Add LICENCE_REMEDIATION.md

LICENCE_REMEDIATION.md

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+# IRexp licence remediation (Track 1)
+
+**Date:** 2026-08-26  
+**Branch:** `cursor/irexp-licence-remediation-9a67`  
+**Audit:** `docs/irexp_scientific_data_audit.md` (§C)
+
+## Problem
+
+PMC Open Access is **not** uniformly CC-BY. A prior blanket CC-BY claim (~19% NC/empty in a 200-PMCID sample) was incorrect for NOTICE / README / HF / Zenodo framing. Chemotion CC-BY-SA-4.0 was already correct.
+
+## What we did
+
+1. **`scripts/join_pmc_licences.py`** — extract unique `PMC:*` accessions from `data/irexp/irexp.jsonl.gz`, batch-query Europe PMC (`resultType=core` → `license`), cache hits, classify, stamp every record, write segregated pools.
+2. **`scripts/split_license_pools.py`** — uses stamped `license_pool` / `license` (not DOI-prefix → CC-BY). Keeps `pool_of()` as provenance-only (`pmc` vs `chemotion`) for manuscript gate A.
+3. Stamped full corpus + pool files under `data/irexp/`.
+4. Honest updates: `data/NOTICE`, `README.md`, `.zenodo.json`, `data/irexp_release/README_HF.md`, minimal `docs/PAPER.md`.
+
+## Classification policy
+
+| Europe PMC / Chemotion | `license` | `license_pool` | Zenodo / Sci Data |
+|---|---|---|---|
+| `cc by`, versioned BY | CC-BY | **commercial** | **Primary redistributable** |
+| `cc0` / public domain | CC0 | **commercial** | Primary |
+| `cc by-nc`, `cc by-nc-nd`, `cc by-nc-sa` | CC-BY-NC* | **non_commercial** | Held-aside file |
+| `cc by-sa` (PMC) | CC-BY-SA | **sharealike** | With Chemotion SA file |
+| Chemotion RADAR4Chem | CC-BY-SA-4.0 | **sharealike** | SA file |
+| `cc by-nd` | CC-BY-ND | **other** | Held aside (ND vs derived extracts) |
+| Missing `license` field | EMPTY | **empty_unknown** | **Exclude from commercial pool** |
+| No EPMC hit | UNKNOWN | **empty_unknown** | **Exclude from commercial pool** |
+
+**Recommendation (implemented):** ship Sci Data / Zenodo **commercial-use pool** as the primary artifact; keep NC in a clearly labelled file; exclude empty/unknown from the commercial deposit; keep Chemotion (+ rare PMC SA) as a separate ShareAlike file.
+
+## Counts (Europe PMC join, 2026-08-26)
+
+### Records (n = 121,233)
+
+| Pool | Records | % of corpus |
+|---|---:|---:|
+| **commercial** (CC-BY + CC0) | **87,617** | 72.3% |
+| non_commercial (NC*) | 20,938 | 17.3% |
+| sharealike (Chemotion 1,888 + PMC SA 9) | 1,897 | 1.6% |
+| empty_unknown | 10,781 | 8.9% |
+| other | 0 | 0.0% |
+| **Total** | **121,233** | 100% |
+
+### By `license` label (records)
+
+| license | Records |
+|---|---:|
+| CC-BY | 87,588 |
+| EMPTY | 10,664 |
+| CC-BY-NC | 10,546 |
+| CC-BY-NC-ND | 9,663 |
+| CC-BY-SA-4.0 (Chemotion) | 1,888 |
+| CC-BY-NC-SA | 729 |
+| UNKNOWN | 117 |
+| CC0 | 29 |
+| CC-BY-SA (PMC) | 9 |
+
+### Unique PMCIDs (15,416 articles)
+
+| license | Articles |
+|---|---:|
+| CC-BY | 11,967 |
+| CC-BY-NC | 1,235 |
+| CC-BY-NC-ND | 1,190 |
+| EMPTY | 864 |
+| CC-BY-NC-SA | 134 |
+| UNKNOWN | 21 |
+| CC0 | 4 |
+| CC-BY-SA | 1 |
+
+Provenance totals unchanged: **119,345** PMC-sourced + **1,888** Chemotion.
+
+## Artefacts
+
+| Path | Role |
+|---|---|
+| `scripts/join_pmc_licences.py` | Join + stamp + write pools |
+| `scripts/split_license_pools.py` | Report / re-materialise from stamps |
+| `data/irexp/irexp.jsonl.gz` | Full corpus **with** `license*` fields |
+| `data/irexp/pmc_licence_lookup.jsonl.gz` | Per-PMCID cache |
+| `data/irexp/pmc_licence_summary.json` | Machine-readable counts |
+| `data/irexp/licence_pools/irexp_commercial.jsonl.gz` | Zenodo primary (87,617) |
+| `data/irexp/licence_pools/irexp_non_commercial.jsonl.gz` | NC held aside |
+| `data/irexp/licence_pools/irexp_sharealike.jsonl.gz` | Chemotion + PMC SA |
+| `data/irexp/licence_pools/irexp_empty_unknown.jsonl.gz` | Excluded from commercial |
+| `data/irexp/licence_pools/irexp_other.jsonl.gz` | Empty placeholder (0 rows) |
+
+Re-run:
+
+```bash
+python scripts/join_pmc_licences.py          # network; resumable via cache
+python scripts/split_license_pools.py        # report
+```
+
+## Hugging Face re-upload (no credentials in-repo)
+
+Public dataset: https://huggingface.co/datasets/ilkhamfy/IRexp  
+
+Previous card/tags overclaimed PMC as CC-BY. After this branch merges:
+
+1. Ensure `HF_TOKEN` with write access to `ilkhamfy/IRexp` (or a staging fork).
+2. Update local card: `data/irexp_release/README_HF.md` (already multi-licence).
+3. Upload stamped files + commercial primary, e.g.:
+
+```bash
+# Preferred: repo helper (requires HF_TOKEN)
+HF_TOKEN=hf_... python scripts/publish_hf.py
+
+# Or huggingface-cli
+huggingface-cli upload ilkhamfy/IRexp \
+  data/irexp/licence_pools/irexp_commercial.jsonl.gz \
+  data/irexp_commercial.jsonl.gz
+huggingface-cli upload ilkhamfy/IRexp \
+  data/irexp/irexp.jsonl.gz data/irexp.jsonl.gz
+huggingface-cli upload ilkhamfy/IRexp \
+  data/irexp_release/README_HF.md README.md
+```
+
+4. Set dataset card `license` list to reflect **cc-by-4.0** (commercial primary) **and** **cc-by-sa-4.0** (Chemotion/SA pool); document NC/empty as non-redistributed or separate configs.
+5. Add a card warning: full `irexp.jsonl.gz` is multi-licence; commercial training should use `license_pool == "commercial"` or the commercial file only.
+
+If `HF_TOKEN` is unavailable in this environment, ship the files above and run the upload from a machine with Hub credentials.
+
+## Zenodo
+
+`.zenodo.json` describes a **multi-licence** deposit: primary file = commercial CC-BY pool; Chemotion/SA as a second file under CC-BY-SA-4.0; NC and empty/unknown not in the commercial artifact (may be uploaded as restricted/supplementary with clear labels). Zenodo’s single `license` metadata field is set to `cc-by-4.0` for the **primary** commercial artifact; description text states the SA companion and exclusions.
+
+## Manuscript / gates
+
+- Full corpus count remains 121,233; PMC/Chemotion provenance counts unchanged → `check_manuscript.py` gate A still passes via `pool_of` provenance split.
+- Filter commercial rows at release time; do not shrink the on-disk research corpus.
+- `docs/paper.tex` intentionally untouched (Track 1 rule).