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BioGRID

BioGRID is a database of Protein, Genetic and Chemical Interactions, a biomedical interaction repository with data compiled through comprehensive curation efforts. The current index searches thousands of publications extracting millions of protein and genetic interactions, thousands of chemical interactions and over a million post translational modifications from major model organism species.

Source File

Data columns (defined here) in the Bulk BioGrid data file are as follows:

  1. ID Interactor A
  2. ID Interactor B
  3. Alt IDs Interactor A
  4. Alt IDs Interactor B
  5. Aliases Interactor A
  6. Aliases Interactor B
  7. Interaction Detection Method
  8. Publication 1st Author
  9. Publication Identifiers
  10. Taxid Interactor A
  11. Taxid Interactor B
  12. Interaction Types
  13. Source Database
  14. Interaction Identifiers
  15. Confidence Values

with a typical row looking like:

  1. entrez gene/locuslink:6416
  2. entrez gene/locuslink:2318
  3. biogrid:112315|entrez gene/locuslink:MAP2K4|uniprot/swiss-prot:P45985|refseq:NP_003001|refseq:NP_001268364
  4. biogrid:108607|entrez gene/locuslink:FLNC|uniprot/swiss-prot:Q14315|refseq:NP_001120959|refseq:NP_001449
  5. entrez gene/locuslink:JNKK(gene name synonym)|entrez gene/locuslink:JNKK1(gene name synonym)|entrez gene/locuslink:MAPKK4(gene name synonym)|entrez gene/locuslink:MEK4(gene name synonym)|entrez gene/locuslink:MKK4(gene name synonym)|entrez gene/locuslink:PRKMK4(gene name synonym)|entrez gene/locuslink:SAPKK-1(gene name synonym)|entrez gene/locuslink:SAPKK1(gene name synonym)|entrez gene/locuslink:SEK1(gene name synonym)|entrez gene/locuslink:SERK1(gene name synonym)|entrez gene/locuslink:SKK1(gene name synonym)
  6. entrez gene/locuslink:ABP-280(gene name synonym)|entrez gene/locuslink:ABP280A(gene name synonym)|entrez gene/locuslink:ABPA(gene name synonym)|entrez gene/locuslink:ABPL(gene name synonym)|entrez gene/locuslink:FLN2(gene name synonym)|entrez gene/locuslink:MFM5(gene name synonym)|entrez gene/locuslink:MPD4(gene name synonym)
  7. psi-mi:"MI:0018"(two hybrid)
  8. "Marti A (1997)"
  9. pubmed:9006895
  10. taxid:9606
  11. taxid:9606
  12. psi-mi:"MI:0407"(direct interaction)
  13. psi-mi:"MI:0463"(biogrid)
  14. biogrid:103

(note: column 15 of this row doesn't report a confidence value).

The BioGRID ingest only uses columns 1, 2 and 9 to generate its output

Concept Nodes

The statement 'subject' (column 1) and 'object' (column 2) nodes are both genes:

  • biolink:Gene
  • id (NCBIGene Entrez ID)

Associations

  • biolink:PairwiseGeneToGeneInteraction:
    • id (random uuid)
    • subject (gene.id)
    • predicate (interacts_with)
    • object (gene.id)
    • has_evidence (ECO codes)
    • publications (LIST[Pubmed ID])
    • aggregating_knowledge_source (["infores:monarchinitiative"])
    • primary_knowledge_source ("infores:biogrid")

Citations

Most Recent

  • Oughtred R, Rust J, Chang C, Breitkreutz BJ, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 2020 Oct 18. PMID:33070389

Original

  • Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan 1, 2006; 34:D535-9; PMID:16381927.