Reactome and the Gene Ontology: digital convergence of data resources
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.
Additional Information
© The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 23 December 2020; Revision received: 18 March 2021; Editorial decision: 19 April 2021; Accepted: 27 April 2021; Published: 08 May 2021. This work was supported by grants from the National Institutes of Health [U41 HG02273 to support the GO Consortium; U41 HG 003751 to support the Reactome Knowledgebase], and by funds from the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [Contract No. DE-AC02-05CH11231 to C.J.M. and S.C.]. Conflict of Interest: none declared.Attached Files
Published - btab325.pdf
Supplemental Material - btab325_supplementary_data.pdf
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Additional details
- PMCID
- PMC8504636
- Eprint ID
- 109122
- Resolver ID
- CaltechAUTHORS:20210513-141147825
- U41 HG02273
- NIH
- U41 HG 003751
- NIH
- DEAC02-05CH11231
- Department of Energy (DOE)
- Created
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2021-05-13Created from EPrint's datestamp field
- Updated
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2021-10-15Created from EPrint's last_modified field