データセット詳細

Reactome RDF

REACTOMEは、オープンソース、オープンアクセスで、マニュアルキュレーションされ、ピアレビューされた、パスウェイデータベースです。

データセット仕様

タグ	Interaction/Pathway
提供元	Original
登録区分	Added by RDF portal
データ提供者	Reactome Team (https://reactome.org/)
作成者	Reactome Team (https://reactome.org/)
公開日	2023
ライセンス	Creative Commons Public Domain (CC0) License
バージョン	84
ダウンロード	https://rdfportal.org/download/reactome
SPARQLエンドポイント	https://rdfportal.org/ebi/sparql

データセット統計

Triples: 21317159

Subjects: 3705512

Properties: 45

Objects: 6831167

Classes: 33

SPARQLクエリ例

例 1

エンドポイントで実行

# 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

例 2

エンドポイントで実行

# 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

例 3

エンドポイントで実行

# 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

スキーマ図