[ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/Head", "@graph": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci dataset-resolvability assessor (Gemini 4 Argon)" } ], "http://www.w3.org/ns/prov#actedOnBehalfOf": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "https://w3id.org/delphi/ontology/usesModel": [ { "@id": "https://w3id.org/delphi/resource/model/gemini-4-argon-medium" } ] }, { "@id": "https://w3id.org/delphi/resource/model/gemini-4-argon-medium", "http://purl.org/dc/terms/identifier": [ { "@value": "gemini-4-argon-medium" } ], "@type": [ "https://w3id.org/delphi/ontology/LanguageModel" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini", "http://purl.org/dc/terms/description": [ { "@value": "The mathematical derivation extending Bell's theory is directly checkable, and its empirical content—that protein domain strength follows from H-bond cluster hierarchy—can be tested against published AFM/optical-tweezers force spectra and steered MD data. However, experimental force-velocity data are fragmented across the literature, and the abstract does not state the full closed-form multi-hierarchy coupling, leaving parameter identifiability only partially constrained." } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Proposed test with existing data: Fit the hierarchical Bell expression F(v) with cluster-size-scaled barrier E_b and transition-state distance x_b to published dynamic force spectroscopy and steered MD unfolding force-velocity curves across diverse protein domains, testing whether architecture-derived b values predict rupture forces without free fitting of x_b." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon on buehler-2007-hierarchies-03: partially-resolvable, resolvability 0.65" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0" } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Because single-bond energy E_1 and distance x_1 depend on local microenvironment and solvent exposure, fitting b can become degenerate with effective bond parameters." }, { "@value": "Experimental single-molecule force spectroscopy datasets across multiple pulling velocities are scattered across individual papers rather than unified in one open repository." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.75", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2007-hierarchies-03--gemini--dataset-1" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.653", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "partially-resolvable" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2007-hierarchies-03--gemini--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "Three-dimensional protein structures from which H-bond topology and parallel cluster sizes b can be extracted" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Candidate dataset: RCSB Protein Data Bank" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.rcsb.org/" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--analysis-feasibility", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-analysis-feasibility" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Analysis feasibility of buehler-2007-hierarchies-03 by Gemini 4 Argon: 0.75" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/analysis-feasibility" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.75", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--data-adequacy", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-adequacy" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Data adequacy of buehler-2007-hierarchies-03 by Gemini 4 Argon: 0.55" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/data-adequacy" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.55", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--data-existence", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-existence" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Data existence of buehler-2007-hierarchies-03 by Gemini 4 Argon: 0.6" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/data-existence" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.6", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--discriminating-power", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-discriminating-power" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Discriminating power of buehler-2007-hierarchies-03 by Gemini 4 Argon: 0.65" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/discriminating-power" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.65", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--operationalizability", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-operationalizability" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Operationalizability of buehler-2007-hierarchies-03 by Gemini 4 Argon: 0.75" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/operationalizability" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.75", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/buehler-2007-hierarchies-03", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--analysis-feasibility" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--data-adequacy" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--data-existence" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--discriminating-power" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini--operationalizability" } ] } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/provenance", "@graph": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/assessment/raw/gemini/batch-1.json" }, { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0" } ], "http://www.w3.org/ns/prov#wasGeneratedBy": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assessment" } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assessment", "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/ns/prov#qualifiedAssociation": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assessmentPlan" } ], "http://www.w3.org/ns/prov#wasAssociatedWith": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/assessmentPlan", "http://www.w3.org/ns/prov#hadPlan": [ { "@id": "https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/README.md" } ] } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/pubinfo", "@graph": [ { "@id": "https://w3id.org/delphi/resource/domain/buehler-protein-materials", "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "buehler-protein-materials" } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs", "http://purl.org/dc/terms/created": [ { "@value": "2026-11-08T04:48:50.317Z", "@type": "http://www.w3.org/2001/XMLSchema#dateTime" } ], "http://purl.org/dc/terms/creator": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "http://purl.org/dc/terms/license": [ { "@id": "https://creativecommons.org/licenses/by/4.0/" } ], "http://purl.org/nanopub/x/hasNanopubType": [ { "@id": "https://w3id.org/delphi/ontology/LLMClaimAssessment" } ], "http://purl.org/nanopub/x/introduces": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2007-hierarchies-03--gemini" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon on buehler-2007-hierarchies-03: partially-resolvable, resolvability 0.65" } ], "https://w3id.org/delphi/ontology/domain": [ { "@id": "https://w3id.org/delphi/resource/domain/buehler-protein-materials" } ] }, { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs/sig", "http://purl.org/nanopub/x/hasAlgorithm": [ { "@value": "RSA" } ], "http://purl.org/nanopub/x/hasPublicKey": [ { "@value": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB" } ], "http://purl.org/nanopub/x/hasSignature": [ { "@value": "MZgnvI646KnxhW87ZM7Sw+7v80c4BsaKTct1UsX8rk8BDetdpD+572Zq0q8KDHWhHooiBqhiPQUQQOILARGMCYo7MIU0BeU9ojRaQSncypKZzbwJJ5EHvseB2/AX5VTDGG60sXvHZv7mI/BDf5dYgke7zxlusMqQugXerw7M1DUtDUirysMOqcTwKBCyfUKehcLTPmYnG8CNfHO3umNmQKeYa/FCYQq3Hcb2pEK1AAs5M80P2lV3a6r63WD5xIFrGTwK0g0aoHTT9x2T/TxaQjzEQgp8RDRjYNtwoF+pfxK68ZD+EeBhTEPMqY0uNvtDujs2oeXqZy824rehGIKV4A==" } ], "http://purl.org/nanopub/x/hasSignatureTarget": [ { "@id": "https://w3id.org/np/RARCmsXyXvoG6sfWUywcUdh9oJcXlTxGwID9Q-vii4tQs" } ], "http://purl.org/nanopub/x/signedBy": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ] } ] } ]