https://w3id.org/np/RAlKWZT_fYEypAcxT-UKqR0e11iFea4cU0-g6pmKhpu4E
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@prefix this: <https://w3id.org/np/RAlKWZT_fYEypAcxT-UKqR0e11iFea4cU0-g6pmKhpu4E> .
@prefix sub: <https://w3id.org/np/RAlKWZT_fYEypAcxT-UKqR0e11iFea4cU0-g6pmKhpu4E/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix grlc: <https://w3id.org/kpxl/grlc/> .
@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 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-mvikg-gene-variants a grlc:grlc-query;
dct:description "Lists the sequence variant records of the MVIKG knowledge graph that belong to a gene ('partid'), with the sample they were observed in, Sequence Ontology type, effect and review status. 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).";
dct:license <https://creativecommons.org/licenses/by/4.0/>;
rdfs:label "Get MVIKG variants of a gene";
grlc:endpoint <https://w3id.org/np/l/nanopub-query-1.1/repo/full>;
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 ?variant ?variant_label ?sample ?sample_label ?type ?effect ?status ?np ?np_label where {
{
select ?variant ?np (sample(?l) as ?vl) (sample(coalesce(?samc, ?sam)) as ?sample) (min(?saml) as ?sl) (group_concat(distinct ?tl; separator=', ') as ?type) (sample(?e) as ?effect) (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 ?a { ?_partid_iri biolink:has_sequence_variant ?variant . ?variant a biolink:SequenceVariant ; dct:isPartOf <https://w3id.org/spaces/mvikg/r/kg> . }
graph npa:graph {
?np np:hasAssertion ?a ; npx:introduces ?variant ; dct:created ?date ;
npa:hasValidSignatureForPublicKeyHash ?pubkey .
filter not exists { ?inv npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . }
}
filter(contains(?memberKeys, ?pubkey))
optional {
graph npa:graph {
?np2 npx:introduces ?variant ; dct:created ?date2 ; npa:hasValidSignatureForPublicKeyHash ?pubkey2 .
filter not exists { ?inv2 npx:invalidates ?np2 ; npa:hasValidSignatureForPublicKeyHash ?pubkey2 . }
}
filter(contains(?memberKeys, ?pubkey2) && concat(str(?date2), '>', str(?np2)) > concat(str(?date), '>', str(?np)))
}
filter(!bound(?np2))
optional { graph ?a { ?variant rdfs:label ?l } }
optional { graph ?a { ?variant mvikg:effect ?e } }
optional { graph ?a { ?variant a ?t . filter(?t != biolink:SequenceVariant) } bind(if(?t = obo:SO_0000159, 'deletion', if(?t = obo:SO_0000667, 'insertion', if(?t = obo:SO_0000694, 'SNP', if(?t = obo:SO_0001483, 'SNV', if(?t = obo:SO_0001059, 'sequence alteration', if(?t = obo:SO_1000002, 'substitution', if(?t = obo:SO_1000032, 'delins', if(?t = obo:SO_0002007, 'MNV', replace(replace(str(?t), '^.*[/#]', ''), '_', ':'))))))))) as ?tl) }
optional { graph ?a { ?_partid_iri sosa:isFeatureOfInterestOf ?sam } }
optional {
graph npa:graph {
?samonp npx:introduces ?sam . ?samnp npx:supersedes* ?samonp ; npx:introduces ?samc ; rdfs:label ?saml ;
npa:hasValidSignatureForPublicKeyHash ?sampk .
filter not exists { ?saminv npx:invalidates ?samnp ; npa:hasValidSignatureForPublicKeyHash ?sampk . }
}
}
optional {
values ?vpred { npx:approvesOf npx:disapprovesOf }
graph ?va { ?vagent ?vpred ?np . }
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 ?variant ?np
}
bind(coalesce(str(?vl), replace(str(?variant), '^.*/np/', '')) as ?variant_label)
bind(coalesce(str(?sl), replace(str(?sample), '^.*/np/', '')) as ?sample_label)
bind(if(!bound(?mv), '⏳ pending', if(strends(?mv, 'd'), '�� rejected', '✅ approved')) as ?status)
bind('^' as ?np_label)
}
order by ?variant_label""" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 .
}
sub:pubinfo {
this: dct:created "2026-11-12T13:26:12.587+01:00"^^xsd:dateTime;
dct:creator orcid:0000-0002-1267-0234;
dct:license <https://creativecommons.org/licenses/by/4.0/>;
npx:embeds sub:get-mvikg-gene-variants;
rdfs:label "Get MVIKG variants of a gene";
nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA7lSq6MuK_TIC6JMSHvLtee3lpLoZDOqLJCLXevnrPoU>;
nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA-N4_kFxcruvBTlo1yJv29E4SLOXsx5KO_th69PprMrA>,
<https://w3id.org/np/RACJ58Gvyn91LqCKIO9zu1eijDQIeEff28iyDrJgjSJF8>;
nt:wasCreatedFromTemplate <https://w3id.org/np/RAEFAt-QcFK0ZhqfvlsmS10BnzGJA0xwOICZXkO-ai87k> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwUtewGCpT5vIfXYE1bmf/Uqu1ojqnWdYxv+ySO80ul8Gu7m8KoyPAwuvaPj0lvPtHrg000qMmkxzKhYknEjq8v7EerxZNYp5B3/3+5ZpuWOYAs78UnQVjbHSmDdmryr4D4VvvNIiUmd0yxci47dTFUj4DvfHnGd6hVe5+goqdcwIDAQAB";
npx:hasSignature "HguU3mxaPNid16sHokcs+pOAYbB53kW3StSFQeQ6cCM7aJ1oqSf32YiqLfuv6cLMe3v+wpdKu36BPb/P5tao81zJfM+n+Uw9oHCua7c4CIETXzeIoVC9je+gouSIMKMg1/jwMEr/fdETkgq88Ia38jVjt0id552Ty7QbOXrBr+Y=";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0002-1267-0234 .
}