The Renal Gene Ontology Annotation Initiative

Abstract

The gene ontology (go) resource provides dynamic controlled vocabularies to aid in the description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). A renal-focused curation initiative, funded by Kidney Research UK and supported by the GO Consortium, has started at the European Bioinformatics Institute and aims to provide a detailed GO resource for mammalian proteins implicated in renal development and function. This report outlines the aims of this initiative and explains how the renal community can become involved to help improve the availability, quality and quantity of GO terms and their association to specific proteins.

Keywords: annotation; biocuration; gene ontology; kidney; renal.

Figure 1

(A) A QuickGO view of a single Molecular Function GO term (i.e., GO:0015378 sodium:chloride symporter activity) showing it’s “parent” relations within the hierarchical DAG. (B) Clicking on a particular GO term box (i.e., Anion transmembrane transporter activity) brings up a window providing the GO term name, it’s stable GO ID, the definition of the term and its “child” terms.

Figure 2

View of a combination of manual and electronic annotations for protein Q9H267, displayed by the QuickGO browser (http://www.ebi.ac.uk/ego/GProtein?ac=Q9H267). Annotations include information on (1) the sequence accession number from a named database (e.g., UniProtKB), (2) gene symbol, (3) species taxon ID , (5) GO term stable ID (6) GO term name, (7) the reference ID of the source of the manual or electronic annotation, (8) a three-letter acronym of the GO evidence code, (10) a date stamp of when the annotation was made/updated. The “Qualifier” column (4) is an optional addition to an annotation that acts to modify the interpretation of the associated GO term; similarly the ‘With’ column (9) provides further functional information such as the name/accession number of an interacting partner of the annotated protein (manual annotation) or the accession number from the underlying mapped source of the electronic annotation.