Datasets:
Add files using upload-large-folder tool
Browse files- README.md +54 -77
- _POSTPROCESS_MANIFEST.json +63 -0
- indexes/sprot.metadata_index.json +21 -0
- indexes/sprot_varsplic.metadata_index.json +21 -0
- indexes/trembl.metadata_index.json +2041 -0
- tables/source_set=sprot/split=test/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=sprot/split=train/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=sprot/split=validation/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=sprot_varsplic/split=test/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=sprot_varsplic/split=train/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=sprot_varsplic/split=validation/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000175.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000176.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000177.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000178.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000179.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000180.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000181.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000182.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000183.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000184.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000185.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000186.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000187.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000188.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000189.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000190.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000191.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000192.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000194.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000195.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000196.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000197.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000198.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000199.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000200.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000201.jsonl.gz +3 -0
- tables/source_set=trembl/split=test/protein_entries_shard-000202.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000000.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000001.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000004.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000005.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000006.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000007.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000008.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000009.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000010.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000011.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000012.jsonl.gz +3 -0
- tables/source_set=trembl/split=train/protein_entries_shard-000013.jsonl.gz +3 -0
README.md
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---
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license: cc-by-4.0
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pretty_name: UniProtKB
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size_categories:
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- 100M<n<1B
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task_categories:
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language:
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- en
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tags:
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- biology
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- proteins
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- sequences
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- fasta
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- uniprot
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---
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# UniProtKB
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Normalized FASTA shards of UniProt Knowledgebase entries (curated Swiss-Prot plus TrEMBL), processed by the MegaData pipeline.
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Processed and uploaded by the [MegaData](https://github.com/) post-download pipeline
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(internal repo). Original source: <https://www.uniprot.org/help/downloads>.
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## Statistics
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|---|---|
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| Source files | 3 |
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| Shards | 205 |
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| Compressed shard bytes | 43.31 GiB (46,504,287,641) |
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| Records (per-source manifest sum) | 203,172,274 |
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| Residues (per-source manifest sum) | 75,747,523,712 |
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| Aggregate manifest `total_records` | 203172274 |
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## Layout
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```
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.
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├── _MANIFEST.json # aggregate manifest written by the pipeline
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├── manifests/<source_slug>.json # per-source manifest (records, residues, shards)
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├── metadata/<source_slug>.records.jsonl # per-record provenance
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└── sequences/<source_slug>/shard-NNNNNN.fasta.zst
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```
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`<source_slug>` corresponds 1:1 with an upstream source archive; e.g.
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`sequence_uniprotkb_uniprot_sprot.fasta.gz`.
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## Loading
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Stream every shard of one source (replace `<source_slug>` with the directory of
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interest under `sequences/`):
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```bash
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hf download LiteFold/UniProtKB --repo-type dataset \
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--include 'sequences/<source_slug>/shard-*.fasta.zst' \
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--local-dir ./uniprotkb
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zstd -dc ./uniprotkb/sequences/<source_slug>/shard-*.fasta.zst | head
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```
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Programmatic streaming with [`zstandard`](https://pypi.org/project/zstandard/):
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```python
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from huggingface_hub import snapshot_download
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from pathlib import Path
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import zstandard as zstd
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local = snapshot_download(
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repo_id="LiteFold/UniProtKB",
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repo_type="dataset",
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allow_patterns=["sequences/*/shard-*.fasta.zst"],
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)
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dctx = zstd.ZstdDecompressor()
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for shard in sorted(Path(local).rglob("shard-*.fasta.zst")):
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with shard.open("rb") as f, dctx.stream_reader(f) as reader:
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buf = b""
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while chunk := reader.read(1 << 20):
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buf += chunk
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*lines, buf = buf.split(b"\n")
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for line in lines:
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... # naive splitter; swap in your FASTA parser
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```
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Pipeline source: `megadata-post normalize --dataset uniprotkb`.
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---
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license: cc-by-4.0
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pretty_name: UniProtKB Processed
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size_categories:
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- 100M<n<1B
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task_categories:
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- feature-extraction
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language:
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- en
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tags:
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- biology
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- proteins
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- uniprot
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- fasta
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- protein-sequences
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- bioinformatics
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- train-validation-test-split
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configs:
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- config_name: default
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data_files:
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- split: train
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path:
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- tables/source_set=*/split=train/*.jsonl.gz
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- split: validation
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path:
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- tables/source_set=*/split=validation/*.jsonl.gz
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- split: test
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path:
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- tables/source_set=*/split=test/*.jsonl.gz
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---
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# UniProtKB Processed
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Processed UniProtKB protein entries derived from LiteFold/UniProtKB FASTA shards.
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The processing pipeline parses UniProt FASTA headers, computes exact amino-acid
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sequence SHA-256 hashes, assigns deterministic train/validation/test splits, and
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writes queryable table files.
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## Files
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- `tables/source_set=*/split=*/*.jsonl.gz` - Hugging Face viewer/loadable JSONL tables.
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- `_POSTPROCESS_MANIFEST.json` - processing metadata and split counts.
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- `split_counts.tsv` and `source_counts.tsv` - quick validation summaries.
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## Columns
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Each row is one UniProtKB FASTA record. Important columns include:
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- `record_id`, `accession`, `base_accession`, `entry_name`
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- `source_db`, `reviewed`, `source_set`, `is_isoform`
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- `protein_name`, `organism_name`, `taxon_id`, `gene_name`
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- `protein_existence`, `sequence_version`, `length`
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- `sequence_sha256`, `source_slug`, `shard`, `record_index`
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- `split_strategy`, `split_version`, `split_group`, `split`
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## Splits
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Splits are deterministic and assigned by `sequence_hash`.
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Default fractions are 80% train, 10% validation, and 10% test. Exact duplicate
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sequences are kept together when `SPLIT_KEY=sequence_hash`.
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## Source
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Derived from LiteFold/UniProtKB, which was built from UniProtKB.
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## License
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CC BY 4.0.
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_POSTPROCESS_MANIFEST.json
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{
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"created_at_unix": 1778683558,
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"dataset_id": "uniprotkb",
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"jsonl_compression": "gzip",
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"partition_by_split": true,
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"postprocess_script_version": "2026-05-13.3",
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"root": "/workspace/UniProtKB",
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"sources": [
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{
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"records_written": 574627,
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"source_file": "sequence/uniprotkb/uniprot_sprot.fasta.gz",
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"source_set": "sprot",
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"source_slug": "sequence_uniprotkb_uniprot_sprot.fasta.gz",
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"split_counts": {
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"test": 57478,
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"train": 459912,
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"validation": 57237
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},
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"sqlite_shards": 0
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},
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+
{
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| 22 |
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"records_written": 41333,
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"source_file": "sequence/uniprotkb/uniprot_sprot_varsplic.fasta.gz",
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"source_set": "sprot_varsplic",
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"source_slug": "sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz",
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| 26 |
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"split_counts": {
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"test": 4148,
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| 28 |
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"train": 33089,
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| 29 |
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"validation": 4096
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| 30 |
+
},
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| 31 |
+
"sqlite_shards": 0
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| 32 |
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},
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{
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| 34 |
+
"records_written": 202556314,
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| 35 |
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"source_file": "sequence/uniprotkb/uniprot_trembl.fasta.gz",
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"source_set": "trembl",
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| 37 |
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"source_slug": "sequence_uniprotkb_uniprot_trembl.fasta.gz",
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| 38 |
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"split_counts": {
|
| 39 |
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"test": 20253150,
|
| 40 |
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"train": 162055964,
|
| 41 |
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"validation": 20247200
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},
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| 43 |
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"sqlite_shards": 0
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| 44 |
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}
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| 45 |
+
],
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| 46 |
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"split_counts": {
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| 47 |
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"test": 20314776,
|
| 48 |
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"train": 162548965,
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| 49 |
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"validation": 20308533
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},
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| 51 |
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"split_fractions": {
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| 52 |
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"test": 0.1,
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"train": 0.8,
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| 54 |
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"validation": 0.1
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},
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| 56 |
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"split_key": "sequence_hash",
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| 57 |
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"split_version": "uniprotkb_exact_sequence_hash_v1",
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| 58 |
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"sqlite": null,
|
| 59 |
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"store_sequences_in_sqlite": false,
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| 60 |
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"total_records": 203172274,
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"workers": 16,
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"write_jsonl": true
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}
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indexes/sprot.metadata_index.json
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{
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"metadata_mtime_ns": 1778680365000000000,
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| 3 |
+
"metadata_path": "/workspace/UniProtKB/metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl",
|
| 4 |
+
"metadata_size": 203301433,
|
| 5 |
+
"partial": false,
|
| 6 |
+
"records": 574627,
|
| 7 |
+
"shards": [
|
| 8 |
+
{
|
| 9 |
+
"count": 574627,
|
| 10 |
+
"ranges": [
|
| 11 |
+
{
|
| 12 |
+
"count": 574627,
|
| 13 |
+
"offset": 0
|
| 14 |
+
}
|
| 15 |
+
],
|
| 16 |
+
"shard": "shard-000000.fasta.zst"
|
| 17 |
+
}
|
| 18 |
+
],
|
| 19 |
+
"source_set": "sprot",
|
| 20 |
+
"source_slug": "sequence_uniprotkb_uniprot_sprot.fasta.gz"
|
| 21 |
+
}
|
indexes/sprot_varsplic.metadata_index.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"metadata_mtime_ns": 1778680365000000000,
|
| 3 |
+
"metadata_path": "/workspace/UniProtKB/metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl",
|
| 4 |
+
"metadata_size": 14200051,
|
| 5 |
+
"partial": false,
|
| 6 |
+
"records": 41333,
|
| 7 |
+
"shards": [
|
| 8 |
+
{
|
| 9 |
+
"count": 41333,
|
| 10 |
+
"ranges": [
|
| 11 |
+
{
|
| 12 |
+
"count": 41333,
|
| 13 |
+
"offset": 0
|
| 14 |
+
}
|
| 15 |
+
],
|
| 16 |
+
"shard": "shard-000000.fasta.zst"
|
| 17 |
+
}
|
| 18 |
+
],
|
| 19 |
+
"source_set": "sprot_varsplic",
|
| 20 |
+
"source_slug": "sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz"
|
| 21 |
+
}
|
indexes/trembl.metadata_index.json
ADDED
|
@@ -0,0 +1,2041 @@
|
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