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README.md

@@ -11,7 +11,9 @@ tags:
   - biology
   - proteins
   - uniprot
-  - fasta
+  - uniprotkb
+  - swiss-prot
+  - trembl
   - protein-sequences
   - bioinformatics
   - train-validation-test-split
@@ -27,55 +29,176 @@ configs:
       - split: test
         path:
           - tables/source_set=*/split=test/*.jsonl.gz
+  - config_name: sprot
+    data_files:
+      - split: train
+        path:
+          - tables/source_set=sprot/split=train/*.jsonl.gz
+      - split: validation
+        path:
+          - tables/source_set=sprot/split=validation/*.jsonl.gz
+      - split: test
+        path:
+          - tables/source_set=sprot/split=test/*.jsonl.gz
+  - config_name: sprot_varsplic
+    data_files:
+      - split: train
+        path:
+          - tables/source_set=sprot_varsplic/split=train/*.jsonl.gz
+      - split: validation
+        path:
+          - tables/source_set=sprot_varsplic/split=validation/*.jsonl.gz
+      - split: test
+        path:
+          - tables/source_set=sprot_varsplic/split=test/*.jsonl.gz
+  - config_name: trembl
+    data_files:
+      - split: train
+        path:
+          - tables/source_set=trembl/split=train/*.jsonl.gz
+      - split: validation
+        path:
+          - tables/source_set=trembl/split=validation/*.jsonl.gz
+      - split: test
+        path:
+          - tables/source_set=trembl/split=test/*.jsonl.gz
 ---
 
 # UniProtKB Processed
 
-Processed UniProtKB protein entries derived from LiteFold/UniProtKB FASTA shards.
+This dataset is a table-friendly, split-aware version of LiteFold/UniProtKB.
+It converts UniProtKB FASTA headers into normalized records that can be browsed
+in the Hugging Face Dataset Viewer and loaded with the `datasets` library.
 
-The processing pipeline parses UniProt FASTA headers, computes exact amino-acid
-sequence SHA-256 hashes, assigns deterministic train/validation/test splits, and
-writes queryable table files.
+The table contains parsed protein metadata and deterministic train/validation/test
+split assignments. To keep the dataset practical for table viewing, full amino
+acid sequences are not duplicated here; each record includes `sequence_sha256`
+for sequence-level identity and deduplication.
 
-## Files
+## Dataset Summary
 
-- `tables/source_set=*/split=*/*.jsonl.gz` - Hugging Face viewer/loadable JSONL tables.
+| Source set | Description | Records |
+|---|---|---:|
+| `sprot` | Swiss-Prot reviewed canonical proteins | 574,627 |
+| `sprot_varsplic` | Swiss-Prot alternative isoform sequences | 41,333 |
+| `trembl` | TrEMBL unreviewed proteins | 202,556,314 |
+| **Total** |  | **203,172,274** |
 
-- `_POSTPROCESS_MANIFEST.json` - processing metadata and split counts.
-- `split_counts.tsv` and `source_counts.tsv` - quick validation summaries.
+## Splits
 
-## Columns
+Splits are deterministic and assigned from the exact amino-acid sequence hash.
+Exact duplicate sequences are kept in the same split.
 
-Each row is one UniProtKB FASTA record. Important columns include:
+| Split | Records |
+|---|---:|
+| `train` | 162,548,965 |
+| `validation` | 20,308,533 |
+| `test` | 20,314,776 |
 
-- `record_id`, `accession`, `base_accession`, `entry_name`
-- `source_db`, `reviewed`, `source_set`, `is_isoform`
-- `protein_name`, `organism_name`, `taxon_id`, `gene_name`
-- `protein_existence`, `sequence_version`, `length`
-- `sequence_sha256`, `source_slug`, `shard`, `record_index`
-- `split_strategy`, `split_version`, `split_group`, `split`
+These are exact-sequence splits, not homology-cluster splits. For strict
+homology-aware model evaluation, split again by UniRef/MMseqs cluster ids.
 
-## Missing Values
+## Loading
 
-For Hugging Face Dataset Viewer compatibility, this dataset does not use JSON
-`null` values in table files.
+Load all source sets:
 
-- Missing optional integer values are encoded as `-1`.
-- Missing optional string values are encoded as `""`.
+```python
+from datasets import load_dataset
 
-## Splits
+ds = load_dataset("LiteFold/UniProtKB", "default")
+train = ds["train"]
+valid = ds["validation"]
+test = ds["test"]
+```
+
+Load only Swiss-Prot reviewed entries:
+
+```python
+from datasets import load_dataset
+
+sprot = load_dataset("LiteFold/UniProtKB", "sprot")
+```
+
+Load only TrEMBL:
+
+```python
+from datasets import load_dataset
 
-Splits are deterministic and assigned by `sequence_hash`.
+trembl = load_dataset("LiteFold/UniProtKB", "trembl", streaming=True)
+for row in trembl["train"]:
+    print(row["accession"], row["protein_name"])
+    break
+```
 
-Default fractions are 80% train, 10% validation, and 10% test. Exact duplicate
-sequences are kept together when `SPLIT_KEY=sequence_hash`.
+Filter examples:
 
+```python
+from datasets import load_dataset
+
+ds = load_dataset("LiteFold/UniProtKB", "sprot", split="train")
+human = ds.filter(lambda x: x["taxon_id"] == 9606)
+reviewed_kinases = human.filter(lambda x: "kinase" in x["protein_name"].lower())
+```
+
+For large-scale TrEMBL use, prefer streaming:
+
+```python
+from datasets import load_dataset
+
+rows = load_dataset("LiteFold/UniProtKB", "trembl", split="train", streaming=True)
+for row in rows:
+    ...
+```
+
+## Columns
 
+| Column | Type | Description |
+|---|---|---|
+| `record_id` | string | Full UniProt FASTA record id, e.g. `sp|Q6GZX4|001R_FRG3G` |
+| `accession` | string | UniProt accession |
+| `base_accession` | string | Accession without isoform suffix |
+| `entry_name` | string | UniProt entry name |
+| `reviewed` | bool | `true` for Swiss-Prot reviewed entries |
+| `source_set` | string | `sprot`, `sprot_varsplic`, or `trembl` |
+| `is_isoform` | bool | Whether the row is an isoform entry |
+| `isoform_number` | int | Isoform suffix number, or `-1` if not applicable |
+| `protein_name` | string | Parsed protein name from the FASTA header |
+| `organism_name` | string | Parsed organism name |
+| `taxon_id` | int | NCBI taxonomy id |
+| `gene_name` | string | Parsed gene name, or `""` if unavailable |
+| `protein_existence` | int | UniProt PE value, or `-1` if unavailable |
+| `sequence_version` | int | UniProt sequence version, or `-1` if unavailable |
+| `length` | int | Amino-acid sequence length |
+| `sequence_sha256` | string | SHA-256 hash of the amino-acid sequence |
+| `split` | string | `train`, `validation`, or `test` |
+
+## Missing Values
+
+For stable Hugging Face Dataset Viewer schema inference, table files do not use
+JSON `null` values.
+
+- Missing optional integer values are encoded as `-1`.
+- Missing optional string values are encoded as `""`.
+
+## Processing Notes
+
+The public tables intentionally omit internal provenance columns such as raw
+FASTA header, source shard, source file, record index, and split internals.
+The postprocessing manifest is available in `_POSTPROCESS_MANIFEST.json`.
 
 ## Source
 
-Derived from LiteFold/UniProtKB, which was built from UniProtKB.
+Derived from LiteFold/UniProtKB, which was built from UniProtKB FASTA releases.
+
+Original source: UniProtKB.
 
 ## License
 
 CC BY 4.0.
+
+## Citation
+
+If you use this dataset, cite UniProt:
+
+The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023.
+Nucleic Acids Research, 51(D1):D523-D531, 2023.

_POSTPROCESS_MANIFEST.json

@@ -1,6 +1,17 @@
 {
   "created_at_unix": 1778683558,
   "dataset_id": "uniprotkb",
+  "dropped_columns": [
+    "source_db",
+    "shard",
+    "record_index",
+    "source_file",
+    "source_slug",
+    "raw_header",
+    "split_strategy",
+    "split_version",
+    "split_group"
+  ],
   "hf_null_repair": {
     "files": 615,
     "null_values_replaced": 214328163,
@@ -10,7 +21,31 @@
   "jsonl_compression": "gzip",
   "partition_by_split": true,
   "postprocess_script_version": "2026-05-13.3",
+  "public_columns": [
+    "record_id",
+    "accession",
+    "base_accession",
+    "entry_name",
+    "reviewed",
+    "source_set",
+    "is_isoform",
+    "isoform_number",
+    "protein_name",
+    "organism_name",
+    "taxon_id",
+    "gene_name",
+    "protein_existence",
+    "sequence_version",
+    "length",
+    "sequence_sha256",
+    "split"
+  ],
   "root": "/workspace/UniProtKB",
+  "slim_rewrite": {
+    "files": 615,
+    "rows": 203172274
+  },
+  "slimmed_for_hf_viewer": true,
   "sources": [
     {
       "records_written": 574627,

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