BioGRID: a general repository for interaction datasets
Open accessAbstract
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.
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Based on BioGRID, trans associations between TMEM119 and SELPLG, as well as GAL3ST2 and MUC-16 had no supporting interactions.
“Based on BioGRID42,43, trans associations between TMEM119 and SELPLG, as well as GAL3ST2 and MUC-16 had no supporting interactions.”
From Genetic determinants of plasma protein levels in the Estonian population (2024) · cites this paper as [42]
The Introduction identifies BioGRID as a repository of physical and genetic interactions, supporting its use as the cited resource. Neither that section nor the retrieved passages report whether TMEM119–SELPLG or GAL3ST2–MUC-16 have supporting interactions, so the specific negative finding is not verified by this paper. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn the case of BioGRID, none of the trans associations had support for a functional connection with GDF-15.
“In the case of BioGRID42,43, none of the trans associations had support for a functional connection with GDF-15.”
From Genetic determinants of plasma protein levels in the Estonian population (2024) · cites this paper as [42]
Graphs can model long-range dependencies or interactions, so chromatin elements and effects of their binding to regions across the genome can be modeled as a network.
“Additionally, because graphs can model long-range dependencies or interactions, we can model chromatin elements and the effects of their binding to regions across the genome as a network [220, 221].”
From Graph representation learning in biomedicine and healthcare (2022) · cites this paper as [220]
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- Authors
- Stark, C.
- Affiliations
- Princess Margaret Cancer Centre (CA)
- Corresponding author
- Stark, C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-01
- Volume
- 34
- Issue
- 90001
- Pages
- D535-D539
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1347471
- OpenAlex
- W2163485494
- Cited by
- 3,960
- References
- 34
- Citations by year
- 2026: 109 · 2025: 153 · 2024: 180 · 2023: 183 · 2022: 260 · 2021: 299 · 2020: 278 · 2019: 260 · 2018: 218 · 2017: 215 · 2016: 225 · 2015: 208 · 2014: 200 · 2013: 191 · 2012: 178
- FWCI
- 34.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Terry Fox Foundation
- Canadian Institutes of Health Research
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- BioGRID, protein-protein interaction, genetic interactions, INTERACTION dataset, biological networks, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, human, literature curation, network visualization, Pandion haliaetus
- MeSH terms
- Animals, Computer Graphics, Drosophila melanogaster, Genes, Humans, Models, Genetic, Saccharomyces cerevisiae, User-Computer Interface, Caenorhabditis elegans, Systems Integration, Internet, Protein Interaction Mapping, Databases, Genetic, Multiprotein Complexes
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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