simulation/graph-viewer.html at main · REagent-LABrador/simulation · GitHub

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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<title>Evidence graph viewer — research-evidence-mapper</title>
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</head>
<body>
<div class="viz-root">
<div class="wrap">

<header>
  <div>
    <h1>Evidence graph viewer</h1>
    <p class="sub">research-evidence-mapper output &mdash; things, links, verbatim-quoted findings, gaps</p>
  </div>
  <div class="bar">
    <select id="ds" aria-label="Graph"></select>
    <button id="v-graph" aria-pressed="true">Graph</button>
    <button id="v-table" aria-pressed="false">Table</button>
    <button id="theme">Toggle dark</button>
  </div>
</header>

<div class="card qcard">
  <div class="qlabel">The question &mdash; <code>{"ask":"new_question","target":"&hellip;"}</code></div>
  <p class="q" id="q"></p>
  <div class="qmeta" id="qmeta"></div>
  <div class="blurb" id="blurb"></div>
</div>

<div id="banner"></div>
<div class="cov" id="cov"></div>

<div class="cols" id="graph-view">
  <div class="card">
    <div class="plot">
      <svg id="svg" viewBox="0 0 980 640" role="img"
        aria-label="Node-link diagram of the evidence graph. A table view is available above.">
        <defs>
          <marker id="a-agreed" viewBox="0 0 8 8" refX="7" refY="4" markerWidth="5.5" markerHeight="5.5" orient="auto-start-reverse"><path d="M0,0 L8,4 L0,8 z" fill="var(--state-agreed)"/></marker>
          <marker id="a-disagreed" viewBox="0 0 8 8" refX="7" refY="4" markerWidth="5.5" markerHeight="5.5" orient="auto-start-reverse"><path d="M0,0 L8,4 L0,8 z" fill="var(--state-disagreed)"/></marker>
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    </div>
    <div class="legend">
      <span class="item"><svg viewBox="0 0 30 10"><line x1="1" y1="5" x2="29" y2="5" stroke="var(--state-agreed)" stroke-width="2.5"/></svg>agreed</span>
      <span class="item"><svg viewBox="0 0 30 10"><line x1="1" y1="5" x2="29" y2="5" stroke="var(--state-disagreed)" stroke-width="3" stroke-dasharray="7 3"/></svg>disagreed</span>
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      <span class="item"><svg viewBox="0 0 30 10"><line x1="1" y1="5" x2="29" y2="5" stroke="var(--gap)" stroke-width="2" stroke-dasharray="5 5"/></svg>gap &mdash; never stated</span>
      <span class="item" style="color:var(--text-muted)">circle size = papers mentioning</span>
    </div>
  </div>
  <div class="card panel" id="panel"></div>
</div>

<div class="card" id="table-view" hidden>
  <table>
    <caption id="cap"></caption>
    <thead><tr><th>id</th><th>relationship</th><th>state</th><th>basis</th>
      <th class="num">yes</th><th class="num">no</th><th class="num">conf.</th><th>note</th></tr></thead>
    <tbody id="tbody"></tbody>
  </table>
  <table style="margin-top:8px">
    <caption>Findings &mdash; the verbatim quotes. Every one was string-matched against the fetched text before it was written; a quote that would not match was dropped, not repaired.</caption>
    <thead><tr><th>id</th><th>paper</th><th>triple</th><th>says</th><th>where</th><th>quote</th></tr></thead>
    <tbody id="fbody"></tbody>
  </table>
</div>

<p class="foot" id="foot"></p>

</div>
</div>

<script>
const GRAPHS = {"g_e041":{"schema_version":"1.1","graph_id":"g_e041","question":"In inflammatory bowel disease, do small-molecule MR1 antagonist ligands (isobutyl 6-formyl pterin / i6-FP, 6-formylpterin; versus the riboflavin-derived agonist precursor 5-A-RU) block presentation of microbial riboflavin metabolites and thereby suppress MAIT (mucosal-associated invariant T) cell-driven colonic inflammation in ulcerative colitis, or does MR1 blockade instead remove a MAIT-CCL2-AHR-IL-22 epithelial repair program whose loss aggravates barrier injury — and does the sign of that effect track the colitis model (hapten/oxazolone versus DSS barrier injury) rather than the compartment?","round":2,"status":"ok","generated_at":"2026-08-16T06:00:00Z","error":null,"delta":{"round":2,"things_added":[],"papers_added":[],"findings_added":["fg2"],"links_added":["L30"],"links_changed":["L18","L20","L21","L23","L24","L25","L26"],"gaps_added":[],"gaps_resolved":[]},"rounds":[{"n":1,"ask":"new_question","target":null,"depth":"standard","papers_added":8,"outcome":"new_evidence"},{"n":2,"ask":"new_question","target":null,"depth":"standard","papers_added":8,"outcome":"promoted"}],"coverage":{"depth":"standard","found":91,"read":8,"used":8,"truncated":true,"no_quote_discarded":0,"limits":{"max_papers":25,"max_queries":4},"figures_read":0,"duplicates_dropped":36,"stop_reason":"queries_exhausted","has_disease_node":true,"proteins_without_accession":[],"proteins_without_accession_count":0,"interventions_without_target":["t19","t7"],"interventions_without_target_count":2,"confidence_profile":{"n":37,"min":0.5,"max":0.9,"below_0_65":4,"hedged_but_confident":[]}},"things":[{"id":"t1","name":"MAIT cell activation","kind":"process","aliases":["MAIT cells","MAIT17 cells","colonic MAIT cells","mucosal-associated invariant T cells"],"mentions":2,"round":1,"merged_from":[{"name":"MAIT cell activation","via":"name"}]},{"id":"t2","name":"MR1","kind":"protein","aliases":["MHC class I-related molecule","major histocompatibility complex class I-related protein 1","major histocompatibility complex-related molecule 1"],"uniprot_accession":"Q95460","gene_symbol":"MR1","resolved_by":"f-Q_L12 quote (i6-FP) and Q7_1 (5-A-RU) both name MR1 as the human antigen-presenting molecule these ligands act on; species is human per the clinical/human-PBMC and human-cell-line experiments in p1 and p7","mentions":2,"round":1,"merged_from":[{"name":"MR1","via":"accession"}]},{"id":"t3","name":"ulcerative colitis","kind":"disease","aliases":["UC"],"mentions":2,"round":1,"merged_from":[{"name":"ulcerative colitis","via":"name"}]},{"id":"t4","name":"Crohn's disease","kind":"disease","aliases":["CD"],"mentions":2,"round":1,"merged_from":[{"name":"Crohn's disease","via":"name"}]},{"id":"t5","name":"inflammatory bowel disease","kind":"disease","aliases":["IBD"],"mentions":2,"round":1,"merged_from":[{"name":"inflammatory bowel disease","via":"name"}]},{"id":"t6","name":"i6-FP","kind":"small_molecule","aliases":["antagonistic MR1 ligand","isobutyl 6-formyl pterin","isobutyryl 6-formyl pterin"],"mentions":2,"round":1,"merged_from":[{"name":"i6-FP","via":"name"}]},{"id":"t7","name":"oxazolone colitis","kind":"method","aliases":["hapten colitis model","oxazolone-induced colitis"],"mentions":2,"round":1,"merged_from":[{"name":"oxazolone colitis","via":"name"}]},{"id":"t8","name":"DSS colitis","kind":"method","aliases":["DSS-induced colitis","dextran sodium sulfate colitis","dextran sulfate sodium colitis"],"mentions":2,"round":1,"merged_from":[{"name":"DSS colitis","via":"name"}]},{"id":"t9","name":"CCL2","kind":"protein","aliases":["C-C motif chemokine 2","MCP-1","monocyte chemoattractant protein-1"],"uniprot_accession":"P13500","gene_symbol":"CCL2","resolved_by":"f-Q2_4/Q2_5 quotes name CCL2 as the MAIT-derived secreted mediator in the mouse DSS colitis model (p2); human accession used as the canonical protein-concept node, mouse ortholog P10148 is the species actually assayed and is recorded in the finding's where field via paper context","ambiguity":["P10148 Ccl2 (mouse) — the species actually measured in p2; human P13500 used as the canonical cross-species node per convention"],"mentions":2,"round":1,"merged_from":[{"name":"CCL2","via":"name"}]},{"id":"t10","name":"AHR","kind":"protein","aliases":["aryl hydrocarbon receptor"],"uniprot_accession":"P35869","gene_symbol":"AHR","resolved_by":"f-Q2_6 quote names AHR and its target CYP1A1 as the pathway reduced in MR1-/- mouse colon (p2); human accession used as canonical node, mouse study","mentions":2,"round":1,"merged_from":[{"name":"AHR","via":"accession"}]},{"id":"t11","name":"IL-22","kind":"protein","aliases":["interleukin-22"],"uniprot_accession":"Q9GZX6","gene_symbol":"IL22","resolved_by":"f-Q2_9/Q2_8 quotes name IL-22 as the downstream cytokine mediator rescued by recombinant IL-22 and by CCL2 in MR1-/- mice (p2); 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It has also attracted significant research interest with regard to its role in cancer progression, although the mechanisms involved remain controversial and poorly understood. Here, using murine models of breast cancer metastasis, we found that systemic NAC administration significantly enhanced pulmonary metastasis without altering primary tumor growth in immunocompetent mice, whereas this metastasis-promoting property of NAC was abrogated in T cell-deficient mice.","round":1,"says":"yes","section":"abstract","to":"t13","where":"immunocompetent mice"},{"confidence":0.75,"flags":["direction_from_context"],"from":"t1","hedged":false,"how":"increases","id":"f13","is_own_result":true,"paper":"p4","quote":"N-acetylcysteine (NAC) is a widely used antioxidant. It has also attracted significant research interest with regard to its role in cancer progression, although the mechanisms involved remain controversial and poorly understood. 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Here, using murine models of breast cancer metastasis, we found that systemic NAC administration significantly enhanced pulmonary metastasis without altering primary tumor growth in immunocompetent mice, whereas this metastasis-promoting property of NAC was abrogated in T cell-deficient mice.","round":1,"says":"no_effect","section":"abstract","to":"t14","where":"immunocompetent mice"},{"confidence":0.85,"flags":[],"from":"t1","hedged":false,"how":"increases","id":"f1","is_own_result":true,"paper":"p1","quote":"Here, we show that supplementation with the antioxidants N-acetylcysteine (NAC) and vitamin E promotes intestinal tumor progression in the ApcMin mouse model for familial adenomatous polyposis, a hereditary form of colorectal cancer, driven by Wnt signaling.","round":1,"says":"yes","section":"abstract","to":"t15","where":"apcmin mice"},{"confidence":0.9,"flags":[],"from":"t1","hedged":false,"how":"increases","id":"f16","is_own_result":true,"paper":"p5","quote":"RES and NAC enhance HCC formation in both DEN/HFD and AKT/Ras mice.","round":1,"says":"yes","section":"abstract","to":"t16","where":"den/hfd and akt/ras mice"},{"confidence":0.85,"flags":[],"from":"t1","hedged":false,"how":"increases","id":"f40","is_own_result":true,"paper":"p18","quote":"Rather, NAC treatment increased epithelial cell proliferation and promoted the expression of a pro-proliferative gene signature.","round":1,"says":"yes","section":"abstract","to":"t17","where":"nkx3.1 mutant mice"},{"confidence":0.8,"flags":[],"from":"t1","hedged":false,"how":"activates","id":"f14","is_own_result":true,"paper":"p4","quote":"Mechanistically, we demonstrated that NAC endows neutrophils with an immunosuppressive phenotype, which is characterized by the upregulation of immunosuppressive genes, and these NAC-educated neutrophils potently suppress the activation and effector functions of T cells.","round":1,"says":"yes","section":"abstract","to":"t24","where":"murine breast cancer metastasis model"},{"confidence":0.85,"flags":[],"from":"t1","hedged":false,"how":"increases","id":"f18","is_own_result":true,"paper":"p5","quote":"We therefore performed Western blot to detect GST-pi, and found that GST-pi expression was increased in the liver tissues of both the RES- or NAC-treated mice, whereas nucleoprotein γH2AX was decreased (Figure 5F).","round":1,"says":"yes","section":"results","to":"t9","where":"den/hfd mice, liver tissue"},{"confidence":0.85,"flags":[],"from":"t2","hedged":false,"how":"decreases","id":"f5","is_own_result":true,"paper":"p2","quote":"Trolox, an antioxidant vitamin E derivative, administered in vivo, decreased metastatic growth.","round":1,"says":"yes","section":"abstract","to":"t11","where":"melanoma xenograft mice"},{"confidence":0.85,"flags":[],"from":"t2","hedged":false,"how":"increases","id":"f2","is_own_result":true,"paper":"p1","quote":"Here, we show that supplementation with the antioxidants N-acetylcysteine (NAC) and vitamin E promotes intestinal tumor progression in the ApcMin mouse model for familial adenomatous polyposis, a hereditary form of colorectal cancer, driven by Wnt signaling.","round":1,"says":"yes","section":"abstract","to":"t15","where":"apcmin mice"},{"confidence":0.9,"flags":[],"from":"t2","hedged":false,"how":"decreases","id":"f39","is_own_result":true,"paper":"p17","quote":"vitamin E drastically decreased the incidence of lung tumor and tumor multiplicity which were 17.0% and 0.32 ± 0.16, respectively (p < 0.05)","round":1,"says":"yes","section":"results","to":"t23","where":"smoking-induced lung tumor, swiss mice"},{"confidence":0.85,"flags":[],"from":"t2","hedged":false,"how":"decreases","id":"f31","is_own_result":true,"paper":"p11","quote":"Supplemental alpha-tocopherol, beta-carotene, or both, relative to placebo, did not reduce the risk of liver cancer or CLD, either overall, during the intervention or during the post-intervention period.","round":1,"says":"no_effect","section":"results","to":"t26","where":"atbc trial, finnish male smokers"},{"confidence":0.85,"flags":[],"from":"t2","hedged":false,"how":"increases","id":"f34","is_own_result":true,"paper":"p12","quote":"Vitamin E in a dose above the RDA (> 15 mg) significantly increased mortality (RR 1.03, 95% CI 1.00 to 1.05, I 2 = 0%).","round":1,"says":"yes","section":"abstract","to":"t27","where":"meta-analysis of rcts, adults, dose above rda"},{"confidence":0.7,"flags":[],"from":"t2","hedged":false,"how":"increases","id":"f41","is_own_result":false,"paper":"p18","quote":"Results from the large-scale Selenium and Vitamin E Cancer Prevention Trial (SELECT) showed that antioxidants failed to prevent, and in some cases promoted, prostate cancer formation in men without a history of the disease.","round":1,"says":"yes","section":"discussion","to":"t28","where":"select trial, human"},{"confidence":0.9,"flags":[],"from":"t3","hedged":false,"how":"increases","id":"f6","is_own_result":true,"paper":"p3","quote":"Four diet-relevant compounds from this list—VitC, β-carotene, retinyl palmitate, and canthaxanthin—were selected and found to accelerate metastasis in mice with BRAF V600E -driven malignant melanoma.","round":1,"says":"yes","section":"abstract","to":"t11","where":"braf v600e-driven melanoma, mouse"},{"confidence":0.9,"flags":[],"from":"t3","hedged":false,"how":"increases","id":"f20","is_own_result":true,"paper":"p6","quote":"Ascorbate-supplemented gulo KO mice injected with B16FO melanoma cells demonstrated significant reduction (by 71%, p=0.005) in tumor metastasis compared to gulo KO mice on the control diet.","round":1,"says":"no","section":"abstract","to":"t11","where":"b16f0 melanoma, gulo ko mice"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"decreases","id":"f22","is_own_result":true,"paper":"p7","quote":"restoration of wild-type ascorbate levels led to a reduction in growth of B16-F10 (log phase P < 0.001) and LL/2 tumors (lag growth P < 0.001, log phase P < 0.05).","round":1,"says":"yes","section":"abstract","to":"t12","where":"gulo-/- mice, b16-f10 melanoma"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"decreases","id":"f21","is_own_result":true,"paper":"p6","quote":"The mean tumor weight in ascorbate supplemented mice injected with 4T1 cells was reduced by 28% compared to tumor weight in scorbutic mice.","round":1,"says":"yes","section":"abstract","to":"t14","where":"4t1 breast cancer, gulo ko mice"},{"confidence":0.6,"flags":["effect_size_dropped"],"from":"t3","hedged":false,"how":"decreases","id":"f35","is_own_result":true,"paper":"p13","quote":"The combination of pharmacological ascorbate with genotoxic agents, including oxaliplatin and irinotecan, synergistically inhibited gastric tumor growth in mouse models.","round":1,"says":"yes","section":"results","to":"t18","where":"gastric cancer xenograft + oxaliplatin/irinotecan, mouse"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"decreases","id":"f42","is_own_result":true,"paper":"p19","quote":"Taken together, these in vitro and in vivo data indicated that, pharmacological ascorbate inhibited pancreatic cancer growth and metastasis through a pro-oxidative mechanism, subsequently induced NAD+/ATP depletion selectively in cancer cells, and resulted in inhibition of cell proliferation and induction of cell death.","round":1,"says":"yes","section":"results","to":"t19","where":"panc-1 orthotopic xenograft, mouse"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"suppresses","id":"f37","is_own_result":true,"paper":"p15","quote":"Collectively, these single‐cell resolution results indicate that APM suppresses tumor growth by inducing cell cycle arrest in malignant cells and interfering with prometastatic signaling pathways.","round":1,"says":"yes","section":"results","to":"t20","where":"apm, renal cancer stem-like cells, mouse"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"suppresses","id":"f38","is_own_result":true,"paper":"p16","quote":"Additionally, AA prevented liver cancer metastasis in a xenotransplantation model without suppressing stemness gene expression in liver CSCs.","round":1,"says":"yes","section":"abstract","to":"t21","where":"liver cancer xenotransplantation, mouse"},{"confidence":0.9,"flags":[],"from":"t3","hedged":false,"how":"suppresses","id":"f36","is_own_result":true,"paper":"p14","quote":"Here, we showed that vitamin C inhibited spheroid formation and metastasis in ID8 ovarian cancer-bearing mice.","round":1,"says":"yes","section":"abstract","to":"t22","where":"id8 ovarian cancer, mouse"},{"confidence":0.85,"flags":[],"from":"t3","hedged":false,"how":"decreases","id":"f23","is_own_result":true,"paper":"p7","quote":"restoration of wild-type ascorbate levels led to a reduction in growth of B16-F10 (log phase P < 0.001) and LL/2 tumors (lag growth P < 0.001, log phase P < 0.05).","round":1,"says":"yes","section":"abstract","to":"t29","where":"gulo-/- mice, ll/2 lewis lung carcinoma"},{"confidence":0.85,"flags":[],"from":"t30","hedged":false,"how":"increases","id":"f28","is_own_result":true,"paper":"p9","quote":"Here, we administered the mitochondria-targeted antioxidants MitoQ and MitoTEMPO to mice with BRAF-induced malignant melanoma and KRAS-induced lung cancer, and found that these compounds had no impact on the number of primary tumors and metastases; and did not influence mitochondrial and nuclear DNA damage levels.","round":1,"says":"no_effect","section":"abstract","to":"t11","where":"braf-driven melanoma, mouse"},{"confidence":0.85,"flags":[],"from":"t30","hedged":false,"how":"increases","id":"f27","is_own_result":true,"paper":"p9","quote":"Here, we administered the mitochondria-targeted antioxidants MitoQ and MitoTEMPO to mice with BRAF-induced malignant melanoma and KRAS-induced lung cancer, and found that these compounds had no impact on the number of primary tumors and metastases; and did not influence mitochondrial and nuclear DNA damage levels.","round":1,"says":"no_effect","section":"abstract","to":"t12","where":"braf-driven melanoma, mouse"},{"confidence":0.85,"flags":[],"from":"t30","hedged":false,"how":"increases","id":"f29","is_own_result":true,"paper":"p9","quote":"Here, we administered the mitochondria-targeted antioxidants MitoQ and MitoTEMPO to mice with BRAF-induced malignant melanoma and KRAS-induced lung cancer, and found that these compounds had no impact on the number of primary tumors and metastases; and did not influence mitochondrial and nuclear DNA damage levels.","round":1,"says":"no_effect","section":"abstract","to":"t31","where":"kras-driven lung cancer, mouse"},{"confidence":0.9,"flags":[],"from":"t4","hedged":false,"how":"increases","id":"f15","is_own_result":true,"paper":"p5","quote":"RES and NAC enhance HCC formation in both DEN/HFD and AKT/Ras mice.","round":1,"says":"yes","section":"abstract","to":"t16","where":"den/hfd and akt/ras mice"},{"confidence":0.85,"flags":[],"from":"t4","hedged":false,"how":"increases","id":"f17","is_own_result":true,"paper":"p5","quote":"We therefore performed Western blot to detect GST-pi, and found that GST-pi expression was increased in the liver tissues of both the RES- or NAC-treated mice, whereas nucleoprotein γH2AX was decreased (Figure 5F).","round":1,"says":"yes","section":"results","to":"t9","where":"den/hfd mice, liver tissue"},{"confidence":0.9,"flags":[],"from":"t5","hedged":false,"how":"increases","id":"f7","is_own_result":true,"paper":"p3","quote":"Four diet-relevant compounds from this list—VitC, β-carotene, retinyl palmitate, and canthaxanthin—were selected and found to accelerate metastasis in mice with BRAF V600E -driven malignant melanoma.","round":1,"says":"yes","section":"abstract","to":"t11","where":"braf v600e-driven melanoma, mouse"},{"confidence":0.9,"flags":[],"from":"t5","hedged":false,"how":"increases","id":"f30","is_own_result":true,"paper":"p10","quote":"The findings indicate that beta-carotene supplementation was associated with an increased risk of lung cancer (RR = 1.16, 95% CI = 1.06–1.26).","round":1,"says":"yes","section":"abstract","to":"t25","where":"meta-analysis of rcts, smokers and general population"},{"confidence":0.85,"flags":[],"from":"t5","hedged":false,"how":"decreases","id":"f32","is_own_result":true,"paper":"p11","quote":"Supplemental alpha-tocopherol, beta-carotene, or both, relative to placebo, did not reduce the risk of liver cancer or CLD, either overall, during the intervention or during the post-intervention period.","round":1,"says":"no_effect","section":"results","to":"t26","where":"atbc trial, finnish male smokers"},{"confidence":0.9,"flags":[],"from":"t5","hedged":false,"how":"increases","id":"f33","is_own_result":true,"paper":"p12","quote":"Beta-carotene in a dose above 9.6 mg significantly increased mortality (relative risk (RR) 1.06, 95% confidence interval (CI) 1.02 to 1.09, I 2 = 13%).","round":1,"says":"yes","section":"abstract","to":"t27","where":"meta-analysis of rcts, adults, dose above rda"},{"confidence":0.9,"flags":[],"from":"t6","hedged":false,"how":"increases","id":"f8","is_own_result":true,"paper":"p3","quote":"Four diet-relevant compounds from this list—VitC, β-carotene, retinyl palmitate, and canthaxanthin—were selected and found to accelerate metastasis in mice with BRAF V600E -driven malignant melanoma.","round":1,"says":"yes","section":"abstract","to":"t11","where":"braf v600e-driven melanoma, mouse"},{"confidence":0.9,"flags":[],"from":"t7","hedged":false,"how":"increases","id":"f9","is_own_result":true,"paper":"p3","quote":"Four diet-relevant compounds from this list—VitC, β-carotene, retinyl palmitate, and canthaxanthin—were selected and found to accelerate metastasis in mice with BRAF V600E -driven malignant melanoma.","round":1,"says":"yes","section":"abstract","to":"t11","where":"braf v600e-driven melanoma, mouse"},{"confidence":0.8,"flags":[],"from":"t8","hedged":false,"how":"activates","id":"f10","is_own_result":true,"paper":"p3","quote":"Genomics analyses revealed that the transcription factor BACH1 is activated following antioxidant administration and knockout of Bach1 in mouse melanoma cells reduced lymph node and liver metastasis in xenograft mouse models.","round":1,"says":"yes","section":"abstract","to":"t11","where":"xenograft mouse, bach1 knockout"},{"confidence":0.8,"flags":[],"from":"t9","hedged":false,"how":"drives","id":"f19","is_own_result":true,"paper":"p5","quote":"Collectively, these results indicate that GST-pi mediates the promoting effect of antioxidants in HCC initiation and 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age","basis":"primary","confidence":{"overall":0.41,"label":"medium","evidence_quality":0.45,"agreement":0.5,"independence":0.5},"changed_in_round":2},{"id":"L7","from":"t7","how":"contributes_to","to":"t5","yes":["f8"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.72,"label":"high","evidence_quality":0.8,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L8","from":"t2","how":"slows","to":"t11","yes":["f9"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.8,"label":"high","evidence_quality":0.95,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L9","from":"t3","how":"drives","to":"t7","yes":["f10"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.63,"label":"medium","evidence_quality":0.6,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L10","from":"t12","how":"sustains","to":"t3","yes":["f11"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.61,"label":"medium","evidence_quality":0.6,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L11","from":"t10","how":"measures","to":"t4","yes":["f12"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.52,"label":"medium","evidence_quality":0.45,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L12","from":"t12","how":"contributes_to","to":"t5","yes":["f14"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.7,"label":"high","evidence_quality":0.6,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L13","from":"t2","how":"inhibits","to":"t3","yes":["f15"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.5,"label":"medium","evidence_quality":0.45,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L14","from":"t1","how":"inhibits","to":"t4","yes":["f16"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.58,"label":"medium","evidence_quality":0.45,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L15","from":"t2","how":"inhibits","to":"t4","yes":["f17"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.54,"label":"medium","evidence_quality":0.45,"agreement":1.0,"independence":0.0},"changed_in_round":2}],"gaps":[{"id":"g1","missing":["t8","t5"],"implied_by":["L5","L6","L7"],"note":"nobody states metformin affects IPF directly","confidence":0.38,"searched_in_round":null},{"id":"g2","missing":["t1","t11"],"implied_by":["L1","L8"],"note":"pirfenidone is never linked to SSc-ILD despite the shared antifibrotic target","confidence":0.31,"searched_in_round":2}],"_meta":{"key":"g_demo1","blurb":"Hypothesis-generator fixture (IPF repositioning) — the graph shape hyp_gen enumerates over.","path":"hypothesis-generator/fixtures/example_graph.json"}},"g_ra4k":{"_fixture":true,"_fixture_note":"SYNTHETIC FIXTURE. Papers, DOIs and quotes are illustrative and were NOT retrieved from any corpus. Do not cite. Regenerate against Paperclip before using as a real Stage 1 output.","schema_version":"1.1","graph_id":"g_ra4k","question":"can a small-molecule IRAK4 inhibitor suppress synovial fibroblast-driven inflammation in rheumatoid arthritis, or is its effect confined to the myeloid compartment?","round":2,"generated_at":"2026-08-15T14:20:00Z","rounds":[{"n":1,"ask":"new_question","target":null,"depth":"standard","papers_added":25},{"n":2,"ask":"resolve_link","target":"L3","depth":"deep","papers_added":18}],"coverage":{"depth":"deep","found":1180,"read":50,"used":41,"truncated":true,"no_quote_discarded":6,"limits":{"max_papers":50,"max_queries":6,"hit_limit":"max_papers"}},"things":[{"id":"t1","name":"IRAK4","kind":"protein","aliases":["interleukin-1 receptor-associated kinase 4","IRAK-4"],"mentions":31},{"id":"t2","name":"zimlovisertib","kind":"small_molecule","aliases":["PF-06650833"],"mentions":12},{"id":"t3","name":"MyD88 signalosome","kind":"process","aliases":["Myddosome"],"mentions":18},{"id":"t4","name":"synovial fibroblast","kind":"process","aliases":["fibroblast-like synoviocyte","FLS"],"mentions":22},{"id":"t5","name":"IL-6","kind":"protein","aliases":["interleukin-6"],"mentions":27},{"id":"t6","name":"rheumatoid arthritis","kind":"disease","aliases":["RA"],"mentions":44},{"id":"t7","name":"TLR/IL-1R signaling","kind":"process","aliases":["Toll-like receptor signaling"],"mentions":20},{"id":"t8","name":"macrophage TNF release","kind":"process","aliases":["monocyte TNF-alpha secretion"],"mentions":16}],"papers":[{"id":"p1","title":"Discovery of a selective IRAK4 inhibitor","year":2018,"journal":"J. Med. Chem.","doi":"10.0000/fixture.p1","first_author":"Lee","study_type":"test_tube","is_preprint":false,"round":1},{"id":"p2","title":"Target engagement of IRAK4 inhibition in human whole blood","year":2019,"journal":"Clin. Pharmacol. Ther.","doi":"10.0000/fixture.p2","first_author":"Okafor","study_type":"test_tube","is_preprint":false,"round":1},{"id":"p3","title":"The Myddosome in innate immune signaling","year":2016,"journal":"Nat. Rev. Immunol.","doi":"10.0000/fixture.p3","first_author":"Verma","study_type":"review","is_preprint":false,"round":1},{"id":"p4","title":"IRAK4 kinase activity controls monocyte TNF output","year":2020,"journal":"J. Immunol.","doi":"10.0000/fixture.p4","first_author":"Brandt","study_type":"test_tube","is_preprint":false,"round":1},{"id":"p5","title":"Fibroblast-like synoviocytes as a source of IL-6 in RA","year":2017,"journal":"Arthritis Rheumatol.","doi":"10.0000/fixture.p5","first_author":"Iwasaki","study_type":"test_tube","is_preprint":false,"round":1},{"id":"p6","title":"IL-6 pathway blockade in rheumatoid arthritis: a meta-analysis","year":2021,"journal":"Lancet Rheumatol.","doi":"10.0000/fixture.p6","first_author":"Duarte","study_type":"meta_analysis","is_preprint":false,"round":1},{"id":"p7","title":"IRAK4 inhibition spares TNF-driven fibroblast activation","year":2023,"journal":"Ann. Rheum. Dis.","doi":"10.0000/fixture.p7","first_author":"Nowak","study_type":"test_tube","is_preprint":false,"round":2},{"id":"p8","title":"A phase 2 trial of zimlovisertib in active rheumatoid arthritis","year":2022,"journal":"Arthritis Rheumatol.","doi":"10.0000/fixture.p8","first_author":"Chen","study_type":"clinical_trial","is_preprint":false,"round":2}],"findings":[{"id":"f1","from":"t2","how":"inhibits","to":"t1","says":"yes","quote":"compound 12 inhibited IRAK4 kinase activity with an IC50 of 0.2 nM","paper":"p1","where":"biochemical assay","is_own_result":true,"hedged":false,"confidence":0.95,"flags":[],"round":1},{"id":"f2","from":"t2","how":"inhibits","to":"t1","says":"yes","quote":"PF-06650833 produced dose-dependent target engagement in human whole blood","paper":"p2","where":"human whole blood","is_own_result":true,"hedged":false,"confidence":0.9,"flags":[],"round":1},{"id":"f3","from":"t7","how":"activates","to":"t1","says":"yes","quote":"ligation of TLR and IL-1R receptors recruits IRAK4 to the receptor complex","paper":"p3","where":null,"is_own_result":false,"hedged":false,"confidence":0.85,"flags":["background"],"round":1},{"id":"f4","from":"t1","how":"activates","to":"t3","says":"yes","quote":"IRAK4 nucleates assembly of the MyD88 signalosome","paper":"p3","where":null,"is_own_result":false,"hedged":false,"confidence":0.88,"flags":["background"],"round":1},{"id":"f5","from":"t1","how":"drives","to":"t8","says":"yes","quote":"loss of IRAK4 kinase activity reduced TNF secretion by 78% in stimulated monocytes","paper":"p4","where":"LPS-stimulated human monocytes","is_own_result":true,"hedged":false,"confidence":0.92,"flags":[],"round":1},{"id":"f6","from":"t4","how":"secretes","to":"t5","says":"yes","quote":"RA fibroblast-like synoviocytes were the dominant source of IL-6 in explant culture","paper":"p5","where":"RA synovial explant","is_own_result":true,"hedged":false,"confidence":0.9,"flags":[],"round":1},{"id":"f7","from":"t5","how":"drives","to":"t6","says":"yes","quote":"IL-6 receptor blockade reduced ACR20 non-response across 14 randomized trials","paper":"p6","where":"pooled RCTs","is_own_result":true,"hedged":false,"confidence":0.93,"flags":[],"round":1},{"id":"f8","from":"t2","how":"reduces","to":"t5","says":"yes","quote":"IRAK4 inhibition suppressed LPS-induced IL-6 release in a concentration-dependent manner","paper":"p2","where":"LPS-stimulated whole blood","is_own_result":true,"hedged":false,"confidence":0.88,"flags":[],"round":1},{"id":"f9","from":"t2","how":"reduces","to":"t5","says":"no","quote":"IL-6 output from TNF-stimulated synovial fibroblasts was unchanged by IRAK4 inhibition","paper":"p7","where":"TNF-stimulated RA synovial fibroblasts","is_own_result":true,"hedged":false,"confidence":0.8,"flags":[],"round":2},{"id":"f10","from":"t2","how":"reduces","to":"t5","says":"yes","quote":"serum IL-6 trended lower in the treatment arm, which may reflect target engagement","paper":"p8","where":"phase 2, serum","is_own_result":true,"hedged":true,"confidence":0.6,"flags":["hedged"],"round":2},{"id":"f11","from":"t2","how":"improves","to":"t6","says":"yes","quote":"ACR50 at week 12 was 32% versus 18% for placebo","paper":"p8","where":"phase 2 RCT, n=269","is_own_result":true,"hedged":false,"confidence":0.87,"flags":[],"round":2}],"links":[{"id":"L1","from":"t2","how":"inhibits","to":"t1","yes":["f1","f2"],"no":[],"no_effect":[],"state":"agreed","why":null,"basis":"primary","confidence":{"overall":0.88,"label":"high","evidence_quality":0.5,"agreement":1.0,"independence":1.0},"changed_in_round":null},{"id":"L2","from":"t1","how":"activates","to":"t3","yes":["f4"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"background_only","confidence":{"overall":0.38,"label":"low","evidence_quality":0.2,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L3","from":"t2","how":"reduces","to":"t5","yes":["f8","f10"],"no":["f9"],"no_effect":[],"state":"disagreed","why":"different conditions — myeloid stimulation (LPS, whole blood) versus fibroblast stimulation (TNF)","basis":"mixed","confidence":{"overall":0.42,"label":"medium","evidence_quality":0.55,"agreement":0.5,"independence":0.67},"changed_in_round":2},{"id":"L4","from":"t1","how":"drives","to":"t8","yes":["f5"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.52,"label":"medium","evidence_quality":0.5,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L5","from":"t4","how":"secretes","to":"t5","yes":["f6"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.55,"label":"medium","evidence_quality":0.5,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L6","from":"t5","how":"drives","to":"t6","yes":["f7"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.78,"label":"high","evidence_quality":1.0,"agreement":1.0,"independence":0.0},"changed_in_round":null},{"id":"L7","from":"t2","how":"improves","to":"t6","yes":["f11"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"primary","confidence":{"overall":0.6,"label":"medium","evidence_quality":0.8,"agreement":1.0,"independence":0.0},"changed_in_round":2},{"id":"L8","from":"t7","how":"activates","to":"t1","yes":["f3"],"no":[],"no_effect":[],"state":"single_source","why":null,"basis":"background_only","confidence":{"overall":0.35,"label":"low","evidence_quality":0.2,"agreement":1.0,"independence":0.0},"changed_in_round":null}],"gaps":[{"id":"g1","missing":["t2","t4"],"implied_by":["L1","L3","L5"],"note":"nobody states that zimlovisertib acts directly on synovial fibroblasts; the myeloid path is covered, the fibroblast path is inferred","confidence":0.34,"searched_in_round":null},{"id":"g2","missing":["t1","t4"],"implied_by":["L2","L5"],"note":"IRAK4 dependence of the fibroblast compartment is never stated; f9 implies it may be absent but tests the inhibitor, not the target","confidence":0.41,"searched_in_round":null}],"_meta":{"key":"g_ra4k","blurb":"Hypothesis-generator fixture — the same IRAK4 question modelled at protein granularity. This is the graph the earlier hand-built viewer rendered.","path":"hypothesis-generator/fixtures/example-graph-1.json"}}};
const NS = "http://www.w3.org/2000/svg";
const el = (n,a) => { const e=document.createElementNS(NS,n); for(const k in a) if(a[k]!=null) e.setAttribute(k,a[k]); return e; };
const esc = s => String(s==null?"":s).replace(/[&<>"]/g,c=>({"&":"&amp;","<":"&lt;",">":"&gt;",'"':"&quot;"}[c]));
const n2 = v => (v==null||Number.isNaN(v)) ? "—" : (+v).toFixed(2);
const pct = v => Math.round((v||0)*100)+"%";

const STROKE = {agreed:"var(--state-agreed)", disagreed:"var(--state-disagreed)",
                single_source:"var(--state-single)", derived:"var(--text-muted)"};
const DASH   = {agreed:null, disagreed:"7 3", single_source:"1.5 3", derived:"4 3"};
const WIDTH  = {agreed:2.5, disagreed:3, single_source:2, derived:2};
const MARKER = {agreed:"a-agreed", disagreed:"a-disagreed", single_source:"a-single", derived:"a-derived"};

const W=980, H=640;
let G=null, TH={}, EDGES=[], TOUCH={}, VIEW_GRAPH=true;

/* ---------- fixture detection --------------------------------------------
   graph-intake failure mode 8: a graph carrying _fixture:true has papers,
   DOIs and quotes that were never retrieved from any corpus, and must never
   be cited. Failure mode 17: a real graph is told from a synthetic one only
   by the ABSENCE of that flag, so also look at whether the DOIs resolve to
   anything real. g_demo1 is unflagged and its DOIs are stubs.            */
function fixtureCheck(g){
  const papers = g.papers||[];
  const stub = papers.filter(p=>{
    const d = String(p.doi||"");
    return !d || /^10\.0000\//.test(d) || /\/x\d+$/.test(d) || /fixture/i.test(d);
  });
  if (g._fixture === true || String(g._fixture)==="true")
    return {level:"flagged", stub:stub.length, total:papers.length};
  if (papers.length && stub.length === papers.length)
    return {level:"unflagged", stub:stub.length, total:papers.length};
  return null;
}

/* ---------- layout: deterministic force sim, then label side -------------- */
function mulberry32(a){return function(){a|=0;a=a+0x6D2B79F5|0;let t=Math.imul(a^a>>>15,1|a);t=t+Math.imul(t^t>>>7,61|t)^t;return((t^t>>>14)>>>0)/4294967296}}
const R = t => 13 + 3.0*Math.sqrt(Math.max(1, t.mentions||1));

function layout(nodes, edges){
  const rnd = mulberry32(0x1a4f), n = nodes.length||1;
  const LINK = Math.max(185, Math.min(320, 880/Math.sqrt(n)));
  const REP  = LINK*LINK*1.5;
  nodes.forEach((v,i)=>{
    const a = 2*Math.PI*i/n;
    v.x = W/2 + Math.cos(a)*(W*0.33) + (rnd()-0.5)*40;
    v.y = H/2 + Math.sin(a)*(H*0.32) + (rnd()-0.5)*40;
    v.vx = v.vy = 0;
  });
  const ix = new Map(nodes.map((v,i)=>[v.id,i]));
  const E = edges.filter(e=>ix.has(e.a)&&ix.has(e.b)).map(e=>[ix.get(e.a),ix.get(e.b)]);
  for(let it=0; it<700; it++){
    const k = 1 - it/700;
    for(let i=0;i<nodes.length;i++) for(let j=i+1;j<nodes.length;j++){
      const a=nodes[i], b=nodes[j];
      let dx=b.x-a.x, dy=b.y-a.y, d2=Math.max(dx*dx+dy*dy,400), d=Math.sqrt(d2);
      const f=REP/d2; dx/=d; dy/=d;
      a.vx-=dx*f; a.vy-=dy*f; b.vx+=dx*f; b.vy+=dy*f;
    }
    for(const [i,j] of E){
      const a=nodes[i], b=nodes[j];
      let dx=b.x-a.x, dy=b.y-a.y, d=Math.hypot(dx,dy)||1;
      const f=(d-LINK)*0.035; dx/=d; dy/=d;
      a.vx+=dx*f; a.vy+=dy*f; b.vx-=dx*f; b.vy-=dy*f;
    }
    /* labels stack under or over the circle, so separate harder in y */
    for(let i=0;i<nodes.length;i++) for(let j=i+1;j<nodes.length;j++){
      const a=nodes[i], b=nodes[j], dy=b.y-a.y, dx=b.x-a.x;
      if (Math.abs(dy)<64 && Math.abs(dx)<215){
        const p=(64-Math.abs(dy))*0.30*(dy<0?-1:1);
        a.vy-=p; b.vy+=p;
      }
    }
    for(const v of nodes){
      v.vx += (W/2-v.x)*0.004; v.vy += (H/2-v.y)*0.005;
      v.x += v.vx*k*0.5; v.y += v.vy*k*0.5; v.vx*=0.84; v.vy*=0.84;
      v.x = Math.max(115,Math.min(W-115,v.x));
      v.y = Math.max(78,Math.min(H-84,v.y));
    }
  }
  /* put the label where the edges are not: sum unit vectors to neighbours,
     then place the label block on the opposite side */
  const nb = {};
  edges.forEach(e=>{ (nb[e.a] ||= []).push(e.b); (nb[e.b] ||= []).push(e.a); });
  const byId = Object.fromEntries(nodes.map(v=>[v.id,v]));
  for(const v of nodes){
    let sy = 0;
    for(const o of (nb[v.id]||[])){ const u=byId[o]; if(!u) continue;
      const d=Math.hypot(u.x-v.x,u.y-v.y)||1; sy += (u.y-v.y)/d; }
    v.lp = sy > 0.15 ? "above" : (sy < -0.15 ? "below" : (v.y > H*0.62 ? "above" : "below"));
    /* a label block is up to two name lines plus a kind line; if that would
       run off the top or bottom edge, the edge wins over the traffic rule */
    const need = R(v) + 58;
    if (v.y - need < 6)     v.lp = "below";
    if (v.y + need > H - 6) v.lp = "above";
  }
}

/* ---------- build ---------------------------------------------------------- */
/* A round input carries findings but no links. assemble.py groups findings on
   (from,how,to) to make links, so do the same and label the result derived. */
function deriveLinks(g){
  if (g.links && g.links.length) return g.links;
  const by = new Map();
  for(const f of (g.findings||[])){
    const k = f.from+"|"+f.how+"|"+f.to;
    if(!by.has(k)) by.set(k,{id:"(derived) "+k, from:f.from, how:f.how, to:f.to,
      state:"derived", basis:null, why:null, yes:[], no:[], no_effect:[],
      confidence:null, derived:true});
    const l=by.get(k);
    (f.says==="no"?l.no : f.says==="no_effect"?l.no_effect : l.yes).push(f.id);
  }
  return [...by.values()];
}

function build(key){
  G = GRAPHS[key];
  const links = deriveLinks(G), gaps = G.gaps||[];

  /* every id a link or gap points at becomes a node, so a dangling reference
     is visible rather than silently dropped */
  const map = new Map((G.things||[]).map(t=>[t.id,{...t, resolved:true}]));
  const touch = id => { if(id && !map.has(id)) map.set(id,{id, name:id, kind:null, mentions:1, resolved:false}); };
  links.forEach(l=>{touch(l.from);touch(l.to)});
  gaps.forEach(x=>(x.missing||[]).forEach(touch));
  const nodes = [...map.values()];
  TH = Object.fromEntries(nodes.map(v=>[v.id,v]));

  EDGES = links.map(l=>({...l, kind:"link", a:l.from, b:l.to}))
    .concat(gaps.map(x=>({id:x.id, kind:"gap", a:(x.missing||[])[0], b:(x.missing||[])[1],
      missing:x.missing, note:x.note, confidence:x.confidence,
      implied_by:x.implied_by, searched_in_round:x.searched_in_round})));

  /* parallel edges between one pair get bowed apart, both directions counted
     as the same pair so an A->B and B->A do not draw on top of each other */
  const groups = {};
  EDGES.forEach(e=>{ const k=[e.a,e.b].sort().join("~"); (groups[k] ||= []).push(e); });
  for(const k in groups){
    const set = groups[k], m = set.length;
    set.forEach((e,i)=>{ e.bow = m===1 ? 0 : (i-(m-1)/2) * 150; });
  }

  layout(nodes, EDGES);
  head(links, gaps);
  coverage(links);
  drawAll(nodes);
  intro(links, gaps);
  tables(links, gaps);
  location.hash = "";
}

function head(links, gaps){
  document.getElementById("q").textContent = G.question || "(no question recorded)";
  const rounds = (G.rounds||[]).map(r =>
    `round ${r.n}: <code>${esc(r.ask)}</code>${r.target?" → "+esc(r.target):""}${r.outcome?" · "+esc(r.outcome):""}`).join(" &nbsp;|&nbsp; ");
  document.getElementById("qmeta").innerHTML =
    `<code>${esc(G.graph_id||"—")}</code> &nbsp; round ${esc(G.round)} &nbsp; status <b>${esc(G.status||"—")}</b>`
    + ` &nbsp; ${(G.things||[]).length} things · ${links.length} links · ${(G.findings||[]).length} findings · ${gaps.length} gaps`
    + (rounds ? `<br>${rounds}` : "");
  document.getElementById("blurb").innerHTML =
    esc(G._meta.blurb) + ` &nbsp; <code>managed/${esc(G._meta.path)}</code>`;

  const fx = fixtureCheck(G);
  document.getElementById("banner").innerHTML = !fx ? "" :
    fx.level === "flagged"
      ? `<p class="banner"><b>Synthetic fixture — carries <code>_fixture: true</code>.</b>
         Its papers, DOIs and quotes were never retrieved from any corpus. Do not cite a line of it.
         <code>graph_read.py</code> refuses a graph like this unless <code>--allow-fixture</code> is passed,
         and that guard should never be lifted for a real run.</p>`
      : `<p class="banner"><b>Synthetic, but carrying no <code>_fixture</code> flag.</b>
         All ${fx.total} papers have placeholder DOIs, so nothing here resolves to a real record —
         yet nothing in the file says so. This is the gap the fixture guard does not close:
         a real graph is told from a synthetic one only by the <i>absence</i> of a flag we invented
         and upstream has never heard of.</p>`;
}

function coverage(links){
  const c = G.coverage||{}, L = c.limits||{};
  const out = [];
  const cell = (k,v,note,warn) =>
    `<div class="${warn?"warn":""}">${esc(k)}<b>${v}</b>${note?`<span class="note">${note}</span>`:""}</div>`;

  if (c.found!=null) out.push(cell("found", c.found, "returned by search"));
  if (c.read!=null)  out.push(cell("read", c.read, "actually fetched"));
  if (c.used!=null)  out.push(cell("yielded a finding", c.used, "search is cheap; extraction is the bottleneck"));
  if (c.depth) out.push(cell("depth", esc(c.depth), `the budget — ${L.max_papers??"?"} papers / ${L.max_queries??"?"} queries`));
  if (c.truncated!=null || c.stop_reason)
    out.push(cell("coverage", c.stop_reason==="complete" ? "complete" : (c.truncated ? "truncated" : "—"),
      c.stop_reason==="complete" ? "literature exhausted — an absence here means something"
        : `stop_reason: ${esc(c.stop_reason||"—")} · absence proves nothing`,
      c.stop_reason!=="complete"));
  if (c.no_quote_discarded!=null)
    out.push(cell("discarded, no quote", c.no_quote_discarded, "claims dropped for failing string-match", c.no_quote_discarded>0));
  if (c.depth==="quick")
    out.push(cell("quick", "page 1 lies", "at this depth absence means unknown, whatever stop_reason says", true));
  document.getElementById("cov").innerHTML = out.join("");
}

/* ---------- draw ----------------------------------------------------------- */
function curve(a,b,bow){
  const cx=(a.x+b.x)/2, cy=(a.y+b.y)/2;
  const dx=b.x-a.x, dy=b.y-a.y, len=Math.hypot(dx,dy)||1;
  const qx=cx-(dy/len)*(bow||0), qy=cy+(dx/len)*(bow||0);
  const trim=(p,q,r)=>{const ux=q.x-p.x,uy=q.y-p.y,m=Math.hypot(ux,uy)||1;
    return {x:p.x+(ux/m)*r, y:p.y+(uy/m)*r}};
  const s=trim(a,{x:qx,y:qy},R(a)+3), e=trim(b,{x:qx,y:qy},R(b)+9);
  return {d:`M${s.x.toFixed(1)},${s.y.toFixed(1)} Q${qx.toFixed(1)},${qy.toFixed(1)} ${e.x.toFixed(1)},${e.y.toFixed(1)}`,
          mx:(s.x+2*qx+e.x)/4, my:(s.y+2*qy+e.y)/4};
}

function drawAll(nodes){
  const gE=document.getElementById("edges"), gN=document.getElementById("nodes");
  gE.textContent=""; gN.textContent=""; TOUCH={};
  const mark=(t,id)=>((TOUCH[t] ||= new Set()).add(id));

  for(const e of EDGES){
    const a=TH[e.a], b=TH[e.b]; if(!a||!b) continue;
    const isGap = e.kind==="gap";
    const {d,mx,my} = curve(a,b,e.bow);
    const g = el("g",{"data-edge":e.id});
    g.appendChild(el("path",{d,
      stroke: isGap ? "var(--gap)" : STROKE[e.state],
      "stroke-width": isGap ? 2 : WIDTH[e.state],
      "stroke-dasharray": isGap ? "5 5" : DASH[e.state],
      "stroke-linecap": e.state==="single_source" ? "round" : "butt",
      fill:"none",
      "marker-end": isGap ? null : `url(#${MARKER[e.state]})`}));
    g.appendChild(el("path",{d, class:"edge-hit"}));

    if(isGap){
      /* a gap is a hypothesis candidate, not background — badge it */
      const bg = el("g",{class:"gap-badge"});
      bg.appendChild(el("circle",{cx:mx,cy:my,r:9,fill:"var(--surface-1)",
        stroke:"var(--gap)","stroke-width":1.5,"stroke-dasharray":"3 2.6"}));
      const q = el("text",{x:mx,y:my+4,"text-anchor":"middle",fill:"var(--text-secondary)","font-size":11,"font-weight":700});
      q.textContent="?"; bg.appendChild(q); g.appendChild(bg);
    } else {
      const t = el("text",{x:mx, y:my-7, "text-anchor":"middle", class:"edge-lab",
        "font-size":10.5, fill:"var(--text-muted)"});
      t.textContent = e.how; g.appendChild(t);
    }
    g.addEventListener("click", ()=>select(e.id));
    gE.appendChild(g);
    mark(a.id,e.id); mark(b.id,e.id);
  }

  /* Nodes are neutral: a node-link diagram is an all-pairs case, so kind-hues
     could not clear the CVD floors. Kind rides in the label instead, and hue
     is spent entirely on link state. */
  for(const v of nodes){
    const g = el("g",{"data-node":v.id, class:"node-hit"});
    g.appendChild(el("circle",{cx:v.x, cy:v.y, r:R(v), fill:"var(--node-fill)",
      stroke: v.resolved===false ? "var(--gap)" : "var(--text-muted)",
      "stroke-width":1.5, "stroke-dasharray": v.resolved===false ? "3 3" : null}));

    const words = String(v.name).split(" ");
    let lines = [v.name];
    if (v.name.length>17 && words.length>1){
      const mid = Math.ceil(words.length/2);
      lines = [words.slice(0,mid).join(" "), words.slice(mid).join(" ")];
    }
    const above = v.lp==="above";
    const top = above ? v.y - R(v) - 12 - lines.length*14 : v.y + R(v) + 17;
    const lab = el("text",{x:v.x, y:top, "text-anchor":"middle", fill:"var(--text-primary)",
      "font-size":12.5, "font-weight":600});
    lines.forEach((ln,i)=>{ const ts=el("tspan",{x:v.x, dy:i?14:0}); ts.textContent=ln; lab.appendChild(ts); });
    g.appendChild(lab);

    const k = el("text",{x:v.x, y:top+lines.length*14, "text-anchor":"middle",
      fill:"var(--text-muted)", "font-size":10.5});
    k.textContent = v.resolved===false ? "not in this file"
      : String(v.kind||"?").replace(/_/g," ") + (v.mentions!=null ? " · "+v.mentions : "");
    g.appendChild(k);
    g.addEventListener("click", ()=>focusNode(v.id));
    gN.appendChild(g);
  }
}

/* ---------- panel ---------------------------------------------------------- */
const panel = () => document.getElementById("panel");
const dimTo = ids => document.querySelectorAll("[data-edge]").forEach(e =>
  e.classList.toggle("dim", ids!==null && !ids.has(e.dataset.edge)));

function intro(links, gaps){
  const dis = links.filter(l=>l.state==="disagreed");
  panel().innerHTML = `<h2>Detail</h2>
    <p class="hint">Click a line to read the findings behind it, or a circle to isolate what touches it.
    Dashed gray lines are gaps &mdash; the hypothesis candidates.</p>
    ${dis.length?`<p class="hint" style="margin-top:10px">Start with
      <b>${dis.map(d=>esc(d.id)).join(", ")}</b> &mdash; the disagreed link${dis.length>1?"s":""}.
      That is where the question actually got answered.</p>`:""}
    <table style="margin-top:12px"><thead><tr><th>id</th><th>relationship</th><th>state</th><th class="num">conf</th></tr></thead>
    <tbody>${links.map(l=>`<tr><td><code>${esc(l.id)}</code></td>
      <td>${esc(nm(l.from))} <span style="color:var(--text-muted)">${esc(l.how)}</span> ${esc(nm(l.to))}</td>
      <td>${esc(String(l.state).replace(/_/g," "))}</td>
      <td class="num">${n2(l.confidence&&l.confidence.overall)}</td></tr>`).join("")}</tbody></table>`;
}
const nm = id => (TH[id] ? TH[id].name : id);

function select(id){
  dimTo(new Set([id]));
  const e = EDGES.find(x=>String(x.id)===String(id));
  if(!e) return;
  if (e.kind==="gap") return renderGap(e);
  renderLink(e);
}

function findingsOf(ids){
  const all = G.findings||[];
  return (ids||[]).map(i=>all.find(f=>f.id===i)).filter(Boolean);
}
const paperOf = pid => (G.papers||[]).find(p=>p.id===pid);

function renderFinding(f, says){
  const p = paperOf(f.paper);
  return `<div class="f">
    <q>${esc(f.quote)}</q>
    <div class="src">${p ? `${esc(p.first_author||"")} ${esc(p.year||"")} · <i>${esc(p.journal||"")}</i> · ${esc(String(p.study_type||"").replace(/_/g," "))}`
                        : `paper ${esc(f.paper)} — not in this file`}
      ${f.where ? " · "+esc(f.where) : ` · <i>where: null — the sentence stated no conditions</i>`}
      ${p&&p.title ? `<br>${esc(p.title)}` : ""}</div>
    <div class="tags">
      <span class="tag ${says==="no"?"no":says==="yes"?"yes":""}">says: ${esc(says)}</span>
      ${f.confidence!=null?`<span class="tag">confidence ${n2(f.confidence)}</span>`:""}
      ${f.hedged?`<span class="tag warn">hedged</span>`:""}
      ${f.is_own_result===false?`<span class="tag warn">citing others, not its own result</span>`:""}
      ${p&&p.is_preprint?`<span class="tag">preprint</span>`:""}
      ${p&&p.retracted?`<span class="tag no">RETRACTED</span>`:""}
      ${f.section?`<span class="tag">${esc(f.section)}</span>`:""}
    </div></div>`;
}

function renderLink(l){
  const c = l.confidence||{};
  const yes=findingsOf(l.yes), no=findingsOf(l.no), ne=findingsOf(l.no_effect);
  const total = yes.length+no.length+ne.length;
  panel().innerHTML = `
    <h2>Link · ${esc(l.id)}</h2>
    <p class="ttl">${esc(nm(l.from))} <span style="color:var(--text-muted);font-weight:400">${esc(l.how)}</span> ${esc(nm(l.to))}</p>
    <p class="meta"><span class="chip" style="color:${STROKE[l.state]}">${esc(String(l.state).replace(/_/g," "))}</span>
      ${l.basis?`&nbsp;basis: ${esc(String(l.basis).replace(/_/g," "))}`:""}
      ${l.changed_in_round?`&nbsp;· <b>changed in round ${esc(l.changed_in_round)}</b>`:""}</p>
    ${l.derived?`<p class="why">Derived here by grouping findings on <code>(from, how, to)</code>.
      This file is a round input, so <code>assemble.py</code> has not scored it yet — there is no confidence to show.</p>`:""}
    ${l.why?`<p class="why"><b>Boundary condition detected.</b> ${esc(l.why)}<br>
      <span style="color:var(--text-muted)">Disjoint <code>where</code> sets mean the two camps measured different
      things — usually more informative than “they disagree”.</span></p>`:""}
    ${c.overall!=null?`<div class="scores">
      <span>overall${c.label?` (${esc(c.label)})`:""}</span><em>${n2(c.overall)}</em>
      <div class="track"><i style="width:${pct(c.overall)}"></i></div>
      <span>agreement — yes vs no, own results only</span><em>${n2(c.agreement)}</em>
      <span>evidence quality — study type, ×0.8 preprint</span><em>${n2(c.evidence_quality)}</em>
      <span>independence — distinct first authors${c.independence===0?" (0.00 = one lab)":""}</span><em>${n2(c.independence)}</em>
    </div>`:""}
    <h2>${total} finding${total===1?"":"s"} — yes ${yes.length} · no ${no.length} · no_effect ${ne.length}</h2>
    ${no.map(f=>renderFinding(f,"no")).join("")}
    ${ne.map(f=>renderFinding(f,"no_effect")).join("")}
    ${yes.map(f=>renderFinding(f,"yes")).join("")}`;
}

function renderGap(g){
  panel().innerHTML = `
    <h2>Gap · ${esc(g.id)}</h2>
    <p class="ttl">${esc(nm(g.a))} &mdash; ${esc(nm(g.b))}</p>
    <p class="meta"><span class="chip" style="color:var(--gap)">never stated</span>
      ${g.implied_by?`&nbsp;implied by ${g.implied_by.map(esc).join(", ")}`:""}</p>
    <p class="why">${esc(g.note||"")}</p>
    <p class="why">An <b>open triangle</b>: both ends connect to a shared neighbour and nobody has stated a
      direct relationship between them. Computed from graph shape alone, so it is a <b>question</b>, not a candidate.</p>
    <div class="scores">
      <span>confidence (capped low on purpose — a proposal, not a finding)</span><em>${n2(g.confidence)}</em>
      <div class="track"><i style="width:${pct(g.confidence)}"></i></div>
    </div>
    <p class="meta"><b>searched_in_round: ${g.searched_in_round ?? "null"}</b> —
      ${g.searched_in_round ? "somebody has looked." : "nobody has looked yet."} Issue
      <code>{"ask":"test_gap","target":"${esc(g.id)}","depth":"deep"}</code> to promote it to a link
      or harden it into a real absence. A pair that was looked for and not found is a far stronger claim
      than one nobody searched.</p>`;
}

function focusNode(tid){
  const ids = TOUCH[tid] || new Set();
  dimTo(ids);
  const t = TH[tid];
  const ls = EDGES.filter(e=>e.kind==="link" && ids.has(e.id));
  const gs = EDGES.filter(e=>e.kind==="gap"  && ids.has(e.id));
  panel().innerHTML = `<h2>Thing · ${esc(t.id)}</h2>
    <p class="ttl">${esc(t.name)}</p>
    <p class="meta">${esc(String(t.kind||"unresolved").replace(/_/g," "))}${t.mentions!=null?` · mentioned in ${t.mentions} paper${t.mentions===1?"":"s"}`:""}</p>
    ${t.resolved===false?`<p class="why">This id is referenced but is not declared in this file. In a round
      input that is expected — the node lives in the prior graph. In an assembled graph it is a dangling id,
      and <code>graph_read.py</code> reports it under <code>integrity</code>.</p>`:""}
    ${t.aliases&&t.aliases.length?`<p class="why"><b>aliases:</b> ${t.aliases.map(esc).join(" · ")}<br>
      <span style="color:var(--text-muted)">The reagents live here, as aliases and in <code>where</code> —
      not as their own nodes. A node is a concept, not a reagent.</span></p>`:""}
    <p class="meta">${ls.length} link${ls.length===1?"":"s"}${gs.length?`, ${gs.length} gap${gs.length===1?"":"s"}`:""}</p>
    ${ls.map(l=>`<div class="f"><q>${esc(nm(l.from))} ${esc(l.how)} ${esc(nm(l.to))}</q>
      <div class="src">${esc(l.id)} · ${esc(String(l.state).replace(/_/g," "))}${l.confidence?` · confidence ${n2(l.confidence.overall)}`:""}</div></div>`).join("")}
    ${gs.map(g=>`<div class="f"><q>${esc(nm(g.a))} — ${esc(nm(g.b))}</q>
      <div class="src">${esc(g.id)} · gap, never stated · ${n2(g.confidence)}</div></div>`).join("")}
    <p class="hint" style="margin-top:14px">Click a line for the findings and quotes. Ask for more with
      <code>{"ask":"expand_node","target":"${esc(t.id)}"}</code>.</p>`;
}

/* ---------- tables --------------------------------------------------------- */
function tables(links, gaps){
  document.getElementById("cap").innerHTML =
    `Links and gaps &mdash; the same data as the graph. Confidence is arithmetic computed by
     <code>assemble.py</code> from findings + papers, valid for this <code>(graph_id, round)</code> only;
     recompute it with your own weights if you disagree.`;
  document.getElementById("tbody").innerHTML =
    links.map(l=>`<tr><td><code>${esc(l.id)}</code></td>
      <td>${esc(nm(l.from))} ${esc(l.how)} ${esc(nm(l.to))}</td>
      <td>${esc(String(l.state).replace(/_/g," "))}</td>
      <td>${esc(String(l.basis||"—").replace(/_/g," "))}</td>
      <td class="num">${(l.yes||[]).length}</td><td class="num">${(l.no||[]).length}</td>
      <td class="num">${n2(l.confidence&&l.confidence.overall)}</td>
      <td>${esc(l.why || (l.changed_in_round?"changed in round "+l.changed_in_round:""))}</td></tr>`).join("")
    + gaps.map(g=>`<tr><td><code>${esc(g.id)}</code></td>
      <td>${(g.missing||[]).map(nm).map(esc).join(" — ")}</td>
      <td>gap</td><td>—</td><td class="num">0</td><td class="num">0</td>
      <td class="num">${n2(g.confidence)}</td><td>${esc(g.note||"")}</td></tr>`).join("");
  document.getElementById("fbody").innerHTML =
    (G.findings||[]).map(f=>`<tr><td><code>${esc(f.id)}</code></td><td>${esc(f.paper)}</td>
      <td>${esc(f.from)} ${esc(f.how)} ${esc(f.to)}</td>
      <td>${esc(f.says)}${f.hedged?" (hedged)":""}</td>
      <td>${f.where?esc(f.where):"<i>null</i>"}</td>
      <td>&ldquo;${esc(f.quote)}&rdquo;</td></tr>`).join("");
}

/* ---------- chrome --------------------------------------------------------- */
const sel = document.getElementById("ds");
sel.innerHTML = Object.keys(GRAPHS).map(k=>`<option value="${k}">${k}</option>`).join("");
sel.addEventListener("change", ()=>build(sel.value));

document.getElementById("svg").addEventListener("click", e=>{
  if(e.target.tagName==="svg"){ dimTo(null); intro(deriveLinks(G), G.gaps||[]); }
});

const bG=document.getElementById("v-graph"), bT=document.getElementById("v-table");
const show = g => { VIEW_GRAPH=g;
  document.getElementById("graph-view").hidden=!g;
  document.getElementById("table-view").hidden=g;
  bG.setAttribute("aria-pressed",g); bT.setAttribute("aria-pressed",!g); };
bG.onclick=()=>show(true); bT.onclick=()=>show(false);

document.getElementById("theme").onclick = ()=>{
  const dark = matchMedia("(prefers-color-scheme: dark)").matches;
  const cur = document.documentElement.dataset.theme || (dark?"dark":"light");
  document.documentElement.dataset.theme = cur==="dark" ? "light" : "dark";
};

/* deep link: #L3 / #g1 / #t4 opens that row */
const openHash = ()=>{
  const id = location.hash.slice(1); if(!id) return;
  if(TH[id]) focusNode(id);
  else if(EDGES.some(e=>String(e.id)===id)) select(id);
};
addEventListener("hashchange", openHash);

document.getElementById("foot").innerHTML =
  `Nodes are neutral and carry their kind in the label; hue is spent entirely on link state, because a
   node-link diagram is an all-pairs case and six kind-hues could not clear the colour-vision floors.
   Circle size is <code>mentions</code>. Every graph here is read from committed JSON on
   <code>labrador/main</code> — no network, no build step, no hand-transcribed data.`;

build(Object.keys(GRAPHS)[0]);
openHash();
</script>
</body>
</html>