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B2G-FAR, a Species-Centered GO Annotation Repository Vol. 27 no. 7 2011, pages 919–924 BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btr059 Genome analysis Advance Access publication February 18, 2011 B2G-FAR, a species-centered GO annotation repository Stefan Götz1,∗, Roland Arnold2, Patricia Sebastián-León1, Samuel Martín-Rodríguez1, Patrick Tischler2, Marc-André Jehl2, Joaquín Dopazo1,3,4, Thomas Rattei2,5 and Ana Conesa1,∗ 1Bioinformatics and Genomics Department, Centro de Investigaciones Príncipe Felipe (CIPF), Valencia, Spain, 2Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany, 3CIBER de Enfermedades Raras (CIBERER), 4Functional Genomics Node (National Institute for Bioinformatics, INB), Centro de Investigaciones Príncipe Felipe (CIPF), Valencia, Spain and 5Department of Computational Systems Biology, Ecology Centre, University of Vienna, 1090 Vienna, Austria Downloaded from https://academic.oup.com/bioinformatics/article-abstract/27/7/919/232238 by guest on 22 November 2018 Associate Editor: John Quackenbush ABSTRACT high-throughput technologies. Beyond traditional model species, Motivation: Functional genomics research has expanded also non-model organisms are in the genomics race and today it enormously in the last decade thanks to the cost reduction in high- is hard to find a biological domain without a functional genomics throughput technologies and the development of computational initiative. This expansion would not have been that successful tools that generate, standardize and share information on gene and without the accompanying development of computational tools protein function such as the Gene Ontology (GO). Nevertheless, that generate, standardize and share information on gene and many biologists, especially working with non-model organisms, still protein function. The Gene Ontology (GO) project is one such suffer from non-existing or low-coverage functional annotation, or standard. GO is a collaborative effort aiming at the establishment simply struggle retrieving, summarizing and querying these data. of a controlled vocabulary that provides biologically meaningful Results: The Blast2GO Functional Annotation Repository (B2G- annotations for gene (products) across species (Ashburner et al., FAR) is a bioinformatics resource envisaged to provide functional 2000). There are two main aspects of this project: (a) the definition of information for otherwise uncharacterized sequence data and offers a comprehensive ontology of functional terms and (b) the generation data mining tools to analyze a larger repertoire of species than of an annotation database containing the assignment of GO terms currently available. This new annotation resource has been created to genes and proteins (The Gene Ontology Consortium, 2008). by applying the Blast2GO functional annotation engine in a strongly Annotation for each organism in the GO database is supplied high-throughput manner to the entire space of public available and maintained by the respective consortium member. Evidence sequences. The resulting repository contains GO term predictions codes (ECs) are added to each individual annotation to reflect the for over 13.2 million non-redundant protein sequences based on information source used in a GO term assignment. ECs indicate BLAST search alignments from the SIMAP database. We generated if the annotation is supported by some (and which) experimental GO annotation for approximately 150 000 different taxa making evidence, whether it was transferred (and how) from related genes available 2000 species with the highest coverage through B2G-FAR. or if it was generated by other prediction methods. The large majority A second section within B2G-FAR holds functional annotations for of GO annotations is centralized in the Gene Ontology Annotation 17 non-model organism Affymetrix GeneChips. (GOA) Database (Camon et al., 2004). This resource contains high- Conclusions: B2G-FAR provides easy access to exhaustive quality functional annotations for proteins mostly obtained from the functional annotation for 2000 species offering a good balance UniProt Knowledgebase (The Uniprot Consortium, 2007). However, between quality and quantity, thereby supporting functional the great majority (∼95%) of GO corresponds to automatically genomics research especially in the case of non-model organisms. transferred annotations based on InterProScan (Quevillon et al., Availability: The annotation resource is available at 2005) results. Currently, only a small number of assignments have http://www.b2gfar.org. experimental evidence or are revised by expert curators. While the Contact: [email protected]; [email protected] GO project is improving the ontology definition and quality of the Supplementary information: Supplementary data are available at GOA database (Barrell et al., 2009), it is still far from providing Bioinformatics online. extensive functional annotation for the wealth of sequence data that populate public databases. However, thanks to the structured and Received on September 25, 2010; revised on January 4, 2011; universal nature of GO, large-scale annotation using an automated accepted on February 1, 2011 process is conceivable and could be feasible given that adequate computational resources are available. Such an annotation effort 1 INTRODUCTION complement current established annotation initiatives by generating Functional genomics research has gained importance in the last preliminary functional labels for sequences not yet covered by any of decade thanks to the fast improvement and cost reduction in the reference projects of the GO consortium. Examples of functional data-intensive resources in the field of functional genomics such ∗To whom correspondence should be addressed. as the Integr8 (Kersey et al., 2005) and PEDANT (Riley, 1993) © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. [13:17 17/3/2011 Bioinformatics-btr059.tex] Page: 919 919–924 S.Götz et al. projects, which offer genome-oriented views on different types of annotation data, can be found. An example of a specialized resource in the area of functional plant genomics is the PlexDB (Wise et al., 2007), a project to support transcriptomics studies on plants and plant pathogens. Although these resources provide comprehensive information on many genomic aspects, they do not represent a universal resource where up-to-date large-scale functional data on species can be readily accessed and analyzed. The Blast2GO project started in 2005 to build an universal bioinformatics platform for the functional annotation and analysis of novel sequence data (Conesa et al., 2005). The tool was designed to provide high-throughput and quality assignments with a user interface strongly based on visualization and intuitive use (Götz et al., 2008) (Conesa and Götz, 2008). So far, Blast2GO has been used in nearly 300 functional profiling projects involving a wide range of model and non-model Downloaded from https://academic.oup.com/bioinformatics/article-abstract/27/7/919/232238 by guest on 22 November 2018 species, from bacteria and fungi, through arthropods and mollusks, to plants, avian, fish and mammals, which evidences the strong need for functional annotations beyond that provided by public Fig. 1. The B2G-FAR annotation pipeline. The scheme shows how the sequence databases. During the last 5 years of Blast2GO, we have different data-sources are related and contribute to the generation of witnessed many cases of redundant annotation of public data by the B2G-FAR annotations, all passing through the Blast2GO annotation different labs and limitations for keeping results updated. These algorithm. facts, in combination with the annotation gaps mentioned above, have encouraged us to consider the generation of an extensive homologues;, (ii) mapping of the corresponding GO terms and their evidence repository of automatic functional annotation making use of the codes for all BLAST hits; and (iii) the annotation step applying the Blast2GO widely accepted functional annotation engine Blast2GO. Lastly annotation rule taking into account GO evidence codes, the GO hierarchy and advances in supercomputing and distributed computing have paved the degree of sequence similarity (an extensive explanation of the Blast2GO the way for undertaking highly intensive genome analysis tasks as annotation rule can be found in the Supplementary Material). In a final step, demonstrated by many examples in different research fields such protein domains, families and motifs are identified through InterProScan and the corresponding GO terms are merged with the already transferred as proteomics (Marti-Renom et al., 2007), phylogenomics (Huerta- annotations taking care of redundancies and GO hierarchy. Cepas et al., 2007; Sjölander, 2004) and sequence analysis (Rattei et al., 2008). In this work, we have made use of these technologies Simap2GO data and processing: Simap2GO is the result of the collaboration to create the Functional Annotation Repository (B2G-FAR), a web- between the SIMAP (Rattei et al., 2008) and Blast2GO projects. SIMAP is based large-scale resource of precomputed functional annotations. a database first published in 2005 (Arnold et
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