@prefix this: <https://w3id.org/np/RAscAYxnNIO0454VneCKWHW6sq6-HLGGH6cz9_bgbYMfA> .
@prefix sub: <https://w3id.org/np/RAscAYxnNIO0454VneCKWHW6sq6-HLGGH6cz9_bgbYMfA/> .
@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/morgan1915-04--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
    dc:description "Seven loci (y, w, bi, v, m, s, B) looked up by symbol; 1915 map distance for each of the 21 pairs from the book's percentages versus genomic distance between gene midpoints (Mb); Spearman rank correlation.";
    <http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.9662 Spearman rho between 1915 map distance and genomic distance over 21 locus pairs (n = 21, Pearson r 0.972; 7 loci on one chromosome). Interpretation: The 1915 map values are the ones quoted in the claims file from the book (yellow-white 1, white-bifid 5, yellow-bifid 6, white-miniature 33, miniature-Bar 22, vermilion-sable 10, sable-Bar 14), not FlyBase's recombination_loc column, which for most genes is interpolated from cytology and would be circular. The test is one chromosome and seven loci: it tests the law where Morgan stated it, not genome-wide.";
    <http://www.w3.org/2000/01/rdf-schema#label> "Claim test of morgan1915-04: supports, confidence 0.8";
    <http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/evolution-after-darwin/morgan1915-04/result.json>;
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1>;
    <https://w3id.org/delphi/ontology/admissibleDatasets> "Planned datasets: flybase-gene-map-table";
    <https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
    <https://w3id.org/delphi/ontology/dataKind> "biological";
    <https://w3id.org/delphi/ontology/disconfirmingObservation> "Spearman < 0.70: refutes. Between 0.70 and 0.90: mixed. Any of the seven loci not found in the map table with an X-chromosome sequence location: inconclusive.";
    <https://w3id.org/delphi/ontology/evidenceAgainst> "Seven loci on the X only: it tests the law where Morgan stated it. Genome-wide, recombination rate varies along chromosomes (hotspots, centromere suppression), so the relation is monotone, not linear.",
      "The 1915 map values come from the book's quoted percentages, not from FlyBase's recombination_loc column, which is largely interpolated from cytology.",
      "sable and Bar are resolved through the FlyBase synonym table to Ype (Yippee) and B-H1 (BarH1); the Bar mutation itself is a duplication of 16A with no single coordinate, so B-H1 stands for its position.";
    <https://w3id.org/delphi/ontology/expectedObservation> "Over the 21 pairs of the seven loci, Spearman rank correlation between 1915 map distance and genomic distance (midpoints of FlyBase sequence locations on X, Release 6) is >= 0.90: supports.";
    <https://w3id.org/delphi/ontology/failCriterion> "Spearman < 0.70: refutes. Between 0.70 and 0.90: mixed. Any of the seven loci not found in the map table with an X-chromosome sequence location: inconclusive.";
    <https://w3id.org/delphi/ontology/hasConfidence> "0.8"^^xsd:double;
    <https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/morgan1915-04--claim-test--dataset-1>;
    <https://w3id.org/delphi/ontology/hasVerdict> "supports";
    <https://w3id.org/delphi/ontology/hypothesis> "If crossing over between two factors increases with their distance apart, the 1915 X-chromosome map distances between yellow, white, bifid, vermilion, miniature, sable and Bar (read from the book's own percentages: y 0, w 1, bi 6, v 32, m 34, s 42, B 56) increase with the genomic distance between those genes.";
    <https://w3id.org/delphi/ontology/inferenceMethod> "Seven loci (y, w, bi, v, m, s, B) looked up by symbol; 1915 map distance for each of the 21 pairs from the book's percentages versus genomic distance between gene midpoints (Mb); Spearman rank correlation.";
    <https://w3id.org/delphi/ontology/passCriterion> "Over the 21 pairs of the seven loci, Spearman rank correlation between 1915 map distance and genomic distance (midpoints of FlyBase sequence locations on X, Release 6) is >= 0.90: supports.";
    <https://w3id.org/delphi/ontology/preregistered> "true"^^xsd:boolean .
  
  <https://w3id.org/delphi/resource/claim/morgan1915-04> <https://w3id.org/delphi/ontology/hasAssessment>
      <https://w3id.org/delphi/resource/assessment/morgan1915-04--claim-test> .
  
  <https://w3id.org/delphi/resource/evidence/morgan1915-04--claim-test--dataset-1> a
      <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "";
    dc:license "CC BY 4.0";
    <http://www.w3.org/2000/01/rdf-schema#label> "Dataset: FlyBase precomputed gene map table FB2026_03 (D. melanogaster Release 6 coordinates)";
    prov:atLocation <https://s3ftp.flybase.org/releases/current/precomputed_files/genes/gene_map_table_fb_2026_03.tsv.gz>,
      <https://s3ftp.flybase.org/releases/current/precomputed_files/synonyms/fb_synonym_fb_2026_03.tsv.gz>;
    prov:wasDerivedFrom <https://flybase.org/downloads/>;
    <https://w3id.org/delphi/ontology/hasChecksum> "sha256:1fc2f20e1fbf82bbec198f268aeff8bfcea3345f7777e2b9ded43a801ddada5c",
      "sha256:e229f1a3be7124fa04fd70e04db4432e9bddcde38408d8840af2caedd002ecce" .
}

sub:provenance {
  <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1> a
      prov:SoftwareAgent;
    <http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (claude-fable-5.1; evolution-after-darwin-tests-1)";
    prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
    <https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/claude-fable-5-1> .
  
  <https://w3id.org/delphi/resource/model/claude-fable-5-1> a <https://w3id.org/delphi/ontology/LanguageModel>;
    dc:identifier "claude-fable-5.1" .
  
  sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1>;
    prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/evolution-after-darwin/morgan1915-04/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-claude-fable-5-1> .
}

sub:pubinfo {
  this: dc:created "2026-11-08T16:24:31.868Z"^^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/morgan1915-04--claim-test>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Claim test of morgan1915-04: supports, confidence 0.8";
    <https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/evolution-after-darwin> .
  
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    npx:hasSignatureTarget this:;
    npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
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