BIOGRID: AN OPEN RESOURCE FOR BIOLOGICAL INTERACTIONS AND NETWORK ANALYSIS
Michael David Tyers
Mt Sinai Hosp-samuel Lunenfeld Res Inst, Research Administration, Toronto, On M5t 3-l9
Grant 5R01RR024031-04 from National Center For Research Resources
Abstract: Project Summary Cellular behavior is dictated by complex networks of protein interactions, which are reflected in dense networks of genetic interactions. Recent high throughput (HTP) determination of interactions and phenotypes affords the potential of systems-level understanding of biological responses. However, these approaches are hampered by a dearth of software tools to manage, integrate and query large datasets. We have developed an open database called the BioGRID (www.thebiogrid.org) that now contains over 150,000 interaction from many species including humans. BioGRID is widely used, with on average 80,000 queries and millions of retrieved interactions per month. BioGRID is dynamically linked to a visualization tool called Osprey that allows users to build, query and visualize fully annotated biological interaction networks in graphical format. To augment HTP data, we exhaustively curated the budding yeast literature for over 30,000 reliable protein and genetic interactions, and thereby greatly facilitated prediction of protein function and network attributes. Here, we propose to elaborate BioGRID and Osprey as follows (i) curation of the yeast, worm, fly, plant and human literature for interactions and post translational modifications; (ii) expansion of the BioGRID platform to allow rapid access to and manipulation of many data types; and (iii) a major new release of Osprey that will enable cross-species network predictions, data integration and network interrogation. All software will be open source and engineered towards compatibility with the Generic Model Organism Database (GMOD) Project. The BioGRID will provide its interaction data and software tools to SGD, Wormbase, Flybase and other interested parties without restriction. The BioGRID/Opsrey platform will thus enable the biomedical and life sciences communities to access fully comprehensive datasets across multiple model organisms for hypothesis generation and network analysis. Relevance Complex biological networks underlie human development, health and disease. Because human networks are highly analogous to networks in tractable model organisms such as yeast, worms and flies, it is essential that the hundreds of thousands of biological interactions that form networks in all species are housed in a freely available manner that is amenable to rigorous analysis. The BioGRID and Osprey software platforms serve this function for the international research community
Keywords: Acetylation; Advanced Development; Amino Acid Sequence; Animal Model; Animal Models and Related Studies; Architecture; Back; Behavior; Biologic Sciences; Biological; Biological Function; Biological Process; Biological Sciences; Biology; C elegans; C.elegans; Caenorhabditis elegans; Cells; Code; Coding System; Communities; Complex; Computer Programs; Computer Software Tools; Computer software; Custom; Data; Data Banks; Data Bases; Data Files; Data Set; Data Storage and Retrieval; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Development; Devices; Disease; Disorder; Dorsum; Drugs, Nonproprietary; Endomycetales; Engineering; Engineering / Architecture; Engineerings; Files, Data; Fission Yeast; Flies; Future; Gene Expression; Generations; Generic Drugs; Genetic; Genome; Grouping; Hand; Health; Housing; Human; Human Development; Human, General; Imagery; Individual; International; Investigators; Java; Laboratories; Life Sciences; Link; Linux; Literature; Man (Taxonomy); Man, Modern; Modeling; Modification; Molecular Biology, Protein Sequencing; Network Analysis; On-Line Systems; Online Systems; PSI; Pathway Analysis; Pathway interactions; Peptide Sequence Determination; Phenotype; Phosphorylation; Plants; Plants, General; Plug-in; Post-Translational Modifications; Post-Translational Protein Processing; Posttranslational Modifications; Protein Modification; Protein Modification, Post-Translational; Protein Phosphorylation; Protein Processing, Post-Translational; Protein Processing, Posttranslational; Protein Sequencing; Protein Structure Initiative; Protein Structure, Primary; Protein/Amino Acid Biochemistry, Post-Translational Modification; Proteins; Publications; Quantitative Genetics; Research; Research Personnel; Research Resources; Researchers; Resources; Running; S cerevisiae; S pombe; Saccharomyces; Saccharomyces cerevisiae; Saccharomycetales; Schizosaccharomyces pombe; Scientific Publication; Sequence Determinations, Amino Acid; Sequence Determinations, Protein; Site; Software; Software Tools; Source; System; System, LOINC Axis 4; TXT; Text; Time; Tools, Software; Translations; Update; Visualization; Writing; Yeast, Baker`s; Yeast, Brewer`s; Yeast, Budding; Yeast, Fission; Yeasts; base; clinical data repository; clinical data warehouse; computer program/software; data integration; data repository; data retrieval; data storage; databases, model organisms; density; disease/disorder; experiment; experimental research; experimental study; fly; gene product; generic; genome database; groupings; improved; interest; interoperability; model organism; model organisms databases; online computer; open source; pathway; protein function; protein sequence; relational database; repository; research study; response; small molecule; tool; web based; web interface
Project start date: 2007-05-15
Project end date: 2011-02-28
Budget start date: 1-MAR-2010
Budget end date: 28-FEB-2011
5R01RR024031-04 (2010): $603323
Sponsored Links Excellgen http://Excellgen.com
BioGRID: An Open Resource For Biological Interactions And Network Analysis
Michael David Tyers
Mt Sinai Hosp-samuel Lunenfeld Res Inst
Grant 5R01RR024031-03 from National Center For Research Resources IRG: ZRG1
Abstract: Project Summary Cellular behavior is dictated by complex networks of protein interactions, which are reflected in dense networks of genetic interactions. Recent high throughput (HTP) determination of interactions and phenotypes affords the potential of systems-level understanding of biological responses. However, these approaches are hampered by a dearth of software tools to manage, integrate and query large datasets. We have developed an open database called the BioGRID (www.thebiogrid.org) that now contains over 150,000 interaction from many species including humans. BioGRID is widely used, with on average 80,000 queries and millions of retrieved interactions per month. BioGRID is dynamically linked to a visualization tool called Osprey that allows users to build, query and visualize fully annotated biological interaction networks in graphical format. To augment HTP data, we exhaustively curated the budding yeast literature for over 30,000 reliable protein and genetic interactions, and thereby greatly facilitated prediction of protein function and network attributes. Here, we propose to elaborate BioGRID and Osprey as follows (i) curation of the yeast, worm, fly, plant and human literature for interactions and post translational modifications; (ii) expansion of the BioGRID platform to allow rapid access to and manipulation of many data types; and (iii) a major new release of Osprey that will enable cross-species network predictions, data integration and network interrogation. All software will be open source and engineered towards compatibility with the Generic Model Organism Database (GMOD) Project. The BioGRID will provide its interaction data and software tools to SGD, Wormbase, Flybase and other interested parties without restriction. The BioGRID/Opsrey platform will thus enable the biomedical and life sciences communities to access fully comprehensive datasets across multiple model organisms for hypothesis generation and network analysis. Relevance Complex biological networks underlie human development, health and disease. Because human networks are highly analogous to networks in tractable model organisms such as yeast, worms and flies, it is essential that the hundreds of thousands of biological interactions that form networks in all species are housed in a freely available manner that is amenable to rigorous analysis. The BioGRID and Osprey software platforms serve this function for the international research community
Keywords: information system, protein Caenorhabditis elegans, Diptera, Saccharomyces, acetylation, back, base, behavior, biological model, biology, cell, community, density, flying, gait, gene expression, gene expression profiling, genetics, genome, hand, health, housing, human, model, molecular biology information system, motivation, organism, phenotype, phosphorylation, plant, protein sequence, publication, small molecule, yeast
Project start date: 2007-05-15
Project end date: 2011-02-28
Grants awarded to Michael David Tyers
Michael David Tyers
Mt Sinai Hosp-samuel Lunenfeld Res Inst
Project start date: 2007-05-15
Project end date: 2016-01-31