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chembl-rdf

ChEMBL-RDF:!: SPARQL Endpoint

  • Molecule(化合物)の情報
## molecule
SELECT DISTINCT *
WHERE
{
?molecule <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity>
      OPTIONAL {?molecule <http://www.w3.org/2002/07/owl#equivalentClass> ?equivalentClassOfMolecule}
      OPTIONAL {?molecule <http://www.w3.org/2000/01/rdf-schema#label> ?label}
      OPTIONAL {?molecule <http://purl.org/spar/cito/citesAsDataSource> ?dataSourceOfMolecule}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/smiles> ?smiles}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/inchi> ?inchi}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/inchikey> ?inchikey}
}
  • Activity(活性)の情報
## activity
SELECT DISTINCT *
WHERE
{
?activity <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity>
      OPTIONAL {?activity <http://purl.org/spar/cito/citesAsDataSource> ?dataSourceOfActivity}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> ?molecule}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#standardValue> ?standardValue}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> ?Assay}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#type> ?typeOfActivity}
}
  • Assayの情報
## assay
SELECT DISTINCT *
{
?assay <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay>
         OPTIONAL {?assay <http://www.w3.org/2002/07/owl#equivalentClass> ?equivalentClassOfAssay}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> ?description}
         OPTIONAL {?assay <http://purl.org/spar/cito/citesAsDataSource> ?dataSourceOfAssay}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTargetScore> ?targetScore}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> ?assayType}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTarget> ?targetOfAssay}
}
  • Target(ターゲットタンパク質)の情報
## target
SELECT DISTINCT *
WHERE
{
?target <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Target>
      OPTIONAL {?target <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?typeOfTarget}
      OPTIONAL {?target <http://www.w3.org/2002/07/owl#sameAs> ?sameAs}
      OPTIONAL {?target <http://purl.org/dc/elements/1.1/title> ?title}
      OPTIONAL {?target <http://www.w3.org/2002/07/owl#equivalentClass> ?equivalentClassOfTarget}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#organism> ?organism}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#hasTaxonomy> ?taxonomy}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#classL1> ?class1}
}
  • molecule(化合物)「CHEMBL1200462」(Doxepin)から、ターゲットタンパク質(生物種)を検索
SELECT DISTINCT ?label ?equivalentClassOfAssay ?assayType ?targetOfequivalentClass ?sameAs ?title ?organism ?taxonomy ?class1
WHERE
{
## moleculeの情報(CHEMBL1200462=>?molecule)
?molecule <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL1200462>
      OPTIONAL {?molecule <http://www.w3.org/2000/01/rdf-schema#label> ?label}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/smiles> ?smiles}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/inchi> ?inchi}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/inchikey> ?inchikey}

## Activityの情報(?molecule=>?activity=>?assay)
?activity <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> ?molecule
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> ?assay}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#type> ?typeOfActivity}

## Assayの情報(?assay=>?target)
?assay <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay>
         OPTIONAL {?assay <http://www.w3.org/2002/07/owl#equivalentClass> ?equivalentClassOfAssay}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> ?description}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTargetScore> ?targetScore}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> ?assayType}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTarget> ?target}

## Targetの情報(?target=>)
?target <http://www.w3.org/2002/07/owl#equivalentClass> ?targetOfequivalentClass
      OPTIONAL {?target <http://www.w3.org/2002/07/owl#sameAs> ?sameAs}
      OPTIONAL {?target <http://purl.org/dc/elements/1.1/title> ?title}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#organism> ?organism}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#hasTaxonomy> ?taxonomy}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#classL1> ?class1}
}
  • molecule(化合物)「InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3」(caffeine)から、ターゲットタンパク質(生物種)を検索
SELECT DISTINCT ?label ?equivalentClassOfAssay ?assayType ?targetOfequivalentClass ?sameAs ?title ?organism ?taxonomy ?class1
WHERE
{
## moleculeの情報(chebi:100443=>?molecule)
{?molecule <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3"} 
UNION {?molecule <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3>}
      OPTIONAL {?molecule <http://www.w3.org/2000/01/rdf-schema#label> ?label}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/smiles> ?smiles}
      OPTIONAL {?molecule <http://www.blueobelisk.org/chemistryblogs/inchikey> ?inchikey}

## Activityの情報(?molecule=>?activity=>?assay)
?activity <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> ?molecule
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> ?assay}
      OPTIONAL {?activity <http://rdf.farmbio.uu.se/chembl/onto/#type> ?typeOfActivity}

## Assayの情報(?assay=>?target)
?assay <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay>
         OPTIONAL {?assay <http://www.w3.org/2002/07/owl#equivalentClass> ?equivalentClassOfAssay}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> ?description}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTargetScore> ?targetScore}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> ?assayType}
         OPTIONAL {?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasTarget> ?target}

## Targetの情報(?target=>)
?target <http://www.w3.org/2002/07/owl#equivalentClass> ?targetOfequivalentClass
      OPTIONAL {?target <http://www.w3.org/2002/07/owl#sameAs> ?sameAs}
      OPTIONAL {?target <http://purl.org/dc/elements/1.1/title> ?title}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#organism> ?organism}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#hasTaxonomy> ?taxonomy}
      OPTIONAL {?target <http://rdf.farmbio.uu.se/chembl/onto/#classL1> ?class1}
}
  • 化合物の数
SELECT count(?molecule)
WHERE
{
?molecule <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity>
}
  • Assayの種類別件数
SELECT ?assayType count((?assayType) as ?totalAssayType)
WHERE
{
?assay <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> ?assayType.
}
GROUP BY ?assayType
  • 化合物の識別子(InChI, InChIKey, smilesなど)の記述例
## molecule
SELECT DISTINCT *
WHERE
{
{<http://linkedchemistry.info/chembl/molecule/m16485> <http://www.w3.org/2002/07/owl#equivalentClass> ?inchiURI}
    FILTER(regex(?inchiURI, "InChI", ""))
       OPTIONAL {<http://linkedchemistry.info/chembl/molecule/m16485> <http://www.blueobelisk.org/chemistryblogs/inchi> ?inchiLiteral}
       OPTIONAL {<http://linkedchemistry.info/chembl/molecule/m16485> <http://www.blueobelisk.org/chemistryblogs/smiles> ?smiles}
       OPTIONAL {<http://linkedchemistry.info/chembl/molecule/m16485> <http://www.blueobelisk.org/chemistryblogs/inchikey> ?inchikey}

}
chembl-rdf.txt · 最終更新: 2013/02/20 18:19 +0900 by kushidat