{
  "version": "20260604_core_validation_v45",
  "chapters": [
    {
      "title": "Introduction",
      "summary": "OligoVigil is a no-login resource for ASO/siRNA safety evidence, provenance, and benchmark reuse.",
      "items": [
        "Release evidence is separated from machine-derived candidates.",
        "Accepted release rows require curator verification and source-level provenance.",
        "Grade A/B rows are eligible for reference benchmark splits; Grade C rows remain contextual evidence."
      ]
    },
    {
      "title": "Getting started",
      "summary": "Start from a safety question, a sequence/design question, or a benchmark reuse question.",
      "items": [
        "Use the Overview search box for molecule, target, endpoint, PMID, DOI, chemistry, or off-target mechanism.",
        "Use Examples for one-click GalNAc, seed off-target, ASO/gapmer hepatotoxicity, and benchmark workflows.",
        "Use Record pages when you need a citable source/audit packet."
      ]
    },
    {
      "title": "Input data",
      "summary": "The portal accepts text terms and sequence-like strings for evidence lookup, not anonymous writes.",
      "items": [
        "Sequence workbench accepts A/C/G/T/U/N characters and reports seed windows.",
        "Safety Triage accepts sequence, target, chemistry, delivery, endpoint, species, and cell-type terms.",
        "Evidence filters accept domain, grade, modality, endpoint/category, and free-text query.",
        "Contribution packets use curator_review_template_v1.csv and require exact source location."
      ]
    },
    {
      "title": "Safety Triage Report",
      "summary": "The report converts a design question into a provenance-first evidence packet.",
      "items": [
        "It is not a de novo safety predictor and does not label an oligo as clinically safe.",
        "Each concern is marked as release-supported, candidate-gap-supported, mixed, or not assessable from current release.",
        "Matched release records are citable; candidate gaps are only used to prioritize additional curation."
      ]
    },
    {
      "title": "Evidence grades",
      "summary": "Grades are defensive evidence strata for database reuse, not clinical recommendations.",
      "items": [
        "Grade A: direct experimental or regulatory safety/off-target evidence with strong provenance.",
        "Grade B: relevant observed evidence with lower granularity or indirect but defensible linkage.",
        "Grade C: contextual evidence retained for discovery, excluded from benchmark reference splits."
      ]
    },
    {
      "title": "Exploring results",
      "summary": "Use source packets and record pages to move from aggregate counts to exact evidence.",
      "items": [
        "Open a record to inspect source, audit trail, source location, citation text, and BibTeX.",
        "Open source detail to view linked queue tasks, candidate signals, and verified evidence.",
        "Use Coverage and Release pages to inspect gaps before drawing claims."
      ]
    },
    {
      "title": "Benchmark reuse",
      "summary": "Benchmark splits are a supplement to the database, not the main claim.",
      "items": [
        "Download benchmark_reference_splits.csv and benchmark_task_cards.csv together.",
        "Group leakage is controlled by source identifier plus molecule/cohort name.",
        "Report AUROC, AUPRC, macro-F1, PCC/Spearman, or MSE according to task card target."
      ]
    },
    {
      "title": "Downloads and API",
      "summary": "All release tables and manifests are available without login.",
      "items": [
        "Use /api/download/evidence_release.csv for the unified verified release.",
        "Use /api/download/all_tables.zip for a full reproducible snapshot.",
        "Use /api/openapi.json for endpoint discovery and lightweight client generation."
      ]
    },
    {
      "title": "Audit path",
      "summary": "Use the Trust page to reproduce the release boundary before citing or reusing the resource.",
      "items": [
        "Open /#trust or /api/curation_protocol to inspect release/candidate separation, audit coverage, and redistribution policy.",
        "Join evidence_release.csv to curation_audit.csv by entity_table and evidence_id/entity_id.",
        "Use source_license_manifest_v1.csv before making source-level redistribution claims."
      ]
    },
    {
      "title": "Contribution and correction",
      "summary": "Corrections and new evidence must preserve source provenance and the curation decision trail. Release rows are human curator-verified (AI-assisted: a primary human curator adjudicated v2 LLM proposals over the source passages, re-curating the v1 machine pre-curated candidates — not blind; a blinded second curator (HY) independently re-scored a 100-row mixed inter-rater sample, giving Cohen κ_binary = 0.42 (moderate, Landis-Koch) under the drop-abstain convention (n=92 non-abstain rows) and 0.34 (fair) under the safety-conservative collapse-abstain convention (n=100), raw agreement 66% (66/100); a third-adjudicator consensus pass is in progress); machine-only candidates are labelled machine_precurated_v1 and are not release evidence.",
      "items": [
        "Use /#submit or curator_review_template_v1.csv for proposed new records.",
        "Required fields include source PMID/DOI/URL, exact source location, proposed evidence label, evidence grade, and curator note.",
        "Candidate rows remain non-citable until accepted by curator audit and promoted through the release gate."
      ]
    },
    {
      "title": "FAQ and troubleshooting",
      "summary": "Most confusing cases are caused by release/candidate separation.",
      "items": [
        "A candidate hit is not release evidence until accepted by curator audit.",
        "Use the archived data DOI (10.5281/zenodo.20633779); cite the public portal only after the Cloudflare Pages HTTPS URL resolves.",
        "Do not cite localhost screenshots; cite the frozen release version and public record URL after deployment."
      ]
    },
    {
      "title": "Citation",
      "summary": "Cite the resource version, exact record pages for claims, and benchmark split checksums for ML reuse.",
      "items": [
        "Use the Cite page for global citation text and BibTeX.",
        "Use record-level BibTeX for individual evidence claims.",
        "Use benchmark task cards when reporting model baselines."
      ]
    }
  ],
  "quick_links": {
    "examples": "/#examples",
    "trust": "/#trust",
    "release_status": "/#release",
    "citation": "/#cite",
    "openapi": "/api/openapi.json",
    "downloads": "/#downloads",
    "data_availability": "/api/data_availability"
  }
}