https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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@prefix sub: <https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/> .
@prefix np: <http://www.nanopub.org/nschema#> .
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@prefix prov: <http://www.w3.org/ns/prov#> .
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@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/assessment/buehler-2008-hbond-confinement-04--claim-test>
a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "A script (analysis.py in this directory) downloads the cluster file, selects representatives, queries the PDBe secondary_structure endpoint for each selected entry, extracts strand lengths for the representative chain, builds the histogram and computes (A)-(D). All raw per-chain strand lengths are written to strand_lengths.csv; the histogram to histogram.json. Every HTTP request carries the User-Agent 'delphisci-claim-test/1.0 (https://delphibio.org)' and no personal identifier.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: undefined undefined. Interpretation: ";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of buehler-2008-hbond-confinement-04: supports, confidence 0.9";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/buehler-protein-materials/buehler-2008-hbond-confinement-04/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Planned datasets: RCSB PDB 30%-sequence-identity cluster file (https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-30.txt); one representative polymer entity per cluster, the first listed, PDBe API secondary structure per entry (https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/{pdb_id}); strands per chain with start and end residue numbers, RCSB search API (https://search.rcsb.org/rcsbsearch/v2/query) or PDBe summary API to restrict to X-ray entries with resolution <= 2.5 A and polymer entity type protein";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "physical";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Refutes if the mode is >= 8 residues or <= 2 residues, or if more than 30% of strands are longer than 10 residues. Any other failure of (A)-(D) -> mixed. If fewer than 2,000 representative chains with at least one strand can be retrieved, -> inconclusive.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "All four pre-registered criteria pass on 60,263 strands from 5,000 representative chains, so the verdict is 'supports' for the distributional reading only; the causal reading was pre-registered as not testable here. The verdict depends on the pre-registered rule that excludes strand segments shorter than 2 residues: PDBe returns 17,577 one-residue strand segments among 77,840 raw segments (22.6%), and had they been kept the mode would be 1 residue, which the fail criterion labels 'refutes'. One-residue segments are most plausibly isolated beta-bridges rather than strands, which is why the exclusion was pre-registered, but a reader who regards them as strands should read the result as 'refutes'. Criterion (A) is passed narrowly: length 5 has 9,555 strands and length 4 has 9,404 (1.6% apart), with length 6 at 8,666 and lengths 2 and 3 at 8,327 and 8,016; the distribution is a broad plateau over 2 to 6 residues rather than a sharp peak, so the mode is in [3, 6] but would be fragile to a different assignment method. Strand assignments are PDBe's as served by the secondary_structure endpoint. The PDBe API documentation (openapi.json, retrieved 2026-11-08) describes them only as 'residue ranges of regular secondary structures (alpha helices and beta strands)' and does not name the method; whether they are the depositors' mmCIF struct_sheet_range records or a DSSP-style recomputation is not stated there and was not verified. Lengths use PDBe's mmCIF residue_number, so author numbering gaps do not affect them. Lengths are in residues, mapped to the model's 3-4 hydrogen bonds by the pre-registered assumption (band [3, 6] residues); no hydrogen bonds were measured. Sampling biases: the PDB over-represents crystallisable, well-folded proteins and the filter keeps only X-ray entries at or better than 2.5 A; the representative is the first entity of each cluster in file order (an arbitrary, not a quality-based, choice) and the first chain listed for that entity; clusters are at 30% sequence identity at the entity level, so fold-level redundancy remains; the 15,500 representatives screened are the first 5.7% of the 272,527 clusters, and the cluster file is sorted by cluster size, so the sample is drawn from the largest families; 631 chains with no strand of at least 2 residues were excluded by design, so the distribution is conditional on a chain having a strand; the exptl.method exact match on 'X-RAY DIFFRACTION' also admits hybrid X-ray entries. Eight filtered entries returned HTTP 404 from the secondary_structure endpoint and were skipped.";
<https://w3id.org/delphi/ontology/expectedObservation> "All of: (A) the mode of the strand-length histogram over the filtered set lies in [3, 6] residues; (B) the median strand length is <= 7 residues; (C) fewer than 15% of strands are longer than 10 residues; (D) the histogram is unimodal in the sense that counts decrease monotonically from the mode up to length 12 (ties allowed). -> supports (distributional reading only).";
<https://w3id.org/delphi/ontology/failCriterion> "Refutes if the mode is >= 8 residues or <= 2 residues, or if more than 30% of strands are longer than 10 residues. Any other failure of (A)-(D) -> mixed. If fewer than 2,000 representative chains with at least one strand can be retrieved, -> inconclusive.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.9"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2>,
<https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<https://w3id.org/delphi/ontology/hypothesis> "Across a non-redundant set of experimentally determined protein structures, the distribution of beta-strand lengths is concentrated at short strands, with its mode in the range that corresponds to the 3-4 hydrogen-bond cluster the Keten & Buehler (2008) model identifies as the shear-strength optimum, and long strands are rare.";
<https://w3id.org/delphi/ontology/inferenceMethod> "A script (analysis.py in this directory) downloads the cluster file, selects representatives, queries the PDBe secondary_structure endpoint for each selected entry, extracts strand lengths for the representative chain, builds the histogram and computes (A)-(D). All raw per-chain strand lengths are written to strand_lengths.csv; the histogram to histogram.json. Every HTTP request carries the User-Agent 'delphisci-claim-test/1.0 (https://delphibio.org)' and no personal identifier.";
<https://w3id.org/delphi/ontology/passCriterion> "All of: (A) the mode of the strand-length histogram over the filtered set lies in [3, 6] residues; (B) the median strand length is <= 7 residues; (C) fewer than 15% of strands are longer than 10 residues; (D) the histogram is unimodal in the sense that counts decrease monotonically from the mode up to length 12 (ties allowed). -> supports (distributional reading only).";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/buehler-2008-hbond-confinement-04> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test> .
<https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "";
dc:license "RCSB PDB data, free to use (https://www.rcsb.org/pages/usage-policy)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: RCSB PDB sequence clusters at 30% identity, entity level (one line per cluster, members as PDBID_ENTITY)";
prov:atLocation <https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-30.txt>;
prov:wasDerivedFrom <https://www.rcsb.org/docs/programmatic-access/file-download-services#sequence-clusters-data>;
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<https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "";
dc:license "RCSB PDB data, free to use";
<http://www.w3.org/2000/01/rdf-schema#comment> "Location (not a URL): https://search.rcsb.org/rcsbsearch/v2/query (POST, 31 batches of up to 500 entity ids)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: RCSB Search API v2: entity ids in batch AND exptl.method = X-RAY DIFFRACTION AND rcsb_entry_info.resolution_combined <= 2.5 AND entity_poly.rcsb_entity_polymer_type = Protein; return_type polymer_entity";
prov:wasDerivedFrom <https://search.rcsb.org/> .
<https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "";
dc:license "PDBe data, CC0 (https://www.ebi.ac.uk/pdbe/about/terms)";
<http://www.w3.org/2000/01/rdf-schema#comment> "Location (not a URL): https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/{pdb_id} (GET, one per filtered representative entry, gzip transfer)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: PDBe API secondary_structure per entry: helix and strand residue ranges per chain, mmCIF residue_number used";
prov:wasDerivedFrom <https://www.ebi.ac.uk/pdbe/api/doc/pdb.html> .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit> a prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (inherit; cursor/buehler-hbond-confinement-04-run-3cf4)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/inherit> .
<https://w3id.org/delphi/resource/model/inherit> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "inherit" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/buehler-protein-materials/buehler-2008-hbond-confinement-04/result.json>;
prov:wasGeneratedBy sub:test .
sub:plan prov:hadPlan <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md> .
sub:test a prov:Activity;
prov:qualifiedAssociation sub:plan;
prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.803Z"^^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/Assessment>;
npx:introduces <https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of buehler-2008-hbond-confinement-04: supports, confidence 0.9";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/buehler-protein-materials> .
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npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
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