https://w3id.org/np/RAInOw1lM5F_-Ja2kWkPWyWDmgsh1FztPpZ-Ax9_Swokc
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAInOw1lM5F_-Ja2kWkPWyWDmgsh1FztPpZ-Ax9_Swokc> .
@prefix sub: <https://w3id.org/np/RAInOw1lM5F_-Ja2kWkPWyWDmgsh1FztPpZ-Ax9_Swokc/> .
@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-ch08-02--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "analysis.py: for each wall flagged in *_new_walls.tif, the mother is the union of the two sisters; the observed interface area (anisotropic voxel faces) is compared with planar cuts at 500 Fibonacci-lattice orientations at the observed volume fraction. Per-division rows in derived/divisions.csv (regenerated by analysis.py, not committed); per-archive figures in derived/summary.json.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.062 median over divisions of the percentile of the observed new-wall area among 500 planar cuts of the mother at the observed volume ratio (voxel-face areas) (n = 27249, 27249 divisions in 8 shoot apices; IQR of percentile 0.016-0.156). Interpretation: Errera's rule as Thompson states it: the incipient partition has the least area that can divide the given space-content. The 'given space-content' is the observed volume split of the two sisters, so asymmetric divisions are included. Real walls may be curved; the minimum is taken over planes, so a curved minimal wall can have q < 1, which still counts as consistent. Sisters are identified from the dataset's own detection of recently formed walls (its pipeline flags thin, recent walls), not from lineage tracking; mis-identified pairs work against the claim. Sachs's subordinate rule (right-angle alternation) is tested separately under thompson1917-ch08-01. The test is on one model plant tissue (Arabidopsis shoot apex), within the claim's scope 'dividing cells, especially plant cells'.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch08-02: mixed, confidence 0.55";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch08-02/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "3D segmentations of plant tissue in which recently divided sister cells can be identified (lineage tracking or detection of new walls), with known voxel size; independent of Thompson; public licence.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "New walls are no smaller than cuts of random orientation (percentile around 0.5) or are usually much larger than the least-area cut.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Completed by the parent agent from the tester run output after the tester subagent stopped; the analysis ran unmodified.",
"Mixed by the pre-registered thresholds: median percentile 0.062 passes (<= 0.10), but only 24.7% of divisions have q <= 1.10 (needs >= 50%; refutes below 20%). New walls are far smaller than random cuts (median 0.68 of the median random-cut area) but usually 10-40% above the least-area plane.",
"Old walls (not flagged as new, analysed identically, not pre-registered) give median q 0.96 and 89% within 1.10. Either established walls relax towards least area after division, or the new-wall flags from the dataset pipeline pick thin, irregular walls that are measured less accurately.",
"One tissue (Arabidopsis inflorescence shoot apex, 8 apices, 27,249 divisions); the minimum is taken over planes only.",
"Sisters are identified from the dataset flag for recently formed walls, not from lineage tracking; 3990 divisions touching the image border were excluded.",
"The q criterion is sensitive to how area is measured. The voxel-face rule inflates staircase surfaces that are oblique to the voxel grid. A sensitivity analysis that was not pre-registered (dividing face area by |n_x|+|n_y|+|n_z|) gives median q 1.04 and 65% within 1.10, which would pass. The pre-registered verdict stands.";
<https://w3id.org/delphi/ontology/expectedObservation> "The new wall's area is near the minimum over planar cuts of the mother at the same volume ratio (q close to or below 1) and in the lowest tail of the area distribution over cut orientations.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES if the median p is >= 0.35 (observed walls are no smaller than typical random-orientation cuts) OR fewer than 20% of divisions have q <= 1.10. Any other outcome is MIXED. Fewer than 30 analysable divisions: inconclusive (underpowered).";
<https://w3id.org/delphi/ontology/hasConfidence> "0.55"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/thompson1917-ch08-02--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "mixed";
<https://w3id.org/delphi/ontology/hypothesis> "In recently divided plant cells, the new wall between two sister cells has close to the least area of any planar cut that divides the reconstructed mother cell in the same volume ratio, and much less area than a cut of random orientation.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Reconstruct mother = union of sisters; compare observed interface area with the planar cut-area distribution over 500 orientations at the observed volume fraction; median percentile and fraction within 10% of the minimum against the pre-registered thresholds.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered. Data: the 8 alphabetically first meristem archives of Zenodo record 18711581 (Yates et al. 2026, Arabidopsis inflorescence shoot apices, 3D confocal, watershed-segmented). For each wall marked in *_new_walls.tif, the two cells it separates are sisters; the mother is their union (including the wall voxels between them). Both sisters must have volume >= 40 um^3 and must not touch the image border. Observed area A_obs = area of the voxel faces shared between the two sister regions in the mother mask (anisotropic voxel face areas from Metadata.txt). For 500 plane orientations spread uniformly over the hemisphere (Fibonacci lattice), the plane offset is set so the smaller side holds the observed smaller-sister volume fraction, and the cut area A(n) is measured with the same voxel-face rule. A_min = min over orientations; q = A_obs / A_min; percentile p = fraction of orientations with A(n) < A_obs. SUPPORTS if the median p over all divisions is <= 0.10 AND at least 50% of divisions have q <= 1.10.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/thompson1917-ch08-02> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/thompson1917-ch08-02--claim-test> .
<https://w3id.org/delphi/resource/evidence/thompson1917-ch08-02--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "watershed segmentations of 3D confocal stacks of Arabidopsis inflorescence shoot apices (voxel 0.1832 x 0.1832 x 0.334 um), the dataset's own flags for recently formed walls (New wall filter = 1, the labels in *_new_walls.tif) and their two flanking cells";
dc:license "CC BY 4.0";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Image processing data for manuscript: Control of plant organ growth through cell division orientation in inner tissues (Yates & Sablowski)";
prov:atLocation <https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_260_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_263_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_274_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_280_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_289_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_291_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_301_t0_40x.zip?download=1>,
<https://zenodo.org/records/18711581/files/20230922_mPS-PI_Meristem_311_t0_40x.zip?download=1>;
prov:wasDerivedFrom <https://zenodo.org/records/18711581> .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5> a
prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (claude-opus-5.5; cursor local subagent)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/claude-opus-5-5> .
<https://w3id.org/delphi/resource/model/claude-opus-5-5> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "claude-opus-5.5" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch08-02/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-claude-opus-5-5> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.903Z"^^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-ch08-02--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch08-02: mixed, confidence 0.55";
<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 "kCEjq8P1o+9VsN7o20GxjcjyerG0Od5rAMUZES6NgeijmQKvPrpjX/m3TDNBP+k7J2+LvneV8Gp0dCaDQRn78IsULju/mbwzRJPkqIsxZjC6c5UVIINL2hKTTnp/koXSXVex4qmXJNqdN41WaTn7oLZxkIaZVzil5Ky6w3FxJ89us6C0eqNk4WQN0IbPRLLk1T6ke1PEA6AnW0ACFQxq5/6/aFPELtFSpXgZdz/RdPK9xsC/JDdWP+QcA8JOdp9RAiDJImtTiVxT8BANlJUmvrdRl24hmIWbpAbvL8ZJ4rJtaXDqyGGZj+gcIVczlDmwxPGmPgFZ4jXJkJirS+Q8Kw==";
npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}