https://w3id.org/np/RAY6Ta_8m3K6k9KeX-VVLPZU-DTpC9aywq4ojMiM6xxus
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAY6Ta_8m3K6k9KeX-VVLPZU-DTpC9aywq4ojMiM6xxus> .
@prefix sub: <https://w3id.org/np/RAY6Ta_8m3K6k9KeX-VVLPZU-DTpC9aywq4ojMiM6xxus/> .
@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-phenotype-info a grlc:grlc-query;
dct:description "Key-value Info card for a phenotype or antibiogram observation record ('partid') of the MVIKG knowledge graph: name, description, baseline, sample, associated variant, the antibiogram fields where present (antibiotic, susceptibility call, MIC, typing method, breakpoint standard, platform), 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).";
dct:license <https://creativecommons.org/licenses/by/4.0/>;
rdfs:label "Get MVIKG phenotype info";
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 ?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('Description:' as ?Property_label)
bind(str(?v) as ?val0) bind('' as ?lab0)
}
union
{
graph ?da { ?_partid_iri dct:description ?v }
bind(3 as ?ord) bind(dct:description as ?Property_noheader) bind('Source sentence:' as ?Property_label)
bind(str(?v) as ?val0) bind('' as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:comparedTo ?v }
bind(4 as ?ord) bind(mvikg:comparedTo as ?Property_noheader) bind('Compared to:' as ?Property_label)
bind(str(?v) as ?val0) bind('' as ?lab0)
}
union
{
graph ?da { ?_partid_iri sosa:isResultOf ?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:isResultOf 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:isAssociatedWithVariant ?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(6 as ?ord) bind(mvikg:isAssociatedWithVariant as ?Property_noheader) bind('Variant:' 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:antibiotic ?v }
bind(7 as ?ord) bind(mvikg:antibiotic as ?Property_noheader) bind('Antibiotic:' as ?Property_label)
bind(str(?v) as ?val0) bind('' as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:antibioticAroId ?iri }
bind(8 as ?ord) bind(mvikg:antibioticAroId as ?Property_noheader) bind('Antibiotic (ARO):' as ?Property_label)
bind(str(?iri) as ?val0) bind(replace(replace(str(?iri), '^.*[/#]', ''), '_', ':') as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:susceptibilityCall ?iri }
bind(9 as ?ord) bind(mvikg:susceptibilityCall as ?Property_noheader) bind('Susceptibility:' as ?Property_label)
bind(str(?iri) as ?val0) bind(if(strends(str(?iri), 'ARO_3004300'), 'intermediate', if(strends(str(?iri), 'ARO_3004301'), 'resistant', if(strends(str(?iri), 'ARO_3004302'), 'susceptible', replace(replace(str(?iri), '^.*[/#]', ''), '_', ':')))) as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:micValue ?v . optional { ?_partid_iri mvikg:micUnit ?mu } }
bind(10 as ?ord) bind(mvikg:micValue as ?Property_noheader) bind('MIC:' as ?Property_label)
bind(concat(str(?v), coalesce(concat(' ', replace(str(?mu), '^.*/', '')), '')) as ?val0) bind('' as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:typingMethod ?iri }
bind(11 as ?ord) bind(mvikg:typingMethod as ?Property_noheader) bind('Typing method:' as ?Property_label)
bind(str(?iri) as ?val0) bind(replace(replace(str(?iri), '^.*[/#]', ''), '_', ':') as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:breakpointStandard ?iri }
bind(12 as ?ord) bind(mvikg:breakpointStandard as ?Property_noheader) bind('Breakpoint standard:' as ?Property_label)
bind(str(?iri) as ?val0) bind(replace(replace(str(?iri), '^.*[/#]', ''), '_', ':') as ?lab0)
}
union
{
graph ?da { ?_partid_iri mvikg:platform ?iri }
bind(13 as ?ord) bind(mvikg:platform as ?Property_noheader) bind('Platform:' as ?Property_label)
bind(str(?iri) as ?val0) bind(replace(replace(str(?iri), '^.*[/#]', ''), '_', ':') as ?lab0)
}
union
{
bind(15 as ?ord) bind(dct:isPartOf as ?Property_noheader) bind('Part of:' as ?Property_label)
graph ?da { ?_partid_iri dct:isPartOf ?iri }
bind(str(?iri) as ?val0) bind('MVIKG knowledge graph' as ?lab0)
}
} }
union
{
bind(16 as ?ord) bind(npa:viaNanopub as ?Property_noheader) bind('Defined in:' as ?Property_label)
bind('DNP' as ?val0)
}
union
{
bind(14 as ?ord) bind(npx:approvesOf as ?Property_noheader) bind('Review status:' as ?Property_label)
bind('STATUS' as ?val0)
}
bind(if(?val0 = 'DNP', str(?dnp), if(?val0 = 'STATUS', if(!bound(?mv), '⏳ pending', if(strends(?mv, 'd'), '�� rejected', '✅ approved')), ?val0)) as ?val)
bind(if(?val0 = 'DNP', substr(replace(str(?dnp), '^.*/np/', ''), 1, 10), if(?val0 = 'STATUS', '', ?lab0)) as ?vallabelRaw)
} group by ?ord ?Property_noheader ?Property_label ?val
}
}
group by ?ord ?Property_noheader ?Property_label
order by ?ord""" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 .
}
sub:pubinfo {
this: dct:created "2026-11-12T12:26:36.769+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-phenotype-info;
rdfs:label "Get MVIKG phenotype info";
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 "IO2mf55mUYaA+/BWuNmFAkFxxfx80FKQFbmILKe3Th/b5JI3mpc5wQrZ/6Arlo/OffRmn54F5u72k/CCESaFCyd/xsa5LNYCYpRZVPlbOJFpPqss/UeNROYr55fvM3hDw1diiYJ4tn3i7JxMfI0hytXe/fqqRqsxyfDnnM/CY3E=";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0002-1267-0234 .
}