Annual Scientific Report 2015

Functional Genomics
Alvis Brazma
• Released the BioStudies Database for storing descriptions of
biological studies and unstructured data at EMBL-EBI;
• Led the effort to integrate data from large genomics and
proteomics studies in the Expression Atlas;
• In the context of the ICGC Pan-cancer analysis project,
analysed data from over 1400 cancer genomes and
transcriptomes.
Proteomics Services
Henning Hermjakob and Juan Vizcaino
• As part of the ProteomeXchange consortium, processed over
1500 submitted proteomics datasets in 2015, with downloads
reaching 200 Terabytes;
• 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;
• Developed the Omics Discovery Index (OmicsDI), a
dataset-discovery tool providing access to nine different
data repositories for proteomics, metabolomics and accessrestricted
studies in the EGA.
Functional Genomics Development
Ugis Sarkans
• Released the BioStudies Database;
• In collaboration with the Literature Services team, populated
the BioStudies database with supplementary materials from
articles in Europe PMC;
• In the context of the BioMedBridges project, developed a
secure information access pilot, demonstrating the linkage
of biobank data across different infrastructures and levels of
access control.
Gene Expression
Robert Petryszak
• Led the development of the new, high-quality Expression
Atlas and its Baseline Atlas, which comprises large genomics
and proteomics studies;
• Co-developed a pipeline for large-scale automatic analysis of
public RNA-seq data;
• Led the submissions handling effort for ArrayExpress;
• Brokered sequencing data for the ENA.
2015 EMBL-EBI Annual Scientific Report 17