Annual Scientific Report 2015

Ugis Sarkans
Functional Genomics Development
PhD in Computer Science, University of Latvia,
1998. Postdoctoral research at the University of
Wales, Aberystwyth, 2000.
At EMBL-EBI since 2000.
Future plans
In 2016 we will release the BioStudies submission tool
and, in the interests of providing users with a consistent
experience, we will work with teams throughout
EMBL-EBI to align further developments with those of
other submission systems.
To make BioStudies an appealing destination for
supplementary data files in the life sciences, we will
work on the presentation of content. In particular, we
will further improve the BioStudies ‘project’ feature, by
which information on studies can be rendered in such
a way that they reflect the project/domain to which
they belong.
We will work with large projects that generate data on
diverse ‘omics platforms to ensure that the data ends up
in the correct structured repositories. We will use the
BioStudies database to tie various modalities together,
and provide study metadata and robust links to the
BioSamples database. This work will support to the
institute’s efforts to build a multi-omics atlas.
The BioStudies and BioSamples databases represent
two orthogonal components for dealing with
multi-omics data at EMBL-EBI. BioStudies contains
overall study descriptions and grouping assays, and
BioSamples groups samples and provides annotation.
We will continue integrating the two systems, such
that information on samples in BioSamples is readily
available for BioStudy submissions.
We will further develop the Annotare tool for data
submissions and, as for the BioStudies submission
tool, will align it with other submission tools. We will
also further simplify and automate the ArrayExpress
data flow.
Our continued participation in medical informatics
projects will provide us with a better understanding of
the data types and data-management patterns in a
range of life-science communities, and this knowledge
will be essential for our work in developing the
BioStudies database.
Selected publications
Hendrickx DM, Aerts HJ, Caiment F, et al. (2015) diXa:
a data infrastructure for chemical safety assessment.
Bioinformatics (Oxford, England) 31:1505-1507
Kirsanova C, Brazma A, Rustici G, Sarkans U (2015)
Cellular phenotype database: a repository for systems
microscopy data. Bioinformatics (Oxford, England)
31:2736-2740
Kolesnikov N, Hastings E, Keays M, et al. (2015)
ArrayExpress update--simplifying data submissions.
Nucleic Acids Res. 43:d1113-d1116
McEntyre J, Sarkans U, Brazma A (2015) The BioStudies
database. Mol. Syst.Biol. 11:847
The BioStudies database is a repository for
supplementary data files from published
life-science experiments that do not fit in the
structured archives at EMBL-EBI.
2015 EMBL-EBI Annual Scientific Report 98