| # NOTICE — upstream attribution, provenance and licensing |
|
|
| This package is a **derived benchmark manifest**, not a re-release of the MSnLib spectra. |
| It contains compound identities (raw and RDKit canonical SMILES), molecular formulas, |
| source-row pointers into `MSnLib.csv`, precursor m/z, adduct, collision energy and the |
| train / validation / test assignments of two independent, frozen benchmark splits. The |
| manifest itself contains no mass spectra (`mzs` / `intensities`). |
|
|
| The Hugging Face dataset that mirrors this manifest additionally hosts two large source |
| files, because every table points into them: |
|
|
| | hosted file | bytes | SHA-256 | content | |
| | --- | ---: | --- | --- | |
| | `MSnLib.csv` | 752,707,651 | `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07` | one row per MSnLib spectrum (560,084 rows), including the `mzs` / `intensities` peak lists | |
| | `MSnLib_candidates.json` | 1,368,264,026 | `125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc` | candidate SMILES lists behind the single-spectrum candidate-ranking task (JSON object: query SMILES → candidate SMILES list; 9,886 query entries) | |
|
|
| Both hosted files derive from the MSnLib release and remain under **CC BY 4.0** with |
| attribution to the MSnLib authors; the candidate lists are derived from the MSnLib compound |
| set by UltraMS. |
|
|
| ## Upstream resource: MSnLib |
|
|
| * Brungs C., Schmid R., Pluskal T. *MSnLib: efficient generation of open multi-stage |
| fragmentation mass spectral libraries.* Nature Methods (2025), |
| doi:[10.1038/s41592-025-02813-0](https://doi.org/10.1038/s41592-025-02813-0). |
| * Data release: *MSnLib mass spectral libraries*, |
| Zenodo [10.5281/zenodo.11163380](https://doi.org/10.5281/zenodo.11163380) (2024). |
| * License: **Creative Commons Attribution 4.0 International (CC BY 4.0)**. |
| Attribution to the MSnLib authors is required for any reuse of the material derived from |
| it, including the compound identities, formulas and metadata distributed here. |
|
|
| The 18 MSnLib original per-file MS2 JSONL releases contain exactly **560,084 records**, |
| equal to the number of data rows of the `MSnLib.csv` file this package indexes. `MSnLib.csv` |
| is the UltraMS CSV conversion of those records (one row per spectrum; peaks stored as |
| comma-separated strings; 752,707,651 bytes; SHA-256 |
| `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07`). It is not part of this |
| manifest; it is hosted with the Hugging Face mirror (see `README.md` §8.1). |
|
|
| ## Retention times |
|
|
| `split_A_full_msnlib/msnlib_rt.csv.gz` contains the per-spectrum retention time |
| (`row_index, rt` in seconds). RT is **source metadata from the MSnLib records** and remains |
| under CC BY 4.0 with attribution to the MSnLib authors. The table was exported from |
| `MSnLib_with_rt.csv` (755,984,910 bytes, SHA-256 |
| `a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964`) after verifying that |
| its row order and first seven columns are identical to `MSnLib.csv` (560,084 rows, 0 |
| mismatches; see `split_A_full_msnlib/VERIFY.md` §5.4). |
|
|
| ## What UltraMS added (the original contribution of this package) |
|
|
| * the CSV representation of the MSnLib release and the source-row pointers, |
| * the frozen **formula-level split A** (all adducts: 21,107 formulas; 16,885 / 2,110 / 2,112 |
| formulas and 446,667 / 55,980 / 57,437 spectra for train / validation / test), |
| * the frozen **strict-adduct molecule-level split B** (70/15/15 by canonical isomeric |
| SMILES, per polarity, with frozen query and library definitions), |
| * the query / library / voting tables, row metadata, protocol arrays, rebuild scripts and |
| verification artifacts derived from them. |
|
|
| The split assignments themselves are an original creation of this work and may be reused |
| with attribution. The compound identities and metadata derived from MSnLib remain under |
| CC BY 4.0. |
|
|
| ## UltraMS code (rebuild scripts only) |
|
|
| * Li Y., Zhong Y., Liu P., Xia J. *UltraMS.* Apache License 2.0 |
| (repository: <https://github.com/Dsadd4/UltraMS>). |
| * `rebuild/build_library_manifest.py` and `rebuild/baseline_common.py` are byte-identical |
| copies of files from the UltraMS public release |
| (`benchmarks/molecular_identification/source_code/original/`). Their license text is |
| reproduced in `rebuild/LICENSE-APACHE-2.0.txt`; the files keep their original copyright |
| and attribution. |
| * `rebuild/verify_release.py` and `split_A_full_msnlib/build_split_a.py` are original |
| verifier / replay scripts of this release. |
|
|
| ## Recommended license for this package |
|
|
| **CC BY 4.0.** Rationale: |
|
|
| * the largest share of the derived content (compound identities, molecular formulas, |
| metadata, source-row pointers) comes from MSnLib under CC BY 4.0, so redistribution must |
| keep at least that attribution requirement; |
| * the split assignments and the derived tables added by UltraMS are released under the same |
| permissive, attribution-preserving terms so that the whole package has one simple |
| license; |
| * a single license keeps the benchmark usable for academic and commercial research. |
|
|
| If you redistribute this package, keep `NOTICE.md`, `README.md` and `SHA256SUMS`, and cite |
| MSnLib and UltraMS as described in `README.md` §12. |
|
|
| ## Third-party names |
|
|
| MSnLib, UltraMS, RDKit, Nature Methods and Zenodo are names/trademarks of their respective |
| owners. Their use here is descriptive only and does not imply endorsement. |
|
|
