https://w3id.org/np/RAOzUgfG1xDWBbUFp1OofITQzimlj4Od_abnSFvd8663I
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAOzUgfG1xDWBbUFp1OofITQzimlj4Od_abnSFvd8663I> .
@prefix sub: <https://w3id.org/np/RAOzUgfG1xDWBbUFp1OofITQzimlj4Od_abnSFvd8663I/> .
@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/assessment/thompson1917-ch05-08--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "Downloaded Meshes.zip from Zenodo 2593861 and the measurement tables. Specimen identifiers are matched case-insensitively, and macOS resource-fork members whose names start with '._' are skipped. For each internal chamber mesh (SampleID-CH#.stl, numbered from the final chamber) and the shrink-wrapped whole test (SampleID-WRAP.stl), up to 5000 vertices are sampled and an algebraic sphere is fit. The specimen score is the median normalized RMS residual of the chambers, excluding the earliest, minus the whole-test residual. A one-sided Wilcoxon test across specimens is compared with the pre-registered threshold. The isoperimetric quotient from the measurement table is computed and not used, because the meshes are present.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: -0.008931936051936817 median across specimens of (median chamber sphere-fit residual minus whole-test residual); negative means chambers are closer to a sphere (n = 37, one-sided Wilcoxon p (chambers closer to a sphere) = 0.03262675827863859). Interpretation: Thompson's 'figure of equilibrium shaped by surface tension' for a new chamber is read as a spherical segment, the closed surface of constant mean curvature available from a mesh. The comparison is to the whole test, which the same sentence says is not itself a figure of minimal area. Globigerina and Rotalia are the named examples; planktonic foraminifera in the archive are in that class of multichambered shells, and any absence of Rotalia or of desmids is a limit on scope, not a reason to drop the specimens that are present. The moment of solidification is not in a mesh of the finished shell.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch05-08: supports, confidence 0.35";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch05-08/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7-high-fast>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Segmented per-chamber surfaces, or per-chamber volume and surface area, for multichambered foraminifera, with a whole-test surface or measurement for the same specimen and a way to tell chambers apart. Public and licensed for reuse. Desmid semicells and live images of chamber formation would be admissible for the clauses this test leaves out; they are not required for the geometric reading.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Chamber surfaces depart from a sphere by as much as, or by more than, the whole multichambered test.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "A sphere fit on the finished chamber mesh, including the septal wall, is a geometric comparison. It does not show that surface tension shaped the chamber.",
"Globigerina bulloides, the named genus present in the archive, has median paired difference -0.06252824301103344 (9 of 10 negative). Other genera in the same table are near zero or positive. The verdict uses all 37 specimens, not Globigerina alone.",
"No Rotalia and no desmids are in this archive. The shells are finished calcite. Nothing here records a chamber while it was fluid or the moment it solidified, so the surface-tension mechanism and the fluid-to-rigid timing are untested.",
"Six specimen ids in the chamber table (RS11-5, RS11-6, RS12-1, RS12-3, RS14-3, T1) have no joined shrink-wrap whole-test mesh and are absent from the test. One mesh id has no species label in the chamber table.",
"The isoperimetric quotients from the volume and area table are not the verdict. Some chamber quotients exceed 1, which a closed surface cannot, so those columns are not a clean sphere comparison. Their paired test does not meet the support rule.",
"The sphere-fit difference is small. Median normalized RMS residual is 0.12088461729839131 for chambers and 0.13400139724767005 for the whole test. The median paired difference is -0.008931936051936817 (mean -0.014913645970034601). 23 of 37 specimens have chambers closer to a sphere than the whole test (one-sided Wilcoxon p 0.03262675827863859).";
<https://w3id.org/delphi/ontology/expectedObservation> "Individual chamber surfaces are closer to a fitted sphere than the surface of the whole test from the same specimen.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES if n_specimens >= 10 and the Wilcoxon test is significant (p < 0.05) in the opposite direction (chambers farther from a sphere than the whole shell). MIXED if one of the majority-sign and the significance requirements holds and the other does not. Inconclusive, reason underpowered, if fewer than 10 specimens can be measured; data-unavailable if neither meshes nor area-and-volume tables can be fetched; not-operationalizable if chamber order or a closed surface cannot be identified. Desmids and the fluid-to-rigid timing are out of scope and are not scored. A sphere fit on a rigid shell does not show that the chamber was a fluid equilibrium when it formed. Thresholds are not revised after the meshes are opened.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.35"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/thompson1917-ch05-08--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<https://w3id.org/delphi/ontology/hypothesis> "Each foraminiferal chamber, once formed, lies closer to a sphere than the whole multichambered shell does.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Paired one-sided Wilcoxon test across specimens of the difference between the median chamber sphere-fit residual and the whole-test residual, p < 0.05, n >= 10, with the majority of specimens in the predicted direction. The isoperimetric quotient is the fallback when meshes are not in the archive.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered geometric reading. For each specimen that has a whole-test mesh and at least one per-chamber mesh with an ontogenetic order, fit a sphere by least squares to the vertices of each chamber mesh and to the whole-test mesh (subsample up to 5000 vertices if a mesh is larger). The residual s is the root-mean-square of |distance to the fitted centre minus radius|, divided by the fitted radius. The specimen value is the median s of its chambers excluding the earliest chamber, minus the whole-test s; negative means the chambers are closer to a sphere than the whole shell. SUPPORTS if n_specimens >= 10, a majority of specimens have a negative value, and a one-sided Wilcoxon signed-rank test of the values against 0 has p < 0.05 in the negative direction. If chamber meshes are absent and the archive instead gives per-chamber surface area and volume, the same test is run on the isoperimetric quotient Q = 36*pi*V^2/A^3, with the sign reversed (chambers should have higher Q than the whole test). Meshes are preferred when both exist. The choice is made from which files the archive contains, not from the sign of the result.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/thompson1917-ch05-08> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/thompson1917-ch05-08--claim-test> .
<https://w3id.org/delphi/resource/evidence/thompson1917-ch05-08--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "per-chamber STL meshes and the shrink-wrapped whole test for planktonic foraminifera, plus the measurement tables used to name species";
dc:license "CC BY 4.0";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera";
prov:atLocation <https://zenodo.org/api/records/2593861/files/Chamber_Measurements.csv/content>,
<https://zenodo.org/api/records/2593861/files/Meshes.zip/content>, <https://zenodo.org/api/records/2593861/files/Sample_Metadata.csv/content>,
<https://zenodo.org/api/records/2593861/files/Whole_Test_Measurements.csv/content>;
prov:wasDerivedFrom <https://zenodo.org/records/2593861>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:93ab4296c45d813c3bbe2f5b71c674434a45a72d98feaf71db8820dc6502e996",
"sha256:a939b1412a4ae9060e608ec05d2f2f0a8b224010c7d86f397a4cc4ad47bb1f7e", "sha256:c749ca03a41d0c7d8affec21c188818eb58f21837eb9eee94c757f985f37f2cb",
"sha256:daa5cb899b8346652d1ad3e75dbff9945abab677d9c950ef4eeede4ae796b683" .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7-high-fast>
a prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (grok-4.7-high-fast; cursor/thompson-form-claims-13cd)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/grok-4-7-high-fast> .
<https://w3id.org/delphi/resource/model/grok-4-7-high-fast> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "grok-4.7-high-fast" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7-high-fast>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch05-08/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-grok-4-7-high-fast> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.897Z"^^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/thompson1917-ch05-08--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch05-08: supports, confidence 0.35";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/thompson-growth-form-1917> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB";
npx:hasSignature "o6RY+AQJTUkCyIJhbjsL572x8mc1pSrpTuIXhGtbGIXWp2bjCFnNSMWGZwnM6hlvqryp0fXQWt7OD8Ppluhq17fDa1hVX+YOrgewylFjM6L2RdEmuZq/UiH9ijJyW9lvQhM6oL330v8RoyM7Rlw85HFoI9dzJAhNyfREte2OAA3lsZjldqmAjc0pGZt/8HGt+19M6F1aoXvF5OvwXmW6oRv7FLTfBHpbTyAcTPgIURMTVsupInThbiooEIPJc+qwIdsU33AhUpTE0ZhnujgI4i+PmSX+cJjif5ooMwBI1HINUuveLCfVcpPM8WyhoNJmjZCJ32hjZndovRTUCcLc6Q==";
npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}