EMBL-EBI Annual Scientific Report 2012

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UniProt contentOne of the central activities of the UniProt Content team is the biocurationof our databases. Biocuration involves the interpretation and integration ofinformation relevant to biology into a database or resource that enablesintegration of the scientific literature as well as large datasets. The primarygoals of biocuration are accurate and comprehensive representation ofbiological knowledge, as well as easy access to this data for workingscientists and a basis for computational analysis.UniProt manual curationThe curation methods we apply to UniProtKB/Swiss-Protinclude manual extraction and structuring of experimentalinformation from the literature, manual verification of resultsfrom computational analyses, quality assessment, integrationof large-scale datasets and continuous updating as newinformation becomes available.UniProt automatic annotationUniProt has developed two complementary approaches inorder to automatically annotate protein sequences with ahigh degree of accuracy. UniRule is a collection of manuallycurated annotation rules, which define annotations that canbe propagated based on specific conditions. The StatisticalAutomatic Annotation System (SAAS) is an automatic,decision-tree-based, rule-generating system. The centralcomponents of these approaches are rules based on themanually curated data in UniProtKB/Swiss-Prot from theexperimental literature and InterPro classification.UniProt GO annotation (GOA)The UniProt GO annotation (GOA) program aims to addhigh-quality GO annotations to proteins in the UniProtKnowledgebase (UniProtKB). We supplement UniProt manualand electronic GO annotations with manual annotationssupplied by external collaborating GO Consortium groups.This ensures that users have a comprehensive GO annotationdataset. UniProt is a member of the GO Consortium.Major achievementsAs a core contributor to the Consensus CDS (CCDS) project,UniProt now has 18 854 manually curated human entries, ofthe total 20 248 records, in synch with the RefSeq annotationgroup (National Center for Biotechnology Information, NCBI)and the Ensembl and HAVANA teams (EMBL-EBI and theWellcome Trust Sanger Institute). A component of this effortinvolves ensuring a curated and complete synchronisationwith the HUGO Gene Nomenclature Committee (HGNC),which has assigned unique gene symbols and names to morethan 33 500 human loci (over 19 000 of these are listed ascoding for proteins).We play a major role in establishing minimal standards forgenome annotation across the taxonomic range, largelythanks to collaborations arising from the annual NCBIGenome Annotation Workshops, which are attended byresearchers from life science organisations worldwide. Thesestandards have contributed significantly to the annotation ofcomplete genomes and proteomes and are helping scientistsexploit these data to their full potential.Our team is working on a ‘gold standard’ dataset to helpusers identify all experimental data for a given proteinfrom a particular strain of a given organism, as well as allexperimentally characterised annotations/proteomes froma proteome or protein family. This work is undertaken incollaboration with model organism databases and theEvidence Code Ontology (ECO).Our curators are key members of the GO ConsortiumReference Genomes Initiative for the human proteome andprovide high-quality annotations for human proteins. In 2012,the electronic GO annotation pipeline was reviewed andimproved, with particular focus on the UniPathway, Ensembland InterPro collaborations.30 2012 EMBL-EBI Annual Scientific Report
Claire O’DonovanBSc (Hons) in Biochemistry, University CollegeCork, 1992. Diploma in Computer ScienceUniversity College Cork, 1993.At EMBL since 1993, at EMBL-EBI since 1994.Team Leader since 2009.Future plansIn 2013 we will continue work on a gold-standard datasetacross the taxonomic range to fully address the requirementsof the biochemical community. We will also continue toexpand and refine our Ensembl and Genome ReferenceConsortium collaborations to ensure that UniProtKB providesthe most appropriate gene-centric view of protein space,allowing a cleaner and more logical mapping of gene andgenomic resources to UniProtKB. We also plan to extend ournomenclature collaborations to include higher-level organisms.We will prioritise the extraction of experimental data fromthe literature and extend our use of data-mining methods toidentify scientific literature of particular interest with regardto our annotation priorities. We are committed to expandingUniRule by adding feature annotation and extending thenumber and range of rules with additional curator resources,both internal and external.Selected publicationsVelankar, S., et al. (2013) SIFTS: Structure Integration withFunction, Taxonomy and Sequences resource. Nucleic AcidsRes 41 (Database issue), D483-489.The UniProt Consortium (2013) Update on activities at theUniversal Protein Resource (UniProt) in 2013. Nucleic AcidsRes 41 (Database issue), D43-D47.Alcantara, R., et al. (2013) The EBI enzyme portal. NucleicAcids Res 41 (Database issue), D773-D780.Pedruzzi, I., et al. (2013) HAMAP in 2013, new developmentsin the protein family classification and annotation system.Nucleic Acids Res 41 (Database issue), D584-D589.Mutowo-Meullenet, P., et al. (2013) Use of Gene OntologyAnnotation to understand the peroxisome proteome inhumans. Database (Oxford) 2013, bas062.Eberhardt, R.Y., et al. (2012) AntiFam: a tool to help identifyspurious ORFs in protein annotation. Database (Oxford) 2012,bas003.Burge, S., et al. (2012) Biocurators and Biocuration: surveyingthe 21st century challenges. Database (Oxford) 2012, bas059.Gaudet, P., et al. (2012) Recent advances in biocuration:Meeting Report from the fifth international BiocurationConference. Database (Oxford) 2012, bas036.Figure. Organisation ofdata and informationin the Universal ProteinResource.www.uniprot.org/help/biocuration2012 EMBL-EBI Annual Scientific Report31
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 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 46 and 47: yMolecular systemsThe genes and gen
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,
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The EMBL International PhDProgramme
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SupportOur support teams provide fo
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T TrainingAs part of EMBL-EBI’s m
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IIndustry programmeSince 1996 the I
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NExternal relationsAs a European In
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sExternal servicesOur team manages
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SSystems and networkingOur team man
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q AdministrationThe EMBL-EBI Admini
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Funding and resource allocationDesp
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Growth of core resourcesIn 2012 the
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CollaborationsEMBL-EBI is a highly
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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
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Major database collaborationsARRAYE
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THE GENE ONTOLOGY CONSORTIUM• Agb
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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
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EMBL - European Bioinformatics Inst
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EMBL-EBI Annual Scientific Report 2012

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