Annual Scientific Report 2015

Protein Function Development
The work of our team spans several major resources under the umbrella of
UniProt, the comprehensive resource of protein sequences and functional
annotation: the UniProt Knowledgebase, the UniProt Archive and the UniProt
Reference Clusters. We develop software and services for protein information
in the UniProt, Gene Ontology (GO) annotation and enzyme data resources at
EMBL-EBI. We are also responsible for developing tools for UniProt and GO
Annotation (GOA) curation, and for the study of novel, automatic methods for
protein annotation.
Major achievements
The UniProt website facilitates the search,
identification and analysis of gene products. In 2015 our
team released new web interfaces and functionalities, all
built in response to user feedback gathered in a number
of user workshops, usability interviews/sessions,
helpdesk reviews and surveys. We now offer better ways
to customise search and present results. A new UniProt
course in Train online allows users to browse, explore
and analyse the profoundly rich, integrated collection of
protein sequence data in this resource.
Prior to the April 2015 release of UniProt, the UniProt
Knowledgebase (UniProtKB) had doubled in size over
the previous year to over 90 million entries, with a
high level of redundancy. This was especially the case
for bacterial species, where different genomes of the
same bacterium have been sequenced and submitted
independently (e.g. 4080 proteomes for Staphylococcus
aureus, comprising 10.88 million entries). To deal with
this redundancy, we developed a procedure to identify
highly redundant proteomes within species groups. We
implemented this procedure for bacterial species and
the sequences corresponding to redundant proteomes
(approximately 47 million entries) were moved from
UniProtKB to the UniProt Archive (UniParc), where
they are still available. This is the first concerted effort
in a public protein database to deal firmly and effectively
with redundancy in big data.
We released a new version of the UniProt Java API that
improved several issues, for example frequent library
updates, retrieval speeds and server availability. With
the new API, users can create their own UniProt service,
query and retrieve sets of proteins of interest, for
instance all records updated in the past few months, or
belonging to a particular family or species.
Our team worked with the UniProt user community
as well as the NCBI RefSeq, Ensembl and
Ensembl Genomes teams to provide a collection of
non-redundant reference proteomes, and to maintain
well-annotated organisms for biomedical and
biotechnological research. New species released in
2015 include Theobroma cacao (cacao / cocoa), Brassica
napus (rapeseed) and Papio anubis (olive baboon),
among others.
In collaboration with genomics resources Ensembl
and COSMIC, we created data links between DNA
sequences and the functional proteins they encode.
Cross-references to specific genomic sequences
are now provided for each protein isoform. We also
began distributing variants with consequences at the
protein level for human and other species, and released
variants from external resources including the Exome
Aggregation Consortium (ExAC) and the Exome
Sequencing Project (ESP) in the protein context.
We introduced new genome annotation track files
in two formats, BED and bigBed, which allows users
to map and visualise UniProtKB sequence feature
annotations including domains, sites and posttranslational
modifications as genome
browser tracks. These can be
visualised in Ensembl, the UCSC
Genome Browser and NCBI
Genome. This beta release of
the UniProt genome annotation
tracks resource contains sequence
annotations only for human; other
species will be added in future.
We worked with the
ProteomeXchange resources such
as PeptideAtlas and MaxQB to
provide experimental peptides
from publicly available massspectrometry
studies for
UniProt proteins for several
reference species.
In 2015 our team extended
the functionality of our
automated annotation
system, which assists
in the curation of the
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2015 EMBL-EBI Annual Scientific Report