Annual Scientific Report 2015

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Molecular Systems Our Molecular Systems teams provide public databases as reference implementations for community standards, for example the IntAct molecular interaction database, the Reactome pathway database, and the BioModels repository of computational models of biological systems. IntAct became an independent project under the leadership of Sandra Orchard in the new Molecular Interactions team in April 2015. We are major contributors to the IMEx Consortium of interaction databases, distributing almost 600 000 binary interaction evidences in 2015. We published a detailed visual analysis of the interactome of LRRK2, a complex, multidomain protein strongly implied in Parkinson’s disease; the dataset represents integrated data from several sources, including IMEx partners and the Reactome database. We redeveloped the Reactome pathway diagram viewer to provide a faster, clearer interface and smooth zooming from the entire reaction network to view the details of individual reactions. All Reactome major components are now available as Web Services or JavaScript-based widgets suitable for integration into third party applications. The Complex Portal, which contained over 1400 manually curated complexes at the end of 2015, now features an innovative graphical tool for visualising complex topology and stoichiometry. Originally developed by the Rappsilber group at the University of Edinburgh, the tool now works with a new Java library. The BioModels database celebrated its tenth anniversary in 2015, and by the end of the year contained more than 1000 literature-based models and featured a new disease summary page. As part of DDMoRe, an IMI project well aligned with the development goals of BioModels, we provided a public platform for sharing models: the Pharmacometrics Markup Language, PharmML. We reached hundreds of scientists in around 20 outreach and training events in 2015, including courses and workshops locally, internationally and virtually throughTrain online and webinars. BioModels BioModels Database is a repository of peer-reviewed, published, computational models, primarily from the field of systems biology but also of general biological interest. BioModels allows biologists to store, search and retrieve published mathematical models. In addition, models in the database can be used to generate sub-models, can be simulated online, and can be converted between different representational formats. This resource also features programmatic access via Web Services. www.ebi.ac.uk/biomodels Complex Portal The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. www.ebi.ac.uk/intact/complex IntAct IntAct provides a freely available, open-source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. www.ebi.ac.uk/intact Reactome Reactome is an open-source, open-access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff, and crossreferenced to many bioinformatics databases. Opposite: Detail from a dataset in IntAct: Phospho-tyrosine dependent protein-protein interaction network, published in 2015 by Grossmann et al., Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany. Mol. Syst. Biol. 11:794. 24 2015 EMBL-EBI Annual Scientific Report
Proteomics Services and Molecular Interactions Henning Hermjakob and Sandra Orchard • IntAct team members and their collaborators added 100,000 binary Interaction evidences to the database; • IntAct published a detailed visual analysis of the interactome of LRRK2, a complex, multidomain protein strongly implied in Parkinson’s disease; • Complex Portal released a novel graphical display enabling the visualisation of the topology of a protein complex; • Reactome released a completely redeveloped pathway diagram viewer to provide a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions; • BioModels team members released the Pharmacometrics Markup Language (PharmML), in the context of the Drug Disease Model Resources (DDMoRe) project. 2015 EMBL-EBI Annual Scientific Report 25
Page 1 and 2: The European Bioinformatics Institu
Page 3 and 4: SERVICE TEAMS TRAINING PROGRAMME RE
Page 5 and 6: Foreword We are pleased to present
Page 7 and 8: awareness amongst some of our stron
Page 9 and 10: Chemical biology The 17 million nov
Page 11 and 12: The most extensive catalogue of str
Page 13 and 14: “ EMBL -EBI services are the back
Page 15 and 16: European Nucleotide Archive The ENA
Page 17 and 18: Vertebrate Genomics Paul Flicek Bro
Page 19 and 20: Functional Genomics Alvis Brazma
Page 21 and 22: Pfam Pfam is a database of protein
Page 23 and 24: Protein Data Bank in Europe Gerard
Page 25: MetaboLights MetaboLights is a data
Page 29 and 30: BioSamples The BioSamples database
Page 31 and 32: “ EMBL -EBI is a critical mass of
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Page 37 and 38: The Birney group used methods devel
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Page 43 and 44: Industry workshops • In silico AD
Page 45 and 46: The work of our institute relies on
Page 47 and 48: Web production Rodrigo Lopez System
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Page 67 and 68: Photo: Uma Maheswari 2015 EMBL-EBI
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269. van den Berg BA, Reinders MJ,
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Director Ewan Birney Admininstratio
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2015 EMBL-EBI Annual Scientific Rep
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Guy Cochrane European Nucleotide Ar
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Vertebrate Genomics Research The mo
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Daniel Zerbino Ensembl Genome Analy
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Future plans We will continue to de
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Andy Yates Genome Technology and In
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Paul Kersey Non-vertebrate Genomics
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Justin Paschall Variation Archive M
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Alvis Brazma Functional Genomics Ph
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Ugis Sarkans Functional Genomics De
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Robert Petryszak Gene Expression MP
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Rob Finn Sequence Families PhD in B
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Maria-Jesus Martin Protein Function
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Claire O’Donovan Protein Function
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(such as the on-going EMDataBank Ma
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Sameer Velankar PDBe Content and In
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containing the mapping between comp
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of 14 leading European labs in Meta
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Henning Hermjakob Proteomic service
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coimmunoprecipitation coimmunopreci
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development of Europe PMC as a plat
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Mouse informatics In 2015 we contin
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Train online, EMBL-EBI’s web-base
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Nils Koelling Quantitative genetics
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Pedro Beltrao PhD in Biology, Unive
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Ewan Birney PhD 2000, Wellcome Trus
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Anton Enright PhD in Computational
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Nick Goldman PhD University of Camb
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John Marioni PhD in Applied Mathema
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Julio-Saez Rodriguez PhD University
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Oliver Stegle PhD in Physics, Unive
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Future plans The Teichmann group wi
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findings regarding association were
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Future plans The Industry Programme
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Reporting on usage We further devel
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to find the support they need. The
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Petteri Jokinen Systems & Networkin
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Standby Facility and Database Disas
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External Relations leads on brand a
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Mark Green EMBL-EBI Administration
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