct | ❔ | Neo4j Dump of KG-Monarch |
| kg-monarch.graph.duckdb | DuckDB database of KG-Monarch | monarch-kg.duckdb (6.4 GB) | GraphProduct | ❔ | DuckDB database of KG-Monarch |
| pheknowlator.graph | PheKnowLator graph | knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator | GraphProduct | owl | PheKnowLator graph files, including s... |
| rna-kg.kg.neo4j | RNA-KG Neo4j Dump | rnakgv20.dump (3.7 GB) | GraphProduct | neo4j | RNA-KG as a Neo4j Dump |
| rna-kg.kg.nodes | RNA-KG Nodes | nodes.csv (4.1 GB) | GraphProduct | csv | RNA-KG Nodes in CSV format |
| rna-kg.kg.edges | RNA-KG Edges | edges.csv (17.1 GB) | GraphProduct | csv | RNA-KG Edges in CSV format |
| kg-monarch.graph.jsonl.edges | KGX JSON-L Distribution of KG-Monarch Edges | monarch-kg_edges.jsonl (14.2 GB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.jsonl.nodes | KGX JSON-L Distribution of KG-Monarch Nodes | monarch-kg_nodes.jsonl (1.1 GB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.neo4j.edges | Neo4j Dump of KG-Monarch Edges | monarch-kg_edges.neo4j.csv (4.1 GB) | GraphProduct | neo4j | Neo4j Dump of KG-Monarch Edges |
| kg-monarch.graph.neo4j.nodes | Neo4j Dump of KG-Monarch Nodes | monarch-kg_nodes.neo4j.csv (333.4 MB) | GraphProduct | neo4j | Neo4j Dump of KG-Monarch Nodes |
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | GraphProduct | neo4j | Integrated graph knowledge base combi... |
| cancer-genome-interpreter.clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | Neo4j database dump of the Clinical K... |
| genecards.pathway.data ⚠ | GeneCards Pathway Data | www.genecards.org | Product | http | Pathway information integrated from R... |
| ibkh.graph | iBKH Knowledge Graph | ❔ | GraphProduct | ❔ | The integrative Biomedical Knowledge ... |
| rampdb.database | RaMP-DB Integrated Database | rampdb.nih.gov | DatabaseProduct | ❔ | Multi-sourced relational database int... |
| cam-kp.reactome-cams | Reactome Pathway CAMs | ❔ | Product | ❔ | Causal Activity Model graphs automati... |
Created: March 17, 2025 | Last modified: December 20, 2025