Datasets:

Synthyra
/

BIOGRID-5.0.253

dataset_info:
  features:
    - name: A
      dtype: string
    - name: B
      dtype: string
    - name: SeqA
      dtype: string
    - name: SeqB
      dtype: string
    - name: OrgA
      dtype: string
    - name: OrgB
      dtype: string
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*

BIOGRID release 5.0.253

This dataset is generated from BioGRID ALL using Synthyra/BIOGRID-5.0.253. BioGRID downloads are hosted here: https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-5.0.253/ The exact zip used for this split: https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-5.0.253/BIOGRID-ALL-5.0.253.tab3.zip

Swiss-Prot and TrEMBL accessions are resolved to current UniProtKB primary accessions using the UniProt ID Mapping service: https://www.uniprot.org/id-mapping We keep interaction pairs only when both partners resolve to a UniProtKB sequence. When multiple accessions are present, Swiss-Prot IDs are preferred over TrEMBL.

Processing Overview

Download and unzip BioGRID
Stream BioGRID tab3 rows in chunks
Normalize accessions (optionally strip isoform suffixes)
Resolve accessions to UniProtKB primary IDs and sequences
Emit rows with A/B, SeqA/SeqB, OrgA/OrgB
Push dataset shards to the Hugging Face Hub

Key Script Snippets

# Download + unzip
zip_path = _ensure_biogrid_zip(version, kind=kind, data_dir=data_dir)

# Stream BioGRID rows from the tab3 file inside the zip
for chunk in _iter_biogrid_chunks(zip_path, chunksize=chunksize):
    ...

# Map accessions to UniProt primary + fetch sequences
id_to_primary, primary_to_seq = _resolve_sequences_for_ids(...)

# Build rows and push to Hub
dataset = Dataset.from_generator(_row_generator, gen_kwargs={...}, features=features)
dataset.push_to_hub(repo_id, token=token, private=args.private, max_shard_size=args.max_shard_size)

Citation

If you use this dataset please cite their work:

@article{Oughtred2020,
  title = {The <scp>BioGRID</scp> database: A comprehensive biomedical resource of curated protein,  genetic,  and chemical interactions},
  volume = {30},
  ISSN = {1469-896X},
  url = {http://dx.doi.org/10.1002/pro.3978},
  DOI = {10.1002/pro.3978},
  number = {1},
  journal = {Protein Science},
  publisher = {Wiley},
  author = {Oughtred,  Rose and Rust,  Jennifer and Chang,  Christie and Breitkreutz,  Bobby‐Joe and Stark,  Chris and Willems,  Andrew and Boucher,  Lorrie and Leung,  Genie and Kolas,  Nadine and Zhang,  Frederick and Dolma,  Sonam and Coulombe‐Huntington,  Jasmin and Chatr‐aryamontri,  Andrew and Dolinski,  Kara and Tyers,  Mike},
  year = {2020},
  month = nov,
  pages = {187–200}
}