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IRexp / 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 + Crossref recovery, 2026-08-27)

Records (n = 121,233)

Pool Records % of corpus
commercial (CC-BY + CC0) 88,545 73.0%
non_commercial (NC*) 21,823 18.0%
sharealike (Chemotion 1,888 + PMC SA 9) 1,897 1.6%
empty_unknown 8,963 7.4%
other (CC-BY-ND) 5 <0.1%
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 (88,545)
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:

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

Status (2026-08-27): remirrored after Crossref recovery — Hub card + pools show commercial 88,545 / NC 21,823 / empty 8,963 / SA 1,897. Re-run only if local stamps drift again:

# 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

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. Card warning: full irexp.jsonl.gz is multi-licence; commercial training should use license_pool == "commercial" or the commercial file only.

Zenodo

.zenodo.json at the repo root currently describes a combined research deposit (IRexp + IRSpectra-Bench). For the Scientific Data archival record, mint a separate data-only Zenodo 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 should be cc-by-4.0 for the primary commercial artifact; description text must state the SA companion and exclusions. Do not invent a DOI in the manuscript until the data-only deposit is minted.

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).