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The BioGRID interaction database: 2015 update.

Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M - Nucleic Acids Res. (2014)

Bottom Line: BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats.In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks.BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada.

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Snapshot of the new IMS curation interface. The main functionalities available to BioGRID curators in the new IMS for the annotation of protein and genetic interactions are shown (A–D). The new system is based on ontologies (E) for the annotation of gene function (Gene Ontology), cell type (Cell Type Ontology), tissue (BRENDA Tissue ontology), small molecules (CheBI), human disease (Human Disease Ontology), human phenotypes (Human Phenotype Ontology, Phenotypic Qualities Ontologies) or anatomical structures (Uberon) and accepts annotation of binary and n-way interactions (F).
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Figure 3: Snapshot of the new IMS curation interface. The main functionalities available to BioGRID curators in the new IMS for the annotation of protein and genetic interactions are shown (A–D). The new system is based on ontologies (E) for the annotation of gene function (Gene Ontology), cell type (Cell Type Ontology), tissue (BRENDA Tissue ontology), small molecules (CheBI), human disease (Human Disease Ontology), human phenotypes (Human Phenotype Ontology, Phenotypic Qualities Ontologies) or anatomical structures (Uberon) and accepts annotation of binary and n-way interactions (F).

Mentions: The web-based IMS curation interface for the BioGRID has recently undergone major revisions in order to allow more sophisticated annotation for future curation projects. The IMS core architecture now enables curation of a broader range of interaction types including for proteins, genes, RNA, small molecules, domains and protein fragments. The overall database architecture has also been improved to allow representation of higher order relationships between interacting partners, such as triple mutant combinations, protein complexes, chemical-genetic interactions and post-translational modifications (Figure 2). The IMS has been elaborated to include more than a dozen comprehensive new ontologies (77–79) that allow curators to unambiguously record new details of any relationship, such as cell lines, phenotypes, small molecules, alleles, diseases, tissues and enzymes (Figure 3). IMS features for curation tracking, fault tolerance and overall curation quality have also been improved. For example, to accommodate more frequent deposition of high-throughput datasets in BioGRID, new tracking tools enable the long-term storage of Supplementary Data files for archival and data reconciliation purposes. The IMS can also track the decision-making processes of each curator for each specific publication, such that it is possible to trace decisions even when the original source material is no longer available or the curator is no longer a member of the BioGRID team. To improve the overall fault tolerance of the underlying database architecture, we have continuously updated our MySQL database platform to utilize enhancements such as InnoDB tables and transactional logging.


The BioGRID interaction database: 2015 update.

Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M - Nucleic Acids Res. (2014)

Snapshot of the new IMS curation interface. The main functionalities available to BioGRID curators in the new IMS for the annotation of protein and genetic interactions are shown (A–D). The new system is based on ontologies (E) for the annotation of gene function (Gene Ontology), cell type (Cell Type Ontology), tissue (BRENDA Tissue ontology), small molecules (CheBI), human disease (Human Disease Ontology), human phenotypes (Human Phenotype Ontology, Phenotypic Qualities Ontologies) or anatomical structures (Uberon) and accepts annotation of binary and n-way interactions (F).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383984&req=5

Figure 3: Snapshot of the new IMS curation interface. The main functionalities available to BioGRID curators in the new IMS for the annotation of protein and genetic interactions are shown (A–D). The new system is based on ontologies (E) for the annotation of gene function (Gene Ontology), cell type (Cell Type Ontology), tissue (BRENDA Tissue ontology), small molecules (CheBI), human disease (Human Disease Ontology), human phenotypes (Human Phenotype Ontology, Phenotypic Qualities Ontologies) or anatomical structures (Uberon) and accepts annotation of binary and n-way interactions (F).
Mentions: The web-based IMS curation interface for the BioGRID has recently undergone major revisions in order to allow more sophisticated annotation for future curation projects. The IMS core architecture now enables curation of a broader range of interaction types including for proteins, genes, RNA, small molecules, domains and protein fragments. The overall database architecture has also been improved to allow representation of higher order relationships between interacting partners, such as triple mutant combinations, protein complexes, chemical-genetic interactions and post-translational modifications (Figure 2). The IMS has been elaborated to include more than a dozen comprehensive new ontologies (77–79) that allow curators to unambiguously record new details of any relationship, such as cell lines, phenotypes, small molecules, alleles, diseases, tissues and enzymes (Figure 3). IMS features for curation tracking, fault tolerance and overall curation quality have also been improved. For example, to accommodate more frequent deposition of high-throughput datasets in BioGRID, new tracking tools enable the long-term storage of Supplementary Data files for archival and data reconciliation purposes. The IMS can also track the decision-making processes of each curator for each specific publication, such that it is possible to trace decisions even when the original source material is no longer available or the curator is no longer a member of the BioGRID team. To improve the overall fault tolerance of the underlying database architecture, we have continuously updated our MySQL database platform to utilize enhancements such as InnoDB tables and transactional logging.

Bottom Line: BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats.In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks.BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada.

Show MeSH