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Difference between revisions of "SemWeb:Bio2RDF Endpoints"
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− | Here are the current working Sparql Endpoints for Bio2RDF | + | Here are the current working Sparql Endpoints for Bio2RDF as of July 7th 2010, 17:23 PM |
* http://pdb.bio2rdf.org/sparql | * http://pdb.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | SELECT | ||
+ | * | ||
+ | WHERE | ||
+ | { | ||
+ | <http://bio2rdf.org/pdb:1GOF> ?p ?o . | ||
+ | optional {?o ?p2 ?o2 .} | ||
+ | optional {?o2 ?p3 ?o3 .} | ||
+ | } | ||
+ | </pre> | ||
+ | |||
* http://geneid-test.bio2rdf.org/sparql | * http://geneid-test.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select distinct ?g ?o | ||
+ | where { | ||
+ | graph ?g | ||
+ | { | ||
+ | ?s ?p ?o . | ||
+ | ?o bif:contains "HK1" . | ||
+ | } | ||
+ | } | ||
+ | </pre> | ||
+ | |||
* http://pubmed.bio2rdf.org/sparql | * http://pubmed.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?label ?o | ||
+ | where | ||
+ | { | ||
+ | graph ?g { | ||
+ | ?s ?p ?o . | ||
+ | ?o bif:contains "HK1" . | ||
+ | } | ||
+ | graph ?g { | ||
+ | ?s2 a <http://bio2rdf.org/pubmed:JournalArticle> . | ||
+ | ?s2 rdfs:label ?label . | ||
+ | } | ||
+ | } | ||
+ | limit 5 | ||
+ | </pre> | ||
+ | |||
* http://refseq.bio2rdf.org/sparql | * http://refseq.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select distinct ?rl ?fs ?fe | ||
+ | where { | ||
+ | ?o <http://bio2rdf.org/ncbi_resource:featureStart> ?fs . | ||
+ | filter (xsd:integer(?fs) < 10000) | ||
+ | ?refseq <http://bio2rdf.org/ncbi_resource:feature> ?o . | ||
+ | ?refseq rdfs:label $rl . | ||
+ | ?o <http://bio2rdf.org/ncbi_resource:featureEnd> ?fe . | ||
+ | } | ||
+ | limit 5 | ||
+ | </pre> | ||
+ | |||
* http://omim.bio2rdf.org/sparql | * http://omim.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?ol ?desc | ||
+ | where { | ||
+ | ?omim a <http://bio2rdf.org/omim_resource:MendelianDisorders> . | ||
+ | ?omim rdfs:label ?ol . | ||
+ | ?omim <http://purl.org/dc/terms/description> ?desc . | ||
+ | ?desc bif:contains "HK1" . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://affymetrix.bio2rdf.org/sparql | * http://affymetrix.bio2rdf.org/sparql | ||
− | * http://atlas.bio2rdf.org/sparql | + | <pre> |
− | * http://quebec.bio2rdf.org/sparql | + | select ?al ?o |
+ | where { | ||
+ | ?s a <http://bio2rdf.org/ns/affymetrix#Probeset> . | ||
+ | ?s rdfs:label ?al . | ||
+ | ?s ?p ?o . | ||
+ | ?o bif:contains "calcium" . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
+ | * http://atlas.bio2rdf.org/sparql and * http://quebec.bio2rdf.org/sparql are the same | ||
+ | <pre> | ||
+ | SELECT ?label1, count(*) | ||
+ | WHERE { | ||
+ | ?s1 ?p1 ?o1 . | ||
+ | ?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 . | ||
+ | ?o1 bif:contains "morissette" . | ||
+ | } | ||
+ | ORDER BY DESC (count(*)) | ||
+ | </pre> | ||
+ | |||
* http://bind.bio2rdf.org/sparql | * http://bind.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?inter ?inter2 ?part1_title ?part2_title ?part3_title | ||
+ | where { | ||
+ | ?inter a <http://bio2rdf.org/bind#Interaction> . | ||
+ | ?inter <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part1 . | ||
+ | ?inter <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part2 . | ||
+ | filter(?part1 != ?part2) . | ||
+ | ?part1 <http://purl.org/dc/elements/1.1/title> ?part1_title . | ||
+ | ?part2 <http://purl.org/dc/elements/1.1/title> ?part2_title . | ||
+ | ?inter2 a <http://bio2rdf.org/bind#Interaction> . | ||
+ | ?inter2 <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part3 . | ||
+ | ?inter2 <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part4 . | ||
+ | filter(?part3 != ?part4) . | ||
+ | ?part3 <http://purl.org/dc/elements/1.1/title> ?part2_title . | ||
+ | ?part4 <http://purl.org/dc/elements/1.1/title> ?part3_title . | ||
+ | filter (?inter != ?inter2) . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://biocarta.bio2rdf.org/sparql | * http://biocarta.bio2rdf.org/sparql | ||
* http://biocyc.bio2rdf.org/sparql | * http://biocyc.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select distinct ?name ?LEFT_name ?RIGHT_name ?inter_name | ||
+ | where { | ||
+ | ?path a <http://bio2rdf.org/ns/biopax#pathway> . | ||
+ | ?path <http://bio2rdf.org/ns/biopax#NAME> ?name . | ||
+ | ?path <http://bio2rdf.org/ns/biopax#PATHWAY-COMPONENTS> ?comp . | ||
+ | ?comp <http://bio2rdf.org/ns/biopax#STEP-INTERACTIONS> ?inter . | ||
+ | ?inter <http://bio2rdf.org/ns/biopax#LEFT> ?LEFT . | ||
+ | ?inter <http://bio2rdf.org/ns/biopax#RIGHT> ?RIGHT . | ||
+ | ?inter <http://bio2rdf.org/ns/biopax#NAME> ?inter_name . | ||
+ | ?LEFT ?p ?o . | ||
+ | ?o <http://bio2rdf.org/ns/biopax#NAME> ?LEFT_name . | ||
+ | ?RIGHT ?p2 ?o2 . | ||
+ | ?o2 <http://bio2rdf.org/ns/biopax#NAME> ?RIGHT_name . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://biopax.bio2rdf.org/sparql | * http://biopax.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?name | ||
+ | where { | ||
+ | ?prot a <http://bio2rdf.org/ns/biopax#protein> . | ||
+ | ?prot <http://bio2rdf.org/ns/biopax#SHORT-NAME> ?name . | ||
+ | } | ||
+ | limit 10 | ||
+ | </pre> | ||
+ | |||
* http://chebi.bio2rdf.org/sparql | * http://chebi.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?comp_label ?mass | ||
+ | where { | ||
+ | ?comp a <http://bio2rdf.org/ns/chebi#Compound> . | ||
+ | ?comp rdfs:label ?comp_label . | ||
+ | ?comp <http://bio2rdf.org/ns/bio2rdf#mass> ?mass . | ||
+ | filter(xsd:double(?mass) > 1500) . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://cpath.bio2rdf.org/sparql | * http://cpath.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?name | ||
+ | where { | ||
+ | ?prot a <http://bio2rdf.org/ns/biopax#protein> . | ||
+ | ?prot <http://bio2rdf.org/ns/biopax#NAME> ?name . | ||
+ | } | ||
+ | limit 10 | ||
+ | </pre> | ||
+ | |||
* http://ec.bio2rdf.org/sparql | * http://ec.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?enzlabel ?sub | ||
+ | where { | ||
+ | ?enz a <http://bio2rdf.org/ns/kegg#Enzyme> . | ||
+ | ?enz rdfs:label ?enzlabel . | ||
+ | ?enz <http://bio2rdf.org/ns/kegg#xSubstrate> ?sub . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://genbank.bio2rdf.org/sparql | * http://genbank.bio2rdf.org/sparql | ||
* http://geneid.bio2rdf.org/sparql | * http://geneid.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?label ?from ?to | ||
+ | where { | ||
+ | ?s a <http://bio2rdf.org/ns/geneid#Gene> . | ||
+ | ?s rdfs:label ?label . | ||
+ | ?s <http://bio2rdf.org/ns/geneid#fromInterval> ?from . | ||
+ | ?s <http://bio2rdf.org/ns/geneid#toInterval> ?to . | ||
+ | filter(xsd:integer(?from) < 100) . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
* http://go.bio2rdf.org/sparql | * http://go.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?golabel ?parentlabel ?greatparentlabel | ||
+ | where { | ||
+ | ?go a <http://bio2rdf.org/ns/go#Term> . | ||
+ | ?go rdfs:label ?golabel . | ||
+ | ?golabel bif:contains "liver" . | ||
+ | ?parent ?p ?go . | ||
+ | ?parent rdfs:label ?parentlabel . | ||
+ | ?greatparent ?p2 ?parent . | ||
+ | ?greatparent rdfs:label ?greatparentlabel . | ||
+ | } | ||
+ | </pre> | ||
+ | |||
* http://hgnc.bio2rdf.org/sparql | * http://hgnc.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?label ?url ?symbol | ||
+ | where { | ||
+ | ?symbol a <http://bio2rdf.org/ns/hgnc#Symbol> . | ||
+ | ?hugo ?p ?symbol . | ||
+ | ?hugo <http://bio2rdf.org/ns/bio2rdf#url> ?url . | ||
+ | ?hugo rdfs:label ?label . | ||
+ | } | ||
+ | limit 200 | ||
+ | </pre> | ||
+ | |||
+ | * http://homologene.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?genelabel ?cluster | ||
+ | where { | ||
+ | ?cluster a <http://bio2rdf.org/homologene#Cluster> . | ||
+ | ?gene ?p ?cluster . | ||
+ | ?gene rdfs:label ?genelabel . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
+ | * http://inoh.bio2rdf.org/sparql | ||
+ | * http://iproclass.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?ident ?go | ||
+ | where { | ||
+ | ?iclass a <http://bio2rdf.org/ns/iproclass#AnnotationClass> . | ||
+ | ?iclass <http://purl.org/dc/elements/1.1/identifier> ?ident . | ||
+ | ?iclass <http://bio2rdf.org/ns/iproclass#xGo> ?go . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
+ | * http://kegg.bio2rdf.org/sparql | ||
+ | <pre> | ||
+ | select ?label ?rel ?entrylabel | ||
+ | where { | ||
+ | ?path a <http://bio2rdf.org/ns/kegg#Pathway> . | ||
+ | ?path rdfs:label ?label . | ||
+ | ?path <http://bio2rdf.org/ns/kegg#xRelation> ?rel . | ||
+ | ?rel <http://bio2rdf.org/ns/kegg#xEntry1> ?entry . | ||
+ | ?entry <http://bio2rdf.org/ns/kegg#xRef> ?o . | ||
+ | ?o rdfs:label ?entrylabel . | ||
+ | } | ||
+ | limit 100 | ||
+ | </pre> | ||
+ | |||
+ | * http://mesh.bio2rdf.org/sparql | ||
+ | * http://mgi.bio2rdf.org/sparql | ||
+ | * http://obo.bio2rdf.org/sparql | ||
+ | * http://pid.bio2rdf.org/sparql | ||
+ | * http://protein.bio2rdf.org/sparql | ||
+ | * http://pubchem.bio2rdf.org/sparql | ||
+ | * http://reactome.bio2rdf.org/sparql | ||
+ | * http://registry.bio2rdf.org/sparql | ||
+ | * http://release.bio2rdf.org/sparql | ||
+ | * http://sgd.bio2rdf.org/sparql | ||
+ | * http://taxonomy.bio2rdf.org/sparql | ||
+ | * http://uniparc.bio2rdf.org/sparql | ||
+ | * http://uniprot.bio2rdf.org/sparql | ||
+ | * http://unists.bio2rdf.org/sparql | ||
+ | * http://uniref.bio2rdf.org/sparql | ||
URI are build with this pattern | URI are build with this pattern |
Latest revision as of 21:15, 8 July 2010
Here are the current working Sparql Endpoints for Bio2RDF as of July 7th 2010, 17:23 PM
SELECT * WHERE { <http://bio2rdf.org/pdb:1GOF> ?p ?o . optional {?o ?p2 ?o2 .} optional {?o2 ?p3 ?o3 .} }
select distinct ?g ?o where { graph ?g { ?s ?p ?o . ?o bif:contains "HK1" . } }
select ?label ?o where { graph ?g { ?s ?p ?o . ?o bif:contains "HK1" . } graph ?g { ?s2 a <http://bio2rdf.org/pubmed:JournalArticle> . ?s2 rdfs:label ?label . } } limit 5
select distinct ?rl ?fs ?fe where { ?o <http://bio2rdf.org/ncbi_resource:featureStart> ?fs . filter (xsd:integer(?fs) < 10000) ?refseq <http://bio2rdf.org/ncbi_resource:feature> ?o . ?refseq rdfs:label $rl . ?o <http://bio2rdf.org/ncbi_resource:featureEnd> ?fe . } limit 5
select ?ol ?desc where { ?omim a <http://bio2rdf.org/omim_resource:MendelianDisorders> . ?omim rdfs:label ?ol . ?omim <http://purl.org/dc/terms/description> ?desc . ?desc bif:contains "HK1" . } limit 100
select ?al ?o where { ?s a <http://bio2rdf.org/ns/affymetrix#Probeset> . ?s rdfs:label ?al . ?s ?p ?o . ?o bif:contains "calcium" . } limit 100
- http://atlas.bio2rdf.org/sparql and * http://quebec.bio2rdf.org/sparql are the same
SELECT ?label1, count(*) WHERE { ?s1 ?p1 ?o1 . ?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 . ?o1 bif:contains "morissette" . } ORDER BY DESC (count(*))
select ?inter ?inter2 ?part1_title ?part2_title ?part3_title where { ?inter a <http://bio2rdf.org/bind#Interaction> . ?inter <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part1 . ?inter <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part2 . filter(?part1 != ?part2) . ?part1 <http://purl.org/dc/elements/1.1/title> ?part1_title . ?part2 <http://purl.org/dc/elements/1.1/title> ?part2_title . ?inter2 a <http://bio2rdf.org/bind#Interaction> . ?inter2 <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part3 . ?inter2 <http://bio2rdf.org/ns/ns/bind#interactionPart> ?part4 . filter(?part3 != ?part4) . ?part3 <http://purl.org/dc/elements/1.1/title> ?part2_title . ?part4 <http://purl.org/dc/elements/1.1/title> ?part3_title . filter (?inter != ?inter2) . } limit 100
select distinct ?name ?LEFT_name ?RIGHT_name ?inter_name where { ?path a <http://bio2rdf.org/ns/biopax#pathway> . ?path <http://bio2rdf.org/ns/biopax#NAME> ?name . ?path <http://bio2rdf.org/ns/biopax#PATHWAY-COMPONENTS> ?comp . ?comp <http://bio2rdf.org/ns/biopax#STEP-INTERACTIONS> ?inter . ?inter <http://bio2rdf.org/ns/biopax#LEFT> ?LEFT . ?inter <http://bio2rdf.org/ns/biopax#RIGHT> ?RIGHT . ?inter <http://bio2rdf.org/ns/biopax#NAME> ?inter_name . ?LEFT ?p ?o . ?o <http://bio2rdf.org/ns/biopax#NAME> ?LEFT_name . ?RIGHT ?p2 ?o2 . ?o2 <http://bio2rdf.org/ns/biopax#NAME> ?RIGHT_name . } limit 100
select ?name where { ?prot a <http://bio2rdf.org/ns/biopax#protein> . ?prot <http://bio2rdf.org/ns/biopax#SHORT-NAME> ?name . } limit 10
select ?comp_label ?mass where { ?comp a <http://bio2rdf.org/ns/chebi#Compound> . ?comp rdfs:label ?comp_label . ?comp <http://bio2rdf.org/ns/bio2rdf#mass> ?mass . filter(xsd:double(?mass) > 1500) . } limit 100
select ?name where { ?prot a <http://bio2rdf.org/ns/biopax#protein> . ?prot <http://bio2rdf.org/ns/biopax#NAME> ?name . } limit 10
select ?enzlabel ?sub where { ?enz a <http://bio2rdf.org/ns/kegg#Enzyme> . ?enz rdfs:label ?enzlabel . ?enz <http://bio2rdf.org/ns/kegg#xSubstrate> ?sub . } limit 100
select ?label ?from ?to where { ?s a <http://bio2rdf.org/ns/geneid#Gene> . ?s rdfs:label ?label . ?s <http://bio2rdf.org/ns/geneid#fromInterval> ?from . ?s <http://bio2rdf.org/ns/geneid#toInterval> ?to . filter(xsd:integer(?from) < 100) . } limit 100
select ?golabel ?parentlabel ?greatparentlabel where { ?go a <http://bio2rdf.org/ns/go#Term> . ?go rdfs:label ?golabel . ?golabel bif:contains "liver" . ?parent ?p ?go . ?parent rdfs:label ?parentlabel . ?greatparent ?p2 ?parent . ?greatparent rdfs:label ?greatparentlabel . }
select ?label ?url ?symbol where { ?symbol a <http://bio2rdf.org/ns/hgnc#Symbol> . ?hugo ?p ?symbol . ?hugo <http://bio2rdf.org/ns/bio2rdf#url> ?url . ?hugo rdfs:label ?label . } limit 200
select ?genelabel ?cluster where { ?cluster a <http://bio2rdf.org/homologene#Cluster> . ?gene ?p ?cluster . ?gene rdfs:label ?genelabel . } limit 100
select ?ident ?go where { ?iclass a <http://bio2rdf.org/ns/iproclass#AnnotationClass> . ?iclass <http://purl.org/dc/elements/1.1/identifier> ?ident . ?iclass <http://bio2rdf.org/ns/iproclass#xGo> ?go . } limit 100
select ?label ?rel ?entrylabel where { ?path a <http://bio2rdf.org/ns/kegg#Pathway> . ?path rdfs:label ?label . ?path <http://bio2rdf.org/ns/kegg#xRelation> ?rel . ?rel <http://bio2rdf.org/ns/kegg#xEntry1> ?entry . ?entry <http://bio2rdf.org/ns/kegg#xRef> ?o . ?o rdfs:label ?entrylabel . } limit 100
- http://mesh.bio2rdf.org/sparql
- http://mgi.bio2rdf.org/sparql
- http://obo.bio2rdf.org/sparql
- http://pid.bio2rdf.org/sparql
- http://protein.bio2rdf.org/sparql
- http://pubchem.bio2rdf.org/sparql
- http://reactome.bio2rdf.org/sparql
- http://registry.bio2rdf.org/sparql
- http://release.bio2rdf.org/sparql
- http://sgd.bio2rdf.org/sparql
- http://taxonomy.bio2rdf.org/sparql
- http://uniparc.bio2rdf.org/sparql
- http://uniprot.bio2rdf.org/sparql
- http://unists.bio2rdf.org/sparql
- http://uniref.bio2rdf.org/sparql
URI are build with this pattern
http://bio2rdf.org/[namespace]:[identifier]
To get information about this URI, you can either ask directly
http://bio2rdf.org/[namespace]:[identifier]
or ask the corresponding endpoint about it. The corresponding endpoints is located at
http://[namespace].bio2rdf.org/sparql
P.S.: The refseq endpoint is experimental. Instead of using the URI pattern http://bio2rdf.org/refseq:[identifier] it use http://bio2rdf.org/ncbi:[identifier]