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https://w3id.org/np/RAlwkr9mQDxu7EwQxrbnLqBtGbWyo4WvkHrnJQPg_-qCM

Formats

.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt

Content

@prefix this: <https://w3id.org/np/RAlwkr9mQDxu7EwQxrbnLqBtGbWyo4WvkHrnJQPg_-qCM> .
@prefix sub: <https://w3id.org/np/RAlwkr9mQDxu7EwQxrbnLqBtGbWyo4WvkHrnJQPg_-qCM/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

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

sub:assertion {
  <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>
    a prov:SoftwareAgent;
    <http://www.w3.org/2000/01/rdf-schema#label> "delphisci dataset-resolvability assessor (Gemini 4 Argon)";
    prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
    <https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/gemini-4-argon-medium> .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:description "Testing whether a bottom-up continuum constitutive law reproduces full-range deformation is feasible in the low-force entropic regime using published optical-tweezer measurements and across higher forces by re-running atomistic simulations on PDB collagen models. However, the public abstract omits the exact functional form of the continuum equation, and no experimental dataset spans the entire deformation range up to covalent backbone rupture of a single tropocollagen molecule. In addition, the 'without empirical parameters' clause rests on treating empirical force-field outputs as ab initio inputs, limiting discriminating power.";
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0>;
    <http://www.w3.org/2000/01/rdf-schema#comment> "Proposed test with existing data: Parameterize an extensible worm-like chain and piecewise energetic stretching continuum model solely from atomistic force-field simulations of a tropocollagen triple helix, then test its predicted force-extension curve against single-molecule optical-tweezer and AFM pulling data as well as reactive MD trajectories up to covalent rupture. Confirmation requires good quantitative agreement across the entropic, helix-uncoiling, and backbone-fracture regimes without post-hoc curve fitting to experimental traces.";
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2007-tropocollagen-entropic-04: partially-resolvable, resolvability 0.48";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0";
    <https://w3id.org/delphi/ontology/evidenceAgainst> "Experimental single-molecule pulling datasets only cover the low- and intermediate-force regimes and do not reach covalent backbone fracture of a triple helix.",
      "The abstract does not give the explicit equations of the continuum model, requiring access to the closed-access full text or independent re-derivation.",
      "Whether parameters extracted from empirical MD force fields qualify as parameter-free is partly a methodological definition rather than an empirical question.";
    <https://w3id.org/delphi/ontology/hasConfidence> "0.65"^^xsd:double;
    <https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/buehler-2007-tropocollagen-entropic-04--gemini--dataset-1>,
      <https://w3id.org/delphi/resource/evidence/buehler-2007-tropocollagen-entropic-04--gemini--dataset-2>;
    <https://w3id.org/delphi/ontology/hasScore> "0.478"^^xsd:double;
    <https://w3id.org/delphi/ontology/hasVerdict> "partially-resolvable" .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--analysis-feasibility>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-analysis-feasibility>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Analysis feasibility of buehler-2007-tropocollagen-entropic-04 by Gemini 4 Argon: 0.55";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/analysis-feasibility";
    <https://w3id.org/delphi/ontology/hasScore> "0.55"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--data-adequacy>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-adequacy>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Data adequacy of buehler-2007-tropocollagen-entropic-04 by Gemini 4 Argon: 0.4";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/data-adequacy";
    <https://w3id.org/delphi/ontology/hasScore> "0.4"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--data-existence>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-existence>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Data existence of buehler-2007-tropocollagen-entropic-04 by Gemini 4 Argon: 0.5";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/data-existence";
    <https://w3id.org/delphi/ontology/hasScore> "0.5"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--discriminating-power>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-discriminating-power>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Discriminating power of buehler-2007-tropocollagen-entropic-04 by Gemini 4 Argon: 0.45";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/discriminating-power";
    <https://w3id.org/delphi/ontology/hasScore> "0.45"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--operationalizability>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-operationalizability>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Operationalizability of buehler-2007-tropocollagen-entropic-04 by Gemini 4 Argon: 0.5";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/operationalizability";
    <https://w3id.org/delphi/ontology/hasScore> "0.5"^^xsd:double .
  
  <https://w3id.org/delphi/resource/claim/buehler-2007-tropocollagen-entropic-04> <https://w3id.org/delphi/ontology/hasAssessment>
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>,
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--analysis-feasibility>,
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--data-adequacy>,
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--data-existence>,
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--discriminating-power>,
      <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini--operationalizability> .
  
  <https://w3id.org/delphi/resource/evidence/buehler-2007-tropocollagen-entropic-04--gemini--dataset-1>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "collagen triple-helix structural templates for bottom-up parameterization of the continuum model";
    <http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: RCSB Protein Data Bank";
    prov:wasDerivedFrom <https://www.rcsb.org/> .
  
  <https://w3id.org/delphi/resource/evidence/buehler-2007-tropocollagen-entropic-04--gemini--dataset-2>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "open simulation package with CHARMM and ReaxFF potentials to generate full-range single-molecule force-extension curves";
    <http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: LAMMPS Molecular Dynamics Simulator";
    prov:wasDerivedFrom <https://www.lammps.org/> .
  
  <https://w3id.org/delphi/resource/model/gemini-4-argon-medium> a <https://w3id.org/delphi/ontology/LanguageModel>;
    dc:identifier "gemini-4-argon-medium";
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon" .
}

sub:provenance {
  sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/assessment/raw/gemini/batch-2.json>,
      <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0>;
    prov:wasGeneratedBy sub:assessment .
  
  sub:assessment a prov:Activity;
    prov:qualifiedAssociation sub:assessmentPlan;
    prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium> .
  
  sub:assessmentPlan prov:hadPlan <https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/README.md> .
}

sub:pubinfo {
  <https://w3id.org/delphi/resource/domain/buehler-protein-materials> <http://www.w3.org/2000/01/rdf-schema#label>
      "buehler-protein-materials" .
  
  this: dc:created "2026-11-08T04:48:50.317Z"^^xsd:dateTime;
    dc:creator <https://orcid.org/0009-0007-4948-9192>;
    dc:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:hasNanopubType <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    npx:introduces <https://w3id.org/delphi/resource/assessment/buehler-2007-tropocollagen-entropic-04--gemini>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2007-tropocollagen-entropic-04: partially-resolvable, resolvability 0.48";
    <https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/buehler-protein-materials> .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB";
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    npx:hasSignatureTarget this:;
    npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}