Major database collaborations

ArrayExpress

  • Gene Expression Omnibus, National Center for Biotechnology Information, Bethesda, Maryland, United States

BioModels database

  • Database of Ouantitative Cellular Signalling, National Center for Biological Sciences, India
  • JWS Online, Stellenbosch University, South Africa
  • Physiome Model Repository, Auckland Bioengineering Institute, New Zealand
  • The Virtual Cell, University of Connecticut Health Center, United States

ChEBI

  • ChemIdPlus, National Library of Medicine, Bethesda, United States
  • DrugBank, University of Alberta, Canada
  • Immune Epitope Database (IEDB) at La Jolla Institute for Allergy and Immunology, United States
  • KEGG Compound, Kyoto University Bioinformatics Centre, Japan
  • OBI Ontology Consortium
  • PubChem, National Institutes of Health, Bethesda, United States
  • UniPathways, Swiss Institute of Bioinformatics, Geneva, Switzerland

ChEMBL

  • BindingDB, University of California San Diego, United States
  • CanSAR, Institute of Cancer Research, London, United Kingdom
  • PubChem, NCBI, National Institutes of Health, Bethesda, United States

Ensembl

Here we list collaborations with the major genome centres and representative collaborations for the human, mouse, rat and chicken genomes. There are many others.

  • Baylor College of Medicine, Houston, United States
  • Broad Institute, Cambridge, United States
  • DOE Joint Genome Institute, Walnut Creek, United States
  • Ensembl at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Genome Browser at the University of California, Santa Cruz, United States
  • Map Viewer at the National Center for Biotechnology Information, Bethesda, United States
  • Mouse Genome Informatics at the Jackson Laboratory, Bar Harbor, United States
  • Rat Genome Database at the Medical College of Wisconsin, Milwaukee, United States
  • The Roslin Institute, Midlothian, Scotland, United Kingdom

Ensembl Genomes

  • Gramene at Cold Spring Harbor Laboratory, United States
  • PomBase with University College London and the University of Cambridge, United Kingdom
  • PhytoPath with Rothamsted Research, Harpenden, United Kingdom
  • VectorBase: a collaboration with University of Notre Dame, United States; Harvard University, United States; Institute of Molecular Biology and Biochemistry, Greece; University of New Mexico, United States; and Imperial College London, United Kingdom
  • Microme, a European collaboration with 14 partners
  • transPLANT, a European project with 11 partners
  • WormBase, a collaboration with the California Institute of Technology and Washington University, United States; Ontario Institute for Cancer Research, Canada; Wellcome Trust Sanger Institute and Oxford University, United Kingdom

The European Nucleotide Archive (ENA)

The ENA is part of the International Nucleotide Sequence Database Collaboration. Other partners include:

  • National Center for Biotechnology Information, Bethesda, United States (GenBank, Trace Archive and Sequence Read Archive)
  • National Institute of Genetics, Mishima, Japan (DNA DataBank of Japan, Trace Archive and Sequence Read Archive)

Other ENA collaborations

Expression Atlas

  • Oregon State University, Corvallis, United States
  • Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
  • Rothamsted Research, Harpenden, United Kingdom
  • Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom

Gene Ontology Consortium

  • Agbase, Mississippi State University, Mississippi, United States
  • The Arabidopsis Information Resource, Carnegie Institution of Washington, Stanford, United States
  • Berkeley Bioinformatics and Ontology Project, Lawrence Berkeley National Laboratory, Berkeley, United States
  • British Heart Foundation, University College London, London, United Kingdom
  • Candida Genome Database, Stanford University, Stanford, United States
  • DictyBase at Northwestern University, Chicago, United States
  • EcoliWiki
  • FlyBase at the University of Cambridge, United Kingdom
  • GeneDB S. pombe and GeneDB for protozoa at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Gramene at Cornell University, Ithaca, United States
  • Institute for Genome Sciences, University of Maryland, Baltimore, United States
  • The J. Craig Venter Institute, Rockville, United States
  • Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, United States
  • Muscle TRAIT, University of Padua, Padua, Italy
  • Plant-Association Microbe Gene Ontology, Virginia Polytechnic Institute and State University, Blacksburg, United States
  • Rat Genome Database at the Medical College of Wisconsin, Milwaukee, United States
  • Reactome at Cold Spring Harbor Laboratory, United States
  • Saccharomyces Genome Database, Stanford University, Stanford, United States
  • WormBase at California Institute of Technology, Pasadena, United States
  • The Zebrafish Information Network at the University of Oregon, Eugene, United States

IMEx Consortium

  • Centro Nacional de Biotecnologia, Madrid, Spain
  • DIP at the University of California, Los Angeles, United States
  • MINT at University Tor Vergata, Rome, Italy
  • MIPS at the National Research Centre for Environment and Health, Munich, Germany
  • Neuroproteomics platform of National Neurosciences Facility, Melbourne, Australia
  • Shanghai Institutes for Biological Sciences, Shanghai, China

InterPro

  • CATH-Gene3D at University College London, United Kingdom
  • HAMAP at the Swiss Institute of Bioinformatics, Geneva, Switzerland
  • InterPro at EMBL-EBI, Hinxton, United Kingdom
  • PANTHER at University of Southern California, Los Angeles, United States
  • Pfam at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • PIRSF at the Protein Information Resource, Georgetown University Medical Centre, Washington DC, United States
  • PRINTS at the University of Manchester, United Kingdom
  • ProDom at INRA and CNRS, Toulouse, France
  • PROSITE at the Swiss Institute of Bioinformatics, Geneva, Switzerland
  • SCOP at the Laboratory of Molecular Biology, University of Cambridge, United Kingdom
  • SMART at EMBL, Heidelberg, Germany
  • SUPERFAMILY at the University of Bristol, United Kingdom
  • TIGRFAMs at The Institute of Genome Research, Rockville, United States

Protein Data Bank in Europe

  • PDBe is a partner in the World Wide Protein Data Bank (wwPDB). Other partners include: 
  • BioMagResBank, University of Wisconsin, Madison, United States
  • PDBj at Osaka University, Japan
  • Research Collaboratory for Structural Bioinformatics, United States

PRIDE

  • Faculty of Life Sciences, The University of Manchester, United Kingdom
  • Ghent University, Ghent, Belgium
  • The Yonsei Proteome Research Center, Yonsei University, Seoul, Korea

RNAcentral

  • dictyBase at Northwestern University, Chicago, United States
  • the Greengenes Consortium, a collaboration with University of Colorado, Boulder, USA; University of Queensland, Australia; Second Genome Inc, San Francisco, United States
  • gtRNAdb at University of California Santa Cruz, Santa Cruz, United States
  • LNCipedia at Ghent University, Ghent, Belgium
  • lncRNAdb at Garvan Institute of Medical Research, Darlinghurst, Australia
  • miRBase at University of Manchester, United Kingdom
  • Modomics at International Institute of Molecular and Cell Biology, Warsaw, Poland
  • NONCODE at Institute of Biophysics at Chinese Academy of Sciences, Beijing, China
  • Pombase at University College London and the University of Cambridge, UK
  • Ribosomal Database Project at Michigan State University, East Lansing, United States
  • RefSeq at National Center for Biotechnology Information, Bethesda, United States
  • Saccharomyces Genome Database, Stanford University, Stanford, United States
  • SILVA at Max Planck Institute for Marine Microbiology, Bremen, Germany
  • snOPY at University of Miyazaki, Miyazaki, Japan
  • SRPDB at University of Texas Health Science Center, San Antonio, United States
  • The Arabidopsis Information Resource (TAIR) at Phoenix Bioinformatics Corporation, Redwood City, United States
  • tmRNA Website at Sandia National Laboratories, Livermore, United States
  • Vega at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Wormbase, a collaboration with the California Institute of Technology and Washington University, United States; Ontario Institute for Cancer Research, CA; Wellcome Trust Sanger Institute and Oxford University, United Kingdom

 

RNAcentral databases at EMBL-EBI

  • Rfam
  • Protein Data Bank in Europe (PDBe)
  • European Nucleotide Archive (ENA)

Europe PubMed Central

Europe PubMed Central is part of PubMed Central International. Other database partners include:

  • PubMed Central, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, United States
  • PubMed Central Canada

Reactome

  • New York University Medical Center, United States
  • Ontario Institute for Cancer Research, Toronto, Ontario, Canada
  • Reactome at Cold Spring Harbor Laboratory, United States

UniProt: The Unified Protein Resource

UniProt at EMBL-EBI is part of the UniProt Consortium. Other partners include:

  • UniProt at the Protein Information Resource, Georgetown University Medical Centre, Washington, DC, United States
  • UniProt at the Protein Information Resource, University of Delaware, United States
  • UniProt at the Swiss Institute of Bioinformatics, Geneva, Switzerland