rhea_reactions — Rhea biochemical reactions (2026)

Description

Bipartite networks of biochemical reactions and the compounds that take part in them, from Rhea, the expert-curated knowledgebase of chemical and transport reactions of biological interest of the SIB Swiss Institute of Bioinformatics, which is the reference vocabulary for the enzymatic reactions annotated in UniProtKB. The data are those of release 142 (September 2, 2026).

reactions: the reactions and their participants. Each reaction of Rhea is described by a reaction with an undefined direction ("master" reaction, written with =), and by its two directional (left-to-right and right-to-left) and its bidirectional versions; only the master reactions are nodes here, and the directional ones are given as properties. An edge goes from each compound of the left side of the equation, as written by Rhea, to the reaction, and from the reaction to each compound of its right side, with the stoichiometric coefficient of the compound and, for transport reactions, the side of the membrane (in or out); since the direction of a master reaction is undefined, the direction of the edges is only that of the written equation. A compound that is transported appears on both sides of a reaction. The compounds are small molecules of the ChEBI ontology, generic compounds (e.g. [protein]-dithiol, described by their reactive parts) and polymers. Obsolete reactions have no participants, and are left out.
hierarchy: the classification of the reactions, where an edge goes from a reaction to a more general reaction of which it is an instance (relation is_a), e.g. the reaction of a specific alcohol to the reaction of "a primary alcohol". The nodes are the master reactions that take part in it; Rhea also lists the same relations between the corresponding directional reactions, which are left out.

The networks have the following properties:

(Node) rhea_id (reactions): the accession of the master reaction (e.g. RHEA:10000), or of the compound: CHEBI:... for small molecules, GENERIC:... for generic compounds, POLYMER:... for polymers.
(Node) is_reaction: whether the node is a reaction (otherwise it is a compound).
(Node) name: the equation of the reaction, with the names of the compounds (e.g. pentanamide + H2O = pentanoate + NH4(+)), or the name of the compound.
(Node) status: the curation status of the reaction (Approved or Preliminary; empty for compounds).
(Node) is_transport, is_balanced: whether the reaction is a transport reaction, and whether it is chemically balanced.
(Node) ec: the EC numbers of the enzymes that catalyze the reaction.
(Node) directional_ids: the accessions of the left-to-right, right-to-left and bidirectional versions of the reaction.
(Node) citations: the PubMed identifiers of the articles that support the reaction.
(Node) compound_class (reactions): the kind of compound: SmallMolecule, GenericPolypeptide, GenericPolynucleotide, GenericHeteropolysaccharide, GenericSmallMolecule, GenericCompound or Polymer (empty for reactions).
(Node) formula, charge: the chemical formula and charge of the compound (empty if not given; for polymers they are given per repeating unit, e.g. (-4)(-1)n, as in Rhea).
(Node) chebi_ids: the ChEBI identifiers of the compound: itself for small molecules, the reactive parts for generic compounds, the underlying ChEBI entity for polymers.
(Edge) coefficient (reactions): the stoichiometric coefficient of the compound (e.g. 1, 2, N, 2n, N+1).
(Edge) location (reactions): the side of the membrane of the compound in a transport reaction (in or out; empty otherwise).

Tags

Biological Metabolic Chemical Unweighted Bipartite Metadata

Added

2026-10-31

Citation

P. Bansal, A. Morgat, K. B. Axelsen, V. Muthukrishnan, E. Coudert, L. Aimo, N. Hyka-Nouspikel, E. Gasteiger, A. Kerhornou, T. B. Neto, M. Pozzato, M.-C. Blatter, A. Ignatchenko, N. Redaschi, A. Bridge, "Rhea, the reaction knowledgebase in 2022." Nucleic Acids Research 50, D693-D700 (2022) 10.1093/nar/gkab1016 Sci-Hub

Upstream URL OK

https://www.rhea-db.org/
https://ftp.expasy.org/databases/rhea/

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
reactions	33,814	90,303	2.67	75.35	88.96	34.99	-0.15	0.00	14	0.99	Directed	Bipartite	rhea_id is_reaction name status is_transport is_balanced ec directional_ids citations compound_class formula charge chebi_ids	coefficient location	1.3 MiB	1.9 MiB	1.9 MiB	1.9 MiB
hierarchy	6,277	5,365	0.85	3.06	3.45	241.99	-0.22	0.00	16	0.03	Directed	Unipartite	rhea_id name status is_transport is_balanced ec directional_ids citations		252 KiB	337 KiB	330 KiB	373 KiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.