A set of SPARQL examples that are used in different SIB resources
Variants with phenotype annotation that map to a 3D structure
PREFIX : <http://nextprot.org/rdf/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?entry (str(?pfname) as ?phenovar) (concat(str(sample(?pdbac)),"...") as ?pdbsample) WHERE {
?entry :gene / :name / rdfs:label ?gen .
?entry :isoform ?iso.
?iso :proteoform ?pf .
?pf rdfs:label ?pfname .
?pf :phenotypicVariation ?pv1 .
?pf :difference ?pfmod .
?pfmod a :Variant .
?pfmod :start ?vstart; :end ?vend .
?iso :pdbMapping ?pdbmap.
?pdbmap rdfs:comment ?pdbac.
?pdbmap :start ?pdbstart ; :end ?pdbend.
filter(?pdbstart <= ?vstart && ?pdbend >= ?vend )
} group by ?entry ?pfname
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v14("?_anon_aaf95e3c346c4c97af230d5bcfeba8ab2668"):::projected
v5("?entry"):::projected
v6("?gen")
v7("?iso")
v13("?pdbac")
v3("?pdbend")
v12("?pdbmap")
v16("?pdbsample")
v1("?pdbstart")
v8("?pf")
v11("?pfmod")
v9("?pfname"):::projected
v15("?phenovar")
v10("?pv1")
v4("?vend")
v2("?vstart")
a1((" "))
a2((" "))
c9([":Variant"]):::iri
f0[["?pdbstart <= ?vstart?pdbend >= ?vend"]]
f0 --> v1
f0 --> v2
f0 --> v3
f0 --> v4
v5 --":gene"--> a1
a1 --":name"--> a2
a2 --"rdfs:label"--> v6
v5 --":isoform"--> v7
v7 --":proteoform"--> v8
v8 --"rdfs:label"--> v9
v8 --":phenotypicVariation"--> v10
v8 --":difference"--> v11
v11 --"a"--> c9
v11 --":start"--> v2
v11 --":end"--> v4
v7 --":pdbMapping"--> v12
v12 --"rdfs:comment"--> v13
v12 --":start"--> v1
v12 --":end"--> v3
bind2[/"sample(?pdbac)"/]
v13 --o bind2
bind2 --as--o v14
bind3[/"str(?pfname)"/]
v9 --o bind3
bind3 --as--o v15
bind4[/"concat(str(),'...')"/]
null --o bind4
bind4 --as--o v16