The BioGRID interaction database: 2019 update

The BioGRID interaction database: 2019 update

2019 | Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma, Andrew Willems, Jasmin Coulombe-Huntington, Andrew Chatr-aryamontri, Kara Dolinski and Mike Tyers
The BioGRID interaction database is an open-access resource that curates and archives protein, genetic, and chemical interactions across major model organisms and humans. As of September 2018, BioGRID contains records for 1,598,688 biological interactions, derived from 55,809 publications, and over 700,000 post-translational modification sites. It now includes chemical interaction data, such as interactions between human drug targets and bioactive compounds, and a new aspect for genome-wide CRISPR/Cas9-based screens. An extension called the Open Repository for CRISPR Screens (ORCS) houses over 500 genome-wide screens in human and mouse cell lines. All data is freely available, downloadable in standard formats, and accessible via web services. BioGRID data are also distributed through partner databases like SGD, WormBase, and UniProt. BioGRID's data growth has increased by 32% since its 2017 update, with 1,598,688 interactions, including 774,460 protein interactions and 824,228 genetic interactions. These data are derived from 55,809 publications, including 1,437 high-throughput (HTP) and 54,372 low-throughput (LTP) studies. BioGRID curates data from a wide range of model organisms, including yeast, plants, and mammals, and has expanded to include post-translational modifications and chemical interactions. The database is curated using controlled vocabularies and text-mining methods, and data are updated monthly and shared with partner databases. BioGRID's curation strategy involves deep curation for specific themed projects on critical biological processes and diseases. It also collaborates with model organism databases (MODs) and meta-databases to facilitate data dissemination. BioGRID has developed a standardized Genetic Interactions Structured Terminology (GIST) to unify genetic interaction terminologies across different model organisms. This framework supports the integration of large volumes of genetic interaction data across species. BioGRID also curates chemical interactions, including data from DrugBank and manually curated small molecule–gene and–protein interactions. It has incorporated chemical–protein interaction records from DrugBank and now manually curates small molecule–gene and–protein interactions. BioGRID has developed a minimal unified record structure for chemical interactions, allowing efficient import and interoperability between multiple chemical databases. BioGRID has also developed the Open Repository for CRISPR Screens (ORCS) to house and distribute CRISPR screen datasets across multiple model organisms. ORCS provides a unified warehouse for all published CRISPR screen data and a user-friendly interface for searching, filtering, and downloading datasets. ORCS reports only published scores for screen data and displays results at the publication-, screen-, and gene-level with original scores and significance thresholds. BioThe BioGRID interaction database is an open-access resource that curates and archives protein, genetic, and chemical interactions across major model organisms and humans. As of September 2018, BioGRID contains records for 1,598,688 biological interactions, derived from 55,809 publications, and over 700,000 post-translational modification sites. It now includes chemical interaction data, such as interactions between human drug targets and bioactive compounds, and a new aspect for genome-wide CRISPR/Cas9-based screens. An extension called the Open Repository for CRISPR Screens (ORCS) houses over 500 genome-wide screens in human and mouse cell lines. All data is freely available, downloadable in standard formats, and accessible via web services. BioGRID data are also distributed through partner databases like SGD, WormBase, and UniProt. BioGRID's data growth has increased by 32% since its 2017 update, with 1,598,688 interactions, including 774,460 protein interactions and 824,228 genetic interactions. These data are derived from 55,809 publications, including 1,437 high-throughput (HTP) and 54,372 low-throughput (LTP) studies. BioGRID curates data from a wide range of model organisms, including yeast, plants, and mammals, and has expanded to include post-translational modifications and chemical interactions. The database is curated using controlled vocabularies and text-mining methods, and data are updated monthly and shared with partner databases. BioGRID's curation strategy involves deep curation for specific themed projects on critical biological processes and diseases. It also collaborates with model organism databases (MODs) and meta-databases to facilitate data dissemination. BioGRID has developed a standardized Genetic Interactions Structured Terminology (GIST) to unify genetic interaction terminologies across different model organisms. This framework supports the integration of large volumes of genetic interaction data across species. BioGRID also curates chemical interactions, including data from DrugBank and manually curated small molecule–gene and–protein interactions. It has incorporated chemical–protein interaction records from DrugBank and now manually curates small molecule–gene and–protein interactions. BioGRID has developed a minimal unified record structure for chemical interactions, allowing efficient import and interoperability between multiple chemical databases. BioGRID has also developed the Open Repository for CRISPR Screens (ORCS) to house and distribute CRISPR screen datasets across multiple model organisms. ORCS provides a unified warehouse for all published CRISPR screen data and a user-friendly interface for searching, filtering, and downloading datasets. ORCS reports only published scores for screen data and displays results at the publication-, screen-, and gene-level with original scores and significance thresholds. Bio
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