Annual Scientific Report 2015

Vertebrate Genomics
Paul Flicek
Bronwen Aken
Andrew Yates
Daniel Zerbino
• Welcomed three new Team Leaders in September: Bronwen
Aken, Andrew Yates and Daniel Zerbino;
• Updated the data from several major projects (e.g. 1000
Genomes Project, BLUEPRINT) to reflect the new GRCh38
human reference assembly;
• Issued five major releases of Ensembl, and provided updates
to other highly used resources, e.g. human (now assembly v.
GRCh37.p8) and mouse (now GRC38m.p4) genomes;
• Published the Ensembl regulatory build and the genome of
the vervet monkey;
• Released important annotation updates to the rat (Rnor_6.0)
and zebrafish (GRCz10) genome assemblies, and introduced
a dynamic gene gain/loss view of these datasets;
• Released BLUEPRINT data via GenomeStats, a web-based
tool for carrying out analyses of epigenomic data;
• Released the beta version of our TrackHub registry;
• Developed new views and tools, enhanced performance and
usability of existing views, extended support for track hubs,
and improved our mirror sites;
• Developed a new BioMart system to provide fast access to all
regulatory data from the new Ensembl Regulatory Build and
added new bindings in Bioconductor;
• Helped launch the Functional Annotation of Animal
Genomes (FAANG) project, in which we lead efforts to define
data and metadata standards;
• Upgraded the HipSci project website to improve the
discoverability of individual cell lines and related data;
• Improved display of variation data tables and introduced
Manhattan plots for linkage disequilibrium data;
• Managed the growth in usage of the Ensembl REST API,
which had over 70 million requests in 2015;
• Introduced a new visualisation tool for long-range
connections between genomic regions;
• Promoted Ensembl resources through social media,
conferences, webinars and 97 workshops;
• Helped complete the relocation of the GWAS Catalog
software infrastructure from the NHGRI in the US to
EMBL-EBI;
• Improved the GWAS Catalog website by updating the search
interface with SOLR technology and supporting ontology
expansion queries.
Non-vertebrate Genomics
Paul Kersey
• Issued six public releases of Ensembl Genomes;
• Contributed to the regular data releases of Vector Base,
Wormbase and PomBase;
• Increased the number of bacterial genomes available through
the Ensembl public interface to nearly 30 000;
• Increased the number of fungal genomes 10-fold and protist
genomes 5-fold;
• Made major contributions to the paper describing the
genome of Anopheles stephensi, the primary mosquito
vector of malaria in urban India;
• Extended community curation to plant pathogens,
and released new data-mining tools for PhytoPath and
WormBase ParaSite;
• Issued a new, more contiguous and complete assembly of the
bread wheat genome to the research community.
Variation
Justin Paschall and Helen Parkinson
• Handled a 50% increase in the volume of data archived in
the European Genome-phenome Archive (EGA) and a 65%
increase in the number of files submitted;
• Deployed a new EGA downloader service, which distributed
over 1.7 Petabytes of data;
• Implemented a Global Alliance for Genomics and Health
‘Beacon’ for the EGA, enabling users to access a limited
collection of variation data through a single, three-tiered
entry point;
• Re-built the EGA pipeline, reducing the quarterly average
processing time from three weeks to one and a half days;
• In collaboration with colleagues at CRG Barcelona, increased
the EGA’s capacity to distribute data via FTP, Aspera and a
customised downloader;
• Managed the growth of the European Variation Archive to
22 datasets on various organisms, including crop species
and domesticated animals;
• Made available datasets from Phase 3 of the 1000 Genomes
Project and from the Exome Aggregation Consortium
(ExAC);
• Improved the EVA browser by integrating variant
annotations generated by the Ensembl Variant Effect
Predictor tool and applying advanced search filters;
• Improved the representation of clinical information with a
new display for data from ClinVar;
• Helped standardise ClinVar data in the context of Open
Targets (formerly CTTV) and developed global standards for
variation data as part of the GA4GH.
2015 EMBL-EBI Annual Scientific Report 15