Major database collaborations

ARRAYEXPRESS

  • Dana Farber Cancer Institute, Boston, USA
  • DDBJ Omics Archive, DNA Databank of Japan, Mishima, Japan
  • Gene Expression Omnibus, NCBI, Bethesda, USA
  • Functional Genomics Data Society
  • Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, USA
  • Stanford Microarray Database, Stanford University, USA

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, USA

ChEBI

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

ChEMBL

  • BindingDB, University of California San Diego, USA
  • CanSAR, Institute of Cancer Research, London, UK
  • PubChem, NCBI, National Institutes of Health, Bethesda, USA

THE EUROPEAN NUCLEOTIDE ARCHIVE

The ENA is part of the International Nucleotide Sequence Database Collaboration. Other partners include:
  • National Center for Biotechnology Information, Bethesda, USA (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:

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

ENSEMBL GENOMES

  • Gramene at Cold Spring Harbor Laboratory, USA
  • PomBase with University College London and the University of Cambridge, UK
  • PhytoPath with Rothamsted Research, Harpenden, UK
  • VectorBase: a collaboration with University of Notre Dame, USA; Harvard University, USA; Institute of Molecular Biology and Biochemistry, Greece; University of New Mexico, USA; and Imperial College London, UK
  • 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, USA; Ontario Institute for Cancer Research, CA; Wellcome Trust Sanger Institute and Oxford University, UK

THE GENE ONTOLOGY CONSORTIUM

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

THE IMEX CONSORTIUM

  • Centro Nacional de Biotecnologia, Madrid, Spain
  • DIP at the University of California, Los Angeles, USA
  • 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, UK
  • HAMAP at the Swiss Institute of Bioinformatics, Geneva, Switzerland
  • InterPro at EMBL-EBI, Hinxton, UK
  • PANTHER at University of Southern California, Los Angeles, USA
  • Pfam at the Wellcome Trust Sanger Institute, Hinxton, UK
  • PIRSF at the Protein Information Resource, Georgetown University Medical Centre, Washington DC, USA
  • PRINTS at the University of Manchester, UK
  • 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, UK
  • SMART at EMBL, Heidelberg, Germany
  • SUPERFAMILY at the University of Bristol, UK
  • TIGRFAMs at The Institute of Genome Research, Rockville, USA

THE PROTEIN DATABANK IN EUROPE

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

PRIDE

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

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, USA
  • PubMed Central Canada

REACTOME

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

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, USA
  • UniProt at the Protein Information Resource, University of Delaware, USA
  • UniProt at the Swiss Institute of Bioinformatics, Geneva, Switzerland