The Gene Ontology resource: enriching a GOld mine

Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Figure 1.

Gene Ontology Causal Activity Model (GO-CAM) of ‘C. elegans defense response to Gram negative bacterium in the intestine’. A GO-CAM is centered around at least one molecular activity that takes place within a specific biological context. This part of the GO-CAM details the flow of causal influences between molecular activities with the vocabulary from the Relation Ontology. For instance, the ‘MAP kinase tyrosine/serine/threonine phosphatase activity’ negatively regulates the MAP kinase activity of pmk-1 Cele that occurs in cytosol, which has the downstream effect of negatively regulating the ‘DNA binding transcription factor activity, RNA polymerase II-specific’ of atf-7 cele that occurs in nucleus.

Figure 2.

Changes in GO ontology statistics over the last two years. The stacked histograms detail the ontology efforts in creating, obsoleting and merging GO terms.

Figure 3.

Noctua curation platform. (A) Editorial page where curators can browse and search, GO-CAMs. (B) Model edited in Noctua form, a simple form-based interface. (C) Noctua graph representation of the GO-CAM seen in (B). Both Noctua form and Noctua graph allow users to create and edit models.

Figure 4.

GO ribbon web component in the Alliance. This new version of the ribbon is fast, easy to integrate and now handles gene sets to quickly compare the function of several genes. In this example, the ribbon is used to highlight the differences between orthologs of TP53. Clicking on a high-level function (GO term) such as ‘cell death’ will open a table detailing all the annotations related to ‘cell death’, while clicking on ‘all molecular function’ will show all the available molecular function annotations for those genes.