BH12.12/EBI RDF

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SPARQLthon13トップへ

SPARQLthon15トップへ

目次

リンク

SWAT4LS 2013 Tutorial

EBI SPARQL Endpoints

Expression Atlas：http://www.ebi.ac.uk/rdf/services/atlas/sparql

ChEMBL：http://www.ebi.ac.uk/rdf/services/chembl/sparql

Reactome：http://www.ebi.ac.uk/rdf/services/reactome/sparql

BioSamples：http://www.ebi.ac.uk/rdf/services/biosamples/sparql

BioModels：http://www.ebi.ac.uk/rdf/services/biomodels/sparql


データセットに関するメタデータを取得して、データセットの概略を知る

  • グラフ名を主語としてstatementを取得する 
sparqling -s http://www.ebi.ac.uk/rdf/services/atlas/sparql -S '<http://rdf.ebi.ac.uk/dataset/atlas/13.07>' | sort | abbrev_prefix


5つのendpointにおいて共通して使われている述語

  • dc:title
  • dc:description
  • dc:license
  • pav:version
  • void:Dataset
  • void:sparqlEndPoint
  • void:triples
  • void:vocabulary

Expression Atlas 

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix expAtlasRes: <http://rdf.ebi.ac.uk/resource/atlas/> .
@prefix expAtlasData: <http://rdf.ebi.ac.uk/dataset/atlas/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix ensemblId: <http://identifiers.org/ensembl/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ebiData: <http://rdf.ebi.ac.uk/dataset/> .
@prefix dbpedRes: <http://dbpedia.org/resource/> .
@prefix ebiTerms: <http://rdf.ebi.ac.uk/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pav: <http://purl.org/pav/2.0/> .
@prefix obo: <http://purl.org/obo/> .

expAtlasData:13.07 dc:creator <http://www.ebi.ac.uk/fgpt> .
expAtlasData:13.07 dc:description "RDF representation of all the experiments loaded into the Gene Expression Atlas database."@en .
expAtlasData:13.07 dc:issued "2013-07-19T20:16:03.0"^^xsd:dateTime .
expAtlasData:13.07 dc:license <http://www.ebi.ac.uk/Information/termsofuse.html> .
expAtlasData:13.07 dc:publisher <http://www.ebi.ac.uk> .
expAtlasData:13.07 dc:subject dbpedRes:Gene_expression .
expAtlasData:13.07 dc:subject <http://edamontology.org/topic_0203> .
expAtlasData:13.07 dc:title "Gene Expression Atlas RDF"@en .
expAtlasData:13.07 pav:derivedFrom <http://www.ebi.ac.uk/gxa> .
expAtlasData:13.07 pav:importedBy <http://www.ebi.ac.uk/fgpt> .
expAtlasData:13.07 pav:importedOn "2013-07-19T20:16:03.0"^^xsd:dateTime .
expAtlasData:13.07 pav:version "13.07"^^xsd:string .
expAtlasData:13.07 void:dataDump <ftp://ftp.ebi.ac.uk//pub/databases/microarray/data/gxa/rdf/atlas-rdf-13.07.tar.gz> .
expAtlasData:13.07 void:exampleResource ensemblId:ENSG00000012048 .
expAtlasData:13.07 void:exampleResource expAtlasRes:A-AFFY-39:gnf1m23755_a_at .
expAtlasData:13.07 void:exampleResource expAtlasRes:E-MEXP-114 .
expAtlasData:13.07 void:exampleResource efo:EFO_0000270 .
expAtlasData:13.07 void:sparqlEndpoint <http://www.ebi.ac.uk/rdf/services/atlas/sparql> .
expAtlasData:13.07 void:triples "447149547"^^xsd:integer .
expAtlasData:13.07 void:vocabulary obo:CHEBI .
expAtlasData:13.07 void:vocabulary obo:CL .
expAtlasData:13.07 void:vocabulary obo:GO .
expAtlasData:13.07 void:vocabulary obo:NCBITaxon .
expAtlasData:13.07 void:vocabulary obo:OBO_REL .
expAtlasData:13.07 void:vocabulary obo:PATO .
expAtlasData:13.07 void:vocabulary ebiTerms:atlas .
expAtlasData:13.07 void:vocabulary <http://semanticscience.org/ontology/sio.owl> .
expAtlasData:13.07 void:vocabulary <http://www.ebi.ac.uk/efo> .
expAtlasData:13.07 rdf:type void:Dataset .
expAtlasData:13.07 rdf:type owl:NamedIndividual .
expAtlasData:13.07 prov:specializationOf ebiData:atlas .
expAtlasData:13.07 foaf:homepage <http://www.ebi.ac.uk/rdf/services/atlas> .
  • foaf:homepage は Atlas RDF
  • pav:derivedFrom は Atras
  • dc:publisher は EBI
  • dc:creator と pav:inportedBy は FGPT
  • prov:specializationOf は Atlas RDF


  • void:exampleResource
  • void:dataDump


  • dc:issued と pav:importedOn が同じ値


  • dc:subject

ChEMBL 

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix chemblData: <http://rdf.ebi.ac.uk/dataset/chembl/> .
@prefix voag: <http://voag.linkedmodel.org/voag#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pav: <http://purl.org/pav/> .

chemblData:17.0 dc:created "2009-10-28T00:00:00.0"^^xsd:dateTime .
chemblData:17.0 dc:description "ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs." .
chemblData:17.0 dc:license <http://creativecommons.org/licenses/by-sa/3.0/> .
chemblData:17.0 dc:modified "2013-08-29T00:00:00.0"^^xsd:dateTime .
chemblData:17.0 dc:publisher <https://www.ebi.ac.uk/> .
chemblData:17.0 dc:title "The ChEMBL Database" .
chemblData:17.0 pav:createdBy <http://orcid.org/0000-0002-8011-0300> .
chemblData:17.0 pav:createdOn "2009-10-28T00:00:00.0"^^xsd:dateTime .
chemblData:17.0 pav:lastUpdateOn "2013-08-29T00:00:00.0"^^xsd:dateTime .
chemblData:17.0 pav:previousVersion chemblData:16.2 .
chemblData:17.0 pav:version "17.0" .
chemblData:17.0 void:exampleResource <http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL941> .
chemblData:17.0 void:sparqlEndpoint <http://www.ebi.ac.uk/rdf/services/chembl/sparql> .
chemblData:17.0 void:subset chemblData:17.0/activity_dataset .
chemblData:17.0 void:subset chemblData:17.0/assay_dataset .
chemblData:17.0 void:subset chemblData:17.0/biocmpt_dataset .
chemblData:17.0 void:subset chemblData:17.0/document_dataset .
chemblData:17.0 void:subset chemblData:17.0/journal_dataset .
chemblData:17.0 void:subset chemblData:17.0/molecule_dataset .
chemblData:17.0 void:subset chemblData:17.0/protclass_dataset .
chemblData:17.0 void:subset chemblData:17.0/source_dataset .
chemblData:17.0 void:subset chemblData:17.0/target_dataset .
chemblData:17.0 void:subset chemblData:17.0/targetcmpt_dataset .
chemblData:17.0 void:subset chemblData:17.0/unichem_dataset .
chemblData:17.0 void:triples "374762364"^^xsd:integer .
chemblData:17.0 void:uriSpace "http://rdf.ebi.ac.uk/resource/chembl/" .
chemblData:17.0 void:vocabulary <http://purl.org/dc/terms> .
chemblData:17.0 void:vocabulary <http://purl.org/ontology/bibo> .
chemblData:17.0 void:vocabulary <http://purl.org/spar/cito> .
chemblData:17.0 void:vocabulary <http://semanticscience.org/ontology/cheminf.owl> .
chemblData:17.0 void:vocabulary <http://semanticscience.org/ontology/sio.owl> .
chemblData:17.0 void:vocabulary <http://www.bioassayontology.org/bao> .
chemblData:17.0 void:vocabulary <http://www.w3.org/1999/02/22-rdf-syntax-ns> .
chemblData:17.0 void:vocabulary <http://www.w3.org/2000/01/rdf-schema> .
chemblData:17.0 void:vocabulary <http://www.w3.org/2001/XMLSchema> .
chemblData:17.0 void:vocabulary <http://www.w3.org/2002/07/owl> .
chemblData:17.0 void:vocabulary <http://www.w3.org/2004/02/skos/core> .
chemblData:17.0 voag:frequencyOfChange <http://purl.org/cld/freq/quarterly> .
chemblData:17.0 rdf:type void:Dataset .
chemblData:17.0 dcat:landingPage <https://www.ebi.ac.uk/chembl> .
chemblData:17.0 foaf:page <ftp://ftp.ebi.ac.uk/pub/databases/chembl/> .
  • foaf:page は ftpサイト
  • dcat:landingPage は ChEMBLサイト
  • dc:publisher は EBI
  • pav:createdBy は 研究者


  • void:uriSpace
  • void:exampleResource


  • dc:created と pav:createdOn は 2009
  • dc:modified と pav:lastUpdateOn は 2013
  • voag:frequencyOfChange


  • pav:previousVersion
  • void:subset

Reactome 

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix reactData: <http://rdf.ebi.ac.uk/dataset/reactome/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pav: <http://purl.org/pav/2.0/> .
@prefix obo: <http://purl.org/obo/> .

reactData:46 dc:description "BioPAX/RDF representation of the Reactome database"^^xsd:string .
reactData:46 dc:license <http://www.ebi.ac.uk/termsofuse> .
reactData:46 dc:publisher <http://www.ebi.ac.uk/rdf/services/reactome/> .
reactData:46 dc:title "Reactome BioPAX/RDF"^^xsd:string .
reactData:46 pav:importedBy <http://www.ebi.ac.uk/rdf/services/reactome/> .
reactData:46 pav:importedFrom <http://www.reactome.org/> .
reactData:46 pav:importedOn "Mon Nov 25 15:54:33 GMT 2013"^^xsd:string .
reactData:46 pav:previousVersion reactData:45 .
reactData:46 pav:version "46"^^xsd:string .
reactData:46 void:dataDump <ftp://ftp.ebi.ac.uk/pub/databases/RDF/reactome/r46/reactome-biopax.tar.bz2> .
reactData:46 void:sparqlEndPoint <http://www.ebi.ac.uk/rdf/services/reactome/sparql> .
reactData:46 void:triples "12487422"^^xsd:integer .
reactData:46 void:uriSpace "http://www.reactome.org/"^^xsd:string .
reactData:46 void:vocabulary obo:CHEBI .
reactData:46 void:vocabulary obo:CL .
reactData:46 void:vocabulary obo:GO .
reactData:46 void:vocabulary obo:NCBITaxon .
reactData:46 rdf:type void:Dataset .
reactData:46 foaf:homepage <http://www.ebi.ac.uk/rdf/services/reactome/> .
  • foaf:homepage は Reactome RDF
  • dc:publisher が Reactome RDF
  • pav:importedBy が Reactome RDF
  • pav:importedFrom Reactomeサイト


  • void:uriSpace
  • void:dataDump


  • pav:importedOn


  • pav:previousVersion

BioSamples 

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix biosamData: <http://rdf.ebi.ac.uk/dataset/biosamples/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix oboLib: <http://purl.obolibrary.org/obo/> .
@prefix ebiData: <http://rdf.ebi.ac.uk/dataset/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pav: <http://purl.org/pav/2.0/> .

biosamData:v20131202 dc:description "RDF representation of the EBI Biosample Database"^^xsd:string .
biosamData:v20131202 dc:license <http://www.ebi.ac.uk/Information/termsofuse.html> .
biosamData:v20131202 dc:publisher <http://rdf.ebi.ac.uk/resource/biosamples/biomedBridgesOrg> .
biosamData:v20131202 dc:publisher <http://rdf.ebi.ac.uk/resource/biosamples/biosamplesTeam> .
biosamData:v20131202 dc:subject <http://dbpedia.org/data/Category:Biological_specimens> .
biosamData:v20131202 dc:subject <http://edamontology.org/topic_3071> .
biosamData:v20131202 dc:subject <http://purl.bioontology.org/ontology/MESH/D019992> .
biosamData:v20131202 dc:subject oboLib:OBI_0000747 .
biosamData:v20131202 dc:title "EBI Biosamples Database"^^xsd:string .
biosamData:v20131202 pav:importedBy <http://rdf.ebi.ac.uk/resource/biosamples/biosamplesTeam> .
biosamData:v20131202 pav:importedFrom <http://www.ebi.ac.uk/biosamples> .
biosamData:v20131202 pav:importedOn "2013-12-02"^^xsd:date .
biosamData:v20131202 pav:previousVersion biosamData:v20131121 .
biosamData:v20131202 pav:version "v20131202" .
biosamData:v20131202 void:dataDump <ftp://ftp.ebi.ac.uk/pub/databases/RDF/biosd/biosamples-rdf-v20131202.tar.gz> .
biosamData:v20131202 void:sparqlEndpoint <http://www.ebi.ac.uk/rdf/services/biosamples/sparql> .
biosamData:v20131202 void:triples "102520402"^^xsd:integer .
biosamData:v20131202 void:uriSpace "http://rdf.ebi.ac.uk/resource/biosamples"^^xsd:string .
biosamData:v20131202 void:vocabulary oboLib:obi.owl .
biosamData:v20131202 void:vocabulary <http://purl.org/dc/terms/> .
biosamData:v20131202 void:vocabulary <http://purl.org/ontology/bibo/> .
biosamData:v20131202 void:vocabulary <http://purl.org/spar/fabio/> .
biosamData:v20131202 void:vocabulary <http://rdf.ebi.ac.uk/terms/biosd/> .
biosamData:v20131202 void:vocabulary <http://schema.org/> .
biosamData:v20131202 void:vocabulary <http://semanticscience.org/ontology/sio.owl> .
biosamData:v20131202 void:vocabulary efo:efo.owl .
biosamData:v20131202 void:vocabulary <http://xmlns.com/foaf/0.1/> .
biosamData:v20131202 rdf:type void:Dataset .
biosamData:v20131202 foaf:homepage ebiData:biosamples .
  • foaf:homepage BioSamples RDF
  • dc:publisher が BioSamplesチーム
  • pav:importedFrom は BioSamples


  • void:uriSpace
  • void:dataDump


  • pav:importedOn


  • pav:previousVersion
  • dc:subject

BioModels 

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix biomodData: <http://rdf.ebi.ac.uk/dataset/biomodels/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix pav: <http://purl.org/pav/2.0/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix obo: <http://purl.org/obo/> .

biomodData:26 dc:description "RDF representation of the BioModels database"^^xsd:string .
biomodData:26 dc:license <http://www.ebi.ac.uk/biomodels-main/termsofuse> .
biomodData:26 dc:publisher <http://www.ebi.ac.uk/rdf/services/biomodels> .
biomodData:26 dc:title "BioModels RDF"^^xsd:string .
biomodData:26 pav:importedBy <http://www.ebi.ac.uk/rdf/services/biomodels> .
biomodData:26 pav:importedFrom <http://www.ebi.ac.uk/biomodels/> .
biomodData:26 pav:importedOn "Mon Nov 25 14:44:17 GMT 2013"^^xsd:string .
biomodData:26 pav:previousVersion biomodData:25 .
biomodData:26 pav:version "26"^^xsd:string .
biomodData:26 void:dataDump <ftp://ftp.ebi.ac.uk/pub/databases/RDF/biomodels/r26/biomodels-rdf.tar.bz2> .
biomodData:26 void:sparqlEndPoint <http://www.ebi.ac.uk/rdf/services/biomodels/sparql> .
biomodData:26 void:triples "11385558"^^xsd:integer .
biomodData:26 void:uriSpace "http://identifiers.org/biomodels.db/"^^xsd:string .
biomodData:26 void:vocabulary obo:CHEBI .
biomodData:26 void:vocabulary obo:CL .
biomodData:26 void:vocabulary obo:GO .
biomodData:26 void:vocabulary obo:NCBITaxon .
biomodData:26 rdf:type void:Dataset .
biomodData:26 foaf:homepage <http://www.ebi.ac.uk/rdf/services/biomodels> .
  • dc:publisher が BioModels RDF
  • foaf:homepage は BioModels RDF
  • pav:importedBy は BioModels RDF
  • pav:importedFrom は BioModels


  • void:dataDump


  • pav:previousVersion
「/mw/BH12.12/EBI_RDF」より作成