Annual Scientific Report 2015

Henning Hermjakob
Proteomic services
MSc Bioinformatics University of Bielefeld,
Germany, 1995. Research Assistant at the German
National Centre for Biotechnology (GBF), 1996.
At EMBL-EBI since 1997.
to nine different data repositories across three ‘omics
types: proteomics, metabolomics and access-restricted
studies in the European Genome-phenome Archive
(EGA).
Outreach and training
In 2015 the Proteomics Services Team contributed
to 18 training events, which collectively reached 510
scientists. Ten of these were face-to-face courses held in
the UK, two were hosted elsewhere in Europe and
six were held outside of Europe. We contributed
content to one new course in Train online, participated
in a webinar and presented in two Industry
Programme events.
Future plans
In 2016 the Proteomics Services Team will continue
to restructure, with PRIDE becoming an independent
team led by Juan Antonio Vizcaino. The Reactome
and BioModels teams will be more closely integrated
to enhance synergy and share both expertise and user
interface components.
We will build on the improvements to the Reactome
code base to provide enhanced functionality both for
web users and third-party software developers, with a
major focus on the integration of molecular interaction
data from IntAct and other sources into a pathway
context. The new JUMMP platform will provide the
underlying infrastructure for two modelling resources:
the DDMoRe model repository for pharmacodynamic
models and the new version of the BioModels database.
These will provide a resource for systems biology model
archiving and dissemination for multiple representation
languages, such as the de facto standard SBML and the
community-based COMBINE archive. In the context
of the Identifiers.org and OmicsDI project, we will
continue to pilot agile strategies for data discovery
and integration.
Selected publications
Porras P, Duesbury M, Fabregat A, et al. (2015) A
visual review of the interactome of LRRK2: Using
deep-curated molecular interaction data to represent
biology. Proteomics 15:1390-404. doi: 10.1002/
pmic.201400390
Fabregat A, Sidiropoulos K, Garapati P, et al. (2016) The
Reactome pathway knowledgebase. Nucleic Acids Res.
44:D481-D487. doi: 10.1093/nar/gkv1351
Chelliah V, Juty N, Ajmera I, et al. (2015) BioModels:
ten-year anniversary. Nucleic Acids Res. 43:D542-D548.
doi: 10.1093/nar/gku1181
Swat MJ, Moodie S, Wimalaratne SM, et al. (2015)
Pharmacometrics Markup Language (PharmML):
Opening new perspectives for model exchange in drug
development. CPT Pharmacometrics Syst Pharmacol.
4:316-319. doi: 10.1002/psp4.57
Perez-Riverol Y, Xu QW, Wang R, et al.. (2016) PRIDE
Inspector Toolsuite: Moving toward a universal
visualization tool for proteomics data standard formats
and quality assessment of ProteomeXchange datasets.
Mol Cell Proteomics 15:305-317. doi: 10.1074/mcp.
O115.050229
2015 EMBL-EBI Annual Scientific Report 116