Annual Scientific Report 2015

Protein Function Content
One of the central activities of the Protein Function Content team is the
biocuration of our databases, interpreting and integrating information relevant
to biology. The primary goals of biocuration are accurate and comprehensive
representation of biological knowledge, as well as facilitating easy access to this
data for working scientists and providing a basis for computational analysis.
The curation methods we apply to UniProtKB/
Swiss-Prot include manual extraction and structuring
of experimental information from the literature, manual
verification of results from computational analyses,
quality assessment, integration of large-scale datasets
and continuous updating as new information
becomes available.
UniProt has two complementary approaches to
automatic annotation of protein sequences with a high
degree of accuracy. UniRule is a collection of manually
curated annotation rules, which define annotations that
can be propagated based on specific conditions. The
Statistical Automatic Annotation System (SAAS) is an
automatic, decision-tree-based, rule-generating system.
The central components of these approaches are rules
based on the manually curated data in UniProtKB/
Swiss-Prot from the experimental literature and
InterPro classification.
The UniProt GO annotation (GOA) program aims to
add high-quality Gene Ontology (GO) annotations to
proteins in the UniProt Knowledgebase (UniProtKB).
We supplement UniProt manual and electronic GO
annotations with manual annotations supplied by
external collaborating GO Consortium groups. This
ensures that users have a comprehensive GO annotation
dataset. UniProt is a member of the GO Consortium.
Major achievements
As a core contributor to the Consensus CDS project,
UniProt is creating an authoritative complete
proteome set for Homo sapiens in close collaboration
with the RefSeq annotation group at the National
Center for Biotechnology Information (NCBI) and
the Ensembl and HAVANA teams at EMBL-EBI and
the Wellcome Trust Sanger Institute. A component of
this effort involves ensuring a curated and complete
synchronisation with the HUGO Gene Nomenclature
Committee (HGNC), which has assigned unique gene
symbols and names to 39 000 human loci (19 003 of
which are listed as coding for proteins). Information
on the reviewed set of 20 199 entries is available on the
UniProt website.
We play a major role in establishing minimum standards
for genome annotation across the taxonomic range,
largely thanks to collaborations arising from the annual
NCBI Genome Annotation Workshops, which are
attended by researchers from life science organisations
worldwide. These standards have contributed
significantly to the annotation of complete genomes and
proteomes and are helping scientists exploit these data
to their full potential.
The UniProt Automatic Annotation effort made great
strides in 2015. We increased the number of UniRules
significantly, with an emphasis on enzymes across
the taxonomic space to enable us to respond to the
need for annotation of uncharacterised genomes. We
began establishing relationships with sequencing and
annotation centres such as Genoscope to share these
rules and to expand into new approaches.
The UniProt GO annotation program provides
high-quality GO annotations to proteins in UniProtKB.
The assignment of GO terms to UniProt records is an
integral part of UniProt biocuration. UniProt manual
and electronic GO annotations are supplemented with
manual annotations supplied by external collaborating
GO Consortium groups, to ensure a comprehensive GO
annotation dataset is supplied to users. Our curators
are key members of the GO Consortium Reference
Genomes Initiative for the human proteome and provide
high-quality annotations for human proteins. In 2014,
we provided a manually curated set of human proteins
for the validation of the computational approaches
submitted to for the Critical Assessment of Function
Annotation experiment (CAFA) and presented a guide to
how best to use and interpret Gene Ontology data at the
Automated Function Prediction SIG at the International
Conference on Intelligent Systems for Molecular
Biology (ISMB).
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2015 EMBL-EBI Annual Scientific Report