EMBL-EBI Annual Scientific Report 2012

Maria-Jesus MartinBSc In Veterinary Medicine, UniversityAutonoma in Madrid. PhD in Molecular Biology(Bioinformatics), 2003.At EMBL-EBI since 1996. Team Leadersince 2009.Bombyx mori (silk moth), Gibberella zeae (wheat head blightfungus), Solanum lycopersicum (tomato), Glycine max(soybean), and Phytophthora ramorum (sudden oak deathagent), amongst many others.Collaborations with Ensembl and Ensembl Genomes haveallowed us to create data links between DNA sequencesand the functional proteins they encode. We have developeda pipeline to map protein sequences in UniProt to theircorresponding transcripts and genes for most of the speciesin Ensembl. This is key to facilitating further integration ofgenome-related data from the 1000 Genomes Project. Weare developing a pipeline to incorporate variation data fromEnsembl sources and to annotate functional variantsin Ensembl.In 2012 we implemented UniRule, a system for automaticannotation of a large volume of uncharacterised proteins;it now contains most of the annotation rules producedby the three consortium members. We also extended theUniRule curation tool to include the annotation of sequencerelatedfeatures. This makes it easier for curators to manageprediction rules and perform statistical assessment of existingand new rules. UniRule annotates over 6 million sequences inUniProtKB/TrEMBL.In 2012 the team also worked on a new user interface forQuickGO, the UniProt GO browser. The initial user-testingphase is complete and we expect the new interface tobe released by Spring 2013. We develop the web-basedProtein2GO tool, which UniProt curators use to contributeannotations to the GOA project. We extended this tool in2012 to include new functionalities as requested by the GOConsortium curators.Future plansIn 2013 we will serve the rule-annotation tool as the centralmechanism for rule predictions for all UniProt curators inthe Consortium. We will provide a UniRule XML format forrule-exchange within UniProt and explore this format forpublic distribution and data-exchange mechanisms withuser communities interested in functional prediction. Wewill implement a UniProt website with a new look and feeland improved functionality that will facilitate easy access toreference and complete proteomes. We will continue to focuson usability issues and engage with our users to ensure wemaintain a global genome/proteome- and gene-productcentricview of the sequence space, and to make it easier forour users to explore in-depth the variations and annotationsfor each specific protein within our resources. We will continueto co-operate with diverse data providers (e.g., Ensembl,RefSeq, PRIDE) to integrate relevant genome andproteome information.Selected publicationsThe UniProt Consortium (2012). Reorganizing the proteinspace at the Universal Protein Resource (UniProt). NucleicAcids Res 40 (Database issue), D71-D75.Quest for Orthologs Consortium. Towards communitystandards in the quest for orthologs (2012) Bioinformatics 28,900-904.Ruth Y.E., et al. (2012) AntiFam: a tool to help identify spuriousORFs in protein annotation. Database, bas003.Gaudet, P., et al. (2012) Recent advances in biocuration:Meeting Report from the fifth International BiocurationConference. Database, bas036.The UniProt Consortium. (2012) UniProtKB amid the turmoilof plant proteomics research. Front. Plant Sci; doi: 10.3389/fpls.2012.00270.The UniProt Consortium. (2012) HAMAP in 2013, newdevelopments in the protein family classification andannotation system. Nucleic Acids Res 41 (Database issue),D584-D589.Velankar, S., et al. (2013) SIFTS: Structure Integration withFunction, Taxonomy and Sequences resource. Nucleic AcidsRes 41(D1), D483-D489.Salazar, G., et al. (2012) MyDas, an Extensible Java DASServer. PLoS One 7.9, e44180.Alcántara R, et al. (2013) The EBI Enzyme Portal. NucleicAcids Res 41 (D1), D773-D780.2012 EMBL-EBI Annual Scientific Report33