EMBL-EBI Annual Scientific Report 2012

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yMolecular systemsThe genes and gene products encoded by genomes do not act inisolation but do so in co-ordinated systems, often containing protein,small molecule and oligonucleotide or oligosaccharide components.TheMolecular Systems Cluster groups together resources that cover systemsbiology: from enzymes and their mechanisms, through protein—proteininteractions and networks, to pathways and approaches to quantitativelymodel entire complex biological systems.The Enzyme Portal, launched in February 2012, draws together enzyme-related data from ten different databases. It is the firstof EMBL-EBI’s resources to be entirely user-led, from conception to interface design (Pavelin et al., 2012). The Enzyme Portalallows easy and reliable searching across many enzyme resources, including two developed and maintained directly in theSteinbeck group: IntEnz and Rhea.In 2012 IntAct, our database of molecular interactions, topped 300 000 pieces of evidence supporting interactions betweenmolecules. The IntAct team also led international efforts to co-ordinate the curation of molecular interaction data (Orchard etal., 2012).Following the departure of Nicolas Le Novère to The Babraham Institute, Cambridge, the leadership of BioModels atEMBL-EBI is now in Henning Hermjakob’s hands. The contents of this resource grew by two orders of magnitude in 2012,owing to the integration of a large set of models from the Path2Models project. This represents a new, ‘top-down’ approach tobuilding quantitative models, starting with pathways from data resources.Enzyme PortalThe Enzyme Portal provides integrated enzyme-relateddata for all EBI enzyme resources as well as the underlyingfunctional and genomic data.http://ebi.ac.uk/enzymeportal/ReactomeReactome is an open-source, open-access, manuallycurated and peer-reviewed pathway database. Pathwayannotations are authored by expert biologists, in collaborationwith Reactome editorial staff, and cross-referenced to manybioinformatics databases.http://ebi.ac.uk/reactome/IntActIntAct provides a freely available, open-source databasesystem and analysis tools for molecular interaction data.All interactions are derived from literature curation or directuser submissions.http://ebi.ac.uk/intact/BioModelsBioModels Database is a repository of peer-reviewed,published, computational models, primarily from the fieldof systems biology and of wide biological application.BioModels allows biologists to store, search and retrievemathematical models covering a wide range of diversesystems. In addition, the database can be used to generatesub-models, can be simulated online and can be convertedbetween different representational formats. This resource alsofeatures programmatic access via web Services.http://ebi.ac.uk/biomodels/44 2012 EMBL-EBI Annual Scientific Report
John OveringtonBSc Chemistry, Bath. PhD in Crystallography,Birkbeck College, London, 1991. Postdoctoralresearch, ICRF, 1990-1992. Pfizer 1992-2000.Inpharmatica 2000-2008.At EMBL-EBI since 2008.Summary of progress 2012Henning HermjakobBiomodels, IntAct& ReactomeChristoph SteinbeckEnzyme Portal,IntEnz & Rhea• Published the IMEx consortiumstrategy for internationallyco-ordinated curation ofmolecular interaction data(Orchard et al, 2012);• Reached 300 000 binaryinteraction evidences in theIntAct molecular interactiondatabase (Kerrien et al, 2012);• Reached the milestone of 6000reactions in the Reactomepathway resource;• Developed and launched theEnzyme Portal;• Issued releases 28 to 36 of theRhea enzyme resource;• Issued releases 75 to 83 of theIntEnz enzyme resource;• Redesigned the Enzyme Portal,IntEnz and Rhea to fit withthe new EMBL-EBI website,scheduled to launch inearly 2013.• Integrated the Path2Modelsdata, increasing the data contentof BioModels Database by twoorders of magnitude to morethan 140 000.2012 EMBL-EBI Annual Scientific Report45
Page 1 and 2: EMBL-European Bioinformatics Instit
Page 3: Table of contentsIntroduction & ove
Page 6 and 7: EMBL-EBI 2012It was a year of trans
Page 8 and 9: New service developments• Underst
Page 10 and 11: Organisation ofEMBL-EBI Leadership
Page 12 and 13: dGenes, genomes and variationThe Eu
Page 14 and 15: dGenes, genomes and variationSummar
Page 16 and 17: European Nucleotide ArchiveOur team
Page 18 and 19: Vertebrate genomicsThe Vertebrate G
Page 20 and 21: Nonvertebrate genomicsWe provide to
Page 22 and 23: gMolecular atlasLife scientists are
Page 24 and 25: Functional genomicsThe Functional G
Page 26 and 27: Functional genomics productionOur t
Page 28 and 29: Functional genomics developmentOur
Page 30 and 31: PProteins and protein familiesUniPr
Page 32 and 33: UniProt contentOne of the central a
Page 34 and 35: UniProt developmentOur team provide
Page 36 and 37: InterProOur team co-ordinates the I
Page 38 and 39: sMolecular and cellular structureUn
Page 40 and 41: Protein Data Bank in EuropeThe majo
Page 42 and 43: PDBe content and integrationOur goa
Page 44 and 45: PDBe databases and servicesOur team
Page 48 and 49: Proteomics servicesThe Proteomics S
Page 50 and 51: Chemical biologyThe importance of s
Page 52 and 53: ChEMBLThe ChEMBL team develops and
Page 54 and 55: Cheminformatics and metabolismOur t
Page 56 and 57: cCross-domain toolsand resourcesSci
Page 58 and 59: Literature servicesScientific liter
Page 60 and 61: Research2012 has seen the further t
Page 62 and 63: Bertone groupPluripotency, reprogra
Page 64 and 65: Birney groupNucleotide dataDNA sequ
Page 66 and 67: Enright groupFunctional genomics an
Page 68 and 69: Goldman groupEvolutionary tools for
Page 70 and 71: Le Novère groupComputational syste
Page 72 and 73: Luscombe groupGenomics and regulato
Page 74 and 75: Marioni groupComputational and evol
Page 76 and 77: Rebholz groupPhenotypes and multili
Page 78 and 79: Saez-Rodriguez groupSystems biomedi
Page 80 and 81: Thornton groupProteins: structure,
Page 82 and 83: The EMBL International PhDProgramme
Page 84 and 85: SupportOur support teams provide fo
Page 86 and 87: T TrainingAs part of EMBL-EBI’s m
Page 88 and 89: IIndustry programmeSince 1996 the I
Page 90 and 91: NExternal relationsAs a European In
Page 92 and 93: sExternal servicesOur team manages
Page 94 and 95: SSystems and networkingOur team man
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q AdministrationThe EMBL-EBI Admini
Page 98 and 99:
Funding and resource allocationDesp
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Growth of core resourcesIn 2012 the
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CollaborationsEMBL-EBI is a highly
Page 104 and 105:
Staff growthOur organisational stru
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Scientific advisory commiteesEMBL S
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The International Nucleotide Sequen
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EMDataBank Advisory Committee• Jo
Page 112 and 113:
Major database collaborationsARRAYE
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THE GENE ONTOLOGY CONSORTIUM• Agb
Page 116 and 117:
REACTOME• New York University Med
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Publications in 2012In 2012, EMBL-E
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Doreleijers, J. F., Vranken W. F.,
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Kruger, F. A., Rostom R. and Overin
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Sahakyan, Aleksandr B., Cavalli And
Page 128:
EMBL - European Bioinformatics Inst
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EMBL-EBI Annual Scientific Report 2012

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