[ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/Head", "@graph": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] }, { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/provenance", "@graph": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://orcid.org/0009-0005-5515-1230" } ] } ] }, { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/assertion", "@graph": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/get-kg-landscape-svg", "http://purl.org/dc/terms/description": [ { "@value": "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." } ], "http://purl.org/dc/terms/license": [ { "@id": "https://creativecommons.org/licenses/by/4.0/" } ], "@type": [ "https://w3id.org/kpxl/grlc/grlc-query" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Get mvikg/r/kg landscape SVG" } ], "https://w3id.org/kpxl/grlc/endpoint": [ { "@id": "https://w3id.org/np/l/nanopub-query-1.1/repo/full" } ], "https://w3id.org/kpxl/grlc/sparql": [ { "@value": "prefix npa: \nprefix gen: \nprefix npx: \nprefix dct: \nprefix sosa: \nprefix biolink: \nprefix mvikg: \n\nselect ?svg where {\n\n {\n select (count(distinct ?taxon_s) as ?nSample) where {\n\n { select distinct ?sampleThing where {\n graph ?da_s { ?sampleThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_s), '/assertion$', '')) as ?dnp_s)\n graph ?vda_s { ?admin_s ?verdictPred_s ?dnp_s . filter(?verdictPred_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_s . }\n graph ?g_s { ?ri_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_s), '/assertion$', '')) as ?vnp_s)\n graph ?vpi_s { ?vnp_s dct:created ?vcreatedRaw_s . }\n bind(xsd:dateTime(?vcreatedRaw_s) as ?vcreated_s)\n filter not exists {\n graph ?vda2_s { ?admin2_s ?verdictPred2_s ?dnp_s . filter(?verdictPred2_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_s . }\n graph ?g2_s { ?ri2_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_s), '/assertion$', '')) as ?vnp2_s)\n graph ?vpi2_s { ?vnp2_s dct:created ?vcreated2Raw_s . }\n filter(xsd:dateTime(?vcreated2Raw_s) > ?vcreated_s)\n }\n filter(?verdictPred_s = npx:approvesOf)\n } }\n\n { select distinct ?sampleThing ?taxon_s where { ?sampleThing biolink:in_taxon ?taxon_s . } }\n }\n }\n\n {\n select (count(distinct ?variantThing) as ?nVariant) where {\n \n { select distinct ?variantThing where {\n graph ?da_v { ?variantThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_v), '/assertion$', '')) as ?dnp_v)\n graph ?vda_v { ?admin_v ?verdictPred_v ?dnp_v . filter(?verdictPred_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_v . }\n graph ?g_v { ?ri_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_v), '/assertion$', '')) as ?vnp_v)\n graph ?vpi_v { ?vnp_v dct:created ?vcreatedRaw_v . }\n bind(xsd:dateTime(?vcreatedRaw_v) as ?vcreated_v)\n filter not exists {\n graph ?vda2_v { ?admin2_v ?verdictPred2_v ?dnp_v . filter(?verdictPred2_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_v . }\n graph ?g2_v { ?ri2_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_v), '/assertion$', '')) as ?vnp2_v)\n graph ?vpi2_v { ?vnp2_v dct:created ?vcreated2Raw_v . }\n filter(xsd:dateTime(?vcreated2Raw_v) > ?vcreated_v)\n }\n filter(?verdictPred_v = npx:approvesOf)\n } }\n\n }\n }\n\n {\n select (count(distinct ?phenoThing) as ?nPheno) where {\n \n { select distinct ?phenoThing where {\n graph ?da_p { ?phenoThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_p), '/assertion$', '')) as ?dnp_p)\n graph ?vda_p { ?admin_p ?verdictPred_p ?dnp_p . filter(?verdictPred_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_p . }\n graph ?g_p { ?ri_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_p), '/assertion$', '')) as ?vnp_p)\n graph ?vpi_p { ?vnp_p dct:created ?vcreatedRaw_p . }\n bind(xsd:dateTime(?vcreatedRaw_p) as ?vcreated_p)\n filter not exists {\n graph ?vda2_p { ?admin2_p ?verdictPred2_p ?dnp_p . filter(?verdictPred2_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_p . }\n graph ?g2_p { ?ri2_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_p), '/assertion$', '')) as ?vnp2_p)\n graph ?vpi2_p { ?vnp2_p dct:created ?vcreated2Raw_p . }\n filter(xsd:dateTime(?vcreated2Raw_p) > ?vcreated_p)\n }\n filter(?verdictPred_p = npx:approvesOf)\n } }\n\n }\n }\n\n {\n select (count(distinct ?taxon_sv) as ?nSampleVariant) where {\n\n { select distinct ?sampleThing where {\n graph ?da_sv_s { ?sampleThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_sv_s), '/assertion$', '')) as ?dnp_sv_s)\n graph ?vda_sv_s { ?admin_sv_s ?verdictPred_sv_s ?dnp_sv_s . filter(?verdictPred_sv_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_sv_s . }\n graph ?g_sv_s { ?ri_sv_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_sv_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_sv_s), '/assertion$', '')) as ?vnp_sv_s)\n graph ?vpi_sv_s { ?vnp_sv_s dct:created ?vcreatedRaw_sv_s . }\n bind(xsd:dateTime(?vcreatedRaw_sv_s) as ?vcreated_sv_s)\n filter not exists {\n graph ?vda2_sv_s { ?admin2_sv_s ?verdictPred2_sv_s ?dnp_sv_s . filter(?verdictPred2_sv_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_sv_s . }\n graph ?g2_sv_s { ?ri2_sv_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_sv_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_sv_s), '/assertion$', '')) as ?vnp2_sv_s)\n graph ?vpi2_sv_s { ?vnp2_sv_s dct:created ?vcreated2Raw_sv_s . }\n filter(xsd:dateTime(?vcreated2Raw_sv_s) > ?vcreated_sv_s)\n }\n filter(?verdictPred_sv_s = npx:approvesOf)\n } }\n\n \n { select distinct ?variantThing where {\n graph ?da_sv_v { ?variantThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_sv_v), '/assertion$', '')) as ?dnp_sv_v)\n graph ?vda_sv_v { ?admin_sv_v ?verdictPred_sv_v ?dnp_sv_v . filter(?verdictPred_sv_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_sv_v . }\n graph ?g_sv_v { ?ri_sv_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_sv_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_sv_v), '/assertion$', '')) as ?vnp_sv_v)\n graph ?vpi_sv_v { ?vnp_sv_v dct:created ?vcreatedRaw_sv_v . }\n bind(xsd:dateTime(?vcreatedRaw_sv_v) as ?vcreated_sv_v)\n filter not exists {\n graph ?vda2_sv_v { ?admin2_sv_v ?verdictPred2_sv_v ?dnp_sv_v . filter(?verdictPred2_sv_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_sv_v . }\n graph ?g2_sv_v { ?ri2_sv_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_sv_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_sv_v), '/assertion$', '')) as ?vnp2_sv_v)\n graph ?vpi2_sv_v { ?vnp2_sv_v dct:created ?vcreated2Raw_sv_v . }\n filter(xsd:dateTime(?vcreated2Raw_sv_v) > ?vcreated_sv_v)\n }\n filter(?verdictPred_sv_v = npx:approvesOf)\n } }\n\n graph ?gda { ?gene sosa:isFeatureOfInterestOf ?sampleThing ; biolink:has_sequence_variant ?variantThing . }\n { select distinct ?sampleThing ?taxon_sv where { ?sampleThing biolink:in_taxon ?taxon_sv . } }\n }\n }\n\n {\n select (count(distinct ?phenoThing) as ?nVariantPheno) where {\n \n { select distinct ?variantThing where {\n graph ?da_vp_v { ?variantThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_vp_v), '/assertion$', '')) as ?dnp_vp_v)\n graph ?vda_vp_v { ?admin_vp_v ?verdictPred_vp_v ?dnp_vp_v . filter(?verdictPred_vp_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_vp_v . }\n graph ?g_vp_v { ?ri_vp_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_vp_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_vp_v), '/assertion$', '')) as ?vnp_vp_v)\n graph ?vpi_vp_v { ?vnp_vp_v dct:created ?vcreatedRaw_vp_v . }\n bind(xsd:dateTime(?vcreatedRaw_vp_v) as ?vcreated_vp_v)\n filter not exists {\n graph ?vda2_vp_v { ?admin2_vp_v ?verdictPred2_vp_v ?dnp_vp_v . filter(?verdictPred2_vp_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_vp_v . }\n graph ?g2_vp_v { ?ri2_vp_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_vp_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_vp_v), '/assertion$', '')) as ?vnp2_vp_v)\n graph ?vpi2_vp_v { ?vnp2_vp_v dct:created ?vcreated2Raw_vp_v . }\n filter(xsd:dateTime(?vcreated2Raw_vp_v) > ?vcreated_vp_v)\n }\n filter(?verdictPred_vp_v = npx:approvesOf)\n } }\n\n \n { select distinct ?phenoThing where {\n graph ?da_vp_p { ?phenoThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_vp_p), '/assertion$', '')) as ?dnp_vp_p)\n graph ?vda_vp_p { ?admin_vp_p ?verdictPred_vp_p ?dnp_vp_p . filter(?verdictPred_vp_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_vp_p . }\n graph ?g_vp_p { ?ri_vp_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_vp_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_vp_p), '/assertion$', '')) as ?vnp_vp_p)\n graph ?vpi_vp_p { ?vnp_vp_p dct:created ?vcreatedRaw_vp_p . }\n bind(xsd:dateTime(?vcreatedRaw_vp_p) as ?vcreated_vp_p)\n filter not exists {\n graph ?vda2_vp_p { ?admin2_vp_p ?verdictPred2_vp_p ?dnp_vp_p . filter(?verdictPred2_vp_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_vp_p . }\n graph ?g2_vp_p { ?ri2_vp_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_vp_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_vp_p), '/assertion$', '')) as ?vnp2_vp_p)\n graph ?vpi2_vp_p { ?vnp2_vp_p dct:created ?vcreated2Raw_vp_p . }\n filter(xsd:dateTime(?vcreated2Raw_vp_p) > ?vcreated_vp_p)\n }\n filter(?verdictPred_vp_p = npx:approvesOf)\n } }\n\n graph ?vpda { ?phenoThing mvikg:isAssociatedWithVariant ?variantThing . }\n }\n }\n\n {\n select (count(distinct ?taxon_sp) as ?nSamplePheno) where {\n\n { select distinct ?sampleThing where {\n graph ?da_sp_s { ?sampleThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_sp_s), '/assertion$', '')) as ?dnp_sp_s)\n graph ?vda_sp_s { ?admin_sp_s ?verdictPred_sp_s ?dnp_sp_s . filter(?verdictPred_sp_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_sp_s . }\n graph ?g_sp_s { ?ri_sp_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_sp_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_sp_s), '/assertion$', '')) as ?vnp_sp_s)\n graph ?vpi_sp_s { ?vnp_sp_s dct:created ?vcreatedRaw_sp_s . }\n bind(xsd:dateTime(?vcreatedRaw_sp_s) as ?vcreated_sp_s)\n filter not exists {\n graph ?vda2_sp_s { ?admin2_sp_s ?verdictPred2_sp_s ?dnp_sp_s . filter(?verdictPred2_sp_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_sp_s . }\n graph ?g2_sp_s { ?ri2_sp_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_sp_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_sp_s), '/assertion$', '')) as ?vnp2_sp_s)\n graph ?vpi2_sp_s { ?vnp2_sp_s dct:created ?vcreated2Raw_sp_s . }\n filter(xsd:dateTime(?vcreated2Raw_sp_s) > ?vcreated_sp_s)\n }\n filter(?verdictPred_sp_s = npx:approvesOf)\n } }\n\n \n { select distinct ?phenoThing where {\n graph ?da_sp_p { ?phenoThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_sp_p), '/assertion$', '')) as ?dnp_sp_p)\n graph ?vda_sp_p { ?admin_sp_p ?verdictPred_sp_p ?dnp_sp_p . filter(?verdictPred_sp_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_sp_p . }\n graph ?g_sp_p { ?ri_sp_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_sp_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_sp_p), '/assertion$', '')) as ?vnp_sp_p)\n graph ?vpi_sp_p { ?vnp_sp_p dct:created ?vcreatedRaw_sp_p . }\n bind(xsd:dateTime(?vcreatedRaw_sp_p) as ?vcreated_sp_p)\n filter not exists {\n graph ?vda2_sp_p { ?admin2_sp_p ?verdictPred2_sp_p ?dnp_sp_p . filter(?verdictPred2_sp_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_sp_p . }\n graph ?g2_sp_p { ?ri2_sp_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_sp_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_sp_p), '/assertion$', '')) as ?vnp2_sp_p)\n graph ?vpi2_sp_p { ?vnp2_sp_p dct:created ?vcreated2Raw_sp_p . }\n filter(xsd:dateTime(?vcreated2Raw_sp_p) > ?vcreated_sp_p)\n }\n filter(?verdictPred_sp_p = npx:approvesOf)\n } }\n\n graph ?spda { ?phenoThing sosa:isResultOf ?sampleThing . }\n { select distinct ?sampleThing ?taxon_sp where { ?sampleThing biolink:in_taxon ?taxon_sp . } }\n }\n }\n\n\n {\n select (count(distinct ?taxon_t) as ?nTriple) where {\n\n { select distinct ?sampleThing where {\n graph ?da_t_s { ?sampleThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_t_s), '/assertion$', '')) as ?dnp_t_s)\n graph ?vda_t_s { ?admin_t_s ?verdictPred_t_s ?dnp_t_s . filter(?verdictPred_t_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_t_s . }\n graph ?g_t_s { ?ri_t_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_t_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_t_s), '/assertion$', '')) as ?vnp_t_s)\n graph ?vpi_t_s { ?vnp_t_s dct:created ?vcreatedRaw_t_s . }\n bind(xsd:dateTime(?vcreatedRaw_t_s) as ?vcreated_t_s)\n filter not exists {\n graph ?vda2_t_s { ?admin2_t_s ?verdictPred2_t_s ?dnp_t_s . filter(?verdictPred2_t_s in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_t_s . }\n graph ?g2_t_s { ?ri2_t_s a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_t_s ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_t_s), '/assertion$', '')) as ?vnp2_t_s)\n graph ?vpi2_t_s { ?vnp2_t_s dct:created ?vcreated2Raw_t_s . }\n filter(xsd:dateTime(?vcreated2Raw_t_s) > ?vcreated_t_s)\n }\n filter(?verdictPred_t_s = npx:approvesOf)\n } }\n\n \n { select distinct ?variantThing where {\n graph ?da_t_v { ?variantThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_t_v), '/assertion$', '')) as ?dnp_t_v)\n graph ?vda_t_v { ?admin_t_v ?verdictPred_t_v ?dnp_t_v . filter(?verdictPred_t_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_t_v . }\n graph ?g_t_v { ?ri_t_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_t_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_t_v), '/assertion$', '')) as ?vnp_t_v)\n graph ?vpi_t_v { ?vnp_t_v dct:created ?vcreatedRaw_t_v . }\n bind(xsd:dateTime(?vcreatedRaw_t_v) as ?vcreated_t_v)\n filter not exists {\n graph ?vda2_t_v { ?admin2_t_v ?verdictPred2_t_v ?dnp_t_v . filter(?verdictPred2_t_v in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_t_v . }\n graph ?g2_t_v { ?ri2_t_v a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_t_v ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_t_v), '/assertion$', '')) as ?vnp2_t_v)\n graph ?vpi2_t_v { ?vnp2_t_v dct:created ?vcreated2Raw_t_v . }\n filter(xsd:dateTime(?vcreated2Raw_t_v) > ?vcreated_t_v)\n }\n filter(?verdictPred_t_v = npx:approvesOf)\n } }\n\n \n { select distinct ?phenoThing where {\n graph ?da_t_p { ?phenoThing a ; dct:isPartOf . }\n bind(iri(replace(str(?da_t_p), '/assertion$', '')) as ?dnp_t_p)\n graph ?vda_t_p { ?admin_t_p ?verdictPred_t_p ?dnp_t_p . filter(?verdictPred_t_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g_t_p . }\n graph ?g_t_p { ?ri_t_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin_t_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda_t_p), '/assertion$', '')) as ?vnp_t_p)\n graph ?vpi_t_p { ?vnp_t_p dct:created ?vcreatedRaw_t_p . }\n bind(xsd:dateTime(?vcreatedRaw_t_p) as ?vcreated_t_p)\n filter not exists {\n graph ?vda2_t_p { ?admin2_t_p ?verdictPred2_t_p ?dnp_t_p . filter(?verdictPred2_t_p in (npx:approvesOf, npx:disapprovesOf)) }\n filter(exists {\n service {\n graph npa:graph { npa:hasCurrentSpaceState ?g2_t_p . }\n graph ?g2_t_p { ?ri2_t_p a gen:RoleInstantiation ; npa:forSpace ; npa:forAgent ?admin2_t_p ; npa:hasRoleType gen:AdminRole . }\n }\n })\n bind(iri(replace(str(?vda2_t_p), '/assertion$', '')) as ?vnp2_t_p)\n graph ?vpi2_t_p { ?vnp2_t_p dct:created ?vcreated2Raw_t_p . }\n filter(xsd:dateTime(?vcreated2Raw_t_p) > ?vcreated_t_p)\n }\n filter(?verdictPred_t_p = npx:approvesOf)\n } }\n\n graph ?tgda { ?gene ?sampleThing ; ?variantThing . }\n graph ?tpda { ?phenoThing mvikg:isAssociatedWithVariant ?variantThing ; sosa:isResultOf ?sampleThing . }\n { select distinct ?sampleThing ?taxon_t where { ?sampleThing biolink:in_taxon ?taxon_t . } }\n }\n }\n\n bind(round(140 + 160*(?nSample/(?nSample + 5.0))) as ?wA) bind(320 as ?Ax2) bind(?Ax2 - ?wA as ?Ax1)\n bind(round(140 + 160*(?nVariant/(?nVariant + 5.0))) as ?wB) bind(280 as ?Bx1) bind(?Bx1 + ?wB as ?Bx2)\n bind(round(160 + 80*(?nPheno/(?nPheno + 5.0))) as ?hC) bind(140 as ?Cy1) bind(?Cy1 + ?hC as ?Cy2)\n bind(if(?nVariantPheno - ?nTriple > 0, ?nVariantPheno - ?nTriple, 0) as ?nVariantPhenoOnly)\n bind(if(?nSamplePheno - ?nTriple > 0, ?nSamplePheno - ?nTriple, 0) as ?nSamplePhenoOnly)\n bind(concat(\n '',\n '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.',\n '',\n '',\n '',\n 'Taxa (', str(?nSample), ')',\n 'Variants (', str(?nVariant), ')',\n 'Phenotypes (', str(?nPheno), ')',\n 'n = ', str(?nSampleVariant), '',\n 'n = ', str(?nSamplePhenoOnly), '',\n 'n = ', str(?nVariantPhenoOnly), '',\n 'n = ', str(?nTriple), '',\n ''\n ) as ?svg)\n}" } ] } ] }, { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/pubinfo", "@graph": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s", "http://purl.org/dc/terms/created": [ { "@value": "2026-11-11T19:38:48Z", "@type": "http://www.w3.org/2001/XMLSchema#dateTime" } ], "http://purl.org/dc/terms/creator": [ { "@id": "https://orcid.org/0009-0005-5515-1230" } ], "http://purl.org/dc/terms/license": [ { "@id": "https://creativecommons.org/licenses/by/4.0/" } ], "http://purl.org/nanopub/x/embeds": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/get-kg-landscape-svg" } ], "http://purl.org/nanopub/x/supersedes": [ { "@id": "https://w3id.org/np/RAcRJ8tCDl9NHKssBwPS6yKwna_EqcOMFy5uoLHvLSuCk" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Get mvikg/r/kg landscape SVG" } ], "http://www.w3.org/2004/02/skos/core#changeNote": [ { "@value": "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." } ], "https://w3id.org/np/o/ntemplate/wasCreatedFromProvenanceTemplate": [ { "@id": "https://w3id.org/np/RA7lSq6MuK_TIC6JMSHvLtee3lpLoZDOqLJCLXevnrPoU" } ], "https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate": [ { "@id": "https://w3id.org/np/RACJ58Gvyn91LqCKIO9zu1eijDQIeEff28iyDrJgjSJF8" }, { "@id": "https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI" } ], "https://w3id.org/np/o/ntemplate/wasCreatedFromTemplate": [ { "@id": "https://w3id.org/np/RAEFAt-QcFK0ZhqfvlsmS10BnzGJA0xwOICZXkO-ai87k" } ] }, { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s/sig", "http://purl.org/nanopub/x/hasAlgorithm": [ { "@value": "RSA" } ], "http://purl.org/nanopub/x/hasPublicKey": [ { "@value": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAjO3oH8Lq/l1oZIUY3FlCz5DnndybGvAhBdmEJ/yq7Nv3GZEYPrEro23rCBCp0GiriOXlVbk61pA/7JFE6tqzTresINW6QQMxE9sIhCBlX4cG66JFD8ud6bMvUyzCR8LQA6zfrSbafGE06rvglJd4MDUcTwvUKqtL9UCnOaowVfnZ3sPOe9EqlmJuO3iHGxBSXMPOPEJZUzMXsFDWFuMZTnrR8gY3r5nVF5a8L/MD135ZH8qW5yGXOB28CmVYCAbw2o07QEKzyzFKN+W1gfnprYZvuKzwGexnzcdzc1S8N/M5bzhWQ40EKCEqgUE8c81OzEMm1HUlUKEJ/o5I/FKKAwIDAQAB" } ], "http://purl.org/nanopub/x/hasSignature": [ { "@value": "SL15yvbU2M5URlKF9hO9VjoKEP688a3xGC2ef8dHYcEZEkw/OHRUe38zb8kZB6OKoimVhOIdhWChwIRXf5ZQUZ6Z5B1JcH8ThfVALK+2oPrh2qUje9pyCpC46Uvh2S+pjV8ZgKeljmWu0zY1tr+yNVlk2rVU4y+2agIlia0N1KUmd+CSw0Yc04+ZowTEB4RX032KXprTToWZbenHf8ZrLXSam6FfsFoM+AFmITvc1/0OIoBYJ3NgthwYqRyDLSP9/k1CC+UIxylcCZkjVIYVSUGbsbkSyKRFYv96BBk/i9f53zt327QqFj/WjAUaNTUAe3qxU5Vaaf/VvahXupvOLA==" } ], "http://purl.org/nanopub/x/hasSignatureTarget": [ { "@id": "https://w3id.org/np/RARZQfZ3IxhLJsivgDDxEgJgX8WCMKjl4Ta4cV5SSIt5s" } ], "http://purl.org/nanopub/x/signedBy": [ { "@id": "https://orcid.org/0009-0005-5515-1230" } ] } ] } ]