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| Kyoto Encyclopedia of Genes and Genomes | |
|---|---|
| Name | Kyoto Encyclopedia of Genes and Genomes |
| Established | 1995 |
| Focus | Bioinformatics, Genomics, Systems Biology |
| Founder | Minoru Kanehisa |
| Country | Japan |
| Headquarters | Kyoto |
Kyoto Encyclopedia of Genes and Genomes is a curated bioinformatics resource integrating genomic, chemical, and systems information to facilitate understanding of cellular and organismal functions. It provides pathway maps, orthology-based annotations, and molecular interaction networks used by researchers worldwide, including teams at University of Tokyo, Harvard University, Massachusetts Institute of Technology, Max Planck Society, and National Institutes of Health. The resource supports comparative genomics, drug discovery, and metabolic engineering studies undertaken at institutions such as Stanford University, University of California, Berkeley, University of Cambridge, University of Oxford, and Riken.
The database assembles genomic sequences, pathway maps, and molecular interaction data linking genes, proteins, small molecules, and phenotypes for organisms studied at Imperial College London, Princeton University, ETH Zurich, California Institute of Technology, and University of Chicago. It offers pathway representations comparable to resources like Reactome, BioCyc, UniProt, Gene Ontology Consortium, and Ensembl. Users from Centers for Disease Control and Prevention, European Molecular Biology Laboratory, Wellcome Trust Sanger Institute, Broad Institute, and Cold Spring Harbor Laboratory employ it for systems-level interpretation alongside datasets from GenBank, Protein Data Bank, ArrayExpress, Sequence Read Archive, and ClinicalTrials.gov.
Founded in 1995 by Minoru Kanehisa at Kyoto University, the project evolved through collaborations with National Bioscience Database Center, Japan Science and Technology Agency, Ministry of Education, Culture, Sports, Science and Technology (Japan), Human Genome Project, and international partners such as European Bioinformatics Institute and National Center for Biotechnology Information. Major milestones include integration of pathway diagrams influenced by conventions from KEGG PATHWAY-style curation and expansion of orthology concepts paralleling work at COG Consortium, OrthoDB, InParanoid, and OMA Project. Funding and institutional interactions involved organizations like Japan Agency for Medical Research and Development, Wellcome Trust, G7 Science Ministers, and collaborations with industrial groups including Pfizer, Novartis, AstraZeneca, and Takeda Pharmaceutical Company.
The resource organizes information into modules connecting genes, proteins, reactions, compounds, reactions networks, and phenotypes used by groups at University of California, San Diego, Johns Hopkins University, Yale University, University of Pennsylvania, and University of Washington. Core modules align with standards from INSDC partners and integrate identifiers shared with PubChem, ChEBI, KEGG COMPOUND-style records, EC (Enzyme Commission), and cross-references to PubMed. Contents include annotated genomes across taxa studied at Scripps Research Institute, Marine Biological Laboratory, Cold Spring Harbor Laboratory, Smithsonian Institution, and Natural History Museum, London. The orthology-based grouping mirrors approaches used by EggNOG, PantherDB, and KEGG Orthology while pathway maps interoperate with standards endorsed by World Health Organization, Food and Agriculture Organization, United Nations Environment Programme, and regulatory bodies like European Medicines Agency.
The platform provides pathway mapping, enrichment analysis, and network visualization tools comparable to those at Cytoscape, DAVID, GSEA, STRING, and Bioconductor. Computational services integrate algorithms developed in collaborations with research teams at Riken Center for Computational Science, Los Alamos National Laboratory, Argonne National Laboratory, IBM Research, and Google DeepMind for large-scale mapping and annotation. Web interfaces and APIs support programmatic access used by engineers at Amazon Web Services, Microsoft Research, Oracle Corporation, GitHub, and academic groups at New York University.
Researchers apply the resource in studies on metabolic engineering at Delft University of Technology, synthetic biology at MIT Media Lab, drug target identification at GlaxoSmithKline, epidemiology modeling at London School of Hygiene and Tropical Medicine, and agricultural biotechnology at Wageningen University & Research. It has informed vaccine and antimicrobial development programs at World Health Organization, Centers for Disease Control and Prevention, Bill & Melinda Gates Foundation, and pharmaceutical projects at Eli Lilly and Company. Cross-disciplinary impact spans publications in journals such as Nature, Science, Cell, Proceedings of the National Academy of Sciences, and Genome Research.
Maintained by teams at Kyoto University and affiliated centers including National Institute of Genetics, Osaka University, Tohoku University, Hokkaido University, and Nagoya University, the resource offers public web access and downloadable datasets used by consortia like ENCODE, GTEx, 1000 Genomes Project, Human Microbiome Project, and Earth Microbiome Project. Licensing and data-sharing policies interface with repositories such as Zenodo, Figshare, Dryad, and standards bodies including Open Biological and Biomedical Ontology Foundry.
Critiques from researchers at University of California, Los Angeles, University of Toronto, McGill University, University of Melbourne, and Australian National University highlight issues of manual curation scalability similar to debates at UniProtKB/Swiss-Prot and concerns about pathway completeness raised in comparisons with Reactome and BioCyc. Limitations cited include lag in integrating latest datasets from The Cancer Genome Atlas, ClinVar, Metabolomics Workbench, and interoperability challenges referenced by Global Alliance for Genomics and Health and FAIR principles advocates.
Category:Bioinformatics databases