{
  "id": "ark:/99999/dp-bodo-endosymbiont.v1",
  "concept": "ark:/99999/dp-bodo-endosymbiont",
  "type": "datasetpaper",
  "title": "How metabolically reduced is the Bodo endosymbiont? A quantified test of host-symbiont complementarity",
  "discipline": "microbial genomics",
  "description": "Endosymbiotic bacteria are widely expected to be metabolically reduced relative to their hosts, retaining a subset of pathways and depending on the host f…",
  "url": "https://datasetpapers.com/papers/bodo-endosymbiont-metabolic-complementarity/",
  "trust_distance": 0,
  "verification": {
    "claims": 4,
    "re_executed": 4,
    "unverified": 0
  },
  "byline": {
    "software_agent": {
      "name": "Claude Opus 4.8",
      "model_id": "claude-opus-4-8"
    },
    "data_creators": [
      "Sally D. Warring",
      "Jamie McGowan",
      "Estelle S. Kilias",
      "James Lipscombe",
      "Elisabet Alacid",
      "Tom Barker",
      "Leah Catchpole",
      "Karim Gharbi",
      "Seanna McTaggart",
      "Thomas A. Richards",
      "David Swarbreck",
      "Neil Hall"
    ],
    "question_asker": "Mark Hahnel"
  },
  "source_dataset": {
    "title": "Single-cell sequencing of Bodo spp. flagellates and their bacterial endosymbionts",
    "doi": "10.6084/m9.figshare.31362613",
    "license": "CC-BY-4.0",
    "landing_url": "https://doi.org/10.6084/m9.figshare.31362613",
    "download_url": "https://figshare.com/articles/dataset/31362613"
  },
  "components": [
    {
      "name": "analysis",
      "type": "code",
      "path": "analysis.py",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/analysis",
      "produced_by": null
    },
    {
      "name": "fig-1",
      "type": "figure",
      "path": "figures/fig-1-paired-completeness.png",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/fig-1",
      "produced_by": "analysis"
    },
    {
      "name": "fig-2",
      "type": "figure",
      "path": "figures/fig-2-category-breakdown.png",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/fig-2",
      "produced_by": "analysis"
    },
    {
      "name": "fig-3",
      "type": "figure",
      "path": "figures/fig-3-per-cell-consistency.png",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/fig-3",
      "produced_by": "analysis"
    },
    {
      "name": "tbl-1",
      "type": "table",
      "path": "tables/tbl-1-module-classification.csv",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/tbl-1",
      "produced_by": "analysis"
    },
    {
      "name": "narrative",
      "type": "narrative",
      "path": "narrative.md",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/narrative",
      "produced_by": null
    }
  ],
  "claims": [
    {
      "n": 1,
      "subject": "Ca. Bodocryptus vickermanii",
      "predicate": "is not significantly less metabolically complete than",
      "object": "its Bodo saltans host",
      "assertion_text": "Across the 106 KEGG modules shared by both genomes, the Bodo host is not significantly more complete than its endosymbiont (Wilcoxon signed-rank p = 0.12; host more complete in 44 modules, endosymbiont in 34, 28 tied; median paired difference 0.0 percentage points). The endosymbiont retains a module-completeness profile close to the host's.",
      "supported_by": [
        "fig-1"
      ],
      "confidence": 0.9,
      "novelty_grade": "B",
      "mode": "confirmatory-test-negative",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/claim-1"
    },
    {
      "n": 2,
      "subject": "host-complete endosymbiont-incomplete KEGG modules",
      "predicate": "outnumber the reverse consistently but not significantly",
      "object": "at completeness thresholds from 50 to 80 percent",
      "assertion_text": "Host-complete, endosymbiont-incomplete modules outnumber the reverse at every threshold tested (50%: 21 vs 13; 67%: 19 vs 10, a 1.9 to 1 ratio; 80%: 11 vs 9), a directionally consistent asymmetry that is not statistically significant at 67% (McNemar exact p = 0.14).",
      "supported_by": [
        "fig-2",
        "tbl-1"
      ],
      "confidence": 0.85,
      "novelty_grade": "B",
      "mode": "confirmatory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/claim-2"
    },
    {
      "n": 3,
      "subject": "the host-symbiont metabolic asymmetry",
      "predicate": "is reproducible across",
      "object": "the seven single-cell host-symbiont pairs",
      "assertion_text": "The host-only module fraction is 15.2% plus or minus 2.1 versus 10.0% plus or minus 2.9 symbiont-only across the seven single cells, with host-only at least symbiont-only in all seven (strictly greater in six). The modest asymmetry is a reproducible feature of the symbiosis, not a single-cell artifact.",
      "supported_by": [
        "fig-3"
      ],
      "confidence": 0.9,
      "novelty_grade": "B",
      "mode": "exploratory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/claim-3"
    },
    {
      "n": 4,
      "subject": "the strong reductive-complementarity expectation for this endosymbiont",
      "predicate": "is refined rather than supported by",
      "object": "KEGG module completeness on shared modules",
      "assertion_text": "At the KEGG-module-completeness level, the endosymbiont is only modestly less complete than its host and the reductive asymmetry, though directionally consistent and reproducible, is small and not significant on the 106 shared modules. This nuances the common expectation of strong host-symbiont metabolic complementarity.",
      "supported_by": [
        "fig-1",
        "fig-2"
      ],
      "confidence": 0.8,
      "novelty_grade": "B",
      "mode": "exploratory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-endosymbiont.v1/claim-4"
    }
  ],
  "exports": {
    "object_json": "object.json",
    "ro_crate": "ro-crate-metadata.json",
    "code": "analysis.py",
    "emissions": [
      {
        "format": "datapackage",
        "file": "datapackage.json"
      }
    ]
  }
}