https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/Head https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/assertion https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/provenance https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/pubinfo https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/assertion https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info http://purl.org/dc/terms/description Key-value Info card for a sequence variant record ('partid') of the MVIKG knowledge graph: name, comment, Sequence Ontology type, gene, sample, effect, alleles, coordinates, length, frequency, evidence text, review status and defining nanopub. Rows of absent fields are omitted. Only records signed by a current admin, maintainer or member of the mvikg space count, in their newest non-invalidated version; the review status is the latest npx:approvesOf / npx:disapprovesOf verdict of a current mvikg admin on that version (none: pending). https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/kpxl/grlc/grlc-query https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info http://www.w3.org/2000/01/rdf-schema#label Get MVIKG variant info https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info https://w3id.org/kpxl/grlc/endpoint https://w3id.org/np/l/nanopub-query-1.1/repo/full https://w3id.org/np/RAmv4e-f80auufldzsWhNsOwaYJqzKaNH8XyCX623byKQ/get-mvikg-variant-info https://w3id.org/kpxl/grlc/sparql prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix gen: <https://w3id.org/kpxl/gen/terms/> prefix sosa: <http://www.w3.org/ns/sosa/> prefix biolink: <https://w3id.org/biolink/vocab/> prefix mvikg: <http://example.org/mvikg/> prefix obo: <http://purl.obolibrary.org/obo/> select ?Property_noheader ?Property_label (group_concat(replace(str(?val), '[\r\n]+', ' '); separator='\n') as ?Value_multi_val_noheader) (group_concat(replace(str(?vallabel), '[\r\n]+', ' '); separator='\n') as ?Value_label_multi) where { { select ?ord ?Property_noheader ?Property_label ?val (min(?vallabelRaw) as ?vallabel) where { { select ?dnp ?da (max(?verdict) as ?mv) where { service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> { select (group_concat(distinct ?pk; separator=' ') as ?memberKeys) (group_concat(distinct ?apk; separator=' ') as ?adminKeys) where { graph npa:graph { npa:thisRepo npa:hasCurrentSpaceState ?sg . } graph ?sg { ?ri a gen:RoleInstantiation ; npa:forSpace <https://w3id.org/spaces/mvikg> ; npa:hasRoleType ?tier ; npa:forAgent ?agent . filter(?tier in (gen:AdminRole, gen:MaintainerRole, gen:MemberRole)) ?acct a npa:AccountState ; npa:agent ?agent ; npa:pubkey ?pk . bind(if(?tier = gen:AdminRole, ?pk, '') as ?apk) } } } graph npa:graph { ?dnp npx:introduces ?_partid_iri ; np:hasAssertion ?da ; dct:created ?ddate ; npa:hasValidSignatureForPublicKeyHash ?dpk . filter not exists { ?dinv npx:invalidates ?dnp ; npa:hasValidSignatureForPublicKeyHash ?dpk . } } filter(contains(?memberKeys, ?dpk)) optional { values ?vpred { npx:approvesOf npx:disapprovesOf } graph ?va { ?vagent ?vpred ?dnp . } graph npa:graph { ?vnp np:hasAssertion ?va ; dct:created ?vdate ; npa:hasValidSignatureForPublicKeyHash ?vpk . filter not exists { ?vinv npx:invalidates ?vnp ; npa:hasValidSignatureForPublicKeyHash ?vpk . } } filter(contains(?adminKeys, ?vpk)) bind(concat(str(?vdate), '>', if(?vpred = npx:disapprovesOf, 'd', 'a')) as ?verdict) } } group by ?dnp ?da ?ddate order by desc(?ddate) limit 1 } { select ?da ?ord ?Property_noheader ?Property_label ?val0 ?lab0 where { { graph ?da { ?_partid_iri rdfs:label ?v } bind(1 as ?ord) bind(rdfs:label as ?Property_noheader) bind('Name:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri rdfs:comment ?v } bind(2 as ?ord) bind(rdfs:comment as ?Property_noheader) bind('Comment:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri rdf:type ?iri . filter(?iri != biolink:SequenceVariant) } bind(3 as ?ord) bind(rdf:type as ?Property_noheader) bind('Type:' as ?Property_label) bind(str(?iri) as ?val0) bind(if(?iri = obo:SO_0000159, 'deletion', if(?iri = obo:SO_0000667, 'insertion', if(?iri = obo:SO_0000694, 'SNP', if(?iri = obo:SO_0001483, 'SNV', if(?iri = obo:SO_0001059, 'sequence alteration', if(?iri = obo:SO_1000002, 'substitution', if(?iri = obo:SO_1000032, 'delins', if(?iri = obo:SO_0002007, 'MNV', replace(replace(str(?iri), '^.*[/#]', ''), '_', ':'))))))))) as ?lab0) } union { graph ?da { ?iri biolink:has_sequence_variant ?_partid_iri } bind(4 as ?ord) bind(biolink:has_sequence_variant as ?Property_noheader) bind('Gene:' as ?Property_label) bind(str(?iri) as ?val0) bind(replace(str(?iri), '^.*[/#]', '') as ?lab0) } union { graph ?da { ?gene biolink:has_sequence_variant ?_partid_iri ; sosa:isFeatureOfInterestOf ?iri } optional { graph npa:graph { ?onp npx:introduces ?iri . ?cnp npx:supersedes* ?onp ; npx:introduces ?ciri ; rdfs:label ?llab ; npa:hasValidSignatureForPublicKeyHash ?cpk . filter not exists { ?cinv npx:invalidates ?cnp ; npa:hasValidSignatureForPublicKeyHash ?cpk . } } } bind(5 as ?ord) bind(sosa:isFeatureOfInterestOf as ?Property_noheader) bind('Sample:' as ?Property_label) bind(str(coalesce(?ciri, ?iri)) as ?val0) bind(coalesce(str(?llab), replace(str(?iri), '^.*[/#]', '')) as ?lab0) } union { graph ?da { ?_partid_iri mvikg:effect ?v } bind(6 as ?ord) bind(mvikg:effect as ?Property_noheader) bind('Effect:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri mvikg:ref ?v } bind(7 as ?ord) bind(mvikg:ref as ?Property_noheader) bind('Reference allele:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri mvikg:alt ?v } bind(8 as ?ord) bind(mvikg:alt as ?Property_noheader) bind('Alternate allele:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri biolink:start_coordinate ?v } bind(9 as ?ord) bind(biolink:start_coordinate as ?Property_noheader) bind('Start:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri biolink:end_coordinate ?v } bind(10 as ?ord) bind(biolink:end_coordinate as ?Property_noheader) bind('End:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri mvikg:length ?v } bind(11 as ?ord) bind(mvikg:length as ?Property_noheader) bind('Length:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri mvikg:frequencyValue ?v . optional { ?_partid_iri mvikg:frequencyUnit ?fu } } bind(12 as ?ord) bind(mvikg:frequencyValue as ?Property_noheader) bind('Frequency:' as ?Property_label) bind(concat(str(?v), if(coalesce(strends(str(?fu), 'PERCENT'), false), ' %', '')) as ?val0) bind('' as ?lab0) } union { graph ?da { ?_partid_iri mvikg:evidenceText ?v } bind(13 as ?ord) bind(mvikg:evidenceText as ?Property_noheader) bind('Evidence:' as ?Property_label) bind(str(?v) as ?val0) bind('' as ?lab0) } union { bind(15 as ?ord) bind(dct:isPartOf as ?Property_noheader) 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