https://w3id.org/np/RAtf0Fs65O71xbLmdQ3Y62crQavyQCkKlH1oNuQqDdwsU
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAtf0Fs65O71xbLmdQ3Y62crQavyQCkKlH1oNuQqDdwsU> .
@prefix sub: <https://w3id.org/np/RAtf0Fs65O71xbLmdQ3Y62crQavyQCkKlH1oNuQqDdwsU/> .
@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-2010-silk-assemblies-01--gemini>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:description "The partitioning of MaSp1 and MaSp2 sequences into beta-sheet-forming poly-Ala tracts and 3_1-helix/beta-turn Gly-rich regions maps onto standard structural observables (DSSP classes and Ramachandran phi-psi angles). Although the authors' REMD coordinates were not deposited in the PDB, the sequences are public in UniProt, independent solid-state NMR and X-ray data exist, and REMD can be re-run in GROMACS. It is rated partially resolvable because re-running converged multi-chain REMD requires substantial compute and only the abstract is vendored locally.";
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: Retrieve Nephila clavipes MaSp1 and MaSp2 repeat sequences from UniProt, perform replica-exchange MD (or inspect solid-state NMR chemical-shift constraints in BMRB), and compute residue-specific secondary structure via DSSP and backbone dihedral distributions on Ramachandran plots separately for poly-Ala segments and Gly-rich motifs. The claim is confirmed if poly-Ala tracts predominantly populate antiparallel beta-sheet states while GGX and GPGXX repeats populate 3_1-helical (polyglycine II-like) and beta-turn conformations.";
<http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2010-silk-assemblies-01: partially-resolvable, resolvability 0.72";
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> "Converging replica-exchange MD for multi-chain silk protein assemblies is computationally intensive and sensitive to force-field backbone dihedral potentials.",
"The replica-exchange MD structural ensemble generated in the 2010 study is not deposited in the PDB or a public trajectory repository.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.85"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-1>,
<https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-2>,
<https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-3>;
<https://w3id.org/delphi/ontology/hasScore> "0.725"^^xsd:double;
<https://w3id.org/delphi/ontology/hasVerdict> "partially-resolvable" .
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--analysis-feasibility>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--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-2010-silk-assemblies-01 by Gemini 4 Argon: 0.6";
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> "0.6"^^xsd:double .
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--data-adequacy>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--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-2010-silk-assemblies-01 by Gemini 4 Argon: 0.65";
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> "0.65"^^xsd:double .
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--data-existence>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--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-2010-silk-assemblies-01 by Gemini 4 Argon: 0.7";
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> "0.7"^^xsd:double .
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--discriminating-power>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--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-2010-silk-assemblies-01 by Gemini 4 Argon: 0.8";
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> "0.8"^^xsd:double .
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--operationalizability>
a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--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-2010-silk-assemblies-01 by Gemini 4 Argon: 0.85";
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> "0.85"^^xsd:double .
<https://w3id.org/delphi/resource/claim/buehler-2010-silk-assemblies-01> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini>,
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--analysis-feasibility>,
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--data-adequacy>,
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--data-existence>,
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--discriminating-power>,
<https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-01--gemini--operationalizability> .
<https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "Public protein sequence records for Nephila clavipes spidroin-1 (MaSp1, P19837) and spidroin-2 (MaSp2, P46804)";
<http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: UniProt Knowledgebase";
prov:wasDerivedFrom <https://www.uniprot.org/> .
<https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "Solid-state NMR chemical shifts and dihedral angle restraints for spider dragline silk poly-Ala and Gly-rich domains";
<http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: Biological Magnetic Resonance Data Bank (BMRB)";
prov:wasDerivedFrom <https://bmrb.io/> .
<https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-01--gemini--dataset-3>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "Open-source MD engine supporting replica-exchange molecular dynamics and Ramachandran/DSSP structural analysis";
<http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: GROMACS Molecular Dynamics Package";
prov:wasDerivedFrom <https://www.gromacs.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-3.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-2010-silk-assemblies-01--gemini>;
<http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2010-silk-assemblies-01: partially-resolvable, resolvability 0.72";
<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";
npx:hasSignature "Xn8P0yXbj4Unday66wbIygA1DX9cR61om3iJzACoJhmkRQWhzomr+qOgUi2L34wk9GsaJ8PAuHxyL9uIHuJf7SOTAS3nOdh3v/XGg7ZhGuoUELuqODyF6Bw9MG/GsXc4TGMVrQx7a56dGgvdD0RFG94MDGkJ0YvqqmX4Jy4bRTSWST/siFkEh4KtmiVk2Z3LboxoqWMPD9coVhNuzsxHbZQ/48F7Kkb9DVRptsknaHrYQA0a/bS8GE1jZzD9+ZCs3x1x8oxvLCb6r6UEeY2dwffhJlN+/r7t+VnumcV7w3ePePXkbFQpbN+F0em3AqCUyWgntKsCFCf9LE9n0L0t+g==";
npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}