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Datasets:
LiteFold
/
UniProtKB

Tasks:
Feature Extraction
Languages:
English
Size:
100M<n<1B
Tags:
biology
proteins
uniprot
uniprotkb
swiss-prot
trembl
License:
Dataset card Files
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  1. .gitattributes +2 -0
  2. README.md +96 -3
  3. _MANIFEST.json +43 -0
  4. manifests/sequence_uniprotkb_uniprot_sprot.fasta.gz.json +11 -0
  5. manifests/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.json +11 -0
  6. manifests/sequence_uniprotkb_uniprot_trembl.fasta.gz.json +11 -0
  7. metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl +3 -0
  8. metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl +3 -0
  9. sequences/sequence_uniprotkb_uniprot_sprot.fasta.gz/shard-000000.fasta.zst +3 -0
  10. sequences/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz/shard-000000.fasta.zst +3 -0
  11. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000000.fasta.zst +3 -0
  12. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000001.fasta.zst +3 -0
  13. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000002.fasta.zst +3 -0
  14. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000003.fasta.zst +3 -0
  15. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000004.fasta.zst +3 -0
  16. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000005.fasta.zst +3 -0
  17. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000006.fasta.zst +3 -0
  18. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000007.fasta.zst +3 -0
  19. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000008.fasta.zst +3 -0
  20. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000009.fasta.zst +3 -0
  21. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000010.fasta.zst +3 -0
  22. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000011.fasta.zst +3 -0
  23. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000012.fasta.zst +3 -0
  24. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000013.fasta.zst +3 -0
  25. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000014.fasta.zst +3 -0
  26. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000015.fasta.zst +3 -0
  27. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000016.fasta.zst +3 -0
  28. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000017.fasta.zst +3 -0
  29. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000018.fasta.zst +3 -0
  30. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000020.fasta.zst +3 -0
  31. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000022.fasta.zst +3 -0
  32. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000023.fasta.zst +3 -0
  33. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000024.fasta.zst +3 -0
  34. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000025.fasta.zst +3 -0
  35. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000026.fasta.zst +3 -0
  36. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000027.fasta.zst +3 -0
  37. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000028.fasta.zst +3 -0
  38. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000029.fasta.zst +3 -0
  39. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000189.fasta.zst +3 -0
  40. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000190.fasta.zst +3 -0
  41. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000191.fasta.zst +3 -0
  42. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000192.fasta.zst +3 -0
  43. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000193.fasta.zst +3 -0
  44. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000194.fasta.zst +3 -0
  45. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000195.fasta.zst +3 -0
  46. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000196.fasta.zst +3 -0
  47. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000197.fasta.zst +3 -0
  48. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000198.fasta.zst +3 -0
  49. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000199.fasta.zst +3 -0
  50. sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz/shard-000200.fasta.zst +3 -0
.gitattributes CHANGED
@@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
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+ metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl filter=lfs diff=lfs merge=lfs -text
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+ metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl filter=lfs diff=lfs merge=lfs -text
README.md CHANGED
@@ -1,3 +1,96 @@
1
- ---
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- license: mit
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- ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ ---
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+ license: cc-by-4.0
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+ pretty_name: UniProtKB (Swiss-Prot + TrEMBL)
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+ size_categories:
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+ - 100M<n<1B
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+ task_categories:
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+ - other
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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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+
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+ # UniProtKB (Swiss-Prot + TrEMBL)
19
+
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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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+
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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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+
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+ ## Statistics
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+
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+ | | |
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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 |
33
+ | Residues (per-source manifest sum) | 75,747,523,712 |
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+ | Aggregate manifest `total_records` | 203172274 |
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+
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+ ## Layout
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+
38
+ ```
39
+ .
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+ ├── _MANIFEST.json # aggregate manifest written by the pipeline
41
+ ├── manifests/<source_slug>.json # per-source manifest (records, residues, shards)
42
+ ├── metadata/<source_slug>.records.jsonl # per-record provenance
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+ └── sequences/<source_slug>/shard-NNNNNN.fasta.zst
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+ ```
45
+
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+ `<source_slug>` corresponds 1:1 with an upstream source archive; e.g.
47
+ `sequence_uniprotkb_uniprot_sprot.fasta.gz`.
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+
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+ ## Loading
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+
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+ Stream every shard of one source (replace `<source_slug>` with the directory of
52
+ interest under `sequences/`):
53
+
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+ ```bash
55
+ hf download LiteFold/UniProtKB --repo-type dataset \
56
+ --include 'sequences/<source_slug>/shard-*.fasta.zst' \
57
+ --local-dir ./uniprotkb
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+ zstd -dc ./uniprotkb/sequences/<source_slug>/shard-*.fasta.zst | head
59
+ ```
60
+
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+ Programmatic streaming with [`zstandard`](https://pypi.org/project/zstandard/):
62
+
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+ ```python
64
+ from huggingface_hub import snapshot_download
65
+ from pathlib import Path
66
+ import zstandard as zstd
67
+
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+ local = snapshot_download(
69
+ repo_id="LiteFold/UniProtKB",
70
+ repo_type="dataset",
71
+ allow_patterns=["sequences/*/shard-*.fasta.zst"],
72
+ )
73
+
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+ dctx = zstd.ZstdDecompressor()
75
+ for shard in sorted(Path(local).rglob("shard-*.fasta.zst")):
76
+ with shard.open("rb") as f, dctx.stream_reader(f) as reader:
77
+ buf = b""
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+ while chunk := reader.read(1 << 20):
79
+ buf += chunk
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+ *lines, buf = buf.split(b"\n")
81
+ for line in lines:
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+ ... # naive splitter; swap in your FASTA parser
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+ ```
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+
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+ ## License
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+
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+ CC BY 4.0 (UniProt Consortium).
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+
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+ ## Citation
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+
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+ > The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523-D531, 2023.
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+
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+ ## Provenance
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+
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+ Built from the local manifest entry `uniprotkb` of `manifests/atlas_download_plan.json`.
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+ Pipeline source: `megadata-post normalize --dataset uniprotkb`.
_MANIFEST.json ADDED
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+ {
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+ "dataset_id": "uniprotkb",
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+ "format": "fasta.zst source-specific shards plus jsonl metadata",
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+ "source_count": 3,
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+ "sources": [
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+ {
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+ "dataset_id": "uniprotkb",
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+ "format": "fasta.zst plus jsonl metadata",
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+ "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl",
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+ "records": 574627,
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+ "shards": 1,
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+ "source_file": "sequence/uniprotkb/uniprot_sprot.fasta.gz",
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+ "source_slug": "sequence_uniprotkb_uniprot_sprot.fasta.gz"
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+ },
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+ {
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+ "dataset_id": "uniprotkb",
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+ "format": "fasta.zst plus jsonl metadata",
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+ "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl",
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+ "records": 41333,
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+ "residues": 24903719,
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+ "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz",
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+ "shards": 1,
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+ "source_file": "sequence/uniprotkb/uniprot_sprot_varsplic.fasta.gz",
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+ "source_slug": "sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz"
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+ },
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+ {
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+ "dataset_id": "uniprotkb",
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+ "source_file": "sequence/uniprotkb/uniprot_trembl.fasta.gz",
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+ "source_slug": "sequence_uniprotkb_uniprot_trembl.fasta.gz"
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+ }
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+ ],
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+ "total_records": 203172274,
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+ "total_residues": 75747523712,
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+ "total_shards": 205
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+ }
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