README.md

---
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.