{
  "id": "ark:/99999/dp-bodo-divergence.v1",
  "concept": "ark:/99999/dp-bodo-divergence",
  "type": "datasetpaper",
  "title": "Do single-cell Bodo genomes form a functional group distinct from the reference? A PFAM-domain divergence analysis",
  "discipline": "microbial genomics",
  "description": "The source paper reports unexpected genetic diversity among single-cell Bodo genomes. We tested that at the level of protein-domain (PFAM) content: are th…",
  "url": "https://datasetpapers.com/papers/bodo-functional-divergence/",
  "trust_distance": 0,
  "verification": {
    "claims": 3,
    "re_executed": 3,
    "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": "analysis2",
      "type": "code",
      "path": "analysis2.py",
      "ark": "ark:/99999/dp-bodo-divergence.v1/analysis2",
      "produced_by": null
    },
    {
      "name": "fig-1",
      "type": "figure",
      "path": "figures/fig-1-dendrogram.png",
      "ark": "ark:/99999/dp-bodo-divergence.v1/fig-1",
      "produced_by": "analysis2"
    },
    {
      "name": "fig-2",
      "type": "figure",
      "path": "figures/fig-2-pcoa.png",
      "ark": "ark:/99999/dp-bodo-divergence.v1/fig-2",
      "produced_by": "analysis2"
    },
    {
      "name": "tbl-1",
      "type": "table",
      "path": "tables/tbl-1-braycurtis-distance.csv",
      "ark": "ark:/99999/dp-bodo-divergence.v1/tbl-1",
      "produced_by": "analysis2"
    },
    {
      "name": "narrative",
      "type": "narrative",
      "path": "narrative2.md",
      "ark": "ark:/99999/dp-bodo-divergence.v1/narrative",
      "produced_by": null
    }
  ],
  "claims": [
    {
      "n": 1,
      "subject": "the seven single-cell Bodo genomes",
      "predicate": "are functionally more distant from the B. saltans reference than from one another",
      "object": "at the PFAM-domain level",
      "assertion_text": "Normalised PFAM-domain profiles place the single cells significantly further from the B. saltans reference (mean Bray-Curtis 0.179) than from one another (0.132), Mann-Whitney p = 0.0024, so the single cells form a coherent functional group distinct from the reference.",
      "supported_by": [
        "fig-1",
        "fig-2"
      ],
      "confidence": 0.85,
      "novelty_grade": "B",
      "mode": "confirmatory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-divergence.v1/claim-1"
    },
    {
      "n": 2,
      "subject": "the B. saltans reference genome",
      "predicate": "is the single most functionally divergent genome",
      "object": "among the eight compared",
      "assertion_text": "B. saltans has the largest mean Bray-Curtis distance to the other genomes (0.179 versus 0.124 to 0.167 for the single cells), consistent with the single cells clustering together and the reference sitting as the outlier.",
      "supported_by": [
        "fig-1"
      ],
      "confidence": 0.85,
      "novelty_grade": "B",
      "mode": "exploratory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-divergence.v1/claim-2"
    },
    {
      "n": 3,
      "subject": "the reference-versus-single-cell separation",
      "predicate": "is real but not fully robust",
      "object": "being metric-sensitive and internally structured",
      "assertion_text": "The separation is significant under Bray-Curtis (p = 0.0024) but not under cosine distance (p = 0.16), and the ordination shows two single cells (B7, F10) diverging from the other five, so the grouping should be read as a tendency rather than a settled result.",
      "supported_by": [
        "fig-2"
      ],
      "confidence": 0.8,
      "novelty_grade": "B",
      "mode": "exploratory",
      "verification_status": "re_executed",
      "ark": "ark:/99999/dp-bodo-divergence.v1/claim-3"
    }
  ],
  "exports": {
    "object_json": "object.json",
    "ro_crate": "ro-crate-metadata.json",
    "code": "analysis2.py",
    "emissions": []
  }
}