Annual Scientific Report 2015

Proteomic Services
The Proteomics Services team develops tools and resources for the representation,
deposition, distribution and analysis of proteomics and systems biology data.
We follow an open-source, open-data approach, and contribute to community
standards, in particular the Proteomics Standards Initiative (PSI) of the
international Human Proteome Organisation (HUPO) and systems biology
standards (COMBINE Network).
Our team provides public databases as reference
implementations for community standards: the
PRIDE proteomics identifications database, the IntAct
molecular interaction database, the Reactome pathway
database, and the BioModels Database, a repository
of computational models of biological systems. IntAct
became an independent project under the leadership of
Sandra Orchard in the Molecular Interactions team in
April 2015.
As a result of long-term engagement with the
community, journal editors and funding organisations,
data deposition in our standards-compliant data
resources is becoming a strongly recommended part
of the publishing process. This has resulted in a rapid
increase in the data content of our resources. Our
curation teams ensure consistency and appropriate
annotation of all data, whether from direct depositions
or literature curation, to provide the community with
high-quality reference datasets. We also contribute
to the development of data-integration technologies,
using protocols like the PSI Common Query Interface
(PSICQUIC) and Semantic Web technologies, and
provide stable identifiers for life science entities through
Identifiers.org.
Major achievements
In 2015, the IntAct molecular interaction database team
published a detailed visual analysis of the interactome
of LRRK2, a complex, multidomain protein strongly
implied in Parkinson’s disease (Porras et al., 2015).
Our study integrated data from consortium partners,
large-scale experiments and targeted literature curation
as well as pathway data from the Reactome database,
providing open data supporting all figures as separate
files for further analysis e.g. in Cytoscape. In April
2015, IntAct became an independent team led by
Sandra Orchard.
The Reactome Knowledgebase (Fabregat et al., 2016)
provides molecular details of signal transduction,
transport, DNA replication, metabolism and other
cellular processes as an ordered network of molecular
transformations-an extended version of a classic
metabolic map in a single, consistent data model.
Reactome functions both as an archive of biological
processes and as a tool for discovering unexpected
functional relationships in data, such as gene-expression
pattern surveys or somatic-mutation catalogues from
tumour cells. In 2015 we completely 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 available
as web services or JavaScript-based widgets suitable
for integration into third party applications; the new
pathway diagram view has already been integrated into
the Target Validation platform and ChEBI website.
The BioModels database (Chelliah et al. 2015), a
standards-compliant resource for systems biology
models, celebrated its tenth anniversary in 2015, and by
the end of the year contained more than 1000 literaturebased
models. Our work on BioModels focused on
targeted curation of disease-related models, and in
2015 we released a new disease summary page. We
further developed the JUMMP software platform, a
flexible infrastructure on which we will build the next
version of BioModels and which will accommodate
the IMI-funded Drug Disease Model Resources
(DDMoRe) project’s model repository. DDMoRe
provides a public dissemination platform for models in
the Pharmacometrics Markup Language (PharmML),
which was released in 2015 (Swat et al., 2015).
The PRIDE database continued to grow rapidly as
a key partner of the ProteomeXchange consortium
of proteomics resources. In 2015, PRIDE processed
over1500 submitted datasets (compared to around 900
datasets in 2014). PRIDE data downloads reached 200
Terabytes. To optimise support for both PRIDE data
depositors and data users, we completely redeveloped
the PRIDE Archive website, developed a REST-based
web service and released a new version of the popular,
stand-alone PRIDE Inspector tool suite (Perez-Riverol
et al., 2015).
Generalising the principles of ProteomeXchange central,
the central search interface for all ProteomeXchange
partners, we developed the Omics Discovery Index
(OmicsDI), a dataset-discovery tool providing access
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2015 EMBL-EBI Annual Scientific Report