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. 2019 Jan 8;47(D1):D330-D338.
doi: 10.1093/nar/gky1055.

The Gene Ontology Resource: 20 years and still GOing strong

The Gene Ontology Consortium

The Gene Ontology Resource: 20 years and still GOing strong

The Gene Ontology Consortium. Nucleic Acids Res. .

Abstract

The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the 'GO ribbon' widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.

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Figures

Figure 1.
Figure 1.
GO structure. (A) Graphical representation of relationships between terms: black lines represent is_a and blue lines represent part_of (representation obtained from https://www.ebi.ac.uk/QuickGO/term/GO:0060887). (B) Equivalence axiom for the term ‘GO:0060887: limb epidermis development’, as displayed in Protégé (12).
Figure 2.
Figure 2.
The molecular function branch, before and after refactoring. The term marked with an ‘x’ in the left-hand panel has been obsoleted. Terms moved (assigned to a new parent) are indicated by arrows. New terms (right panel) are marked with ‘NEW’. 1The class label ‘electron carrier activity’ was changed to ‘electron transfer activity’.
Figure 3.
Figure 3.
Current structure of the ‘GO:0140110 transcription regulator activity’ branch of the ontology.
Figure 4.
Figure 4.
GO ribbon representation. Darker boxes indicate terms with the most annotations; white boxes represent terms that are not annotated for this protein (Mus musculus Sox7, MGI:98369). Screenshot obtained from https://www.alliancegenome.org/gene/MGI:98369.
See this image and copyright information in PMC

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