| --- |
| pretty_name: LuminBench Nano ESMC Raw 70% Cluster Outputs v1 |
| license: other |
| size_categories: |
| - 100M<n<1B |
| tags: |
| - biology |
| - protein |
| - protein-language-model |
| - fasta |
| - clustering |
| - mmseqs2 |
| --- |
| |
| # LuminBench Nano ESMC Raw 70% Cluster Outputs v1 |
|
|
| This repository preserves the source-specific 70%-identity clustering outputs |
| that precede evaluation decontamination and final Parquet packing in |
| [`LuminScience/LuminBench-Nano-ESMC`](https://huggingface.co/datasets/LuminScience/LuminBench-Nano-ESMC). |
|
|
| It contains **241,600,826,413 bytes of representative FASTA data** covering |
| **765,290,002 source-specific cluster representatives**. It also preserves the |
| three cluster-membership maps so the clustering result is not reduced to the |
| representatives alone. |
|
|
| > **Not decontaminated training data.** These FASTAs precede the P@L/P-CORE |
| > evaluation exclusion, cross-source ownership assignment, length gate, and |
| > train/validation split. Use the final repository above for clean training. |
|
|
| ## Files |
|
|
| | Source arm | Representative FASTA | Representatives | Cluster map | Source-specific member rows | |
| |---|---:|---:|---:|---:| |
| | UniRef90 2023_02 | 38,626,189,542 bytes | 92,230,941 | 23,887,338,192 bytes | 165,884,293 | |
| | MGnify Protein DB 2023_02 | 93,319,863,106 bytes | 348,135,082 | 88,097,490,576 bytes | 611,788,129 | |
| | OMG/IMG | 109,654,773,765 bytes | 324,923,979 | 138,768,938,784 bytes | 963,673,186 | |
| | **Total** | **241,600,826,413 bytes** | **765,290,002** | **250,753,767,552 bytes** | **1,741,345,608 source memberships** | |
|
|
| Paths are: |
|
|
| ```text |
| representatives/{uniref90,mgnify,omg_img}.fasta |
| clusters/{uniref90,mgnify,omg_img}.clusters.tsv |
| receipts/{uniref90,mgnify,omg_img}.verification.json |
| ``` |
|
|
| FASTA identifiers are `sha256_<digest>`, where the digest is computed from the |
| normalized ASCII amino-acid sequence. Each cluster-map row is: |
|
|
| ```text |
| representative_sha256<TAB>member_sha256 |
| ``` |
|
|
| The maps are source-specific. The same exact sequence can therefore occur as a |
| member in more than one source arm. |
|
|
| ## Does this preserve every clustered protein? |
|
|
| It preserves the **cluster assignment relation**, but it is not a self-contained |
| copy of every cluster-member sequence: |
|
|
| - the representative FASTAs contain the 765.29M representative sequences; |
| - the `clusters.tsv` files map each representative digest to every member digest; |
| - non-representative member sequences and original upstream accessions are not |
| stored in those TSVs. |
|
|
| To recover all member sequences or original identifiers, redownload the pinned |
| upstream snapshots, rerun normalization and exact deduplication, and join the |
| resulting membership Parquet rows to `member_sha256`. This repository therefore |
| preserves enough information to reproduce cluster membership **when combined |
| with the pinned upstream inputs and build recipe**, but the representative |
| FASTAs alone would not be sufficient. |
|
|
| See [`BUILD_RECIPE.md`](BUILD_RECIPE.md), [`manifest.json`](manifest.json), and |
| [`SOURCE_PROVENANCE.json`](SOURCE_PROVENANCE.json) for the exact pipeline, |
| commands, checksums, and limitations. |
|
|
| ## License and source terms |
|
|
| This is a mixed-terms dataset, so the Hub metadata uses `license: other` rather |
| than pretending that one license replaces all upstream terms. |
|
|
| | Path | Direct source | Governing terms | |
| |---|---|---| |
| | `representatives/uniref90.fasta` | UniRef90 2023_02 | [UniProt CC BY 4.0](https://www.uniprot.org/help/license) | |
| | `representatives/mgnify.fasta` | MGnify Protein DB 2023_02 | [EMBL-EBI Terms of Use](https://www.ebi.ac.uk/about/terms-of-use/) plus applicable original-owner rights; not relicensed by Lumin Science | |
| | `representatives/omg_img.fasta` | JGI/IMG records distributed by [`tattabio/OMG`](https://huggingface.co/datasets/tattabio/OMG) | CC BY-SA 4.0 as declared by the direct distribution | |
| | `clusters/**`, manifests, receipts, and build documentation | Lumin Science selection, arrangement, and derived clustering metadata | CC BY-SA 4.0 | |
|
|
| See [`LICENSE_AND_ATTRIBUTION.md`](LICENSE_AND_ATTRIBUTION.md) before reuse. |
|
|
|
|
