The Gene Ontology resource: enriching a GOld mine

TLDR

The Gene Ontology Consortium provides the most comprehensive resource for computable knowledge of gene and gene product functions. This paper reports the consortium’s advances over the past two years. The consortium improved the GO‑CAM annotation framework with a formal computational schema, updated older annotations, redesigned its website for easier access, and released a 15‑year historical archive to support traceability and reproducibility. Collaborations produced a 10 % increase in GO annotations, a 25 % increase in annotated gene products, over 9,400 newly annotated scientific articles, and the review of 20,000 experimental annotations (2.5 % of all experimental GO annotations).

Abstract

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.