README.md

metadata

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.

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:

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:

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, manifest.json, and 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
representatives/mgnify.fasta	MGnify Protein DB 2023_02	EMBL-EBI Terms of Use plus applicable original-owner rights; not relicensed by Lumin Science
representatives/omg_img.fasta	JGI/IMG records distributed by 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 before reuse.