https://w3id.org/np/RAOOCyhTlYJpH41DF6nswHFXmwhtABqM9g_m2S2mfxKZM
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAOOCyhTlYJpH41DF6nswHFXmwhtABqM9g_m2S2mfxKZM> .
@prefix sub: <https://w3id.org/np/RAOOCyhTlYJpH41DF6nswHFXmwhtABqM9g_m2S2mfxKZM/> .
@prefix qudt: <http://qudt.org/schema/qudt/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix mvikg: <http://example.org/mvikg/> .
@prefix gen: <https://w3id.org/kpxl/gen/terms/> .
@prefix unit: <http://qudt.org/vocab/unit/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix biolink: <https://w3id.org/biolink/vocab/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
mvikg:alt rdfs:label "alternate allele" .
mvikg:comparedTo rdfs:label "compared to" .
mvikg:effect rdfs:label "variant effect" .
mvikg:frequency rdfs:label "frequency" .
mvikg:length rdfs:label "variant length" .
mvikg:ref rdfs:label "reference allele" .
<http://purl.obolibrary.org/obo/ECO_0000305> rdfs:label "evidence" .
dct:description rdfs:label "description" .
qudt:QuantityValue rdfs:label "quantity value" .
qudt:hasUnit rdfs:label "unit" .
qudt:numericValue rdfs:label "numeric value" .
rdf:type rdfs:label "is a" .
rdfs:label rdfs:label "label" .
sosa:isFeatureOfInterestOf rdfs:label "is feature of interest of" .
biolink:Gene rdfs:label "gene" .
biolink:PhenotypicFeature rdfs:label "phenotypic feature" .
biolink:SequenceVariant rdfs:label "sequence variant" .
biolink:end_coordinate rdfs:label "end coordinate" .
biolink:has_evidence rdfs:label "has evidence" .
biolink:has_phenotype rdfs:label "has phenotype" .
biolink:has_sequence_variant rdfs:label "has sequence variant" .
biolink:start_coordinate rdfs:label "start coordinate" .
sub:alt a nt:LiteralPlaceholder;
rdfs:label "alternate allele" .
sub:comparedTo a nt:LiteralPlaceholder;
rdfs:label "compared to (the baseline/control the phenotype outcome was compared against)" .
sub:effect a nt:LiteralPlaceholder;
rdfs:label "variant effect" .
sub:endCoordinate a nt:LiteralPlaceholder;
rdfs:label "end coordinate (variant position)";
nt:hasDatatype xsd:integer .
sub:evidence a nt:EmbeddedResource, nt:LocalResource;
rdfs:label "evidence for this variant" .
sub:evidenceText a nt:LiteralPlaceholder;
rdfs:label "evidence text (quote/description from the source)" .
sub:freq a nt:EmbeddedResource, nt:LocalResource;
rdfs:label "the variant's frequency" .
sub:freqUnit a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
rdfs:label "frequency unit";
nt:possibleValue unit:PERCENT, unit:UNITLESS .
sub:freqValue a nt:LiteralPlaceholder;
rdfs:label "frequency value";
nt:hasDatatype xsd:decimal .
sub:gene a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
rdfs:label "the gene this variant and (optionally) phenotype belong to (search existing genes, or enter an NCBI Gene ID)";
nt:possibleValuesFromApi "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&retmode=json&id=",
"https://w3id.org/np/l/nanopub-query-1.1/api/RAom4OoQ8U2K6A629YRXKo9-XU-ZJM7-KZs1h11OD6c1w/find-things?type=https://w3id.org/biolink/vocab/Gene" .
sub:length a nt:LiteralPlaceholder;
rdfs:label "variant length (free text — not all source rows give a clean integer)" .
sub:phenotype a nt:EmbeddedResource, nt:LocalResource;
rdfs:label "the phenotype associated with this gene" .
sub:phenotypeDescription a nt:LiteralPlaceholder;
rdfs:label "phenotype description (prose, e.g. \"DeltarfaH mutant elicited ROS production...\")" .
sub:ref a nt:LiteralPlaceholder;
rdfs:label "reference allele" .
sub:sample a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
rdfs:label "the sample this gene was observed in (declared via the sample-context template)";
nt:possibleValuesFromApi "https://w3id.org/np/l/nanopub-query-1.1/api/RAom4OoQ8U2K6A629YRXKo9-XU-ZJM7-KZs1h11OD6c1w/find-things?type=http://www.w3.org/ns/sosa/Sample" .
sub:soType a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
rdfs:label "sequence variant type (Sequence Ontology)";
nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols4/api/select?ontology=so&fieldList=iri,label,description&q=" .
sub:st01 rdf:object sub:sample;
rdf:predicate sosa:isFeatureOfInterestOf;
rdf:subject sub:gene .
sub:st08 rdf:object biolink:Gene;
rdf:predicate rdf:type;
rdf:subject sub:gene .
sub:st09 rdf:object sub:variant;
rdf:predicate biolink:has_sequence_variant;
rdf:subject sub:gene .
sub:st10 rdf:object biolink:SequenceVariant;
rdf:predicate rdf:type;
rdf:subject sub:variant .
sub:st11 rdf:object sub:variantName;
rdf:predicate rdfs:label;
rdf:subject sub:variant .
sub:st12 a nt:OptionalStatement;
rdf:object sub:soType;
rdf:predicate rdf:type;
rdf:subject sub:variant .
sub:st13 a nt:OptionalStatement;
rdf:object sub:effect;
rdf:predicate mvikg:effect;
rdf:subject sub:variant .
sub:st14 a nt:OptionalStatement;
rdf:object sub:length;
rdf:predicate mvikg:length;
rdf:subject sub:variant .
sub:st15 a nt:OptionalStatement;
rdf:object sub:alt;
rdf:predicate mvikg:alt;
rdf:subject sub:variant .
sub:st16 a nt:OptionalStatement;
rdf:object sub:ref;
rdf:predicate mvikg:ref;
rdf:subject sub:variant .
sub:st17 a nt:OptionalStatement;
rdf:object sub:startCoordinate;
rdf:predicate biolink:start_coordinate;
rdf:subject sub:variant .
sub:st18 a nt:OptionalStatement;
rdf:object sub:endCoordinate;
rdf:predicate biolink:end_coordinate;
rdf:subject sub:variant .
sub:st19 a nt:GroupedStatement, nt:OptionalStatement;
nt:hasStatement sub:st20, sub:st21, sub:st22 .
sub:st20 rdf:object sub:evidence;
rdf:predicate biolink:has_evidence;
rdf:subject sub:variant .
sub:st21 rdf:object <http://purl.obolibrary.org/obo/ECO_0000305>;
rdf:predicate rdf:type;
rdf:subject sub:evidence .
sub:st22 rdf:object sub:evidenceText;
rdf:predicate dct:description;
rdf:subject sub:evidence .
sub:st23 a nt:GroupedStatement, nt:OptionalStatement;
nt:hasStatement sub:st24, sub:st25, sub:st26, sub:st27 .
sub:st24 rdf:object sub:freq;
rdf:predicate mvikg:frequency;
rdf:subject sub:variant .
sub:st25 rdf:object qudt:QuantityValue;
rdf:predicate rdf:type;
rdf:subject sub:freq .
sub:st26 rdf:object sub:freqValue;
rdf:predicate qudt:numericValue;
rdf:subject sub:freq .
sub:st27 rdf:object sub:freqUnit;
rdf:predicate qudt:hasUnit;
rdf:subject sub:freq .
sub:st28 a nt:GroupedStatement, nt:OptionalStatement;
nt:hasStatement sub:st29, sub:st30, sub:st31, sub:st32 .
sub:st29 rdf:object sub:phenotype;
rdf:predicate biolink:has_phenotype;
rdf:subject sub:gene .
sub:st30 rdf:object biolink:PhenotypicFeature;
rdf:predicate rdf:type;
rdf:subject sub:phenotype .
sub:st31 rdf:object sub:phenotypeDescription;
rdf:predicate rdfs:label;
rdf:subject sub:phenotype .
sub:st32 rdf:object sub:comparedTo;
rdf:predicate mvikg:comparedTo;
rdf:subject sub:phenotype .
sub:startCoordinate a nt:LiteralPlaceholder;
rdfs:label "start coordinate (variant position)";
nt:hasDatatype xsd:integer .
sub:templateVersion a nt:AssertionTemplate, nt:UnlistedTemplate;
dct:description "Declaring an MVIKG observation";
dct:isVersionOf sub:template;
rdfs:label "Declaring an MVIKG observation";
gen:governedBy <https://w3id.org/spaces/mvikg>;
nt:hasNanopubLabelPattern "${variantName}";
nt:hasStatement sub:st01, sub:st08, sub:st09, sub:st10, sub:st11, sub:st12, sub:st13,
sub:st14, sub:st15, sub:st16, sub:st17, sub:st18, sub:st19, sub:st20, sub:st21, sub:st22,
sub:st23, sub:st24, sub:st25, sub:st26, sub:st27, sub:st28, sub:st29, sub:st30, sub:st31,
sub:st32;
nt:hasTag "Biology";
nt:hasTargetNanopubType biolink:SequenceVariant .
sub:variant a nt:IntroducedResource, nt:LocalResource;
rdfs:label "this sequence variant" .
sub:variantName a nt:LiteralPlaceholder;
rdfs:label "variant name/notation (e.g. T77I)" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0009-0005-5515-1230 .
}
sub:pubinfo {
this: dct:created "2026-11-04T12:15:21Z"^^xsd:dateTime;
dct:creator orcid:0009-0005-5515-1230;
dct:license <https://creativecommons.org/licenses/by/4.0/>;
npx:embeds sub:templateVersion;
npx:introduces sub:template;
rdfs:label "Declaring an MVIKG observation";
nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA-yPZEYODCS39dWOWm7NA_ClOGFHzPi8iYhLzoZf19GI>;
nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA4o9JqSxNO2Z47itbAcxvpVfdR97t_7usxmdR90URXQs>;
nt:wasCreatedFromTemplate <https://w3id.org/np/RAgeON_vGgJCt5E4DPMi0eOPaGwNv9tbfFTRZtBwdQL0w> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAjO3oH8Lq/l1oZIUY3FlCz5DnndybGvAhBdmEJ/yq7Nv3GZEYPrEro23rCBCp0GiriOXlVbk61pA/7JFE6tqzTresINW6QQMxE9sIhCBlX4cG66JFD8ud6bMvUyzCR8LQA6zfrSbafGE06rvglJd4MDUcTwvUKqtL9UCnOaowVfnZ3sPOe9EqlmJuO3iHGxBSXMPOPEJZUzMXsFDWFuMZTnrR8gY3r5nVF5a8L/MD135ZH8qW5yGXOB28CmVYCAbw2o07QEKzyzFKN+W1gfnprYZvuKzwGexnzcdzc1S8N/M5bzhWQ40EKCEqgUE8c81OzEMm1HUlUKEJ/o5I/FKKAwIDAQAB";
npx:hasSignature "TL7aHGCrAuvgE0DTe030AIwk3p/2ygAhsC3vsSKL5Mdz1Y/pJUBdmJcPa9xkgUi7lCMFfSCnowa/kveQlXaZw+aw4Vy5PmEbp7Nt+7q50sLXEIQxiUjlINchmV4nDbJjYOK+ynh7+4cyMYxgUXOq8NkZawneeKk5XbwuVVPIAP7P+AqBrmdohJq+T5/Dg6miMFM9q0SSgrqSXMcQaxgmfvLOIBBAGrmBarVdGUNBdWsTH5CsblcHLMDE8pX+slHXnsjNlrE0T1jH/Q5iD4oYW663EwWZOgC/SjtncGxRbywkIaSX7L4IDvpryeAcqOTh97w2pN/yBbXwxiVQXmJ+Zg==";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0009-0005-5515-1230 .
}