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interpro_repeat

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interpro_repeat

Protein-level multi-label dataset sourced from InterPro entry metadata and UniProtKB protein-to-InterPro cross-references.

Intended use

Protein repeat annotation prediction from sequence. This evaluates recovery of curated InterPro classifications, not an experimental assay result.

Source and labels

  • InterPro metadata: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
  • UniProt REST API: https://rest.uniprot.org/uniprotkb/stream
  • Card generated (UTC): 2026-09-28
  • Organism Taxonomy ID: 9606 (all = all organisms).
  • Review status: reviewed (reviewed = Swiss-Prot, unreviewed = TrEMBL, all = both).
  • UniProt query: (organism_id:9606) AND (reviewed:true)
  • UniProt TSV fields: accession,sequence,xref_interpro
  • InterPro entry type: Repeat
  • Keep entries observed in at least 2 proteins and present in the training split.
  • targets is a multi-hot vector ordered by InterPro accession. Accession, display name, and type are recorded in label_vocabulary.json.
  • Proteins without a retained entry before splitting are dropped; after training-only vocabulary filtering, other splits may contain all-zero targets.

Splits

Whole MMseqs2 easy-linclust clusters are assigned to splits targeting {'train': 0.8, 'validation': 0.1, 'test': 0.1}, with minimum identity 0.3, minimum coverage 0.8, and 1 thread(s). Seed: 1957723. When create_split_subsets is enabled, pooled random, stratified, and hold-cluster-out subsets are also included. Hold-cluster-out subsets require enough MMseqs clusters to populate all three roles. The optional maximum sequence length is None and is applied before vocabulary construction and MMseqs2 clustering.

Split sizes

  • test: 1473 rows
  • test_cluster: 1473 rows
  • test_random: 1473 rows
  • test_stratified: 1473 rows
  • train: 11785 rows
  • train_cluster: 11785 rows
  • train_random: 11785 rows
  • train_stratified: 11785 rows
  • validation: 1473 rows
  • validation_cluster: 1473 rows
  • validation_random: 1473 rows
  • validation_stratified: 1473 rows

Vocabulary size: 159.

Dataset statistics

stats.json at the dataset root contains row counts by split, columns, and SeqKit sequence-length metrics.