Annual Scientific Report 2015

Maria-Jesus Martin
Protein Function Development
BSc In Veterinary Medicine, University
Autonoma in Madrid. PhD in Molecular Biology
(Bioinformatics), 2003.
At EMBL-EBI since 1996.
Team Leader since 2009.
millions of proteins in UniProt. Informed by specialist
biocurators, the automated system adds as much useful
information as possible to imported sequences, which
now include domains, signal, transmembrane and
coil regions. We extended UniRule and the Statistical
Automatic Annotation System (SAAS), two systems
for the automatic annotation of large volumes of
uncharacterised proteins. These are now available
through newly implemented interactive web pages,
allowing our users to browse annotation rules. We also
started to work in a service to download and/or use these
rules as a system for genome annotation. We extended
our collaborations with external automatic annotation
communities including the Biofunction Prediction and
Critical Assessment of Function Annotation initiatives,
which will expand our knowledge and use of functional
prediction methods.
In 2015 we further extended the scope of GO
annotation to support annotations to RNA, identified by
RNAcentral identifiers. We made significant changes
to our database and Protein2GO, the web-based GO
curation tool used by UniProt and GO Consortium
curators to contribute annotations to the GOA project,
in order to support a number of changes to annotation
format and rules agreed by the GO Consortium. We
re-engineered our pipeline that verifies the taxonomic
correctness of GO annotations using a much-extended
set of taxonomic constraints that originate from both
GO and other ontologies, principally UBERON.
To make GO protein–protein interaction annotations
available for visualisation in tools such as Cytoscape,
we implemented a PSICQUIC (Proteomics Standards
Initiative Common Query Interface) server, available
through EMBL-EBI’s PSICQUIC portal.
Our team maintains the Enzyme Portal, a resource
that integrates enzyme-related data for all relevant
EMBL-EBI resources and the underlying functional and
genomic data. We re-launched the service, which now
features improved interfaces and functionalities and
provides a one-stop shop for all information available
on enzymes. To further improve the discoverability of
enzyme data, we collaborated with the Web Production
team to refine the enzyme search within the EBI-Search
and EBI Blast sequence search tools.
Future plans
In 2016 we plan to release a protein-sequence feature
viewer that summarises functional sites in the
UniProt web site. We will continue to engage with user
communities working in functional prediction, and
explore methods and data-exchange mechanisms to
improve accuracy and coverage of protein annotations.
We will maintain our focus on usability and engage
with our users to ensure we maintain a global genome/
proteome- and gene-product-centric view of the
sequence space. We aim to expand our collaboration
with the ProteomeXchange resources in the integration
of post-translational modifications in UniProtKB, and in
the provision of experimental, unique peptide mappings
for reference species. We will continue to co-operate
with variation projects such as ExAC to integrate
relevant genome and proteome information.
Restructuring GO electronic annotation pipelines,
principally those based on orthology supplied by
Ensembl, will help us improve the quality of the
projected annotations. We will continue the work
undertaken on behalf of the GO Consortium in 2015
to transition from using UniProt cross-references
rather than MOD-supplied mapping files to map from
“foreign” identifiers to UniProtKB accessions. We also
plan to revise the set of annotation files that we publish
and submit to the GO Consortium. We plan to release
a new QuickGO with re-designed interfaces and new
features to improve the overall user experience. We
will also continue to develop Protein2GO to keep it in
line with changes in annotation strategy agreed by the
GO Consortium, and to introduce additional function
to enhance curators’ workflow. We will make use of
the enhanced set of Web Services provided by the new
QuickGO to provide improved searching capabilities,
and the ability to use any available ECO evidence code.
Following the successful relaunch of the Enzyme Portal
in 2015, we will expand its functionalities in response to
user needs and create new training activities.
Selected publications
Alpi E, Griss J, et al. (2015) Analysis of the tryptic search
space in UniProt databases. Proteomics 15:48-57
Huntley RP, et al. (2015) The GOA database: Gene
Ontology annotation updates for 2015. Nucleic Acids Res.
43:d1057-d1063
Pundir S, Magrane M, Martin MJ, O’Donovan C, UniProt
Consortium (2015) Searching and navigating UniProt
databases. Curr. Protoc. Bioinform. 50:1.27.1–1.27.10
UniProt Consortium (2015) UniProt: a hub for protein
information. Nucleic Acids Res. 43:d204-d212
2015 EMBL-EBI Annual Scientific Report 104