A set of SPARQL examples that are used in different SIB resources
Find zebrafish orthologs of disease-implicated (according to Nextprot SPARQL endpoint) human genes via Vertebrata-level orthogroup/s annotated with both IPR000719 (protein kinase domain) and GO:0048013 (ephrin receptor signaling pathway)
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>
PREFIX : <http://purl.orthodb.org/>
PREFIX np: <http://nextprot.org/rdf#>
PREFIX interpro: <http://www.ebi.ac.uk/interpro/entry/>
SELECT ?gene_zf ?gene_zf_name ?gene ?gene_name ?description ?go ?disease
WHERE {
SERVICE <https://sparql.nextprot.org/> {
select distinct ?entry ?disease WHERE {
?entry np:isoform / np:disease / rdfs:comment ?disease
}
}
?gene rdfs:seeAlso ?entry;
:name ?gene_name ;
:description ?description.
?gene :memberOf ?og .
?og :xref/:xrefResource interpro:IPR000719 , GO:0048013.
?og :ogBuiltAt/up:scientificName "Vertebrata";
:hasMember ?gene_zf.
?gene_zf :name ?gene_zf_name;
up:organism/a [up:scientificName "Danio rerio"].
} ORDER BY ?disease
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v5("?description"):::projected
v1("?disease"):::projected
v2("?entry")
v3("?gene"):::projected
v4("?gene_name"):::projected
v7("?gene_zf"):::projected
v8("?gene_zf_name"):::projected
v6("?og")
a1((" "))
a2((" "))
a3((" "))
a4((" "))
a6((" "))
a5((" "))
c12(["GO:0048013"]):::iri
c17(["Danio rerio"]):::literal
c15(["Vertebrata"]):::literal
c11(["interpro:IPR000719"]):::iri
subgraph s1["https://sparql.nextprot.org/"]
style s1 stroke-width:4px;
v2 --"np:isoform"--> a1
a1 --"np:disease"--> a2
a2 --"rdfs:comment"--> v1
end
v3 --"rdfs:seeAlso"--> v2
v3 --":name"--> v4
v3 --":description"--> v5
v3 --":memberOf"--> v6
v6 --":xref"--> a3
a3 --":xrefResource"--> c11
a3 --":xrefResource"--> c12
v6 --":ogBuiltAt"--> a4
a4 --"up:scientificName"--> c15
v6 --":hasMember"--> v7
v7 --":name"--> v8
a5 --"up:scientificName"--> c17
v7 --"up:organism"--> a6
a6 --"a"--> a5