GleghornLab/taxonomy_order

UniProt search (7/22/2025): * (Swiss-Prot reviewed entries only) download TSV with Taxonomic lineage (Ids), sequence, and length.

Curation steps:

• Filtered for sequence length >=20 and <=2048
• Extract Taxonomic IDs (domain, kingdom, phylum, class, order, family, genus, species) from taxonomic_lineage_ids column
• Keep entry, order, and sequence information
• Drop N/A
• CD-HIT using Docker at 80% similarity threshold and n=5
• Keep representative sequences
• Create labels based on orders
• Remove orders/examples with fewer than 100 samples
• Stratified split: first get test set (5,000), then eval (5,000), rest is train