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Difference between revisions of "SemWeb:Bio2RDF Endpoints"

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Here are the current working Sparql Endpoints for Bio2RDF has of July 7th 2010, 15:48 PM
+
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
 +
<pre>
 +
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
 +
<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://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
 +
<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
 +
<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
 +
<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
 +
<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://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
 +
<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
 +
<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
 +
 +
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]

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

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

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]

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