The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

Abstract

The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of integration of the knowledge represented in UniProt with other databases. This is achieved by converting UniProt annotation into a recognized computational format. GOA provides annotated entries for nearly 60,000 species (GOA-SPTr) and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. By integrating GO annotations from other model organism groups, GOA consolidates specialized knowledge and expertise to ensure the data remain a key reference for up-to-date biological information. Furthermore, the GOA database fully endorses the Human Proteomics Initiative by prioritizing the annotation of proteins likely to benefit human health and disease. In addition to a non-redundant set of annotations to the human proteome (GOA-Human) and monthly releases of its GO annotation for all species (GOA-SPTr), a series of GO mapping files and specific cross-references in other databases are also regularly distributed. GOA can be queried through a simple user-friendly web interface or downloaded in a parsable format via the EBI and GO FTP websites. The GOA data set can be used to enhance the annotation of particular model organism or gene expression data sets, although increasingly it has been used to evaluate GO predictions generated from text mining or protein interaction experiments. In 2004, the GOA team will build on its success and will continue to supplement the functional annotation of UniProt and work towards enhancing the ability of scientists to access all available biological information. Researchers wishing to query or contribute to the GOA project are encouraged to email: goa@ebi.ac.uk.

Enrichment of HapMap recombination hotspot predictions around human nervous system genes: evidence for positive selection ?

“…23 Ensembl genes 22 were cross-referenced via the International Protein Index (version April 2006) 24 to the Gene Ontology (GO) Annotation database (version April 2006). 25 Obeying the 'true path rule', GO annotations were transitively assigned for all parent categories. GO categories 26 were analyzed, if annotated to 20 or more human Ensembl genes.…”

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

“…Foundry ontologies are created and maintained by biologists with a thorough knowledge of the underlying science. Where domain experts jointly control ontology, data, and annotations (as in the case of the GO/ Uniprot collaboration), all three can be curated in tandem in a way that provides a reality check at each stage of the process 34 . As results of experiments are described in annotations, this leads to extensions or corrections of the ontology, which in turn lead to better annotation35.…”

Single nucleotide polymorphisms as a prerequisite for autoantigens

“…As illustrated in Table 2, human preproinsulin contains seven synonymous and two non-synonymous SNP. Interestingly, the single non-synonymous SNP located in mature insulin (position 38 of preproinsulin) is contained in two of the six known class-II-restricted T cell epitopes (33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51), and directly flanking the only known class-I-restricted epitope (39)(40)(41)(42)(43)(44)(45)(46)(47) in human insulin ( [22] and references therein).…”

“…Human gene structure was from Ensembl [36], human release 34c (accessed via Ensembl perl API and Bioperl modules [37]). For gene annotation we used the GO database [38] with human annotation release 18.0 [39]. For disease-associated genes, we used the OMIM database [27], downloaded on 04/27/2004.…”