Frequently asked questions

What is Rhea?

Rhea is a freely available knowledgebase of biochemical reactions. This knowledge is curated by experts from peer-reviewed literature.

How frequently is Rhea updated?

Rhea is updated approximately on a monthly basis. Rhea updates are synchronized with those of UniProt.

What types of reaction are included in Rhea?

Rhea describes reactions that are relevant to biological systems, including enzyme-catalyzed reactions, transport reactions, and spontaneous reactions.

What is the relationship between Rhea and the enzyme classification of the IUBMB?

Rhea aims to cover all chemically explicit reactions described by the enzyme classification of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). The relationship between the two is complex: a single enzyme class may catalyse several reactions, while many enzyme classes may catalyze the same reaction. There are currently around two times as many reactions in Rhea as there are known enzyme classes in the IUBMB enzyme classification.

Where can I find information about the enzymes that catalyze Rhea reactions?

UniProt curators now use Rhea to annotate enzymes in the UniProt Knowledgebase (UniProtKB, available at UniProt users can search UniProtKB using the names and identifiers of compounds (from ChEBI) and the identifiers of Rhea reactions; find out more at the UniProt documentation and news page.

Is there any significance to the order of reaction participants?

There is no particular significance to the order of reaction participants. For those reactions with a specified direction, the position of the reaction participants with respect to the reaction operator (such as an arrow) reflects their role as substrates or products.

What types of molecules are included in Rhea?

Rhea reactions feature naturally occurring compounds, including natural products such as primary and secondary metabolites and synthetic products such as drugs or environmental chemicals. Rhea also includes genetically encoded macromolecules such as proteins and nucleic acids, as well as polymers.

How does Rhea represent molecules in reactions?

Rhea represents reactants – including small molecules and the reactive groups of large macromolecules such as proteins – using species from the ChEBI ontology of Chemical Entities of Biological Interest. Rhea represents reactant structures using the ChEBI entity that describes the predominant charge state – also known as the major microspecies – at pH7.3.

Which ChEBIs are used in Rhea?

Rhea uses the major species at pH 7.3 (we call it normalized ChEBI). For external users we provide a mapping file that allows them to do this mapping for their own data. See chebi_pH7_3_mapping.tsv file in the Download page.

Why does the name of a given compound differ in ChEBI and Rhea?

Rhea curators will assign names to compounds that facilitate their recognition by biologists. These names may differ from the primary name assigned by ChEBI curators; they appear in ChEBI as a specific type of synonym called the "UniProt name".

How can I search Rhea for reactions?

With the simple search, users can search for reactions using compound names, identifiers, pubmed IDs or cross-references.
With the advanced search, users can search by structures (represented as InChI keys for example).

What is an InChI key?

The IUPAC International Chemical Identifier, or InChI, is a textual representation for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. The condensed InChI key is a hashed version of the full InChI (created using the SHA-256 algorithm), designed to allow for easy searches of chemical compounds. InChI keys can be used to quickly match identical structures or those that differ only in charge or stereochemistry.