Annual Scientific Report 2015

containing the mapping between compound structures
and the patents they appear in. We also developed a
data client feed that enables users to maintain a regular
stream of the patent data behind a firewall and integrate
the data with their in-house data. Using SciBite’s
Termite software, we annotated the patent corpus
with dictionaries and ontologies for biological terms
including gene and diseases. The mapping is available
through the OpenPHACTS API.
In 2015 we intensified our work on the annotation
of marketed drugs and clinical candidates with their
intended therapeutic targets and diseases. This provides
a rich source of data for researchers interested in
validating therapeutic targets and identifying novel
ones. This was carried out as part of the NIH-funded
Illuminating the Druggable Genome (IDG) project and n
Open Targets (formerly CTTV) project.
We continued to participate in two EU-funded
projects, eTOX and HeCaTos, which aim to better
identify and curate toxicity data and apply it to the
prediction of toxicological endpoints. We continued
our work on OpenPHACTS, an Innovative Medicines
Initiative project that integrates pharmacological
data across diverse resources. We also participated
in the IDG project, Open Targets and Corbel, the
European infrastructure project that follows on from
BioMedBridges.
Research
We developed methods to predict molecular targets
and off-targets using structural information from
phenotypic screening data, an essential step in lead
optimisation, polypharmacology and the study of side
effects. Through collaborations, we validated three Mtb
targets from our predictions for potential tuberculosis
drug leads using biochemical and biophysical methods,
and from the generation of target-ligand structures. In
addition to developing a general theoretical model of
drug resistance and drug combinations, we performed
extensive data mining to retrieve information on
the relationship between the type of target and the
physicochemical properties of antibiotics – information
that is important for the development of new drugs.
John Overington
Chemogenomics
BSc Chemistry, Bath. PhD in Crystallography,
Birkbeck College, London, 1991. Postdoctoral
research, ICRF, 1990-1992. Pfizer 1992-2000.
Inpharmatica 2000-2008.
At EMBL-EBI from 2008 to 2015.
Anne Hersey
Acting Team Leader, ChEMBL
BSc Chemistry, University of Kent, PhD in
Physical Chemistry, University of Kent, 1982,
GlaxoSmithKline and former companies1982-
2009.
At EMBL-EBI since 2009.
Future projects and goals
In 2016 we will continue to broaden the utility and
content of ChEMBL and SureChEMBL by adding
additional annotation, for example on diseases, targets
and data measured using genetic variants of proteins.
We will expand our use of ontologies to increase
indexing of the ChEMBL data, particularly for complex
and high-value endpoints such as ADMET, and in vivo
pharmacology assays. We will develop technologies
that enable us to build curation and data submission
interfaces in a flexible and extendable way, and use
text-mining methodologies to identify journal articles
that enhance our coverage of chemical space. We will
continue to develop automation methods for ChEMBL
to enable the database to be updated more regularly
and simply. We will also develop a sub-structure and
similarity search facility for UniChem.
Selected publications
Davies M, et al. (2015) ChEMBL web services:
streamlining access to drug discovery data and utilities.
Nucleic Acids Res. 43: W612-W620
Gaulton A, et al. (2015) A large-scale crop protection
bioassay data set. Scientific Data 2:150032
Mugumbate G, et al. (2015) Mycobacterial dihydrofolate
reductase inhibitors identified using chemogenomic
methods and in vitro validation. PLoS One 10:e0121492
Papadatos G, et al. (2016) SureChEMBL: a large-scale,
chemically annotated patent document database Nucleic
Acids Res. 44:D1220-D1228
Papadatos G, (2015) Activity, assay and target data
curation and quality in the ChEMBL database. J.
Computer-Aided Mol. Design 29:885-896
2015 EMBL-EBI Annual Scientific Report 112