Annual Scientific Report 2015

of 14 leading European labs in Metabolomics,
and in 2015 successfully delivered new standards
including the NMR markup language (NMR-ML)
open standard for Nuclear Magnetic Resonance data.
COSMOS also agreed procedures for the management
and dissemination of data in metabolomics. The
success of the project led to the formation of the
MetabolomeXchange consortium, which continues the
honoured tradition of global data exchange in biology.
The MetabolomeXchange platform made more than 350
datasets publicly available in 2015.
PhenoMeNal e-infrastructure for
metabolic computational workflows
A large volume of medical molecular phenotyping and
genotyping data will be generated by metabolomics
applications now entering research and the clinic.
In 2015 the PhenoMeNal project was funded with
€8 million by the European Commission’s Horizon
2020 Programme to develop and deploy an integrated,
secure, permanent, on-demand, service-driven,
privacy-compliant, sustainable e-infrastructure for
the processing, analysis, and information-mining
of such data. This e-infrastructure will support the
data processing and analysis pipeline for molecular
phenotype data from the moment of its acquisition
to high-level medical and biological conclusions
and interpretations.
Outreach
We represented MetaboLights and ChEBI at
28 scientific conferences, training sessions and
knowledge-exchange events in the UK and other
European countries as well as China, India and the US.
MetaboLights is now the recommended metabolomics
repository several journals, including Nature Scientific
Data, Metabolomics, PLOS and the EMBO journals.
Future plans
We select projects that are aligned with the goals of our
services. Our research will focus on the development
of efficient methods and algorithms for the assembly,
analysis and dissemination of information on small
molecules of relevance for biological systems. This
includes information about primary and secondary
metabolites, and also on xenobiotics and other molecules
of relevance, such as epitopes. We will continue our work
in related areas of ontology development, research on the
computational representation of related data, inference
of metabolomes from all types of available information,
processing of metabolic and metabolomics information
and reconstruction of metabolic networks. We will work
on extending the ChEBI database to offer greater utility
Christoph Steinbeck
Cheminformatics and Metabolism
PhD Rheinische Friedrich-Wilhelm-Universität,
Bonn, 1995. Postdoc at Tufts University, Boston,
1996-1997. Group leader, Max Planck Institute
of Chemical Ecology, Jena, 1997-2002. Group
leader, Cologne University 2002-2007. Lecturer in
Cheminformatics, University of Tübingen, 2007.
At EMBL-EBI since 2008.
for metabolism and natural-products researchers, and
to extend MetaboLights. We will enrich MetaboLights
with curated knowledge, including reference spectra,
pathways, protocols and references to a wider range
of resources. We will develop new online data analysis
capabilities to strengthen the position of MetaboLights
as an important research tool.
PhenoMeNal will provide computational and
data analysis services to the European biomedical
community to improve understanding of aetiology,
pathogenesis, pathways, and mechanisms of common
human diseases. PhenoMeNal will create a federated,
secure, high-performance e-infrastructure to handle and
analyse large research datasets make their application
available via national and European grid and cloud
infrastructures where appropriate. By doing so, the 13
partners will address serious challenges arising from
rapidly growing data volumes in molecular phenotyping.
PhenoMeNal’s cloud-based, virtualised compute engines
will enable users to bring the compute to potentially
sensitive data, rather than necessitating the movement
of such data to potentially insecure environments.
Selected publications
Beisken S, et al. (2015) SpeckTackle: JavaScript charts
for spectroscopy. J. Cheminform. 7:17
Hastings J, Jeliazkova N, Owen G, et al. (2015)
eNanoMapper: harnessing ontologies to enable data
integration for nanomaterial risk assessment. J. Biomed.
Semantics 6:10
Hastings J, Owen G, Dekker A, et al. (2016) ChEBI in
2016: Improved services and an expanding collection of
metabolites. Nucleic Acids Res. 44:D1214-D1219.
Moreno P, Beisken S, Harsha B, et al. (2015) BiNChE: a
web tool and library for chemical enrichment analysis
based on the ChEBI ontology. BMC Bioinformatics 16:56
Salek RM, Neumann S, Schober D, et al. (2015)
COordination of Standards in MetabOlomicS
(COSMOS): facilitating integrated metabolomics data
access. Metabolomics 11:1587-1597
Morgat A, Axelsen KB, Lombardot T, et al. (2015)
Updates in Rhea--a manually curated resource of
biochemical reactions. Nucleic Acids Res. 43:d459-d464
2015 EMBL-EBI Annual Scientific Report 114