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.
This ingest uses the Bulk BioGRID MITAB data file. The PSI-MITAB format columns (defined here) are:
- 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
This ingest uses columns 1, 2, 7 and 9 to generate its output.
Only interactions where both interactor IDs can be resolved to NCBIGene or UniProtKB identifiers are included. Rows with other identifier types (e.g. BioGRID internal IDs) are filtered out.
| Property | Value | Notes |
|---|---|---|
| id | UUID | |
| subject | CURIE | Genes captured from NCBI or UniProt. |
| predicate | interacts_with |
|
| object | CURIE | See subject. |
| has_evidence | CURIE list | ECO codes derived from the Interaction Detection Method column. |
| publications | CURIE list | PMIDs derived from the Publication Identifiers column. |
| primary_knowledge_source | infores:biogrid |
|
| aggregator_knowledge_source | infores:monarchinitiative |
|
| knowledge_level | knowledge_assertion |
|
| agent_type | not_provided |
Interaction detection methods from the PSI-MI ontology are mapped to ECO evidence codes:
| Detection Method | ECO Code | ECO Label |
|---|---|---|
| two hybrid | ECO:0000024 | yeast 2-hybrid evidence |
| affinity chromatography technology | ECO:0000079 | affinity chromatography evidence |
| genetic interference | ECO:0000011 | genetic interaction evidence |
| pull down | ECO:0000025 | co-purification evidence |
| enzymatic study | ECO:0000005 | enzyme assay evidence |
| x-ray crystallography | ECO:0001823 | x-ray crystallography evidence |
| far western blotting | ECO:0000076 | far western blot evidence |
| fluorescent resonance energy transfer | ECO:0001048 | FRET evidence |
| imaging technique | ECO:0000324 | imaging assay evidence |
| protein complementation assay | ECO:0006256 | protein complementation assay evidence |
| biochemical | ECO:0000172 | biochemical trait evidence |
Unknown methods default to ECO:0000006 (experimental evidence).
- ID normalization:
entrez gene/locuslink:prefixes are mapped toNCBIGene:CURIEs;uniprot/swiss-prot:toUniProtKB:. All other identifier types are passed through but interactions with unrecognized ID types are filtered out. - Evidence mapping: Several mappings are approximate (pull down, imaging technique, protein complementation assay, biochemical) since the PSI-MI detection methods don't map 1:1 to ECO codes.
- Publication parsing: Only PubMed IDs (
pubmed:prefix) are captured from the Publication Identifiers column.
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
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.
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