Reactome RDF
Reactome RDF is a BioPAX Level 3 representation of Reactome, an expert-curated and peer-reviewed biological pathway database. It describes pathways and reactions involved in metabolism, signaling, gene regulation, and disease, linking participating proteins, complexes, and small molecules with supporting literature and external databases.
Dataset specifications
| Tags |
|
| Provenance |
Original
|
| Registration |
Added by RDF portal
|
| Data provider |
- Reactome Team (https://reactome.org/)
|
| Creator |
-
Reactome Team (https://reactome.org/)
|
| Issued |
2026-06-30 |
| Licenses |
-
Creative Commons Public Domain (CC0) License
|
| Version |
97 |
| Download |
/website/download/#reactome
|
| SPARQL Endpoint |
https://rdfportal.org/ebi/sparql
|
Dataset statistics
- Triples
- 21610772
- Subjects
- 3751401
- Properties
- 45
- Objects
- 6912981
- Classes
- 33
SPARQL example queries
# Endpoint: https://rdfportal.org/ebi/sparql
# Description: Pathway
PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
SELECT ?pathway_display_name ?pathway_db ?pathway_id ?biochemical_reaction_display_name ?left_molecule_db ?right_molecule_db ?left_molecule_id ?right_molecule_id ?left_protein_db ?right_protein_db ?left_protein_id ?right_protein_id
FROM <http://rdf.ebi.ac.uk/dataset/reactome>
WHERE {
?Pathway a biopax:Pathway ;
biopax:displayName ?pathway_display_name .
?BiochemicalReaction a biopax:BiochemicalReaction ;
biopax:displayName ?biochemical_reaction_display_name .
OPTIONAL {
?Pathway biopax:xref ?UnificationXref .
?UnificationXref a biopax:UnificationXref ;
biopax:db ?pathway_db ;
biopax:id ?pathway_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:left / biopax:entityReference / biopax:xref ?LeftSmallMoleculeRefXref .
?LeftSmallMoleculeRefXref a biopax:UnificationXref ;
biopax:db ?left_molecule_db ;
biopax:id ?left_molecule_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:right / biopax:entityReference / biopax:xref ?RightSmallMoleculeRefXref .
?RightSmallMoleculeRefXref a biopax:UnificationXref ;
biopax:db ?right_molecule_db ;
biopax:id ?right_molecule_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:left / biopax:entityReference / biopax:xref ?LeftProteinRefXref .
?LeftProteinRefXref a biopax:UnificationXref ;
biopax:db ?left_protein_db ;
biopax:id ?left_protein_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:right / biopax:entityReference / biopax:xref ?RightProteinRefXref .
?RightProteinRefXref a biopax:UnificationXref ;
biopax:db ?right_protein_db ;
biopax:id ?right_protein_id .
}
}
LIMIT 100
# Endpoint: https://rdfportal.org/ebi/sparql
# Description:
PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
SELECT ?pathway_display_name ?pathway_db ?pathway_id ?left_protein_db ?left_protein_id ?right_protein_db ?right_protein_id
FROM <http://rdf.ebi.ac.uk/dataset/reactome>
WHERE {
?Pathway a biopax:Pathway ;
biopax:displayName ?pathway_display_name .
OPTIONAL {
?Pathway biopax:xref ?UnificationXref .
?UnificationXref a biopax:UnificationXref ;
biopax:db ?pathway_db ;
biopax:id ?pathway_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:left / biopax:entityReference / biopax:xref ?LeftProteinRefXref .
?LeftProteinRefXref a biopax:UnificationXref ;
biopax:db ?left_protein_db ;
biopax:id ?left_protein_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:right / biopax:entityReference / biopax:xref ?RightProteinRefXref .
?RightProteinRefXref a biopax:UnificationXref ;
biopax:db ?right_protein_db ;
biopax:id ?right_protein_id .
}
}
LIMIT 100
# Endpoint: https://rdfportal.org/ebi/sparql
# Description:
PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
SELECT ?pathway_display_name ?pathway_db ?pathway_id ?left_molecule_db ?left_molecule_id ?right_molecule_db ?right_molecule_id
FROM <http://rdf.ebi.ac.uk/dataset/reactome>
WHERE {
?Pathway a biopax:Pathway ;
biopax:displayName ?pathway_display_name .
OPTIONAL {
?Pathway biopax:xref ?UnificationXref .
?UnificationXref a biopax:UnificationXref ;
biopax:db ?pathway_db ;
biopax:id ?pathway_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:left / biopax:entityReference / biopax:xref ?LeftSmallMoleculeRefXref .
?LeftSmallMoleculeRefXref a biopax:UnificationXref ;
biopax:db ?left_molecule_db ;
biopax:id ?left_molecule_id .
}
OPTIONAL {
?Pathway biopax:pathwayComponent / biopax:right / biopax:entityReference / biopax:xref ?RightSmallMoleculeRefXref .
?RightSmallMoleculeRefXref a biopax:UnificationXref ;
biopax:db ?right_molecule_db ;
biopax:id ?right_molecule_id .
}
}
LIMIT 100