Update dataset card for public release

README.md

@@ -4,40 +4,161 @@ license: cc-by-4.0
 tags:
   - biology
   - protein
+  - protein-sequences
   - uniref
   - uniref50
+  - proteomics
+  - bioinformatics
 pretty_name: UniRef50
 size_categories:
   - 10M<n<100M
+task_categories:
+  - feature-extraction
+configs:
+  - config_name: default
+    data_files:
+      - split: train
+        path: "train-*.parquet"
+dataset_info:
+  features:
+    - name: id
+      dtype: string
+    - name: name
+      dtype: string
+    - name: updated
+      dtype: string
+    - name: member_count
+      dtype: int32
+    - name: common_taxon
+      dtype: string
+    - name: common_taxon_id
+      dtype: int32
+    - name: seed_id
+      dtype: string
+    - name: go_mf
+      sequence: string
+    - name: go_bp
+      sequence: string
+    - name: go_cc
+      sequence: string
+    - name: member_ids
+      sequence: string
+    - name: rep_member_id
+      dtype: string
+    - name: rep_member_id_type
+      dtype: string
+    - name: rep_organism
+      dtype: string
+    - name: rep_organism_tax_id
+      dtype: int32
+    - name: rep_protein_name
+      dtype: string
+    - name: rep_accessions
+      sequence: string
+    - name: rep_uniparc_id
+      dtype: string
+    - name: rep_uniref90_id
+      dtype: string
+    - name: rep_uniref100_id
+      dtype: string
+    - name: rep_is_seed
+      dtype: bool
+    - name: sequence
+      dtype: large_string
+    - name: sequence_length
+      dtype: int32
+    - name: sequence_crc64
+      dtype: string
+    - name: sequence_xxh128
+      dtype: string
+  splits:
+    - name: train
+      num_examples: 60315044
+  download_size: 18113417832
 ---
 
 # UniRef50
 
-Complete UniRef50 dataset from UniProt, converted from XML to sharded Parquet.
+Complete [UniRef50](https://www.uniprot.org/uniref?query=identity:0.5) dataset from UniProt, converted to sharded Parquet. UniRef50 clusters protein sequences at 50% sequence identity, providing the most aggressively deduplicated view in the UniRef family. It is commonly used for fast sequence searches, domain-level analyses, and as a compact training set for protein language models.
 
-## Contents
+**Part of the [ConvergeBio Protein Database Collection](https://huggingface.co/collections/ConvergeBio/protein-database)** — see also [UniRef100](https://huggingface.co/datasets/ConvergeBio/uniref100), [UniRef90](https://huggingface.co/datasets/ConvergeBio/uniref90), and [UniClust30](https://huggingface.co/datasets/ConvergeBio/uniclust30).
 
-Each row represents a UniRef50 cluster with:
-- Cluster metadata (ID, name, common taxon, member count)
-- Representative member sequence and annotations
-- GO terms (molecular function, biological process, cellular component)
-- Cross-references (UniRef90, UniRef100, UniParc)
-- All member IDs per cluster
+## Dataset Summary
 
-## Source
+| | |
+|---|---|
+| **Clusters** | 60,315,044 |
+| **Shards** | 130 |
+| **Compressed size** | ~17 GB (zstd) |
+| **Sequence lengths** | 11–49,499 aa (median 189, mean 287) |
+| **Members per cluster** | 1–321,476 (median 1, mean 8.7) |
+| **GO annotation coverage** | MF 18.6% · BP 12.0% · CC 12.4% |
+| **Updated range** | 2006-10-31 to 2026-01-28 |
 
-- **Origin:** [UniProt UniRef50](https://www.uniprot.org/uniref?query=identity:0.5)
-- **Format:** Converted from `uniref50.xml.gz` using stream parsing
-- **Compression:** zstd
+## Schema
+
+Each row represents one UniRef50 cluster with its representative sequence and metadata.
+
+| Column | Type | Description |
+|--------|------|-------------|
+| `id` | `string` | Cluster identifier (e.g. `UniRef50_P12345`) |
+| `name` | `string` | Cluster name from UniProt |
+| `updated` | `string` | Last update date (`YYYY-MM-DD`) |
+| `member_count` | `int32` | Number of sequences in the cluster |
+| `common_taxon` | `string` | Lowest common taxon across members |
+| `common_taxon_id` | `int32` | NCBI Taxonomy ID of common taxon |
+| `seed_id` | `string` | ID of the seed sequence |
+| `go_mf` | `list<string>` | GO Molecular Function terms (`GO:XXXXXXX`) |
+| `go_bp` | `list<string>` | GO Biological Process terms |
+| `go_cc` | `list<string>` | GO Cellular Component terms |
+| `member_ids` | `list<string>` | All member sequence IDs |
+| `rep_member_id` | `string` | Representative member ID |
+| `rep_member_id_type` | `string` | ID type (e.g. `UniProtKB ID`, `UniParc ID`) |
+| `rep_organism` | `string` | Source organism of representative |
+| `rep_organism_tax_id` | `int32` | NCBI Taxonomy ID of representative organism |
+| `rep_protein_name` | `string` | Protein name of representative |
+| `rep_accessions` | `list<string>` | UniProtKB accessions of representative |
+| `rep_uniparc_id` | `string` | UniParc ID of representative |
+| `rep_uniref90_id` | `string` | Child UniRef90 cluster ID |
+| `rep_uniref100_id` | `string` | Child UniRef100 cluster ID |
+| `rep_is_seed` | `bool` | Whether the representative is the seed sequence |
+| `sequence` | `large_string` | Representative protein sequence (uppercase amino acid alphabet) |
+| `sequence_length` | `int32` | Length of the sequence in residues |
+| `sequence_crc64` | `string` | CRC64 checksum from UniProt (hex) |
+| `sequence_xxh128` | `string` | xxHash-128 of the sequence (hex, computed at build time) |
 
 ## Usage
 
 ```python
 from datasets import load_dataset
 
+# Stream without downloading everything
+ds = load_dataset("ConvergeBio/uniref50", streaming=True)
+for row in ds["train"]:
+    print(row["id"], row["sequence_length"])
+    break
+
+# Or load fully
 ds = load_dataset("ConvergeBio/uniref50")
 ```
 
+## Data Processing
+
+- **Source:** `uniref50.xml.gz` from the [UniProt FTP](https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/)
+- **Parsing:** Streaming XML parse with `lxml.etree.iterparse`, multi-process
+- **Integrity:** xxHash-128 computed per sequence; CRC64 preserved from source XML
+- **Validation:** Passed all tiers — schema conformance, zero null/empty sequences, xxHash roundtrip, CRC64 format, GO term format, member ID consistency, and field-by-field comparison against source XML
+- **Format:** Sharded Parquet with zstd compression
+
+## Source & Citation
+
+UniRef is produced by the [UniProt Consortium](https://www.uniprot.org/):
+
+> Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium.
+> "UniRef clusters: a comprehensive and scalable alternative for improving
+> sequence similarity searches." *Bioinformatics* 31(6):926–932 (2015).
+> [doi:10.1093/bioinformatics/btu739](https://doi.org/10.1093/bioinformatics/btu739)
+
 ## License
 
 UniProt data is available under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).