Nanopublication

ID

https://w3id.org/np/RA6_pOabaeorsg_3G0C-SqZUsvODlrcnWuCio2R-1aYrA
Formats

Content

@prefix this: <https://w3id.org/np/RA6_pOabaeorsg_3G0C-SqZUsvODlrcnWuCio2R-1aYrA> .
@prefix sub: <https://w3id.org/np/RA6_pOabaeorsg_3G0C-SqZUsvODlrcnWuCio2R-1aYrA/> .
@prefix schema: <http://schema.org/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix edam: <http://edamontology.org/> .
@prefix pav: <http://purl.org/pav/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .

sub:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo .
}

sub:assertion {
  <http://purl.org/coloc-seq/dataset-hek293> a edam:data_0955, schema:Dataset;
    schema:description "Transcriptome data from human Flp-In T-REx 293 cells"@en;
    schema:isPartOf <https://doi.org/10.1093/nar/gkac1205>;
    schema:name "HEK293 cell mitochondrial transcriptome"@en;
    sio:SIO_000228 "300000000"^^xsd:integer .
  
  <http://purl.org/coloc-seq/experiment-human-mitochondria> a edam:data_0955, schema:Thing;
    schema:name "CoLoC-seq validation in human mitochondria"@en;
    schema:result <http://purl.org/coloc-seq/result-mtdna-transcripts>, <http://purl.org/coloc-seq/result-ndna-contamination>;
    schema:studySubject <http://purl.org/coloc-seq/dataset-hek293>;
    sio:SIO_000062 "13338"^^xsd:integer;
    sio:SIO_000228 "351"^^xsd:integer .
  
  <http://purl.org/coloc-seq/result-mtdna-transcripts> a schema:Thing;
    schema:name "mtDNA-encoded transcript protection"@en;
    sio:SIO_000225 "100"^^xsd:float;
    rdfs:comment "mt-tRNAVal and mt-tRNALys fully resistant to RNase A; rapidly degraded in Mock CoLoC-seq"@en .
  
  <http://purl.org/coloc-seq/result-ndna-contamination> a schema:Thing;
    schema:name "nDNA-encoded contaminant identification"@en;
    rdfs:comment "5.8S rRNA and U6 snRNA rapidly degraded in both CoLoC-seq and Mock CoLoC-seq"@en .
  
  <http://purl.org/coloc-seq/validation-correlation> a schema:Thing;
    schema:measurementTechnique "Spearman's correlation"@en;
    schema:name "Validation against northern blotting"@en;
    schema:statisticalSignificance "8.7e-73"^^xsd:float;
    sio:SIO_000225 "0.888"^^xsd:float;
    rdfs:comment "90.6% of measurements within 0.3 of northern blotting values; high concordance of P0 values (ρ = 0.822, P = 1.6e-5)"@en .
  
  this: a <https://w3id.org/np/RA6_pOabaeorsg_3G0C-SqZUsvODlrcnWuCio2R-1aYrA/o/ntemplate/AIDA-Sentence>;
    npx:relatesTo <https://w3id.org/np/RAqWgWTy_lLfUrvdgqP0lggMHH_Of_5TgmpDWkpxe16gg>;
    schema:about <https://doi.org/10.1093/nar/gkac1205>;
    schema:mentions <http://purl.org/coloc-seq/dataset-hek293>;
    schema:text "CoLoC-seq validation in human mitochondria identified 351 transcripts, with mtDNA-encoded transcripts showing 100 percent protection and nDNA-encoded transcripts showing rapid degradation, demonstrating the method's accuracy."@en .
}

sub:provenance {
  <https://doi.org/10.1093/nar/gkac1205> a schema:ScholarlyArticle;
    bibo:doi "10.1093/nar/gkac1205";
    schema:datePublished "2023"^^xsd:gYear;
    schema:isPartOf sub:__1;
    schema:name "CoLoC-seq probes the global topology of organelle transcriptomes"@en .
  
  sub:__1 a schema:Periodical;
    schema:name "Nucleic Acids Research"@en .
  
  sub:assertion prov:wasAttributedTo orcid:0000-0001-8763-6703, orcid:0000-0002-1481-2996,
      orcid:0000-0002-9142-7979;
    prov:wasDerivedFrom <https://doi.org/10.1093/nar/gkac1205>, <https://w3id.org/np/RAqWgWTy_lLfUrvdgqP0lggMHH_Of_5TgmpDWkpxe16gg> .
}

sub:pubinfo {
  orcid:0009-0005-7752-8203 foaf:name "Tiado Kollender" .
  
  this: a npx:ExampleNanopub;
    dct:created "2026-01-11T00:00:00Z"^^xsd:dateTime;
    dct:license <https://creativecommons.org/publicdomain/zero/1.0/>;
    npx:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA0J4vUn_dekg-U1kK3AOEt02p9mT2WO03uGxLDec1jLw>,
      <https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI>;
    pav:createdBy orcid:0009-0005-7752-8203;
    rdfs:comment "AIDA-based assertion about CoLoC-seq validation and experimental results"@en;
    rdfs:label "Nanopublication: CoLoC-seq validation results in human mitochondria"@en;
    prov:wasAttributedTo orcid:0009-0005-7752-8203 .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAoSR/rqhnkTPQO8u4l2JQAemJo5cN83rT54nA5NXHUqaeu26bEjT/rsX1PCVBhhJ3cV2uu4wjI0NfcVaKPKmODSf6p579tdOykOnjbWLbxxPMe5DC5eV1ThMHsFsNU/6vCYIfS00E7wre7fnFYz7FAG7v1MZEyWeSXsHgk9jHoqQQDPqup5PHReKp1dd6J0Nht/OfSYnUancKAgIFyPhkTlThsLK5xSNyNEgiTR7pwkP5pGq2AnD6bPw4G3kiPnIpIGZNsaeIOvhn64gwbrtoJVdoun/namw6FQ7StEC5km/0evaBZc4qIextwO/s32Wru77ukblJ0Xi/YzbC0iLuIQIDAQAB";
    npx:hasSignature "B4WtYYTurVS/m1hQThLywwa1M1mwW+U9p9eHy+IV4lTGez6BGxLsAVtakrO9r7bPwOS1inLZXBoOmENwOceugQiUso+8YHNacds9jZ6fHlVvQPDHMNLuv6oKlKPMlrHkM5Ut8w7BZifGZH4jUzslHV2eZQlJLPuO7S3k5SL8J4Jz/Ae9WnHICS6ZgajwaADfgByvxj4HGOFIML6XBUP9/mx6+Bbxfl7WvWQw0Kl5GfCRB+khLGuL9aSt5EYYNcUYEG6yEd50WKQRBnjOZgqRehrGl1GF2b0j5fIxOOwypGrDtymYKPNHl8iIOXQP65XWLVhpO8agoFSw3OQeA+tGSA==";
    npx:hasSignatureTarget this: .
}