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ranjithraj/cancer-knowledge-base

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Cancer Knowledge Base

Educational knowledge base on cancer types, classification, case studies, treatment regimens, monitoring, clinical trials, and guidelines.

Contents (parquet files)

File	Rows	Description
`documents.parquet`	57	De-identified documents: metadata + body text
`sections.parquet`	396	Markdown headings + verbatim section content
`markdown_tables.parquet`	209	All markdown tables (header/rows as JSON)
`markdown_links.parquet`	145	Internal links between documents
`prognosis.parquet`	168	Lethality/survival tables by cancer type and stage (dated, educational)
`biomarkers.parquet`	72	Mutations, receptors, genetic syndromes
`guidelines.parquet`	142	Guideline-grade treatment statements per cancer (NCCN/ESMO/ASCO)
`subtypes.parquet`	110	Histologic subtypes by cancer
`drugs.parquet`	59	Drugs, class, mechanism, toxicity
`staging.parquet`	31	Staging systems (WHO, BCLC, Gleason, NCCN, Clark, Breslow)
`regimens.parquet`	85	Treatment regimens per case and phase
`monitoring.parquet`	109	Factors to monitor during chemo/targeted/surgery/RT
`diagnostics.parquet`	96	Recommended diagnostics per case
`labs.parquet`	72	Baseline labs (synthetic, clearly flagged)
`imaging_findings.parquet`	59	PET-CT / imaging findings (synthetic, clearly flagged)
`consultations.parquet`	59	Consultation plan evolution (synthetic, clearly flagged)
`case_facts.parquet`	218	Structured case fields (diagnosis, staging, prognosis)
`evidence_levels.parquet`	101	Evidence grading (guidelines + trials) per entity
`codes.parquet`	82	Interop codes: ICD-10 for sites/types, HGNC for biomarkers, LOINC for labs, ICD-O-3 for breast subtypes
`regimen_drugs.parquet`	100	Regimen-to-drug join table
`mcq_questions.parquet`	124	Oncology multiple-choice eval questions with rationale (112 total)
`prognosis_sources.parquet`	32	Prognosis rows linked to verified SEER references (vintage + value)
`locales.parquet`	9	Registered target languages (BCP-47 codes, review requirement, priority)
`glossary.parquet`	421	Code-anchored localization terminology registry: concept -> code (ICD/LOINC/HGNC/ICD-O-3) -> local term per locale
`translations.parquet`	4	Per-document localized bodies with masterhash/contenthash provenance and review status

RAG Benchmark

benchmark/ contains an oncology RAG evaluation suite built from this knowledge base:

—retrieval_pool.parquet — ~1,092 chunked retrieval units (sections, markdown tables, domain tables)
—mcq_benchmark.parquet — 112 multiple-choice questions with golden docs, difficulty, evidence level, and citations
—mcq_robustness.parquet — 336 MedRGB-style variants (sufficiency / noise / counterfactual-robustness)
—mirage_format.jsonl / medrgb_format.jsonl — interchange exports for MIRAGE-family leaderboards and MedRGB harnesses (see benchmark/MIRAGE_INTEGRATION.md)
—leaderboard.json — recorded system results

Evaluate your own system with scripts/eval_mcq.py (BM25 or embedding retrieval, or score your predictions).

Ground-truth validation scorecards

scorecards/ holds the results of screening LLM-synthetic oncology datasets against the KB's cited statements (scripts/validate_synthetic.py). Each claim is tiered supported / partial / unsupported by lexical coverage of site-gated evidence, and every item links to the matching evidence chunk.

—cancerguide.all.summary.md + .scorecard.json + .claims.parquet — CancerGUIDE (316 synthetic patient notes): 238 scorable claims, 87.0% supported, 12.6% partial, 0.4% unsupported.

Localization (l10n)

The KB is being localized with provenance — every translation keeps its citation (via the master document), a master_hash so a change in the English source flags the locale stale, and an explicit review status (auto → reviewed → approved).

—locales.parquet — registered languages (de, zh, es, hi + pipeline candidates)
—glossary.parquet — code-anchored terminology registry: each concept is linked to its language-neutral code (ICD-10 / ICD-O-3 / LOINC / HGNC) and maps to the local clinical term, so structured rows localize for free while codes stay the join key across languages.
—translations.parquet — localized document bodies (pilot: know/breast-ref.md at 100% translatable coverage in de/zh/es/hi) with master_hash/content_hash and status.

Coverage is not clinical approval: status='auto' rows are glossary-generated drafts that must be clinically reviewed (reviewed) before use. See l10n-moat.md and scripts/localize_pilot.py --coverage.

Privacy

This is the de-identified public subset. The real patient case (cases/specific/ — PHI) and all content derived from it are excluded. Documents are filtered by phi = 0.

Synthetic rows in labs, imaging_findings, and consultations are clearly flagged with synthetic = 1 and are illustrative public-case data — they are not real patient values.

Disclaimer

Educational reference only — not medical advice. Survival figures are population averages and may be outdated (prognosis.as_of marks their review date); consult current guidelines and clinicians for patient decisions.