Published online 27 November 2020 Nucleic Acids Research, 2021, Vol. 49, Database issue D29–D37
doi: 10.1093/nar/gkaa1077
The European Bioinformatics Institute: empowering
cooperation in response to a global health crisis
Gaia Cantelli 1,*
, Guy Cochrane 1
, Cath Brooksbank1
, Ellen McDonagh 1,2
, Paul Flicek 1
,
Johanna McEntyre1
, Ewan Birney1
and Rolf Apweiler1
1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome
Campus, Hinxton, Cambridge CB10 1SD, UK and 2
Open Targets, European Bioinformatics Institute (EMBL-EBI),
Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Received September 24, 2020; Revised October 20, 2020; Editorial Decision October 21, 2020; Accepted October 22, 2020
ABSTRACT
The European Bioinformatics Institute (EMBL-EBI;
https://www.ebi.ac.uk/) provides freely available data
and bioinformatics services to the scientific community,
alongside its research activity and training
provision. The 2020 COVID-19 pandemic has
brought to the forefront a need for the scientific
community to work even more cooperatively to effectively
tackle a global health crisis. EMBL-EBI has
been able to build on its position to contribute to
the fight against COVID-19 in a number of ways.
Firstly, EMBL-EBI has used its infrastructure, expertise
and network of international collaborations
to help build the European COVID-19 Data Platform
(https://www.covid19dataportal.org/), which brings
together COVID-19 biomolecular data and connects
it to researchers, clinicians and public health professionals.
By September 2020, the COVID-19 Data Platform
has integrated in excess of 170 000 COVID-19
biomolecular data and literature records, collected
through a number of EMBL-EBI resources. Secondly,
EMBL-EBI has strived to continue its support of the
life science communities through the crisis, with updated
Training provision and improved service provision
throughout its resources. The COVID-19 pandemic
has highlighted the importance of EMBL-EBI’s
core principles, including international cooperation,
resource sharing and central data brokering, and has
further empowered scientific cooperation.
INTRODUCTION
The European Bioinformatics Institute (EMBL-EBI) is
part of the European Molecular Biology Laboratory, an
intergovernmental research organisation focusing on advancing
the study and understanding of molecular biology
across Europe. EMBL-EBI provides freely available
data and bioinformatics services to the scientific community,
contributing to the advancement of biology through
investigator-driven research and supporting scientists at all
levels with advanced bioinformatics training. We host a
suite of open data resources and tools, which cover every
data type in molecular biology, including, among others,
nucleotide sequence data, protein sequences, chemical biology
and the scientific literature (Figure 1). Resources hosted
by EMBL-EBI include deposition databases (which archive
experimental data) and added-value databases (which add
value to archived data by providing annotation, curation,
reanalysis and integration), as well as open-source software
tools. EMBL-EBI resources are central to the life sciences
community. On an average day in 2019, EMBL-EBI resources
received over 62 million requests. Throughout 2019,
EMBL-EBI websites were visited by almost 24 million IP
addresses (the number of IP addresses is an indication of the
number of users, but not an exact count), and EMBL-EBI
trained over 30 000 people through its training programmes.
Moreover, in 2019 EMBL-EBI reached over 300 petabytes
of raw data storage space.
EMBL-EBI is committed to keeping the data it manages
open, freely accessible and FAIR (findable, accessible, interoperable
and reusable (1)). Building on its 25 years of international
collaboration in bioinformatics and data brokering,
EMBL-EBI is working with the international scientific
community to build new scientific partnerships and coordinate
global research efforts. This involves, for example, active
participation in the development of the Global Alliance
for Genomics and Health (https://www.ga4gh.org/), leading
in the creation of standardised methods for accessing largescale
genomic data, and the use of the Data Use Ontology
(2) by the European Genome-phenome Archive (EGA)
to ensure that data use conditions are machine readable
and standardised. Moreover, EMBL-EBI is a key player in
the ARGENT project, an international effort that aims to
create a global, live database of Mycobacterium tuberculosis
genomes to monitor tuberculosis outbreaks around the
world. Through these efforts, EMBL-EBI is developing new
*To whom correspondence should be addressed. Tel: +44 1223 49 4588; Email: gaiacantelli@ebi.ac.uk
C The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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D30 Nucleic Acids Research, 2021, Vol. 49, Database issue
Figure 1. EMBL-EBI Resources. Summary of all EMBL-EBI Data Resources as of September 2020.
ways for researchers, clinicians and public health professionals
to share data, gather new insights and build on each
other’s discoveries.
The 2020 COVID-19 pandemic has re-shaped the landscape
of research and scientific cooperation. The Severe
Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-
2) causes the disease COVID-19: between January and
September 2020, SARS-CoV-2 has been responsible for
over 890 000 deaths. Moreover, the pandemic and the lockdown
measures implemented by governments across the
globe to contain it have caused unprecedented economic
and societal disruption. The pandemic showed that the scientific
community needed effective international collaboration,
backed by trusted expertise and an open dialogue with
the public. The position EMBL-EBI holds as an international
data broker, a service provider and home to cuttingedge
research has allowed the Institute to contribute to the
fight against COVID-19 in a number of ways. Crucially, the
contributions of the Institute hinge not solely on coronavirus
research, but on empowering international cooperation
across research fields, allowing researchers to access
trustworthy information and to cooperate in the face of a
global crisis.
DATA SERVICE RESPONSES TO THE PANDEMIC
In the early months of 2020, the future global impact of
the newly emerged SARS-CoV-2 became apparent. From
March 2020, EMBL-EBI, supported by the European
Commission and other funders, set to work on building
a foundation for the scientific response to COVID-
19 centred on biomolecular data. On the 20th of April
2020 the European COVID-19 Data Platform (https://
www.covid19dataportal.org/) was launched, as announced
by the President of the European Commission (https://
audiovisual.ec.europa.eu/en/video/I-189639). The platform
enables researchers to upload, access and analyse COVID-
19 related reference data and specialist datasets as part of
the global research effort. Drawing on our infrastructure,
membership of ELIXIR and involvement in the European
Open Science Cloud, we developed resources to link the
clinical, epidemiological, and public health worlds. The European
COVID-19 Data Platform comprises three components:
the COVID-19 Data Portal, the SARS-CoV-2 Data
Hub and the Federated EGA (FEGA) (Figure 2).
The COVID-19 Data Portal
The COVID-19 Data Portal (https://www.
covid19dataportal.org, Figure 3) brings together biomolecular
data across the diversity of relevant data types to
provide an integrated search (based on EMBL-EBI’s
central data search service (3)), navigation across data
and data download. In addition, the Portal provides an
entry point to data resources and services beyond the
biomolecular domain, including clinical and epidemiology
data.
In September 2020, the system presents data from 14
of EMBL-EBI’s biomolecular data resources, including
UniProt (4), European Nucleotide Archive (5), Electron
Microscopy Data Bank (5), Protein Data Bank in Europe
(6), Europe PMC (7), PRIDE (8), InterPro (9), ChEMBL
(10), Complex Portal (11), Protein Data Bank in EuropeKnowledge
Base (12), Ensembl (13), Reactome (14) IntAct
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Nucleic Acids Research, 2021, Vol. 49, Database issue D31
Figure 2. Data flow through the components of the European COVID-19 Data Platform. Patient data is collected by national health data infrastructures
and public health laboratories, which can be deposited in specific SARS-CoV-2 Data Hubs (numbering 12 at the time of writing), Federated EGA (FEGA)
and other data resources. This data feed into the COVID-19 Data Portal, which can be accessed by its user community of researchers, practitioners and
public health specialists.
(15) and the European Genome-phenome Archive (16), featuring
many of ELIXIR’s Core Data Resources (17). Data
in the system is growing rapidly and spans viral and host sequences,
gene and protein expression, protein functions and
structures, biochemical pathways and compounds, and the
scientific literature (Box 1).
Data content available from the COVID-19 Data Portal (September
2020).
To integrate and make this data accessible to the user
community and support research into COVID-19, several
of the contributing data resources developed specific
COVID-19 browsers and tools. For example, Ensembl has
developed a SARS-CoV-2 genome browser and related
resources (https://covid-19.ensembl.org/index.html), which
support genome browsing on the sequence of the virus, its
gene functions, variation data and information on its protein
sequence (13). Providing reliable sequence information
for COVID-19 is essential both for our understanding of
the virus and its pathogenicity, and for the development of
any vaccines or treatments. A further essential area of study
is understanding the genetic factors that dictate susceptibility
to the disease from Genome Wide Association Studies
(GWAS). The GWAS Catalog aggregates data from large
cohort studies, making curated SNP-trait associations and
summary statistics from both genome-wide and targeted
studies (18). In the past year, the GWAS Catalog has released
a new data deposition service, recognising the need to
make available data from preprints prior to peer-reviewed
publication. At the time of writing, there were 3997 studies
from pre-prints with summary statistics, 4 of which
were COVID-19 related. There were 8 published studies
and 25 available published associations between SNPs and
COVID-19 susceptibility.
EMBL-EBI resources have also been able to support
drug discovery research to the COVID-19 portal.
ChEMBL, EMBL-EBI’s manually curated database of
bioactive molecules with drug-like properties, has been curating
the bioactivity data of potential anti-SARS-CoV-2
drugs. Drug discovery researchers have been screening candidate
compounds to identify those with potential antiSARS-CoV-2
activity, to identify already approved medications
that can be repurposed for COVID-19. To date, several
large-scale drug screening studies have been described
and made available to the scientific community, either
via preprints or as peer-reviewed publications. ChEMBL
launched a special release in May 2020 (ChEMBL 27) focusing
on studies that assess the potential anti-SARS-CoV-
2 activity of compounds, with a further focus on studies that
use cell-based assays in their screens. To date, ChEMBL has
curated eight datasets on anti-SARS-CoV-2 compounds.
Across all studies, 142 compounds have been shown to have
some anti-SARS-CoV-2 activity (however, some of these
also showed a high degree of cytotoxicity alongside their
antiviral activity). Interestingly, only a few compounds have
so far been shown to be active against SARS-CoV-2 in multiple
studies: 14 compounds have been shown to be active in
more than one study, and only 5 have shown activity across
three or more studies. The ChEMBL 27 release also enables
users to view the COVID-19-related results alongside previously
available information for each compound, and to
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D32 Nucleic Acids Research, 2021, Vol. 49, Database issue
Figure 3. The COVID-19 Data Portal interface. The COVID-19 Data Portal provides a web entry point to services provided by the European COVID-19
Data Platform.
compare results for the same compound from different research
groups.
EMBL-EBI is a partner in, and also hosts, Open Targets,
a public-private partnership that uses human genetics
and genomics data for systematic drug target identification
and prioritisation (19). Open Targets has responded
to the COVID-19 pandemic by developing a unique tool to
aid filtering and prioritisation of human and viral (SARSCoV-1
and SARS-CoV-2) proteins as potential drug targets
for COVID-19 treatment (https://covid19.opentargets.
org/). The tool integrates key datasets from publicly available
resources via a simple user interface and is designed
to filter potential drug targets by key properties of the data
(Figure 4) to answer key questions such as ‘which human
proteins directly interact with a SARS-CoV-2 viral protein,
are expressed in the respiratory system, and have compounds
with in vitro activity against COVID-19 that modulate
this target?’.
Datasets integrated in the tool include:
• Protein interaction and network data on whether the target
interacts directly with a SARS-CoV-1 or -2 viral protein,
or with another virus protein (source: IntAct).
• Expression, distribution, tissue and subcellular location
data for a given human target (source: Human Protein
Atlas and Expression Atlas).
• Whether target abundance is up- or down-regulated during
SARS-CoV-2 infection, and at which time points (20).
• Drugs in clinical trials that modulate the target, including
details on the number of drugs and maximum trial
phase, and whether these trials are for COVID-19 treatment
(source: ChEMBL).
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Nucleic Acids Research, 2021, Vol. 49, Database issue D33
Figure 4. The Open Targets COVID-19 Target Prioritisation Tool. This example displays the results (listed in the centre window) of filters for targets that
are: protein coding, have a direct interaction with a viral protein, have at least two drugs (for any indication) in a phase IV clinical trial, have a modulating
compound in in-vitro assays, and have safety information (left content side bar). The right content sidebar displays further information for targets when
entries in the list are selected. In this example, the small molecule target tractability button was selected for a particular target to display the level of
predicted tractability information for the target.
• Compounds that modulate the target and have been
tested in vitro against SARS-CoV-2 and whether they had
activity against the virus or not (source: ChEMBL).
• Target tractability assessment, including suitability for
modulation with a small molecule or antibody (source:
Open Targets Platform).
• Target safety information including known toxicity and
organs affected (source: Open Targets Platform).
• List of peer-reviewed articles in which human targets cooccur
with COVID-19 (source: Europe PMC).
The COVID-19 Data Portal also provides links to data
submission systems, which provide data to the Platform, a
bulk data download function, and links to currently 56 external
data resources and services, spanning areas such as
computational, clinical and epidemiological content. Ongoing
work on the Portal includes the development of dashboard
functions, integration of SARS-CoV-2 Data Hubs, a
variety of data visualisations and deeper connections into
clinical data (such as via a ‘Cohort Browser’).
The COVID-19 Data Portal also provides connections
with other related resources, which at the time of writing
included 5 other European projects, 7 computing support
resources and 30 other databases and atlases containing information
relevant to COVID-19 research. Examples of related
resources and projects include the Johns Hopkins University
COVID-19 Case Tracker (https://www.covidtracker.
com/), Coronavirus Phylomes from Phylome DB (http:
//beta.phylomedb.org/covid19) and the European Clinical
Research Infrastructure Network (ECRIN) COVID-19
Taskforce (https://ecrin.org/covid-19-taskforce).
The SARS-CoV-2 Data Hubs
The SARS-CoV-2 Data Hubs are the second component
of the European COVID-19 Data Platform. They focus on
providing tools and services for the validation, processing,
analysis, interpretation, sharing and publication of viral sequence
data. The SARS-CoV-2 Data Hubs are deployed to
be used by public health agencies and scientists responsible
for generating viral sequences at national or regional levels,
with substantial user and tool support to help with their
use. Specific tools on offer at the time of writing include a
dedicated raw viral data uploader, a number of cloud-based
processing workflows supporting data from different sequencing
platforms and library preparation methods and a
Notebook-based data exploration and visualisation system.
Ongoing work includes the addition of further workflows,
including phylogenetic analysis. A particular focus has been
placed on ensuring that COVID-19 Data Hubs promote
FAIR Data Principles, ensuring data remains Findable, Accessible,
Interoperable and Reusable (1).
At the time of writing, there were 16 national SARS-CoV-
2 Data Hubs, supporting 70% of data. Viral data included
over 420 000 data records, including 97 000 raw viral sequence
data sets from 38 countries and over 330 institutions.
The Federated European Genome-phenome Archive
The Federated European Genome-phenome Archive
(FEGA) focuses on sensitive human biomolecular data
relating to COVID-19 and is the third component of the
European COVID-19 Data Platform. For these data, which
are often required to remain within national borders,
FEGA offers a unifying technology that allows national
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D34 Nucleic Acids Research, 2021, Vol. 49, Database issue
databases to be deployed and operated as nodes within
a broader federation. This approach allows consistent
interfaces (such as for submission and data access) across
the federation while respecting requirements for national
governance. Public metadata can be shared across the
network so data discovery can operate from any point and
lead to unambiguous endpoints for access requests and,
ultimately, data access.
The COVID-19 pandemic has provided increased impetus
for FEGA to become more widely operational to ensure
rapid availability of COVID-19 host studies. This has led
to an acceleration in the development of FEGA, including
support for its underlying architecture, technical interfaces
and software implementation to establish national nodes.
To date, work has progressed on the governance and legal
framework for FEGA, the technical interfaces, and demonstrator
implementations in collaboration with the ELIXIR
nodes (21). In addition, FEGA has been able to contribute
to global standards for data sharing through the Global
Alliance for Genomics and Health (GA4GH), a policyframing
and technical standards-setting organisation for responsible
genomic data sharing. Its contributions have included
standards for variation formats, secure data streaming,
reference retrieval, data use ontology, encryption containers
and phenotype exchange.
Building the COVID-19 Data Platform
EMBL-EBI was uniquely positioned to rapidly deploy a
COVID-19 Platform due to a number of factors. First,
EMBL-EBI has a 25 year history in operating bioinformatics
infrastructure to provide biomolecular data and services.
This infrastructure includes systems for the at-scale
rapid capture, integration and publication of scientific data
from the research community. Specifically, several EMBLEBI
data resources for relevant data types were already in
place and, in many cases, already holding data of direct relevance
to SARS-CoV-2 and COVID-19 research (e.g. EGA,
PRIDE, Ensembl). Second, drawing on over 600 staff expert
in bioinformatics, software engineering and data science,
we were able to rapidly redirect human and computational
capacity towards the effort. Third, our work over
the last six years with European partners in pathogen data
systems through the EU Horizon 2020 COMPARE project,
particularly around the COMPARE Data Hubs (22), has
allowed us to develop specific extensions to our existing infrastructure.
Fourth, as a part of ELIXIR, with strong connections
to national nodes, we have well-established working
relations with those who operate infrastructure in national
health and public health systems and the relevant
European-level Research Infrastructures that sit alongside
ELIXIR. Finally, our commitment to open science, through
open data, FAIR principles (1) and data standards, has facilitated
the integration of the diversity of data types of relevance
to COVID-19 research.
While the Platform continues to be developed very actively
with the incremental addition of new data, functions
and services, we count a number of key milestones to date:
• Rapid deployment of the three components of the European
COVID-19 Data Platform––the SARS-CoV-2 Data
Hubs, the Federated EGA and the COVID-19 Data Por-
tal;
• Integration of SARS-CoV-2 and COVID-19 data from 14
EMBL-EBI Data Resources and connection into a number
of external resources and services;
• Mobilisation of raw viral sequence data at scale: with
almost no sharing of raw viral sequence data in March
2020, by September the Platform has mobilised some 25
000 data sets, with 80% of these data routed through the
SARS-CoV-2 Data Hubs; raw data are essential for systematic
variation and assembly analysis with appropriate
error handling;
• Establishment of a host of new tools, including a viral
data submission tool (https://ebi-ait.github.io/sars-cov2data-upload/),
a selection of viral data processing workflows
and a SARS-CoV-2 genome browser (https://covid-
19.ensembl.org/index.htm);
• Deep collaboration with a broad range of partners at
scientific and infrastructure level, and creation of a network
of national coordinators and Platform nodes, such
as in Sweden, Japan, Norway, Poland, and Slovenia
(https://covid19dataportal.se, https://covid19dataportal.
jp, https://covid19dataportal.no, https://covidhub.psnc.
pl, https://covid19dataportal.si).
• As of October 2020, the COVID-19 Data Portal had received
over 2.9 million web requests, from over 90 000
unique hosts. Since the COVID-19 Data Portal is an open
resource, it is difficult to estimate the exact number of
users who accessed it. The number of unique hosts, while
not an exact count, is used as a useful indicator of the
number of users.
While the COVID-19 crisis has driven the specific implementation
of the European COVID-19 Data Platform, we
have, by design, built concepts and technologies that will
be sustained long into the future. Drawing on the foundation
of existing EMBL-EBI and ELIXIR Data Resources,
all new data available through the Platform are appropriately
routed towards their respective underlying data resources
for long-term preservation. Using such applications
as EMBL-EBI Search (3), the future discoverability of the
underlying data is assured. The new software elements that
we have developed are reusable not only for rapid deployment
in future infectious disease scenarios, but also in the
service of broader scientific research, such as genetic disease
applications of FEGA. Finally, our network of partners in
the Platform, the data standards that we have worked upon
and the conventions and practices that we have established
will enrich our opportunities for data infrastructure development
in the future.
SUPPORTING THE RESEARCH COMMUNITY
THROUGH A GLOBAL CRISIS
Empowering cooperation in the specific field of coronavirus
research is not the only way EMBL-EBI supports the research
community. EMBL-EBI continues to support the
life sciences research communities, both through its training
programme and its regular service provision.
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Nucleic Acids Research, 2021, Vol. 49, Database issue D35
Training
An essential part of the work at EMBL-EBI, alongside its
data services and research activities, is its Training programme.
The EMBL-EBI Training programme is now in its
tenth year and aims to train scientists at all levels to get the
most out of publicly available biological data (www.ebi.ac.
uk/training). We responded rapidly to the COVID-19 pandemic;
although we had to cancel some courses at short notice,
we have created a robust mechanism for the delivery of
highly interactive virtual courses and have received encouraging
feedback from participants.
The training programme currently has five major compo-
nents:
Live virtual: Aiming to provide the same impact as our faceto-face
courses in a virtual environment, to reduce our carbon
footprint, shield our participants from communicable
disease and increase accessibility.
Train anytime: A comprehensive collection of online bioinformatics
courses, pre-recorded webinars and course materials,
allowing individuals to choose when, where and
how they learn.
Trainer support: Enabling trainer communities to develop
relevant and high-quality training courses, supported by
EMBL-EBI experts and materials, and underpinned by
global standards.
Face-to-face: Delivering courses to develop practical skills
and knowledge, at EMBL-EBI and at host organisations
worldwide (face-to-face training currently suspended).
Visits and secondments: Visiting scientists are embedded in
an EMBL-EBI group for up to 6 months, often leading
to longer-term collaboration (visits and secondments are
currently suspended).
This combination of activities allows us to deliver training
that is both of high quality and scalable: in 2019, we participated
in 305 training and outreach events, and we delivered
three train-the-trainer events, training 26 bioinformatics
instructors. Meanwhile, in 2019 our ‘train online’ collection
was accessed by 599 549 unique IP addresses and we
expanded our online training offerings by adding two new
courses and 59 new webinars. The expansion of our virtual
training content in 2019 allowed us to respond promptly
and effectively to the challenges of 2020, when we were able
to adapt our programme to the restrictions brought on by
the COVID-19 pandemic.
Furthermore, in late 2019 and early 2020 we began testing
the use of commercial cloud-based systems for their potential
to provide on-demand compute capacity for computationally
intensive off-site courses. We can now create virtual
machines (VMs) and Docker containers in the commercial
cloud, support trainers to test their software and then provide
access to the final VM/container/set of containers for
trainees, giving them a very similar user experience to the
experience that they would have if they were being trained
face-to-face at EMBL-EBI. We accelerated our first use of
this system in response to the COVID-19 pandemic.
Empowering access through service provision
Crucially, EMBL-EBI empowers international cooperation
through its regular service activity, enabling searchers from
across the globe to collaborate daily by sharing their data
through EMBL-EBI data resources.
All EMBL-EBI resources have been continuing their service
development capabilities through the past year. Significant
progress has been achieved in a number of core EMBLEBI
resources, including many referenced above (7,9,13) as
well as Pfam (23), Rfam (24), and RNACentral (25).
We have been working to support the research communities
that rely on our resources though both the COVID-19
pandemic and the ever-changing requirements of research.
For example, the MetaboLights team (26) has been engaged
with the metabolomic community in a comprehensive
exercise to redevelop its submission systems to capture
the growing amount and diversity of metabolomic information.
By redeveloping the MetaboLights submission
processes, we have enabled our user community to make
more comprehensive and high-quality data available as easily
as possible. At the time of writing, the database hosts
around 700 publicly available studies with more in preparation
and awaiting public release due to publication requirements.
The MetaboLights team is committed to continually
developing our resources and services to become a central
hub for metabolomics related data and tools in collaboration
with international collaborators and our diverse user
community.
Data submission to other deposition databases has also
changed through the recent COVID-19 pandemic. For instance,
three of the months during the first half of 2020
have seen a record number of submitted data sets in a single
month to the PRIDE database (8), the world-leading proteomics
data repository and part of the ProteomeXchange
Consortium (27), reaching 566 data sets (∼25 datasets per
working day) submitted in June 2020 alone. The total number
of proteomics data sets in PRIDE is currently around
18 000 and the number of proteomics datasets submitted to
PRIDE continues to grow very significantly year by year.
At the time of writing, 30 public data sets in PRIDE were
COVID-19 related.
One of the strengths of EMBL-EBI as an institute is
that it hosts services, training and research programmes
within the same institute. Proteomics has been at the centre
not only of expanded efforts by our services, but also
of coronavirus-related research by our teams. Researchers
from EMBL-EBI, in collaboration with partners from
across the globe, have used proteomics to identify the mechanisms
through which SARS-CoV-2 hijacks human cells
during infection to promote its own replication. In turn
these discoveries have allowed researchers to identify a number
of existing drugs that may be effective at targeting
the virus (28). Similarly, an international research group
including scientists from EMBL-EBI identified hundreds
of interactions between SARS-CoV-2 proteins and human
proteins, which can in turn be used to identify potential
COVID-19 treatments (29).
The activities of PRIDE are increasingly focused on integrating
proteomics information into other added-value
EMBL-EBI resources. In this context, more than 40 human
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D36 Nucleic Acids Research, 2021, Vol. 49, Database issue
and mouse quantitative proteomics datasets (both baseline
and differential) are now available via Expression Atlas.
Additionally, there is an ongoing effort to improve the
annotation (and then facilitate the re-use) of public proteomics
datasets by adopting and extending the file format
SDRF (Sample and Data Relationship Format) used by the
EMBL-EBI resources ArrayExpress and Expression Atlas
(30).
As well as facilitating submission and access to its existing
resources, EMBL-EBI is continually developing its resource
portfolio to keep up with the ever-changing nature
of molecular biology data. To this end, in 2020 EMBL-EBI
has launched the eQTL Catalogue, a compendium of uniformly
processed human gene expression data and splicing
quantitative trait loci (31). The eQTL Catalogue focuses on
expression of genetic variants that are associated with specific
splicing events within genes, or with expression levels
of nearby genes. eQTL datasets are rare, but they are hugely
valuable for the process of drug discovery: data from the
eQTL Catalogue has already been incorporated in the Open
Targets platform for drug target identification and prioriti-
sation.
CONCLUSIONS
International cooperation, resource sharing and central
data brokering are all principles upon which EMBl-EBI
was founded. The COVID-19 pandemic has highlighted
how important these practices are, and how crucial towards
tackling and effectively addressing a global health crisis. International
cooperation drove the creation and implementation
of the European COVID-19 Data Platform, which
in turn has connected scientists and practicing healthcare
professionals not only throughout Europe, but all over the
world. Cooperative resources have enabled new, groundbreaking
research into the structure and mechanisms of action
of the virus, which in turn are essential for the development
of new effective treatments and vaccines.
ACKNOWLEDGEMENTS
The authors would like to acknowledge the work of all
who contributed to this paper. In particular, they would
like to thank Anna Gaulton, Oana Stroe, Spencer Philips,
Jessica Vamathevan, Helen Parkinson, Thomas Keane,
Juan Antonio Vizcaino, Claire O’Donovan and Andrew
Leach for their contributions, input and feedback. The authors
also wish to acknowledge the Open Targets team,
specifically David Ochoa, Daniel Suveges, Asier GonzalezUriarte,
Javier Ferrer, Aldo Segura-Cabrera, Andrew Hercules,
David Hulcoop and Ian Dunham.
FUNDING
EMBL-EBI is indebted to its funders, including the EMBL
member states, the European Commission, Wellcome, UK
Research and Innovation, the US National Institutes of
Health, our Industry Programme and many others; GWAS
Catalog work was supported by National Human Genome
Research Institute of the National Institutes of Health
[5U41HG007823]. Funding for open access charge: European
Molecular Biology Laboratory (www.embl.org).
Conflict of interest statement. None declared.
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