Aleksandra Shypitsyna

Alexander Holmes

Claire O&apos

Elena Speretta

Maria J Martin

Mélanie Courtot

Tony Sawford

Tony Wardell

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UniProt-GOA: A central resource for data
integration and GO annotation.
Mélanie Courtot, Aleksandra Shypitsyna, Elena Speretta, Alexander Holmes,
Tony Sawford, Tony Wardell, Maria J. Martin, and Claire O’Donovan
European Molecular Biology Laboratory, European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom
mcourtot@ebi.ac.uk
Abstract. The Gene Ontology (GO) is a well-established, structured
vocabulary used in the functional annotation of gene products. GO terms
are used to replace the multiple nomenclatures used by scientific databases
that can hamper data integration. Currently, GO consists of more than
41,000 terms describing the molecular function, biological process and
subcellular location of a gene product in a generic cell.
The UniProt-Gene Ontology Annotation (UniProt-GOA) project [1] pro-
vides high-quality manual and electronic GO annotations, historically to
proteins within the UniProt Knowledgebase. Recently, support for anno-
tation of RNAs via RNAcentral IDs and to macromolecular complexes,
identified by IntAct Complex Portal IDs, was added. For many species,
no experimental data is available: electronic annotations are the only
source of information for biological investigation, and it is therefore crit-
ical that solid pipelines for data integration across multiple resources
be implemented. For example, we rely on Ensembl [2] to project GO
annotations automatically according to orthology between species, or
InterPro [3] to identify proteins with similar signatures to which GO
terms describing the conserved function or location can be associated. In
September 2015, an additional 1.5 million annotations from the UniProt
Unified Rule (UniRule [4]) system were added electronically.
In addition to increasing the number of annotations available, UniProt-
GOA also supports, as part of manual curation, the addition of infor-
mation about the context of a GO term, such as the target gene or the
location of a molecular function, via annotations extensions. For exam-
ple, we can now describe that a gene product is located in a specific
compartment of a specific cell type (e.g., gene product that localizes to
the nucleus of a keratinocyte [5]). Annotation extensions are amenable to
sophisticated queries and reasoning. A typical use case is for researchers
studying a protein that is causative of a specific rare cardiac phenotype:
they will be more interested in specific cardiomyocytes cell differentiation
proteins than all proteins involved in cell differentiation.
Annotation files for various reference proteomes are released monthly, in-
cluding human, mouse, rat, zebrafish, cow, chicken, dog, pig, Arabidopsis
and Dictyostelium, as well as a file for the multiple species within UniPro-
tKB. The UniProt-GOA dataset can be queried through our user-friendly
QuickGO browser6 or downloaded in a parsable format via the EMBL-
EBI [7] and GO Consortium FTP [8] sites.
UniProt-GOA is the largest and most comprehensive open-source con-
tributor of annotations to the GO Consortium annotation effort. The
UniProt-GOA dataset has increasingly been integrated into tools that
aid in the analysis of large datasets resulting from high-throughput ex-
periments thus assisting researchers in biological interpretation of their
results.
Keywords: gene ontology, curation, data integration, uniprot
References
1. UniProt-GOA website, http://www.ebi.ac.uk/GOA
2. The Ensembl project, http://www.ensembl.org/index.html
3. InterPro: protein sequence analysis & classification, http://www.ebi.ac.uk/interpro/
4. UniRule, Rule-based evidence for UniProtKB annotation,
http://www.uniprot.org/help/unirule
5. Huntley, Rachael P., et al. A method for increasing expressivity of Gene Ontology
annotations using a compositional approach. BMC bioinformatics 15.1 (2014): 155.
6. QuckGO, A fast browser for Gene Ontology terms and annotations,
http://www.ebi.ac.uk/QuickGO
7. EBI FTP server, ftp://ftp.ebi.ac.uk/pub/databases/GO/goa
8. Gene Ontology FTP, ftp://ftp.geneontology.org/pub/go/gene-associations


UniProt-GOA: A central resource for data integration and GO annotation

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UniProt-GOA: A central resource for data integration and GO annotation

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