A set of SPARQL examples that are used in different SIB resources
Check there are no entries with non-compliant glycosylation sites from UniProt
PREFIX : <http://nextprot.org/rdf/>
PREFIX cv: <http://nextprot.org/rdf/terminology/>
PREFIX source: <http://nextprot.org/rdf/source/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select distinct ?entry where { # Add ?glypos ?qual to idenfiy glycosylation site and quality
?entry :isoform ?iso.
?iso :swissprotDisplayed true ; :glycosylationSite ?glycosite.
?glycosite :start ?glypos; rdfs:comment ?desc; :quality ?qual .
filter(contains(?desc,"N-linked"))
?glycosite :evidence / :assignedBy source:Uniprot.
{
values ?forbiddom
{ cv:DO-00843 cv:DO-00082 cv:DO-00096 cv:DO-00098 cv:DO-00099 cv:DO-00100 cv:DO-00127 cv:DO-00135 cv:DO-00162 cv:DO-00212 cv:DO-00218 cv:DO-00224 cv:DO-00234 cv:DO-00847 cv:DO-00280 cv:DO-00282 cv:DO-00302 cv:DO-00310 cv:DO-00341 cv:DO-00343 cv:DO-00349 cv:DO-00350 cv:DO-00354 cv:DO-00376 cv:DO-00378 cv:DO-00404 cv:DO-00416 cv:DO-00418 cv:DO-00421 cv:DO-00415 cv:DO-00430 cv:DO-00462 cv:DO-00466 cv:DO-00467 cv:DO-00469 cv:DO-00477 cv:DO-00869 cv:DO-00555 cv:DO-00592 cv:DO-00602 cv:DO-00604 cv:DO-00779 cv:DO-00918 cv:DO-00943 cv:DO-00632 cv:DO-00636 cv:DO-00671 cv:DO-00691 cv:DO-00695 cv:DO-00700 cv:DO-00832 cv:DO-00741 cv:DO-00078 cv:DO-00057 cv:DO-00104 cv:DO-00144 cv:DO-00244 cv:DO-00273 cv:DO-00284 cv:DO-00387 cv:DO-00451 cv:DO-00561 cv:DO-00650 cv:DO-00658 cv:DO-00692 cv:DO-00697 cv:DO-00707 }
?iso :domain ?dom .
?dom :term ?forbiddom; :start ?forbidstart; :end ?forbidend .
}
union
{
values ?forbidtopodom
{ cv:CVTO_0001 cv:CVTO_0004 cv:CVTO_0013 cv:CVTO_0015 cv:CVTO_0022 }
?iso :topology ?top .
?top :term ?forbidtopodom; :start ?forbidstart; :end ?forbidend .
}
union
{ ?iso :signalPeptide ?sigpep . ?sigpep :start ?forbidstart; :end ?forbidend . }
union
{ ?iso :mitochondrialTransitPeptide ?trpep . ?trpep :start ?forbidstart; :end ?forbidend . }
filter((?glypos >= ?forbidstart) && (?glypos <= ?forbidend))
}
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v4("?desc")
v10("?dom")
v5("?entry"):::projected
v9("?forbiddom")
v3("?forbidend")
v2("?forbidstart")
v11("?forbidtopodom")
v7("?glycosite")
v1("?glypos")
v6("?iso")
v8("?qual")
v13("?sigpep")
v12("?top")
v14("?trpep")
a1((" "))
c11([":source/Uniprot"]):::iri
c4(["true^^xsd:boolean"]):::literal
f0[["?glypos >= ?forbidstart?glypos <= ?forbidend"]]
f0 --> v1
f0 --> v2
f0 --> v3
f1[["contains(?desc,'N-linked')"]]
f1 --> v4
v5 --":isoform"--> v6
v6 --":swissprotDisplayed"--> c4
v6 --":glycosylationSite"--> v7
v7 --":start"--> v1
v7 --"rdfs:comment"--> v4
v7 --":quality"--> v8
v7 --":evidence"--> a1
a1 --":assignedBy"--> c11
subgraph union0[" Union "]
subgraph union0l[" "]
style union0l fill:#abf,stroke-dasharray: 3 3;
subgraph union1[" Union "]
subgraph union1l[" "]
style union1l fill:#abf,stroke-dasharray: 3 3;
subgraph union2[" Union "]
subgraph union2l[" "]
style union2l fill:#abf,stroke-dasharray: 3 3;
v6 --":mitochondrialTransitPeptide"--> v14
v14 --":start"--> v2
v14 --":end"--> v3
end
subgraph union2r[" "]
style union2r fill:#abf,stroke-dasharray: 3 3;
v6 --":signalPeptide"--> v13
v13 --":start"--> v2
v13 --":end"--> v3
end
union2r <== or ==> union2l
end
end
subgraph union1r[" "]
style union1r fill:#abf,stroke-dasharray: 3 3;
bind2[/VALUES ?forbidtopodom/]
bind2-->v11
bind20([":terminology/CVTO_0001"])
bind20 --> bind2
bind21([":terminology/CVTO_0004"])
bind21 --> bind2
bind22([":terminology/CVTO_0013"])
bind22 --> bind2
bind23([":terminology/CVTO_0015"])
bind23 --> bind2
bind24([":terminology/CVTO_0022"])
bind24 --> bind2
v6 --":topology"--> v12
v12 --":term"--> v11
v12 --":start"--> v2
v12 --":end"--> v3
end
union1r <== or ==> union1l
end
end
subgraph union0r[" "]
style union0r fill:#abf,stroke-dasharray: 3 3;
bind3[/VALUES ?forbiddom/]
bind3-->v9
bind30([":terminology/DO-00843"])
bind30 --> bind3
bind31([":terminology/DO-00082"])
bind31 --> bind3
bind32([":terminology/DO-00096"])
bind32 --> bind3
bind33([":terminology/DO-00098"])
bind33 --> bind3
bind34([":terminology/DO-00099"])
bind34 --> bind3
bind35([":terminology/DO-00100"])
bind35 --> bind3
bind36([":terminology/DO-00127"])
bind36 --> bind3
bind37([":terminology/DO-00135"])
bind37 --> bind3
bind38([":terminology/DO-00162"])
bind38 --> bind3
bind39([":terminology/DO-00212"])
bind39 --> bind3
bind310([":terminology/DO-00218"])
bind310 --> bind3
bind311([":terminology/DO-00224"])
bind311 --> bind3
bind312([":terminology/DO-00234"])
bind312 --> bind3
bind313([":terminology/DO-00847"])
bind313 --> bind3
bind314([":terminology/DO-00280"])
bind314 --> bind3
bind315([":terminology/DO-00282"])
bind315 --> bind3
bind316([":terminology/DO-00302"])
bind316 --> bind3
bind317([":terminology/DO-00310"])
bind317 --> bind3
bind318([":terminology/DO-00341"])
bind318 --> bind3
bind319([":terminology/DO-00343"])
bind319 --> bind3
bind320([":terminology/DO-00349"])
bind320 --> bind3
bind321([":terminology/DO-00350"])
bind321 --> bind3
bind322([":terminology/DO-00354"])
bind322 --> bind3
bind323([":terminology/DO-00376"])
bind323 --> bind3
bind324([":terminology/DO-00378"])
bind324 --> bind3
bind325([":terminology/DO-00404"])
bind325 --> bind3
bind326([":terminology/DO-00416"])
bind326 --> bind3
bind327([":terminology/DO-00418"])
bind327 --> bind3
bind328([":terminology/DO-00421"])
bind328 --> bind3
bind329([":terminology/DO-00415"])
bind329 --> bind3
bind330([":terminology/DO-00430"])
bind330 --> bind3
bind331([":terminology/DO-00462"])
bind331 --> bind3
bind332([":terminology/DO-00466"])
bind332 --> bind3
bind333([":terminology/DO-00467"])
bind333 --> bind3
bind334([":terminology/DO-00469"])
bind334 --> bind3
bind335([":terminology/DO-00477"])
bind335 --> bind3
bind336([":terminology/DO-00869"])
bind336 --> bind3
bind337([":terminology/DO-00555"])
bind337 --> bind3
bind338([":terminology/DO-00592"])
bind338 --> bind3
bind339([":terminology/DO-00602"])
bind339 --> bind3
bind340([":terminology/DO-00604"])
bind340 --> bind3
bind341([":terminology/DO-00779"])
bind341 --> bind3
bind342([":terminology/DO-00918"])
bind342 --> bind3
bind343([":terminology/DO-00943"])
bind343 --> bind3
bind344([":terminology/DO-00632"])
bind344 --> bind3
bind345([":terminology/DO-00636"])
bind345 --> bind3
bind346([":terminology/DO-00671"])
bind346 --> bind3
bind347([":terminology/DO-00691"])
bind347 --> bind3
bind348([":terminology/DO-00695"])
bind348 --> bind3
bind349([":terminology/DO-00700"])
bind349 --> bind3
bind350([":terminology/DO-00832"])
bind350 --> bind3
bind351([":terminology/DO-00741"])
bind351 --> bind3
bind352([":terminology/DO-00078"])
bind352 --> bind3
bind353([":terminology/DO-00057"])
bind353 --> bind3
bind354([":terminology/DO-00104"])
bind354 --> bind3
bind355([":terminology/DO-00144"])
bind355 --> bind3
bind356([":terminology/DO-00244"])
bind356 --> bind3
bind357([":terminology/DO-00273"])
bind357 --> bind3
bind358([":terminology/DO-00284"])
bind358 --> bind3
bind359([":terminology/DO-00387"])
bind359 --> bind3
bind360([":terminology/DO-00451"])
bind360 --> bind3
bind361([":terminology/DO-00561"])
bind361 --> bind3
bind362([":terminology/DO-00650"])
bind362 --> bind3
bind363([":terminology/DO-00658"])
bind363 --> bind3
bind364([":terminology/DO-00692"])
bind364 --> bind3
bind365([":terminology/DO-00697"])
bind365 --> bind3
bind366([":terminology/DO-00707"])
bind366 --> bind3
v6 --":domain"--> v10
v10 --":term"--> v9
v10 --":start"--> v2
v10 --":end"--> v3
end
union0r <== or ==> union0l
end