Annual Scientific Report 2015

Functional Genomics Development
Our team develops software for ArrayExpress, a core EMBL-EBI resource,
and the BioStudies database, a resource for biological datasets that do not
have a dedicated home within the institute’s services. We also contribute to the
development of BioSamples, which centralises biological sample data.
Together with the Expression Atlas team, we build
and maintain data management tools, user interfaces,
programmatic interfaces, and annotation and data
submission systems for functional genomics resources.
We also collaborate on a number of European
‘multi-omics’ and medical informatics projects in a datamanagement
capacity.
Major achievements
BioStudies
The BioStudies database holds descriptions of biological
studies, and links to data from these studies in other
databases at EMBL-EBI and beyond. It is a repository
for supplementary data files from published life-science
experiments that do not fit in the structured archives at
EMBL-EBI.
In 2015 we redeveloped the BioStudies user interface
to reflect the recommendations of a user experience
study. We drew on a wide range of information
sources to compile data for a comprehensive initial
release of the database. This included supplementary
information from articles in Europe PMC, studies from
the EurocanPlatform project, datasets from diXa and
HeCaToS toxicogenomics studies, imaging data from the
Image Data Repository project and original, unsolicited
submissions to BioStudies. This initial work enabled us
to further refine our data-management principles and
fine-tune the functionality of the user interface.
A simple data submission tool will be launched in
early 2016.
ArrayExpress
We continued to maintain ArrayExpress datamanagement
tools and access interfaces, focusing on
a major redesign of the post-submission experiment
management tool. We continued to improve and
automate the management of sequencing data, and
collaborated with the European Nucleotide Archive
team on methods for storing raw sequence data
and information.
We put significant efforts into further improving
Annotare, our main data-submission tool (originally
released in 2014). The emphasis of our work was on
addressing the needs of curators in handling submitted
datasets of varying levels of quality, and improving the
file-upload functionality.
BioSamples
We continued to collaborate with the Samples,
Phenotypes and Ontologies team on the basic
infrastructure components of the BioSamples
database, perhaps most notably in the context of the
BioMedBridges project. We built a prototype system that
links information from biobanks across BioSamples,
the Biobanking and Biomolecular Resources Research
Infrastructure (BBMRI) Hub and the Resource
Entitlement Management System (REMS). The system
now uses the Shibboleth system for authentication and
access-rights control.
Toxicogenomics and
biomedical informatics
Our work on the diXa toxicogenomics data warehouse—
an Innovative Medicines Initiative (IMI) project—fed
into the development of BioStudies from the outset.
In 2015 we transferred datasets from the dedicated
diXa data warehouse to the BioStudies database, and
developed new functionality. We also started work on
the HeCaToS project, which represents the continuation
of diXa in terms of data management.
We participate in a number of medical informatics
projects, for example providing data management
solutions for the EU-AIMS project on autism spectrum
disorder. As a part of the European Medical Information
Framework (EMIF) project for the reuse of patient
health records in clinical research, we are building a
cloud environment for multi-omics data management
and analysis, providing and integrating (among other
components) our R-cloud scientific computation
infrastructure, several Docker-enabled data-analysis
pipelines, and the iRODS data-management system.
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2015 EMBL-EBI Annual Scientific Report