Annual Scientific Report 2015

Mouse informatics
In 2015 we continued to support the archiving, analysis
and dissemination of complex phenotype data being
generated by the International Mouse Phenotyping
Consortium (IMPC). We put considerable efforts into
standardising high-throughput phenotyping data,
which is pivotal to making the bridge between mouse
biology and precision medicine. Outstanding features
of the infrastructure provided by the IMPC, for example
the versionable statistical analysis software package
Phenstat, were highlighted in scholarly publications
in 2015, underscoring their utility to the research
community. The project was used as an example of
how infrastructure can facilitate reproducibility and
replicability of results by incorporating ARRIVE
guidelines into data management.
The IMPC and its informatics platform were named
as one of five case studies in a G7 report on global
research infrastructures, which promoted the further
development of a framework for transitioning national
research infrastructures to international ones.
We also contributed further to other international
collaborations in mouse biology, including
INFRAFRONTIER, which coordinates the global
distribution of mouse models produced in Europe, and
PhenoImageshare, an online, cross-species, crossrepository
tool enabling semantic discovery, browsing
and complex annotations of phenotype images.
Helen Parkinson
Samples, Phenotypes and
Ontologies
PhD Genetics, 1997. Research Associate
in Genetics, University of Leicester
1997-2000.
At EMBL-EBI since 2000.
Our mouse informatics group expects to have phenotype
data for over 5000 new knockout lines as the IMPC
completes the first phase of their mission. They will
develop new infrastructure for the second phase
of phenotyping, including longitudinal analysis for
ageing studies. A major publication centred on embryo
phenotyping is in development.
Selected publications
Group of Senior Officials on Global Research
Infrastructures, Progress Report 2015. Meeting of the
G7 Science Ministers, 8-9 October 2015. Published
online 14 December 2015 at https://www.bmbf.de/files/
G7_Broschuere_BITV.pdf
Karp NA, Meehan TF, et al. (2015) Applying the ARRIVE
guidelines to an in vivo database. PLoS Biol. 13:e1002151
Kurbatova N, Mason JC, Morgan H, et al. (2015)
PhenStat: A tool kit for standardized analysis of high
throughput phenotypic data. PLoS One 10:e0131274
Lloyd KC, Meehan T, Beaudet A, et al. (2015) Precision
medicine: Look to the mice. Science 349:390
Ring N, et al. (2015) A mouse informatics platform for
phenotypic and translational discovery. Mamm Genome.
26:413-421
Future plans
In 2016 we will deliver a new version of the
Ontology Lookup Service and develop this further
to accommodate the needs of the CORBEL and
EXCELERATE user communities.
The Gene Ontology Editorial Office at EMBL-EBI will
continue and expand on existing work to consolidate
across existing resources, improving consistency and
reasoning. For example, taxon constraints integrated
from the Uber Anatomy ontology can be directly used
in the GO, lessening burden on editors and improving
consistency for users. We will develop ontology
content as well, with a focus on synaptic processes and
components as well as microbial domains.
2015 EMBL-EBI Annual Scientific Report 122