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. 2022 Jan 7;50(D1):D693-D700.
doi: 10.1093/nar/gkab1016.

Rhea, the reaction knowledgebase in 2022

Parit Bansal  1 , Anne Morgat  1 , Kristian B Axelsen  1 , Venkatesh Muthukrishnan  1 , Elisabeth Coudert  1 , Lucila Aimo  1 , Nevila Hyka-Nouspikel  1 , Elisabeth Gasteiger  1 , Arnaud Kerhornou  1 , Teresa Batista Neto  1 , Monica Pozzato  1 , Marie-Claude Blatter  1 , Alex Ignatchenko  2 , Nicole Redaschi  1 , Alan Bridge  1
Affiliations

Rhea, the reaction knowledgebase in 2022

Parit Bansal et al. Nucleic Acids Res. .

Abstract

Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities of Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number of key developments in Rhea since our last report in the database issue of Nucleic Acids Research in 2019. These include improved reaction coverage in Rhea, the adoption of Rhea as the reference vocabulary for enzyme annotation in the UniProt knowledgebase UniProtKB (https://www.uniprot.org), the development of a new Rhea website, and the designation of Rhea as an ELIXIR Core Data Resource. We hope that these and other developments will enhance the utility of Rhea as a reference resource to study and engineer enzymes and the metabolic systems in which they function.

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Figures

Figure 1.
Figure 1.
Rhea Reaction page. Each reaction page contains sections providing information on the reaction itself and associated enzymes, as well as reaction participants, cross references, publications, and other information such as comments. Action buttons allow users to copy the reaction equation and download the directed forms of reaction in RXN and RD formats, while a multi-faceted tooltip linked to the name of each participant allows users to launch searches in Rhea, ChEBI and UniProtKB. (A) reaction information section, (B) detailed information regarding reaction participants, (C) cross-references for each member of the Rhea quartet (each member corresponds to different directions but the same transformation).
Figure 2.
Figure 2.
Rhea Advanced Query builder. (A) The Rhea query builder can be accessed by clicking on the Advanced search link. (B) Clicking on the All button allows users to access a list of searchable fields and select Boolean operators (see Supplementary Table 1). (C) A complex query can be constructed using multiple constraints. An exact search option is provided for searches using identifiers from ChEBI and the Gene Ontology. This option allows users to perform searches without using the ‘is a’ relationships. (D) Final query created using the query builder.
Figure 3.
Figure 3.
Search Results. Search results are displayed in tabular form, where each row corresponds to a single reaction. Action buttons (top) allow users to map selected reactions to UniProtKB, to download them, to add or remove columns from the result table, or to create a link (URL) for the result that can be bookmarked, shared and reused.
Figure 4.
Figure 4.
Identifier mapping. (A) By default, Gene Ontology identifier mapping will retrieve Rhea reactions mapped to a user supplied GO term and to all children of that GO term. In this example, the user supplied GO term, GO:0003884 (D-amino-acid oxidase activity), maps directly to RHEA:21816 (grey arrow) as well as to RHEA:12512 (via GO:0008445, D-aspartate oxidase activity) and RHEA:10028 (via GO:0047821, D-glutamate oxidase activity) (red arrows). (B) The Gene Ontology (exact) search option limits mapping to Rhea reactions directly mapped to GO:0003884 (D-amino-acid oxidase activity)—RHEA:21816—and excludes reactions mapped to GO terms that are children of GO:0003884.
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References

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