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:
- ID Interactor A
- ID Interactor B
- Alt IDs Interactor A
- Alt IDs Interactor B
- Aliases Interactor A
- Aliases Interactor B
- Interaction Detection Method
- Publication 1st Author
- Publication Identifiers
- Taxid Interactor A
- Taxid Interactor B
- Interaction Types
- Source Database
- Interaction Identifiers
- Confidence Values
with a typical row looking like:
- entrez gene/locuslink:6416
- entrez gene/locuslink:2318
- biogrid:112315|entrez gene/locuslink:MAP2K4|uniprot/swiss-prot:P45985|refseq:NP_003001|refseq:NP_001268364
- biogrid:108607|entrez gene/locuslink:FLNC|uniprot/swiss-prot:Q14315|refseq:NP_001120959|refseq:NP_001449
- 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)
- 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)
- psi-mi:"MI:0018"(two hybrid)
- "Marti A (1997)"
- pubmed:9006895
- taxid:9606
- taxid:9606
- psi-mi:"MI:0407"(direct interaction)
- psi-mi:"MI:0463"(biogrid)
- 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
Biolink classes and properties captured
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.