News

Rhea web site

Structure search: to make the result page more self-contained, the 2D structure of the query and the search parameters have been added to the result page.

New website

We are proud to announce the release of our new website: a new interface, a new search engine and many new options to serve you better. We welcome your feedback!

Cross-references to UniProt

The mapping to all UniProt enzyme sequences is now available for download on our FTP site:

• rhea2uniprot_sprot.tsv (UniProtKB/Swiss-Prot)
• rhea2uniprot_trembl.tsv.gz (UniProtKB/TrEMBL)

Rhea in UniProt 'Catalytic activity' annotations

Starting from this release, Rhea reactions are used in UniProt for 'Catalytic activity' annotations. See the UniProt 2018_11 news for more details.

Changes to cross-references to UniProt

UniProt now provides direct links between proteins (UniProtKB entries) and Rhea reactions. These data are searchable and downloadable from the UniProt website. As a consequence, we stopped displaying the old indirect cross-references that were computed via EC numbers (Rhea - EC - UniProtKB/Swiss-Prot) on our website and removed the corresponding file rhea2uniprot.tsv from our FTP site. We also replaced the BioPAX files rhea-biopax_lite.owl.gz and rhea-biopax_full.owl.gz by a single file rhea-biopax.owl.gz, which no longer contains links to UniProtKB/Swiss-Prot entries.

ChEBI major microspecies at pH 7.3

The mapping of ChEBI entities to their protonation state at pH 7.3 is now available for download: chebi_pH7_3_mapping.tsv

Change to alphabetic sorting of reaction participants

Starting with this release, the participants on each side of a reaction are sorted alphabetically (case insensitive) by their name (in ASCII representation).

Old:
RHEA:21732
L-glutamine + chorismate = L-glutamate + anthranilate + H(+) + pyruvate

New:
RHEA:21732
chorismate + L-glutamine = anthranilate + H(+) + L-glutamate + pyruvate

This affects the website, APIs and FTP downloads.

Change of EC cross-references from bidirectional to reactions with undefined direction

The cross references from Rhea reactions to EC numbers have been moved from bidirectional reactions (<=>) to reactions with undefined direction (=).

Old:

RHEA:10739
a primary alcohol + NAD() <=> an aldehyde + H() + NADH
Cross reference: EC 1.1.1.1

New:

RHEA:10736
a primary alcohol + NAD() = an aldehyde + H() + NADH
Cross reference: EC 1.1.1.1

This affects the website, APIs and FTP downloads.

The file ec-rhea-dir.tsv has been removed from the FTP site, the files rhea-ec-iubmb.tsv and rhea2ec.tsv remain available.

Change of symbol for reactions with undefined direction

The symbol in reactions with undefined direction ("master" reactions) has been changed from "<?>" to the equals sign "=".

Old format: A + B <?> C + D
New format: A + B = C + D

This affects the website, API and FTP downloads.