Nanopublication

ID

https://w3id.org/np/RAnGxpTDHemPIuRP09a8Qq55oseUT_NnzlkZdSraEM0qY
Formats

Content

@prefix this: <https://w3id.org/np/RAnGxpTDHemPIuRP09a8Qq55oseUT_NnzlkZdSraEM0qY> .
@prefix sub: <https://w3id.org/np/RAnGxpTDHemPIuRP09a8Qq55oseUT_NnzlkZdSraEM0qY/> .
@prefix schema: <http://schema.org/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@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/kinetics-model> a schema:Thing;
    schema:description "Mathematical model describing RNA degradation dynamics using enzymatic kinetics"@en;
    schema:formula "f(A) = (1 - P0) * exp(-k'i * A) + P0"@en;
    schema:name "CoLoC-seq Kinetics Model"@en;
    sio:SIO_000211 "P0"@en, "k'i"@en;
    rdfs:comment "Model assumes fixed time t=10 min; R0 = initial RNA concentration; A = RNase A concentration"@en .
  
  <http://purl.org/coloc-seq/parameter-P0> a schema:Thing;
    schema:description "Proportion of RNA protected from RNase digestion by organellar membranes"@en;
    schema:interpretation "0 < P0 < 1: partially protected"@en, "P0 = 0: entirely accessible contaminant"@en,
      "P0 ≈ 1: fully protected resident RNA"@en;
    schema:name "Protected Pool Parameter (P0)"@en;
    schema:range "0 to 1 (0% to 100%)"@en;
    rdfs:comment "Primary parameter of interest for CoLoC-seq; determined by nonlinear curve fitting"@en .
  
  <http://purl.org/coloc-seq/parameter-k-prime> a schema:Thing;
    schema:description "Pseudo-first-order rate constant for RNA degradation by RNase"@en;
    schema:interpretation "Reflects sensitivity of each transcript to RNase degradation"@en;
    schema:name "Digestion Rate Constant (k'i)"@en;
    schema:unit "per μg/ml RNase A"@en;
    rdfs:comment "Fitted using Leverberg Marquardt regression; higher k' indicates faster degradation"@en .
  
  this: a <https://w3id.org/np/RAnGxpTDHemPIuRP09a8Qq55oseUT_NnzlkZdSraEM0qY/o/ntemplate/AIDA-Sentence>;
    npx:relatesTo <https://w3id.org/np/RA_C-L7pLBKSyHDhS2YIFmqfb_-BLGOldcUb8emWvRltA>;
    schema:about <https://doi.org/10.1093/nar/gkac1205>;
    schema:text "The CoLoC-seq kinetics model uses the protected pool parameter P0 to distinguish genuinely localised organellar transcripts from surface-attached contaminants based on their degradation dynamics."@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:0000-0002-1481-2996;
    prov:wasDerivedFrom <https://doi.org/10.1093/nar/gkac1205>, <https://w3id.org/np/RA_C-L7pLBKSyHDhS2YIFmqfb_-BLGOldcUb8emWvRltA> .
}

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 the CoLoC-seq kinetics model and the P0 parameter"@en;
    rdfs:label "Nanopublication: CoLoC-seq kinetics model and protected pool parameter"@en;
    prov:wasAttributedTo orcid:0009-0005-7752-8203 .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAoSR/rqhnkTPQO8u4l2JQAemJo5cN83rT54nA5NXHUqaeu26bEjT/rsX1PCVBhhJ3cV2uu4wjI0NfcVaKPKmODSf6p579tdOykOnjbWLbxxPMe5DC5eV1ThMHsFsNU/6vCYIfS00E7wre7fnFYz7FAG7v1MZEyWeSXsHgk9jHoqQQDPqup5PHReKp1dd6J0Nht/OfSYnUancKAgIFyPhkTlThsLK5xSNyNEgiTR7pwkP5pGq2AnD6bPw4G3kiPnIpIGZNsaeIOvhn64gwbrtoJVdoun/namw6FQ7StEC5km/0evaBZc4qIextwO/s32Wru77ukblJ0Xi/YzbC0iLuIQIDAQAB";
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    npx:hasSignatureTarget this: .
}