Get started
Work

Reactome and the Gene Ontology: digital convergence of data resources

Year: 2021
Type: article
Abstract: MOTIVATION: Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. RESULTS: To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
DOI: 10.1093/bioinformatics/btab325
Authors: Benjamin M Good, Kimberly Van Auken, David P Hill, Huaiyu Mi, Seth Carbon, James P Balhoff, Laurent-Philippe Albou, Paul D Thomas, Christopher J Mungall, Judith A Blake, Peter D’Eustachio
Institutions: Lawrence Berkeley National Laboratory, California Institute of Technology, Jackson Laboratory, University of Southern California, University of North Carolina at Chapel Hill, Renaissance Computing Institute, New York University
Language: English
Open Access status: hybrid
Estimated APC paid: $3,478
Awards: G1286236842, G1286251239, Gene Ontology Consortium, G2618837358, Reactome: An Open Knowledgebase of Human Pathways, G30714459, G3083819904, G382641700, G419881185, G42916606, G4501827968, G498139845, G650090426, G6652958823, G969889393
OpenAlex ID: W3163048757
FWCI: 1.411
Cites: 23
Cited by: 23
Related to: 10