https://w3id.org/np/RA2JNBmt8RowLUNumUbesZIvkB-s-oyoqlyeIAPepEoSc
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RA2JNBmt8RowLUNumUbesZIvkB-s-oyoqlyeIAPepEoSc> .
@prefix sub: <https://w3id.org/np/RA2JNBmt8RowLUNumUbesZIvkB-s-oyoqlyeIAPepEoSc/> .
@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-ch03-09--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "Downloaded only the pre-registered Add-my-Pet mydata files, using a fallback entry only when the first URL was not HTTP 200. Parsed matrices whose names start with tL or tW. A MATLAB '...' comments out the rest of its line; a trailing transpose and a uniform elementwise scale of the form [numbers]./c or *c were applied so those arrays are age-size pairs. Successive-difference velocities were scored on each species' longest admissible series with the three pre-registered phase checks. AnAge maximum longevity labelled species at the pre-registered 40-year and 15-year cuts. The verdict is that rule applied to the counts.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: undefined undefined. Interpretation: Thompson (1917, ch. III) says long-lived animals (man, the elephant) and short-lived ones (horse, dog) pass through the same phases: growth begins slowly, reaches maximum velocity early, then slows, with temporary accelerations, toward cessation. Size is the raw length or weight series in the Add-my-Pet mydata file, not a von Bertalanffy fit, because that fit places maximum velocity at the origin and cannot show a slow start. 'Early' is read as the first 40 percent of the ages actually observed in that series. Longevity classes use Thompson's own examples and, separately, AnAge maximum longevity at thresholds of 40 and 15 years fixed here. The 70 percent bar is a reading of a shared pattern in noisy published series; it is weaker than the literal 'in all cases', which is reported beside it.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch03-09: refutes, confidence 0.62";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch03-09/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Raw age–length or age–weight measurements transcribed as numeric matrices in public Add-my-Pet mydata files for the pre-registered entries, with at least eight distinct ages and net growth. Fitted growth parameters are not admissible. Longevity labels come from AnAge maximum longevity matched on the binomial, or from Thompson's named examples when that is the class being scored.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "The pass fraction among admissible species is at most 0.40, or the pattern is absent from every admissible human or elephant series, or from every admissible horse or dog series, or one AnAge longevity class shows the pattern and the other, with at least three species, largely does not.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Equus caballus returned HTTP 404 and was not replaced, so Thompson's horse was not tested. The dog series passes. Bos taurus, Drosophila melanogaster and Apis mellifera were also missing. Gallus gallus and the rabbit were retrieved but had no series with eight or more ages.",
"Forty percent of the observed ages is a reading of 'early', not a number Thompson stated. The sample is the pre-registered list, not a random draw of animals.",
"Macaca mulatta is classed long because its AnAge longevity is 40 years, and its only admissible series has 8 ages.",
"Terminal slowdown held on every admissible primary series. Failures are a velocity peak on the first interval, or a peak after 40 percent of the observed age span.",
"The human primary series is head-feet length. Its fastest interval is the first, so it fails 'begins slowly' even though that peak is early. The weight series in the file are shorter.",
"The pass fraction is exactly 6 of 15, which meets the pre-registered refute boundary of 0.40. Separately, species with AnAge longevity of at least 40 years passed 1 of 5, and species with longevity of at most 15 years passed 4 of 5.",
"The sheep primary series is the longest matrix, tLe, prenatal crown-rump length, and it fails. The shorter postnatal weight series in the same file pass and were not used, because the rule selects the longest series.";
<https://w3id.org/delphi/ontology/expectedObservation> "In most pre-registered species with a long enough raw age–size series, interval growth velocity peaks after the first interval and within the first 40 percent of the observed age span, and velocity near the end of the series is under half that peak, in both Thompson's long-lived examples and his short-lived examples.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES, when at least 4 species are admissible, if the pass fraction is <= 0.40, or if every admissible Thompson-long species fails, or if every admissible Thompson-short species fails, or if both AnAge classes have at least 3 admissible species and one of those classes has pass fraction < 0.34 while the other has pass fraction >= 0.67. MIXED if at least 4 species are admissible and the outcome is neither SUPPORTS nor REFUTES. INCONCLUSIVE reason underpowered if files are retrieved but fewer than 4 species have an admissible series. INCONCLUSIVE reason data-unavailable if the Add-my-Pet host cannot be fetched (every entry request fails). A missing entry is recorded and not replaced. If AnAge longevity cannot be joined, the AnAge class clauses are skipped rather than failing the test. The literal statement that every series passes is recorded and is not required for SUPPORTS. Temporary accelerations do not fail a series. Series are not dropped for starting late; a series whose first age exceeds 20 percent of its maximum age is flagged left-truncated and still scored.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.62"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/thompson1917-ch03-09--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/thompson1917-ch03-09--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "On raw age–size series, growth velocity is not highest at the start, peaks within the first 40 percent of the observed age span, and is lower again near the end of the series, and this phase pattern appears both in the animals Thompson called long-lived (human, elephant) and in those he called short-lived (horse, dog).";
<https://w3id.org/delphi/ontology/inferenceMethod> "Per species, successive-difference velocities on the longest admissible series. Three pre-registered phase checks (slow start, peak by 40 percent of the observed span, terminal velocity under half the peak). Verdict from the species pass fraction and from the same fraction inside the pre-registered longevity classes. No series is added or removed after the curves are plotted or inspected.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered. Fetch only the Add-my-Pet mydata files for this fixed entry list (no replacements after seeing a curve): Homo_sapiens, Elephas_maximus, Loxodonta_africana, Equus_caballus, Canis_familiaris, Mus_musculus, Rattus_norvegicus, Danio_rerio, Gallus_gallus_domesticus, Bos_taurus, Drosophila_melanogaster, Oryctolagus_cuniculus, Felis_catus, Sus_scrofa, Cavia_porcellus, Pan_troglodytes, Macaca_mulatta, Caenorhabditis_elegans, Apis_mellifera, Mytilus_edulis, Ovis_aries. URL https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/<Entry>/mydata_<Entry>.m. Name fallbacks, used only when the first URL is not HTTP 200, and never because of the shape of a series: Canis_familiaris then Canis_lupus_familiaris; Gallus_gallus_domesticus then Gallus_gallus. Thompson-long entries are Homo_sapiens, Elephas_maximus, Loxodonta_africana. Thompson-short entries are Equus_caballus and whichever dog entry was fetched. A series is a numeric matrix in that file whose field name begins with tL or tW, with at least 8 distinct ages after sorting and averaging duplicate ages, positive sizes, positive age span, maximum interval velocity > 0, and final size > 1.05 times initial size. Age is column 1 and size is column 2. The species primary series is the admissible matrix with the most distinct ages, then the larger age span, then the alphabetically first field name. Interval velocity is the successive difference in size divided by the difference in age, assigned to the interval midpoint. Begins-slowly: the maximum velocity is not on the first interval, and the mean velocity of intervals whose midpoint lies in the first 20 percent of the age span (or the first interval, if none do) is less than the maximum. Early peak: (age at the earliest maximum-velocity midpoint minus minimum age) / age span <= 0.40. Terminal slowdown: the mean velocity of intervals whose midpoint lies in the last 20 percent of the age span (or the last interval, if none do) is < 0.5 times the maximum velocity. A species passes if its primary series meets all three. AnAge build 15 'Maximum longevity (yrs)' classifies an entry as long if the exact Genus_Species match is >= 40 years and short if it is <= 15 years; other entries are unclassified. SUPPORTS if at least 4 species have an admissible primary series, at least 70 percent of them pass, at least one admissible Thompson-long species passes, at least one admissible Thompson-short species passes, and every AnAge longevity class that contains at least 2 admissible species has a pass fraction of at least 0.5.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
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<https://w3id.org/delphi/resource/assessment/thompson1917-ch03-09--claim-test> .
<https://w3id.org/delphi/resource/evidence/thompson1917-ch03-09--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "Raw age-length and age-weight series";
dc:license "The Add-my-Pet portal says the data, references and code used for estimation are freely available for anyone to download. The landing page and about page, as retrieved 2026-11-02, do not state a public-license identifier.";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Add-my-Pet mydata files for the pre-registered species sample";
prov:atLocation <https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Caenorhabditis_elegans/mydata_Caenorhabditis_elegans.m>,
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<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Felis_catus/mydata_Felis_catus.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Gallus_gallus/mydata_Gallus_gallus.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Homo_sapiens/mydata_Homo_sapiens.m>,
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<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Mytilus_edulis/mydata_Mytilus_edulis.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Oryctolagus_cuniculus/mydata_Oryctolagus_cuniculus.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Ovis_aries/mydata_Ovis_aries.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Pan_troglodytes/mydata_Pan_troglodytes.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Rattus_norvegicus/mydata_Rattus_norvegicus.m>,
<https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/entries/Sus_scrofa/mydata_Sus_scrofa.m>;
prov:wasDerivedFrom <https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:05b7f5f2541eaae7bc5f2c2f72220f2c07a746aa4d052e67dc422f3a8bb759e3",
"sha256:224f4b86591f040fba54c1ca13ac53e1c17905e38451d47f92a38fefae83a367", "sha256:25917321bbc3ccf648b66141191b74fd899f01d78c57d617454837598ca4eba7",
"sha256:31e556b09f4abba37c94fea6fdd28fb719c8cd0d8c4463649501de001f4eb20a", "sha256:534ffd8a387f62f9194dd3ad58413c321fc904c2fa38a6854789b5ad7e18fc9c",
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<https://w3id.org/delphi/resource/evidence/thompson1917-ch03-09--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "Maximum longevity used only to label long-lived and short-lived classes";
dc:license "Copyright Human Ageing Genomic Resources. The build-15 release notes say use is free but subject to the HAGR conditions at https://genomics.senescence.info/legal.html. That page says the resources are copyrighted and come without warranty; it does not state a public-license identifier.";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: AnAge: The Animal Ageing and Longevity Database, build 15";
prov:atLocation <https://genomics.senescence.info/species/dataset.zip>;
prov:wasDerivedFrom <https://genomics.senescence.info/species/>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:e3ddb66e32e973a79932859ba53013e8f60d957c6ec01c6eb573e3ea3018d630" .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7> a prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (grok-4.7; cursor/thompson-growth-claim-tests-e028)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/grok-4-7> .
<https://w3id.org/delphi/resource/model/grok-4-7> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "grok-4.7" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch03-09/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> .
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sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.892Z"^^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-ch03-09--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch03-09: refutes, confidence 0.62";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/thompson-growth-form-1917> .
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