All data in Rhea is freely accessible and available for download from our FTP sites:
Reactions are available in several data formats:
RDF: This is a model of the Rhea data in the RDF (Resource Description Framework) format. It should be considered beta and can change without prior notice. This data can also be queried directly at the Rhea SPARQL endpoint.
BioPAX level 2: This is a community standard data exchange format for biological pathway data in an OWL RDF/XML serialization. It covers the core Rhea data types. Some aspects of the Rhea model can't be expressed in BioPax (e.g. residues of Rhea generic compounds or polymerization indexes of Rhea polymers) and are added as "bp:COMMENT".
RXN: This is a MDL CT file format that represents unidirectional processes. For this reason, bidirectional reactions and reactions with undefined directions cannot be described in this format.
RD: This is a MDL CT file format that consists of a set of records, each of them defining a reaction - in RXN format - and any associated data.
Information about the chemical entities that participate in Rhea reactions is available in the following files:
rhea-mol.tar.gz (and mol directory): A tar file (and directory with individual files) of the 2D structure of each participant in the MDL Molfile format.
rhea.sdf.gz: A single file with the 2D structures of all participants in the MDL Molfile format
chebiId_name.tsv: A list of the participants (ChEBI small molecules only) that are used in Rhea reactions as a tab-separated values file with the columns 1) participant ID, 2) participant name.
chebi_pH7_3_mapping.tsv: A mapping of ChEBI entities to their state at pH 7.3 as a tab-separated values file with the columns 1) ChEBI ID, 2) ChEBI ID mapped at pH 7.3, 3) origin of mapping ('computation' or 'curation'). Major species at pH 7.3 are computed using Marvin pKa calculator from ChemAxon (Software Solutions and Services for Chemistry and Biology), or are defined by curation.
Rhea cross-references to other databases are available as tab-separated values files:
- rhea2xrefs.tsv (all)