https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s> .
@prefix sub: <https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
sub:get-kg-landscape-svg a <https://w3id.org/kpxl/grlc/grlc-query>;
dct:description "Count-only landscape figure for mvikg/r/kg: the number of distinct taxa (via biolink:in_taxon on currently-approved samples) rather than raw samples, alongside variants and phenotypes, and the number of approved cross-type associations among them (taxon-variant via the shared gene on an approved sample of that taxon, variant-phenotype via mvikg:isAssociatedWithVariant, taxon-phenotype via sosa:isResultOf on an approved sample of that taxon). Returns one row with a single ready-to-embed svg column; no geometric area-proportional layout, just three labelled boxes with the counts written on them.";
dct:license <https://creativecommons.org/licenses/by/4.0/>;
rdfs:label "Get mvikg/r/kg landscape SVG";
<https://w3id.org/kpxl/grlc/endpoint> <https://w3id.org/np/l/nanopub-query-1.1/repo/full>;
<https://w3id.org/kpxl/grlc/sparql> """prefix npa: <http://purl.org/nanopub/admin/>
prefix gen: <https://w3id.org/kpxl/gen/terms/>
prefix npx: <http://purl.org/nanopub/x/>
prefix dct: <http://purl.org/dc/terms/>
prefix sosa: <http://www.w3.org/ns/sosa/>
prefix biolink: <https://w3id.org/biolink/vocab/>
prefix mvikg: <http://example.org/mvikg/>
select ?svg where {
{
select (count(distinct ?taxon_s) as ?nSample) where {
{ select distinct ?sampleThing where {
graph ?da_s { ?sampleThing a <http://www.w3.org/ns/sosa/Sample> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_s), '/assertion$', '')) as ?dnp_s)
graph ?vda_s { ?admin_s ?verdictPred_s ?dnp_s . filter(?verdictPred_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_s . }
graph ?g_s { ?ri_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_s), '/assertion$', '')) as ?vnp_s)
graph ?vpi_s { ?vnp_s dct:created ?vcreatedRaw_s . }
bind(xsd:dateTime(?vcreatedRaw_s) as ?vcreated_s)
filter not exists {
graph ?vda2_s { ?admin2_s ?verdictPred2_s ?dnp_s . filter(?verdictPred2_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_s . }
graph ?g2_s { ?ri2_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_s), '/assertion$', '')) as ?vnp2_s)
graph ?vpi2_s { ?vnp2_s dct:created ?vcreated2Raw_s . }
filter(xsd:dateTime(?vcreated2Raw_s) > ?vcreated_s)
}
filter(?verdictPred_s = npx:approvesOf)
} }
{ select distinct ?sampleThing ?taxon_s where { ?sampleThing biolink:in_taxon ?taxon_s . } }
}
}
{
select (count(distinct ?variantThing) as ?nVariant) where {
{ select distinct ?variantThing where {
graph ?da_v { ?variantThing a <https://w3id.org/biolink/vocab/SequenceVariant> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_v), '/assertion$', '')) as ?dnp_v)
graph ?vda_v { ?admin_v ?verdictPred_v ?dnp_v . filter(?verdictPred_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_v . }
graph ?g_v { ?ri_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_v), '/assertion$', '')) as ?vnp_v)
graph ?vpi_v { ?vnp_v dct:created ?vcreatedRaw_v . }
bind(xsd:dateTime(?vcreatedRaw_v) as ?vcreated_v)
filter not exists {
graph ?vda2_v { ?admin2_v ?verdictPred2_v ?dnp_v . filter(?verdictPred2_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_v . }
graph ?g2_v { ?ri2_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_v), '/assertion$', '')) as ?vnp2_v)
graph ?vpi2_v { ?vnp2_v dct:created ?vcreated2Raw_v . }
filter(xsd:dateTime(?vcreated2Raw_v) > ?vcreated_v)
}
filter(?verdictPred_v = npx:approvesOf)
} }
}
}
{
select (count(distinct ?phenoThing) as ?nPheno) where {
{ select distinct ?phenoThing where {
graph ?da_p { ?phenoThing a <https://w3id.org/biolink/vocab/PhenotypicFeature> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_p), '/assertion$', '')) as ?dnp_p)
graph ?vda_p { ?admin_p ?verdictPred_p ?dnp_p . filter(?verdictPred_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_p . }
graph ?g_p { ?ri_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_p), '/assertion$', '')) as ?vnp_p)
graph ?vpi_p { ?vnp_p dct:created ?vcreatedRaw_p . }
bind(xsd:dateTime(?vcreatedRaw_p) as ?vcreated_p)
filter not exists {
graph ?vda2_p { ?admin2_p ?verdictPred2_p ?dnp_p . filter(?verdictPred2_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_p . }
graph ?g2_p { ?ri2_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_p), '/assertion$', '')) as ?vnp2_p)
graph ?vpi2_p { ?vnp2_p dct:created ?vcreated2Raw_p . }
filter(xsd:dateTime(?vcreated2Raw_p) > ?vcreated_p)
}
filter(?verdictPred_p = npx:approvesOf)
} }
}
}
{
select (count(distinct ?taxon_sv) as ?nSampleVariant) where {
{ select distinct ?sampleThing where {
graph ?da_sv_s { ?sampleThing a <http://www.w3.org/ns/sosa/Sample> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_sv_s), '/assertion$', '')) as ?dnp_sv_s)
graph ?vda_sv_s { ?admin_sv_s ?verdictPred_sv_s ?dnp_sv_s . filter(?verdictPred_sv_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_sv_s . }
graph ?g_sv_s { ?ri_sv_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_sv_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_sv_s), '/assertion$', '')) as ?vnp_sv_s)
graph ?vpi_sv_s { ?vnp_sv_s dct:created ?vcreatedRaw_sv_s . }
bind(xsd:dateTime(?vcreatedRaw_sv_s) as ?vcreated_sv_s)
filter not exists {
graph ?vda2_sv_s { ?admin2_sv_s ?verdictPred2_sv_s ?dnp_sv_s . filter(?verdictPred2_sv_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_sv_s . }
graph ?g2_sv_s { ?ri2_sv_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_sv_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_sv_s), '/assertion$', '')) as ?vnp2_sv_s)
graph ?vpi2_sv_s { ?vnp2_sv_s dct:created ?vcreated2Raw_sv_s . }
filter(xsd:dateTime(?vcreated2Raw_sv_s) > ?vcreated_sv_s)
}
filter(?verdictPred_sv_s = npx:approvesOf)
} }
{ select distinct ?variantThing where {
graph ?da_sv_v { ?variantThing a <https://w3id.org/biolink/vocab/SequenceVariant> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_sv_v), '/assertion$', '')) as ?dnp_sv_v)
graph ?vda_sv_v { ?admin_sv_v ?verdictPred_sv_v ?dnp_sv_v . filter(?verdictPred_sv_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_sv_v . }
graph ?g_sv_v { ?ri_sv_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_sv_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_sv_v), '/assertion$', '')) as ?vnp_sv_v)
graph ?vpi_sv_v { ?vnp_sv_v dct:created ?vcreatedRaw_sv_v . }
bind(xsd:dateTime(?vcreatedRaw_sv_v) as ?vcreated_sv_v)
filter not exists {
graph ?vda2_sv_v { ?admin2_sv_v ?verdictPred2_sv_v ?dnp_sv_v . filter(?verdictPred2_sv_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_sv_v . }
graph ?g2_sv_v { ?ri2_sv_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_sv_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_sv_v), '/assertion$', '')) as ?vnp2_sv_v)
graph ?vpi2_sv_v { ?vnp2_sv_v dct:created ?vcreated2Raw_sv_v . }
filter(xsd:dateTime(?vcreated2Raw_sv_v) > ?vcreated_sv_v)
}
filter(?verdictPred_sv_v = npx:approvesOf)
} }
graph ?gda { ?gene sosa:isFeatureOfInterestOf ?sampleThing ; biolink:has_sequence_variant ?variantThing . }
{ select distinct ?sampleThing ?taxon_sv where { ?sampleThing biolink:in_taxon ?taxon_sv . } }
}
}
{
select (count(distinct ?phenoThing) as ?nVariantPheno) where {
{ select distinct ?variantThing where {
graph ?da_vp_v { ?variantThing a <https://w3id.org/biolink/vocab/SequenceVariant> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_vp_v), '/assertion$', '')) as ?dnp_vp_v)
graph ?vda_vp_v { ?admin_vp_v ?verdictPred_vp_v ?dnp_vp_v . filter(?verdictPred_vp_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_vp_v . }
graph ?g_vp_v { ?ri_vp_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_vp_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_vp_v), '/assertion$', '')) as ?vnp_vp_v)
graph ?vpi_vp_v { ?vnp_vp_v dct:created ?vcreatedRaw_vp_v . }
bind(xsd:dateTime(?vcreatedRaw_vp_v) as ?vcreated_vp_v)
filter not exists {
graph ?vda2_vp_v { ?admin2_vp_v ?verdictPred2_vp_v ?dnp_vp_v . filter(?verdictPred2_vp_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_vp_v . }
graph ?g2_vp_v { ?ri2_vp_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_vp_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_vp_v), '/assertion$', '')) as ?vnp2_vp_v)
graph ?vpi2_vp_v { ?vnp2_vp_v dct:created ?vcreated2Raw_vp_v . }
filter(xsd:dateTime(?vcreated2Raw_vp_v) > ?vcreated_vp_v)
}
filter(?verdictPred_vp_v = npx:approvesOf)
} }
{ select distinct ?phenoThing where {
graph ?da_vp_p { ?phenoThing a <https://w3id.org/biolink/vocab/PhenotypicFeature> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_vp_p), '/assertion$', '')) as ?dnp_vp_p)
graph ?vda_vp_p { ?admin_vp_p ?verdictPred_vp_p ?dnp_vp_p . filter(?verdictPred_vp_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_vp_p . }
graph ?g_vp_p { ?ri_vp_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_vp_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_vp_p), '/assertion$', '')) as ?vnp_vp_p)
graph ?vpi_vp_p { ?vnp_vp_p dct:created ?vcreatedRaw_vp_p . }
bind(xsd:dateTime(?vcreatedRaw_vp_p) as ?vcreated_vp_p)
filter not exists {
graph ?vda2_vp_p { ?admin2_vp_p ?verdictPred2_vp_p ?dnp_vp_p . filter(?verdictPred2_vp_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_vp_p . }
graph ?g2_vp_p { ?ri2_vp_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_vp_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_vp_p), '/assertion$', '')) as ?vnp2_vp_p)
graph ?vpi2_vp_p { ?vnp2_vp_p dct:created ?vcreated2Raw_vp_p . }
filter(xsd:dateTime(?vcreated2Raw_vp_p) > ?vcreated_vp_p)
}
filter(?verdictPred_vp_p = npx:approvesOf)
} }
graph ?vpda { ?phenoThing mvikg:isAssociatedWithVariant ?variantThing . }
}
}
{
select (count(distinct ?taxon_sp) as ?nSamplePheno) where {
{ select distinct ?sampleThing where {
graph ?da_sp_s { ?sampleThing a <http://www.w3.org/ns/sosa/Sample> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_sp_s), '/assertion$', '')) as ?dnp_sp_s)
graph ?vda_sp_s { ?admin_sp_s ?verdictPred_sp_s ?dnp_sp_s . filter(?verdictPred_sp_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_sp_s . }
graph ?g_sp_s { ?ri_sp_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_sp_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_sp_s), '/assertion$', '')) as ?vnp_sp_s)
graph ?vpi_sp_s { ?vnp_sp_s dct:created ?vcreatedRaw_sp_s . }
bind(xsd:dateTime(?vcreatedRaw_sp_s) as ?vcreated_sp_s)
filter not exists {
graph ?vda2_sp_s { ?admin2_sp_s ?verdictPred2_sp_s ?dnp_sp_s . filter(?verdictPred2_sp_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_sp_s . }
graph ?g2_sp_s { ?ri2_sp_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_sp_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_sp_s), '/assertion$', '')) as ?vnp2_sp_s)
graph ?vpi2_sp_s { ?vnp2_sp_s dct:created ?vcreated2Raw_sp_s . }
filter(xsd:dateTime(?vcreated2Raw_sp_s) > ?vcreated_sp_s)
}
filter(?verdictPred_sp_s = npx:approvesOf)
} }
{ select distinct ?phenoThing where {
graph ?da_sp_p { ?phenoThing a <https://w3id.org/biolink/vocab/PhenotypicFeature> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_sp_p), '/assertion$', '')) as ?dnp_sp_p)
graph ?vda_sp_p { ?admin_sp_p ?verdictPred_sp_p ?dnp_sp_p . filter(?verdictPred_sp_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_sp_p . }
graph ?g_sp_p { ?ri_sp_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_sp_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_sp_p), '/assertion$', '')) as ?vnp_sp_p)
graph ?vpi_sp_p { ?vnp_sp_p dct:created ?vcreatedRaw_sp_p . }
bind(xsd:dateTime(?vcreatedRaw_sp_p) as ?vcreated_sp_p)
filter not exists {
graph ?vda2_sp_p { ?admin2_sp_p ?verdictPred2_sp_p ?dnp_sp_p . filter(?verdictPred2_sp_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_sp_p . }
graph ?g2_sp_p { ?ri2_sp_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_sp_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_sp_p), '/assertion$', '')) as ?vnp2_sp_p)
graph ?vpi2_sp_p { ?vnp2_sp_p dct:created ?vcreated2Raw_sp_p . }
filter(xsd:dateTime(?vcreated2Raw_sp_p) > ?vcreated_sp_p)
}
filter(?verdictPred_sp_p = npx:approvesOf)
} }
graph ?spda { ?phenoThing sosa:isResultOf ?sampleThing . }
{ select distinct ?sampleThing ?taxon_sp where { ?sampleThing biolink:in_taxon ?taxon_sp . } }
}
}
{
select (count(distinct ?taxon_t) as ?nTriple) where {
{ select distinct ?sampleThing where {
graph ?da_t_s { ?sampleThing a <http://www.w3.org/ns/sosa/Sample> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_t_s), '/assertion$', '')) as ?dnp_t_s)
graph ?vda_t_s { ?admin_t_s ?verdictPred_t_s ?dnp_t_s . filter(?verdictPred_t_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_t_s . }
graph ?g_t_s { ?ri_t_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_t_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_t_s), '/assertion$', '')) as ?vnp_t_s)
graph ?vpi_t_s { ?vnp_t_s dct:created ?vcreatedRaw_t_s . }
bind(xsd:dateTime(?vcreatedRaw_t_s) as ?vcreated_t_s)
filter not exists {
graph ?vda2_t_s { ?admin2_t_s ?verdictPred2_t_s ?dnp_t_s . filter(?verdictPred2_t_s in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_t_s . }
graph ?g2_t_s { ?ri2_t_s a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_t_s ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_t_s), '/assertion$', '')) as ?vnp2_t_s)
graph ?vpi2_t_s { ?vnp2_t_s dct:created ?vcreated2Raw_t_s . }
filter(xsd:dateTime(?vcreated2Raw_t_s) > ?vcreated_t_s)
}
filter(?verdictPred_t_s = npx:approvesOf)
} }
{ select distinct ?variantThing where {
graph ?da_t_v { ?variantThing a <https://w3id.org/biolink/vocab/SequenceVariant> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_t_v), '/assertion$', '')) as ?dnp_t_v)
graph ?vda_t_v { ?admin_t_v ?verdictPred_t_v ?dnp_t_v . filter(?verdictPred_t_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_t_v . }
graph ?g_t_v { ?ri_t_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_t_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_t_v), '/assertion$', '')) as ?vnp_t_v)
graph ?vpi_t_v { ?vnp_t_v dct:created ?vcreatedRaw_t_v . }
bind(xsd:dateTime(?vcreatedRaw_t_v) as ?vcreated_t_v)
filter not exists {
graph ?vda2_t_v { ?admin2_t_v ?verdictPred2_t_v ?dnp_t_v . filter(?verdictPred2_t_v in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_t_v . }
graph ?g2_t_v { ?ri2_t_v a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_t_v ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_t_v), '/assertion$', '')) as ?vnp2_t_v)
graph ?vpi2_t_v { ?vnp2_t_v dct:created ?vcreated2Raw_t_v . }
filter(xsd:dateTime(?vcreated2Raw_t_v) > ?vcreated_t_v)
}
filter(?verdictPred_t_v = npx:approvesOf)
} }
{ select distinct ?phenoThing where {
graph ?da_t_p { ?phenoThing a <https://w3id.org/biolink/vocab/PhenotypicFeature> ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
bind(iri(replace(str(?da_t_p), '/assertion$', '')) as ?dnp_t_p)
graph ?vda_t_p { ?admin_t_p ?verdictPred_t_p ?dnp_t_p . filter(?verdictPred_t_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g_t_p . }
graph ?g_t_p { ?ri_t_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin_t_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda_t_p), '/assertion$', '')) as ?vnp_t_p)
graph ?vpi_t_p { ?vnp_t_p dct:created ?vcreatedRaw_t_p . }
bind(xsd:dateTime(?vcreatedRaw_t_p) as ?vcreated_t_p)
filter not exists {
graph ?vda2_t_p { ?admin2_t_p ?verdictPred2_t_p ?dnp_t_p . filter(?verdictPred2_t_p in (npx:approvesOf, npx:disapprovesOf)) }
filter(exists {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
graph npa:graph { <http://purl.org/nanopub/admin/thisRepo> npa:hasCurrentSpaceState ?g2_t_p . }
graph ?g2_t_p { ?ri2_t_p a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:forAgent ?admin2_t_p ; npa:hasRoleType gen:AdminRole . }
}
})
bind(iri(replace(str(?vda2_t_p), '/assertion$', '')) as ?vnp2_t_p)
graph ?vpi2_t_p { ?vnp2_t_p dct:created ?vcreated2Raw_t_p . }
filter(xsd:dateTime(?vcreated2Raw_t_p) > ?vcreated_t_p)
}
filter(?verdictPred_t_p = npx:approvesOf)
} }
graph ?tgda { ?gene <http://www.w3.org/ns/sosa/isFeatureOfInterestOf> ?sampleThing ; <https://w3id.org/biolink/vocab/has_sequence_variant> ?variantThing . }
graph ?tpda { ?phenoThing mvikg:isAssociatedWithVariant ?variantThing ; sosa:isResultOf ?sampleThing . }
{ select distinct ?sampleThing ?taxon_t where { ?sampleThing biolink:in_taxon ?taxon_t . } }
}
}
bind(round(140 + 160*(?nSample/(?nSample + 5.0))) as ?wA) bind(320 as ?Ax2) bind(?Ax2 - ?wA as ?Ax1)
bind(round(140 + 160*(?nVariant/(?nVariant + 5.0))) as ?wB) bind(280 as ?Bx1) bind(?Bx1 + ?wB as ?Bx2)
bind(round(160 + 80*(?nPheno/(?nPheno + 5.0))) as ?hC) bind(140 as ?Cy1) bind(?Cy1 + ?hC as ?Cy2)
bind(if(?nVariantPheno - ?nTriple > 0, ?nVariantPheno - ?nTriple, 0) as ?nVariantPhenoOnly)
bind(if(?nSamplePheno - ?nTriple > 0, ?nSamplePheno - ?nTriple, 0) as ?nSamplePhenoOnly)
bind(concat(
'<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 600 400\" width=\"600\" height=\"400\">',
'<desc>Count-only landscape of the mvikg knowledge graph: approved taxa (via in_taxon on approved samples), variants and phenotypes, sized by count, with pairwise and triple association counts in their overlaps.</desc>',
'<rect x=\"', str(?Ax1), '\" y=\"40\" width=\"', str(?wA), '\" height=\"160\" rx=\"12\" fill=\"#3C6DB0\" fill-opacity=\"0.18\" stroke=\"#3C6DB0\" stroke-width=\"1.5\"></rect>',
'<rect x=\"', str(?Bx1), '\" y=\"40\" width=\"', str(?wB), '\" height=\"160\" rx=\"12\" fill=\"#C0392B\" fill-opacity=\"0.18\" stroke=\"#C0392B\" stroke-width=\"1.5\"></rect>',
'<rect x=\"160\" y=\"', str(?Cy1), '\" width=\"280\" height=\"', str(?hC), '\" rx=\"12\" fill=\"#3F9E5C\" fill-opacity=\"0.18\" stroke=\"#3F9E5C\" stroke-width=\"1.5\"></rect>',
'<text x=\"', str(?Ax1 + 20), '\" y=\"65\" font-size=\"13\" fill=\"#2f5488\">Taxa (', str(?nSample), ')</text>',
'<text x=\"', str(?Bx2 - 20), '\" y=\"65\" text-anchor=\"end\" font-size=\"13\" fill=\"#8a2d20\">Variants (', str(?nVariant), ')</text>',
'<text x=\"300\" y=\"', str(?Cy2 - 15), '\" text-anchor=\"middle\" font-size=\"13\" fill=\"#2f7048\">Phenotypes (', str(?nPheno), ')</text>',
'<text x=\"300\" y=\"90\" text-anchor=\"middle\" font-size=\"12\" fill=\"#333333\">n = ', str(?nSampleVariant), '</text>',
'<text x=\"220\" y=\"170\" text-anchor=\"middle\" font-size=\"12\" fill=\"#333333\">n = ', str(?nSamplePhenoOnly), '</text>',
'<text x=\"380\" y=\"170\" text-anchor=\"middle\" font-size=\"12\" fill=\"#333333\">n = ', str(?nVariantPhenoOnly), '</text>',
'<text x=\"300\" y=\"170\" text-anchor=\"middle\" font-size=\"12\" fill=\"#333333\">n = ', str(?nTriple), '</text>',
'</svg>'
) as ?svg)
}""" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0009-0005-5515-1230 .
}
sub:pubinfo {
this: dct:created "2026-11-11T19:38:48Z"^^xsd:dateTime;
dct:creator orcid:0009-0005-5515-1230;
dct:license <https://creativecommons.org/licenses/by/4.0/>;
npx:embeds sub:get-kg-landscape-svg;
npx:supersedes <https://w3id.org/np/RAcRJ8tCDl9NHKssBwPS6yKwna_EqcOMFy5uoLHvLSuCk>;
rdfs:label "Get mvikg/r/kg landscape SVG";
skos:changeNote "Deeper performance fix, superseding the previous taxon-pivot fix (RAcRJ8tC..., ~15-20s, borderline against Nanodash's call timeout -- intermittently still failed with 'couldn't refresh, showing old results'). Each sample/variant/phenotype approval check (verdict + admin-role + no-newer-verdict logic) is now wrapped as its own 'select distinct ?entity where {...}' subquery within every leg that joins multiple entity types (sample-variant, variant-phenotype, sample-phenotype, triple), instead of being inlined as plain triple patterns -- forcing early deduplication before the structural edge joins multiply rows, the same fix previously applied only to the taxon lookup but now applied to the much more expensive admin-verdict logic itself. Verified on the test network (RAKqD8KgNPYF0SW5KnvsfmCByrHwDz3GN5_Bj1u8TU5DU) and via _nanopub_trig against the live repo across multiple spaced runs: consistently ~3-3.5s, down from ~15-20s, with identical correct result values.";
nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA7lSq6MuK_TIC6JMSHvLtee3lpLoZDOqLJCLXevnrPoU>;
nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RACJ58Gvyn91LqCKIO9zu1eijDQIeEff28iyDrJgjSJF8>,
<https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI>;
nt:wasCreatedFromTemplate <https://w3id.org/np/RAEFAt-QcFK0ZhqfvlsmS10BnzGJA0xwOICZXkO-ai87k> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAjO3oH8Lq/l1oZIUY3FlCz5DnndybGvAhBdmEJ/yq7Nv3GZEYPrEro23rCBCp0GiriOXlVbk61pA/7JFE6tqzTresINW6QQMxE9sIhCBlX4cG66JFD8ud6bMvUyzCR8LQA6zfrSbafGE06rvglJd4MDUcTwvUKqtL9UCnOaowVfnZ3sPOe9EqlmJuO3iHGxBSXMPOPEJZUzMXsFDWFuMZTnrR8gY3r5nVF5a8L/MD135ZH8qW5yGXOB28CmVYCAbw2o07QEKzyzFKN+W1gfnprYZvuKzwGexnzcdzc1S8N/M5bzhWQ40EKCEqgUE8c81OzEMm1HUlUKEJ/o5I/FKKAwIDAQAB";
npx:hasSignature "SL15yvbU2M5URlKF9hO9VjoKEP688a3xGC2ef8dHYcEZEkw/OHRUe38zb8kZB6OKoimVhOIdhWChwIRXf5ZQUZ6Z5B1JcH8ThfVALK+2oPrh2qUje9pyCpC46Uvh2S+pjV8ZgKeljmWu0zY1tr+yNVlk2rVU4y+2agIlia0N1KUmd+CSw0Yc04+ZowTEB4RX032KXprTToWZbenHf8ZrLXSam6FfsFoM+AFmITvc1/0OIoBYJ3NgthwYqRyDLSP9/k1CC+UIxylcCZkjVIYVSUGbsbkSyKRFYv96BBk/i9f53zt327QqFj/WjAUaNTUAe3qxU5Vaaf/VvahXupvOLA==";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0009-0005-5515-1230 .
}