Annual Scientific Report 2015

European Nucleotide Archive
Our team builds and maintains the European Nucleotide Archive (ENA), an
open, supported platform for the management, sharing, integration, archiving
and dissemination of public-domain sequence data. ENA comprises both the
globally comprehensive data resource that preserves the world’s public-domain
output of sequence data, and a rich portfolio of services that support the research
community in handling and using sequence data.
As nucleotide sequencing becomes increasingly central
to applied areas such as healthcare and environmental
sciences, ENA has become a foundation upon which
scientific understanding may be assembled. Our
users comprise data submitters, data coordinators for
sequence-based studies, direct data consumers and
secondary service providers (e.g., UniProt, RNAcentral,
EBI Metagenomics, Ensembl, Ensembl Genomes,
ArrayExpress) that build on ENA services and content.
By extending and adapting software and services that
started within ENA, we provide technology and datarepository
support beyond ENA, including the CRAM
sequence-data compression technology and the Webin
submissions application.
We nurture communities of scientists and engineers
in building and improving data infrastructure, helping
them incorporate richer, more discoverable content and
enable higher-impact, sequence-based science. The
ENA and its partner databases represent the engine
room of global data sharing in the life sciences, and
our team members help drive progress in our domain.
We focus on data standards driven by domain experts,
technical interoperability and social aspects of data
sharing such as policy and regulatory requirements.
Major achievements
Throughout 2015 we provided services to more than
2000 sequence data submitters. We made the ENA’s
content discoverable and accessible to a user base many
times this size. We improved many of our services,
including the Webin technical infrastructure, which
provides the means for users to transfer and describe
their newly generated data sets. For example, we
made it easier for users to describe the materials they
sequenced, and updated the programmatic interface to
support both tabular and XML formats for metadata
files. We enhanced the ENA website and associated Web
Services through greater data integration and usability.
Improvements to the presentation of assembly data
include options to browse those sets of raw reads that
have been aligned to a given reference. This represents
a major joining together of the reads and sequence
domains of ENA.
We continued to provide support for the global
programmes for which we offer data coordination,
including those handling marine (e.g. Tara Oceans,
Ocean Sampling Day) and, in the context of the
COMPARE project, pathogen-related data.
Pathogen surveillance and genomics
There is growing global enthusiasm for whole-genome
sequencing as a platform for pathogen surveillance.
It offers opportunities to apply a single, affordable
technology across multiple pathogen groups, and
promises to cater for vital analyses spanning public,
animal, food and environmental health/safety areas.
The ENA provides the robust data infrastructure
required for whole-genome sequencing to come to
fruition, supporting the global sharing of sequence data
and providing new technologies, tools and services for
pathogen surveillance. As a partner on the EU-funded
COMPARE project, we are working actively to help
speed up the detection of and response to infectious
disease outbreaks using genome technology.
In 2015 we updated many of the core technologies
required to adapt ENA to support rapid sharing of
pathogen data, for example deploying a dedicated
viral assembly data submission workflow in Webin,
accelerating the validation of incoming data, enhancing
performance in INSDC global data sharing pipelines
and optimising the efficiency of data structures for
the presentation and sharing of assembled bacterial
genomes. We developed data reporting standards for raw
and assembled viral and bacterial pathogen data sets,
such that the descriptive information supplied is well
suited for data discoverability and reuse. We packaged
core technologies, standards and data submission
services into the COMPARE ‘Data Hubs’. These hubs
facilitate the immediate sharing of data amongst
collaborating public-health scientists. Built on the ENA
and the global INSDC system, datasets shared through
these hubs are structured appropriately and described
richly, ready for full public release as soon as any
embargo lifts. To facilitate the systematic interpretation
of pathogen surveillance data flowing into ENA, we
made available an Embassy Cloud compute environment
to support computational workflows.
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2015 EMBL-EBI Annual Scientific Report