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README.md

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+---
+license: cc-by-sa-3.0
+language:
+- en
+pretty_name: ProvBench EGFR Bioactivity (provenance-preserving)
+tags:
+- chemistry
+- drug-discovery
+- bioactivity
+- ic50
+- egfr
+- data-curation
+- provenance
+size_categories:
+- 1K<n<10K
+configs:
+- config_name: consensus
+  data_files: consensus.csv
+- config_name: source_records
+  data_files: source_records.csv
+---
+
+# ProvBench — EGFR Bioactivity (provenance-preserving, multi-source)
+
+A curated catalog of EGFR (UniProt **P00533**, ChEMBL **CHEMBL203**)
+IC50/Ki bioactivity, built to demonstrate rigorous **data provenance**, **metadata cataloging**,
+and **multi-source harmonization**.
+
+- **28689** original measurements preserved (link-tracked, never deleted)
+- **15507** unique compounds (standardized; joined on standard InChIKey)
+- **11107** compound/target consensus values
+- Upstream sources (via ChEMBL): BindingDB Patent Bioactivity Data, Chemical Probe data from Scientific Literature, DrugMatrix, EUbOPEN Chemogenomic Library Literature Data, PubChem BioAssays, SGC Frankfurt - Donated Chemical Probes, Scientific Literature, SureChEMBL Patent Bioactivity Data
+
+## Philosophy: annotate-don't-delete
+
+Every original record is kept and linked to its source. Suspect values are **flagged** with a
+ChEMBL-style `validity_flag` (e.g. *Potential transcription error*, *Outside typical range*), never
+silently dropped. The consensus is a transparent **median** of the exact measurements.
+
+## Data quality (Landrum & Riniker, 2024)
+
+Pairwise agreement of repeat measurements under different curation regimes
+(higher Kendall tau / lower MAE = better):
+
+| curation | n_pairs | Kendall tau | frac >0.3 log | frac >1.0 log | MAE (log) |
+|---|---|---|---|---|---|
+| minimal | 20398 | 0.3716 | 0.6844 | 0.3745 | 0.9483 |
+| maximal | 13255 | 0.401 | 0.6611 | 0.3442 | 0.883 |
+| cross_source | 1993 | 0.2854 | 0.7341 | 0.4305 | 1.0506 |
+
+## Files
+
+- `consensus.csv` — one harmonized row per (compound, target).
+- `source_records.csv` — every original measurement with source, flags, and provenance.
+- `croissant.json` — **enriched** Croissant v1.1 metadata with PROV-O lineage
+  (HuggingFace's auto-generated Croissant is structurally thin by comparison).
+- `provenance.json` — W3C PROV document of the curation chain.
+
+## Provenance & licensing
+
+Derived from ChEMBL (CC BY-SA 3.0) which aggregates the upstream sources listed above.
+Curation/QC methodology follows Landrum & Riniker (2024), *J. Chem. Inf. Model.*,
+DOI 10.1021/acs.jcim.4c00049.
+
+Built by [Nitin Singh](https://github.com/NI3singh) — code:
+https://github.com/NI3singh/provbench-bioactivity-catalog