Rhea Download

How to download a Rhea reaction record?

ProteinIQ retrieves a single Rhea reaction online from its accession and returns the corresponding RDF/XML record as a downloadable file. Enter a Rhea ID such as RHEA:10000 or 10000, fetch the record, then retain the RDF alongside pathway data, enzyme annotations, or software outputs that need a precise reaction identifier.

For RHEA:10000, the file list returns:

rhea-10000-rdf.xml

There is no output-format selector because this tool returns one format, RDF/XML.

What is Rhea Download?

Rhea Download is a record-retrieval tool for Rhea, an expert-curated knowledgebase of biochemical and transport reactions of biological interest. It retrieves the RDF representation of one reaction identified by its Rhea accession, such as RHEA:10000. Rhea uses ChEBI chemical entities to describe reaction participants and provides curated links to enzyme classifications and other biological resources where available.

The tool answers a specific lookup question: “What is the machine-readable Rhea record for this known reaction?” It does not infer a reaction from a protein sequence, search a pathway, or assign an EC number. That distinction matters when preserving the reaction definition behind an enzyme annotation, a metabolic-model entry, or a cross-reference in a report.

Rhea reactions are especially useful as stable, curated identifiers for chemistry that is linked to protein annotation. A reaction can have associated EC numbers, but an EC number and a Rhea ID are not interchangeable: the Rhea record represents a reaction definition, while EC classification groups enzyme-catalyzed reactions.

Input

The input identifies an existing Rhea reaction, not a protein accession, enzyme name, EC number, ChEBI identifier, or free-text reaction query. When only a compound, enzyme, EC number, or reaction description is known, locate the matching Rhea reaction in Rhea first, then use its RHEA: accession here.

Settings

Output

The Files panel provides an RDF/XML description of the reaction from the official Rhea SPARQL service. ProteinIQ requests DESCRIBE for the reaction URI and preserves the returned XML. The export describes that resource and its links; it is not a complete Rhea release or a recursive export of every linked chemical entity. For RHEA:10000, the filename is rhea-10000-rdf.xml.

Understanding the reaction record

RDF, the Resource Description Framework, represents data as linked statements. Rhea publishes this form so reaction definitions and their identifiers can be read by software or queried alongside other RDF data. The downloaded file is therefore most useful for structured data integration, provenance capture, and semantic-web workflows rather than as a human-friendly reaction report.

Inspect reaction equations and linked EC numbers in the downloaded record or on the original Rhea page. The equation describes a curated reaction, not measured flux, rate, or enzyme activity in a particular organism.

Rhea uses ChEBI entities for reaction participants. A participant identifier points to a defined chemical entity, which is more reliable for automated analysis than matching compounds only by a display name. To retain chemical-entity metadata together with a reaction workflow, database search retrieves ChEBI records by accession.

Where Rhea Download fits in an annotation workflow

Rhea Download is most useful after another resource has already produced a Rhea ID. For example, a UniProt enzyme annotation may carry a Rhea cross-reference, or a pathway table may identify reactions with Rhea accessions. Fetching the individual RDF records at that point preserves the versioned, machine-readable definitions used to interpret those identifiers.

• Store the Rhea RDF file with a metabolic-model export or supplementary dataset to preserve the exact reaction reference.
• Use the equation and linked EC-number metadata to check that an annotation table points to the intended chemistry.
• Parse RDF identifiers and links in a graph database or RDF-aware workflow rather than extracting meaning from a file name.
• Pair reaction records with UniProt protein records when both the annotated protein and the catalyzed reaction need to be retained.

This tool retrieves one known record per run. It does not provide batch mapping, full-text discovery, reaction similarity search, pathway reconstruction, kinetic parameters, or protein-specific evidence that an enzyme catalyzes the downloaded reaction. Those questions require the appropriate Rhea search or mapping workflow and, for a particular protein, the relevant sequence and annotation evidence.

Rhea content changes with database releases. The RDF file is a retrieval-time snapshot, so analyses that depend on exact reaction definitions should retain the Rhea accession, download date, and the retrieved file alongside the study or pipeline output.

Download availability

Enter one identifier or compound name on a single line, up to 200 characters. Surrounding spaces are ignored. These lookups need an internet connection: ProteinIQ retrieves the record from the selected database, and file downloads contact its file service.

If a text file cannot be loaded in the browser, a warning appears and its download link stays available. A listed link does not guarantee that the database currently serves that file. Retry the download or check the original database record; a connection failure is different from an unknown entry.

FAQ

Why is the file named .xml rather than .rdf?

The source document is RDF serialized as XML. ProteinIQ labels that format xml, so RHEA:10000 is saved as rhea-10000-rdf.xml. The content is not converted to a different reaction format.

Can I enter an EC number?

Use a Rhea ID here. To find reactions from an EC number or description, use Rhea search first.