Reaction curation

Content:

Introduction

Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner using the chemical dictionary ChEBI (Chemical Entities of Biological Interest) to describe reaction participants.

Collaborations

Rhea collaborates with and complements the work of three related resources:

ResourceData type
Rheareaction
ChEBIreaction participant
UniProtKBenzyme sequence and functional information
ENZYMEenzyme classification (see details)

Rhea curators describe reactions using ChEBI entities. They submit new entities and updates (synonyms, citations, links, relationships, structure) to ChEBI that are then reviewed by CHEBI curators. UniProt provides sequence and functional information for proteins and uses Rhea to describe enzyme-catalyzed and transporter reactions. ENZYME curators create enzyme classes (EC numbers) according to the NC-IUBMB recommendations and link them to Rhea reactions. Both UniProt and ENZYME curators request new reactions from Rhea.

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These collaborations and user requests drive our curation priorities and the scope of Rhea, which includes all enzyme-catalyzed reactions covered by the NC-IUBMB enzyme classification, but also many more that are described in UniProtKB and other resources, as well as spontaneously occurring reactions.

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Curation steps

Identify relevant scientific publications

Rhea curators scan the scientific literature to identify publications on novel reactions. They select the most relevant publication(s) to curate a new Rhea reaction. They cite the publications by their PubMed identifiers. The same publication may provide evidence for multiple reactions.

Rhea also collaborates with PubTator Central (NIH) to identify publications that describe reactions that are missing in Rhea.

Encode the reaction participants with ChEBI

Rhea curators search the ChEBI ontology for compounds that match the description of the reaction participants that they found in the literature. If they cannot find a suitable compound, they submit a draft for a new compound to ChEBI, which is then reviewed by CHEBI curators. For reactions that involve macromolecules or polymers, Rhea curators create compound records in Rhea to encode these molecules (see reaction participants).