Datasets

KNApSAcK RDF

Website

RDFized dataset in the KNApSAcK family database.

Dataset specifications

Tags
Compound Taxonomy Publication Activity
Provenance Original
Registration Submitted
Data provider
  • National Institute of Genetics
Creator
  • Takatomo FujisawaNational Institute of Genetics (NIG)
  • RIKEN BioResource Research Center
  • Yasunori YamamotoDatabase Center for Life Science (DBCLS)
  • Toshiaki TokimatsuNational Institute of Genetics (NIG)
  • Issaku YamadaThe Noguchi Institute
  • Hideki HatanakaDatabase Center for Life Science (DBCLS)
  • Aki Hirai-MoritaNara Institute of Science and Technology (NAIST)
  • Shigehiko KanayaNara Institute of Science and Technology (NAIST)
  • Masanori AritaNational Institute of Genetics (NIG)
Issued 2022-05-30
Licenses
  • Attribution 4.0 International (CC BY 4.0)
Version 0.2.0
Download https://rdfportal.org/download/knapsack
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
3489616
Subjects
715781
Properties
14
Objects
1385729
Classes
8

SPARQL example queries

Example 1

Run on Endpoint 
# Endpoint: https://rdfportal.org/primary/sparql
# Description: Get attribute information for C00000001 in KNApSAcK Core
# Parameter: knapsack_id: (example: C00000001)

PREFIX knapsack: <http://purl.jp/knapsack/resource#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX cheminf: <http://semanticscience.org/resource/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?KNApSAcKCoreRecord ?knapsack_id ?molecular_entity_name ?molecular_formula ?value_mw ?value_smiles ?value_inchikey ?value_inchi ?rdfs_seealso
FROM <http://purl.jp/knapsack/>
WHERE {
    VALUES ?knapsack_id { "C00000001" }
    VALUES ?KNApSAcKCoreRecord__class { knapsack:KNApSAcKCoreRecord knapsack:KNApSAcKMetaboliteRecord }
    ?KNApSAcKCoreRecord a ?KNApSAcKCoreRecord__class ;
        dc:identifier ?knapsack_id ;
        rdfs:seeAlso ?rdfs_seealso ;
        sio:SIO_000008 ?MolecularEntityName ;
        sio:SIO_000008 ?MolecularFormula ;
        sio:SIO_000008 ?MolecularWeight ;
        cheminf:CHEMINF_000200 ?Smiles ;
        cheminf:CHEMINF_000200 ?StandardInchi ;
        cheminf:CHEMINF_000200 ?StandardInchikey .
    ?MolecularEntityName a cheminf:CHEMINF_000043 ;
        sio:SIO_000300 ?molecular_entity_name .
    ?MolecularFormula a cheminf:CHEMINF_000042 ;
        sio:SIO_000300 ?molecular_formula .
    ?MolecularWeight a cheminf:CHEMINF_000334 ;
        sio:SIO_000300 ?value_mw .
    ?Smiles a cheminf:CHEMINF_000018 ;
        sio:SIO_000300 ?value_smiles .
    ?StandardInchikey a cheminf:CHEMINF_000059 ;
        sio:SIO_000300 ?value_inchikey .
    ?StandardInchi a cheminf:CHEMINF_000113 ;
        sio:SIO_000300 ?value_inchi .
}
LIMIT 100

Example 2

Run on Endpoint 
# Endpoint: https://rdfportal.org/primary/sparql
# Description: Get KNApSAcK Core compounds with molecular weights greater than 3000

PREFIX knapsack: <http://purl.jp/knapsack/resource#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX cheminf: <http://semanticscience.org/resource/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?KNApSAcKCoreRecord ?knapsack_id ?molecular_entity_name ?molecular_formula ?value_mw ?rdfs_seealso
FROM <http://purl.jp/knapsack/>
WHERE {
    VALUES ?KNApSAcKCoreRecord__class { knapsack:KNApSAcKCoreRecord knapsack:KNApSAcKMetaboliteRecord }
    ?KNApSAcKCoreRecord a ?KNApSAcKCoreRecord__class ;
        dc:identifier ?knapsack_id ;
        rdfs:seeAlso ?rdfs_seealso ;
        sio:SIO_000008 ?MolecularEntityName ;
        sio:SIO_000008 ?MolecularFormula ;
        sio:SIO_000008 ?MolecularWeight .
    ?MolecularEntityName a cheminf:CHEMINF_000043 ;
        sio:SIO_000300 ?molecular_entity_name .
    ?MolecularFormula a cheminf:CHEMINF_000042 ;
        sio:SIO_000300 ?molecular_formula .
    ?MolecularWeight a cheminf:CHEMINF_000334 ;
        sio:SIO_000300 ?value_mw .
}
ORDER BY ?value_mw

Example 3

Run on Endpoint 
# Endpoint: https://rdfportal.org/primary/sparql
# Description: Get related resources for C00000001 in KNApSAcK Core
# Parameter: knapsack_id: (example: C00000001)

PREFIX knapsack: <http://purl.jp/knapsack/resource#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT ?knapsack_id ?skos_close_match
FROM <http://purl.jp/knapsack/>
WHERE {
    VALUES ?knapsack_id { "C00000001" }
    VALUES ?KNApSAcKCoreRecord__class { knapsack:KNApSAcKCoreRecord knapsack:KNApSAcKMetaboliteRecord }
    ?KNApSAcKCoreRecord a ?KNApSAcKCoreRecord__class ;
        dc:identifier ?knapsack_id .
    OPTIONAL {
        ?KNApSAcKCoreRecord skos:closeMatch ?skos_close_match .
    }
}
LIMIT 100

Schema diagram

Schema diagram for knapsack
Schema diagram for knapsack