https://w3id.org/np/RAbA56nlLjL4aBEipm2hgxxYpKJi3m9K8y3BFxk2XY45U
.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/RAbA56nlLjL4aBEipm2hgxxYpKJi3m9K8y3BFxk2XY45U/> .
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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 .
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/aristotle-ha03-01--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "Queried EBI BioSamples and NCBI BioSample for the 17 pre-registered organisms, keeping a sample only when a tissue, organism-part or isolation-source attribute matched testis, testes, testicle or testicles under the 60-character rule. Also paged 10 EBI result pages for organism part = testis. Lineages came from NCBI Taxonomy. One qualifying fish, snake or axolotl species refutes.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 16 species with a testis-labelled BioSample (n = 17). Interpretation: The claim's own measurable quantity is presence or absence of testes in male fishes and snakes. Testis is read as the male gonad, which is what modern sample registries label, not as an external scrotum. Aristotle's word can mean the scrotal organ; that narrower reading is not what this test measures and is stated as a limit, not as a second verdict. Ambystoma mexicanum stands in for the clause about gill-bearing animals other than fishes. Cetaceans, which the claim excepts, are not queried.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of aristotle-ha03-01: refutes, confidence 0.74";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/aristotle-biology/aristotle-ha03-01/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Public sample registries that state the anatomical source of a biological sample and the organism, with a taxonomy lineage that can be checked. Species accounts that merely use the word in a narrative are not counted. The pre-registered organism panel is Danio rerio, Oryzias latipes, Takifugu rubripes, Gasterosteus aculeatus, Oreochromis niloticus, Salmo salar, Gadus morhua, Sparus aurata, Scyliorhinus canicula, Raja clavata, Python bivittatus, Thamnophis sirtalis, Pantherophis guttatus, Vipera berus, Naja naja, Crotalus viridis and Ambystoma mexicanum, plus up to 10 pages of an open EBI organism-part=testis search.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "One or more BioSamples whose structured tissue attribute is testis or testes, from a species in Actinopterygii, Chondrichthyes, Serpentes, or from Ambystoma mexicanum.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "A testis cell line counts, because the culture was taken from that organ.",
"Aristotle's testicles can be read as external scrotal organs. This test uses the claim file's quantity, testes, which is the male gonad named in the sample registries.",
"BioSamples record that a tissue was sampled. They do not survey species in which nobody looked for a testis, so a miss cannot support the claim.",
"The open page cap can miss species that are not on the panel. Species that were found are still counterexamples.";
<https://w3id.org/delphi/ontology/expectedObservation> "No BioSample from a fish, from Ambystoma mexicanum, or from a snake carries a testis or testes tissue label. That observation would still not confirm the claim, because the databases do not record absence.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. Refute if at least one species whose NCBI lineage contains Actinopterygii or Chondrichthyes, or at least one species whose lineage contains Serpentes, or Ambystoma mexicanum, has at least one BioSample whose tissue or organism-part attribute value matches testis, testes, testicle or testicles. The value rule: the attribute name matches organism part, tissue or isolation source; the value contains that word, is at most 60 characters, and does not contain no, not, without, absent or lacking. Cell lines count. Queries that fail to load are not evidence of absence. If every planned query fails, the verdict is inconclusive with reason data-unavailable. If the queries succeed and no qualifying sample is found, the verdict is inconclusive with reason other, because a missing sample is not a recorded absence.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.74"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/aristotle-ha03-01--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/aristotle-ha03-01--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "If no fish, no other gill-bearing animal and no serpent has testes, then public BioSample records will not label testis tissue from any actinopterygian or chondrichthyan fish, from the gilled amphibian Ambystoma mexicanum, or from any snake.";
<https://w3id.org/delphi/ontology/inferenceMethod> "A species counts once if any retrieved sample passes the attribute rule and the lineage rule. One such species refutes the universal negative. Zero such species, after successful queries, is inconclusive rather than support. Precedence: data-unavailable if the services cannot be read; else refutes if the species count is at least 1; else inconclusive.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered. This presence-only search cannot confirm the claim. A pass would require an explicit anatomical survey that scores male gonads for at least 20 fish species and at least 5 snake species and records testes as absent in every male. No such survey is in the planned datasets. Do not return supports from a negative search.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
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<https://w3id.org/delphi/resource/assessment/aristotle-ha03-01--claim-test> .
<https://w3id.org/delphi/resource/evidence/aristotle-ha03-01--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "tissue or organism-part labels on biological samples";
dc:license "sample-level licenses vary; registry metadata accessed via the public API";
<http://www.w3.org/2000/01/rdf-schema#comment> "Location (not a URL): https://www.ebi.ac.uk/biosamples/samples and https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: EBI BioSamples";
prov:wasDerivedFrom <https://www.ebi.ac.uk/biosamples/>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:90f0b2e157f05bb46b72e458f0b5e8209c0e834dbf046bd722b2f850ab3ac86b" .
<https://w3id.org/delphi/resource/evidence/aristotle-ha03-01--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "BioSample attributes for the same testis query, with NCBI taxonomy lineages";
dc:license "public domain US government work for NCBI records; submitter metadata varies";
<http://www.w3.org/2000/01/rdf-schema#comment> "Location (not a URL): https://www.ebi.ac.uk/biosamples/samples and https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: NCBI BioSample";
prov:wasDerivedFrom <https://www.ncbi.nlm.nih.gov/biosample/>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:90f0b2e157f05bb46b72e458f0b5e8209c0e834dbf046bd722b2f850ab3ac86b" .
}
sub:provenance {
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<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (grok-4.7; cursor/aristotle-claim-tests-7efa)";
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/aristotle-biology/aristotle-ha03-01/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 "2026-11-08T16:24:31.753Z"^^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/aristotle-ha03-01--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of aristotle-ha03-01: refutes, confidence 0.74";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/aristotle-biology> .
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