THE GENE ONTOLOGY CONSORTIUM• Agbase, Mississippi State University, United States• The Arabidopsis Information Resource, Carnegie Institution of Washington, United States• Berkeley Bioinformatics and Ontology Project, Lawrence Berkeley National Laboratory, United States• British Heart Foundation, University College London, United Kingdom• Candida Genome Database, Stanford University, United States• DictyBase at Northwestern University, United States• EcoliWiki• FlyBase at the University of Cambridge, United Kingdom• GeneDB S. pombe and GeneDB for protozoa at the Wellcome Trust Sanger Institute, United Kingdom• Gramene at Cornell University, United States• Institute for Genome Sciences, University of Maryland, United States• The J. Craig Venter Institute, United States• Mouse Genome Informatics, The Jackson Laboratory, United States• Muscle TRAIT, University of Padua, Italy• Plant-Association Microbe Gene Ontology, Virginia Polytechnic Institute and State University, United States• Rat Genome Database at the Medical College of Wisconsin, United States• Reactome at Cold Spring Harbor Laboratory, United States• Saccharomyces Genome Database, Stanford University, United States• WormBase at California Institute of Technology, United States• The Zebrafish Information Network at the University of Oregon, United StatesTHE IMEX CONSORTIUM• Centro Nacional de Biotecnologia, Spain• DIP at the University of California, Los Angeles, United States• MINT at University Tor Vergata, Italy• MIPS at the National Research Centre for Environment and Health, Germany• Neuroproteomics platform of National Neurosciences Facility, Australia• Shanghai Institutes for Biological Sciences, Shanghai, China112 <strong>2012</strong> <strong>EMBL</strong>-<strong>EBI</strong> <strong>Annual</strong> <strong>Scientific</strong> <strong>Report</strong>
INTERPRO• CATH-Gene3D at University College London, United Kingdom• HAMAP at the Swiss Institute of Bioinformatics, Switzerland• InterPro at <strong>EMBL</strong>-<strong>EBI</strong>, United Kingdom• PANTHER at University of Southern California, Los Angeles, United States• Pfam at the Wellcome Trust Sanger Institute, United Kingdom• PIRSF at the Protein Information Resource, Georgetown University Medical Centre, United States• PRINTS at the University of Manchester, United Kingdom• ProDom at INRA and CNRS, France• PROSITE at the Swiss Institute of Bioinformatics, Switzerland• SCOP at the Laboratory of Molecular Biology, University of Cambridge, United Kingdom• SMART at <strong>EMBL</strong>, Heidelberg, Germany• SUPERFAMILY at the University of Bristol, United Kingdom• TIGRFAMs at The Institute of Genome Research, United StatesTHE PROTEIN DATABANK IN EUROPEPDBe is a partner in the World Wide Protein Data Bank (wwPDB). Other partners include:• BioMagResBank, University of Wisconsin, United States• PDBj at Osaka University, Japan• Research Collaboratory for Structural Bioinformatics, United StatesPRIDE• Faculty of Life Sciences, The University of Manchester, United Kingdom• Ghent University, Belgium• The Yonsei Proteome Research Center, Yonsei University, South 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,United States• PubMed Central Canada<strong>2012</strong> <strong>EMBL</strong>-<strong>EBI</strong> <strong>Annual</strong> <strong>Scientific</strong> <strong>Report</strong>113
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EMBL-European Bioinformatics Instit
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Table of contentsIntroduction & ove
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EMBL-EBI 2012It was a year of trans
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New service developments• Underst
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Organisation ofEMBL-EBI Leadership
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dGenes, genomes and variationThe Eu
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dGenes, genomes and variationSummar
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European Nucleotide ArchiveOur team
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Vertebrate genomicsThe Vertebrate G
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Nonvertebrate genomicsWe provide to
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gMolecular atlasLife scientists are
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Functional genomicsThe Functional G
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Functional genomics productionOur t
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Functional genomics developmentOur
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PProteins and protein familiesUniPr
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UniProt contentOne of the central a
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UniProt developmentOur team provide
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InterProOur team co-ordinates the I
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sMolecular and cellular structureUn
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Protein Data Bank in EuropeThe majo
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PDBe content and integrationOur goa
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PDBe databases and servicesOur team
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yMolecular systemsThe genes and gen
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Proteomics servicesThe Proteomics S
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Chemical biologyThe importance of s
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ChEMBLThe ChEMBL team develops and
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Cheminformatics and metabolismOur t
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cCross-domain toolsand resourcesSci
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Literature servicesScientific liter
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Research2012 has seen the further t
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Bertone groupPluripotency, reprogra
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- Page 66 and 67: Enright groupFunctional genomics an
- Page 68 and 69: Goldman groupEvolutionary tools for
- Page 70 and 71: Le Novère groupComputational syste
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- Page 74 and 75: Marioni groupComputational and evol
- Page 76 and 77: Rebholz groupPhenotypes and multili
- Page 78 and 79: Saez-Rodriguez groupSystems biomedi
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- Page 82 and 83: The EMBL International PhDProgramme
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- Page 90 and 91: NExternal relationsAs a European In
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- Page 96 and 97: q AdministrationThe EMBL-EBI Admini
- Page 98 and 99: Funding and resource allocationDesp
- Page 100 and 101: Growth of core resourcesIn 2012 the
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- Page 104 and 105: Staff growthOur organisational stru
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- Page 112 and 113: Major database collaborationsARRAYE
- Page 116 and 117: REACTOME• New York University Med
- Page 118 and 119: Publications in 2012In 2012, EMBL-E
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- Page 122 and 123: Kruger, F. A., Rostom R. and Overin
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