Annual Scientific Report 2015

Guy Cochrane
European Nucleotide Archive
PhD University of East Anglia, 1999.
At EMBL-EBI since 2002.
Team Leader since 2009.
Quality through standards
The ENA team tracks growth in the uptake of
sequencing and the emergence of innovations in the
field, as these directly impact the growth and evolution
of our services. In 2015 we entered the final stages of a
transition from direct, manual submission processing
to a system that focuses curator input using formally
defined checklists and validation rules. Checklists offer
a structured way to collect information about a sample,
presenting attribute names alongside their definitions,
usage conventions and syntactic rules (e.g. conventional
expression, controlled vocabulary). This approach
allows us to optimise datasets for discoverability and
reanalysis across classes of data submission. It also
allows ENA curators to create and edit attributes
efficiently. This supports concurrent working on the
system and allows for safety operations such as rollback.
The system makes it possible for a single editing event
to drive a change to the attribute across all checklists in
which it appears, where appropriate. Such normalisation
ensures a consistent experience for the data submitter,
supports the capture of consistent and reliable data and,
ultimately, improves the presentation of search services.
Data compression
We advanced our CRAM reference-based sequence
data compression technology in 2015. We continued to
offer and support CRAM as a public software package
for its broadest possible use, extended the technology
itself and adopted it more deeply across ENA services.
We transitioned to CRAM v. 3; extended the software
to include more effective, faster compression; adopted
new compression codecs; improved the treatment of
unmapped reads; established greater controls on data
integrity under random access; and provided more
support for external tools such as the widely used
hts-jdk. We enriched services for CRAM as a core data
format within the Webin and ENA systems, providing
full support across the Webin interfaces for CRAM
submission and the systematic reference indexing of all
submitted raw read CRAM data files to make these reads
available through genomic coordinate-based queries.
Future plans
In 2016 we will continue to work with user communities
on data standards, for example extending the established
Marine Microbial Biodiversity, Bioinformatics and
Biotechnology (M2B3) standard, including coverage of
aquaculture and blue biotechnology-related studies. We
also expect further work on pathogen-related standards.
We will actively seek to collaborate with further
communities to target coverage gaps, with a view to
having checklist coverage across all classes of incoming
data. Curation of data submissions representing
non-assembly annotated sequence will
become a fully autonomous strand of
activity in 2016, which will complete our transition to
having all major submission workflows operating in a
scalable, quality-assured mode.
We will implement specific computational workflows
in the COMPARE Embassy Cloud system, initially
covering bacterial assembly and functional annotation
and typing/resistance profiling. We will further develop
the COMPARE Data Hub concept to allow simpler
user management and more integrated access. We
will begin to construct a data portal for the pathogen
surveillance community, with tailored search, browse
and visualisation tools, and will continue to support data
sharing and analysis efforts around emerging outbreaks.
We will extend the existing ENA system for structured
analysis output data, for example for antimicrobial
drug-resistance profiles and abundance profiles from
ecological studies. This will allow for the agile response
to submissions and data presentation for as-yetunsupported
data types. It has already been used as
the basis for assembly and variation data in the EVA,
submission and indexing support. Extending this system
to serve as data infrastructure for EBI Metagenomics
will help us improve submission and retrieval flexibility.
Selected publications
Gibson R, et al. (2016) Biocuration of functional
annotation at the European nucleotide archive. Nucleic
Acids Res. 44:D58-D66. doi:10.1093/nar/gkv1311
Cochrane G, et al. (2016) The International Nucleotide
Sequence Database Collaboration. Nucleic Acids Res.
44:D48-D50. doi:10.1093/nar/gkv1323
Ten Hoopen P, et al. (2015) Marine microbial
biodiversity, bioinformatics and biotechnology (M2B3)
data reporting and service standards. Stand Genomic Sci.
10:20. doi:10.1186/s40793-015-0001-5
Ip CL, et al. (2015) MinION Analysis and Reference
Consortium: Phase 1 data release and analysis.
F1000Res. 4:1075. doi:10.12688/f1000research.7201.1
Mitchell A, et al. (2016) EBI metagenomics in 2016 -
an expanding and evolving resource for the analysis
and archiving of metagenomic data. Nucleic Acids Res.
44:D595-D603. doi:10.1093/nar/gkv1195
2015 EMBL-EBI Annual Scientific Report 82