How to search for Rhea reactions involving specific chemical compounds
Channel: SIB - Swiss Institute of Bioinformatics
Date: 2021-06-14

What you will discover: How to search Rhea reactions involving specific chemical compounds, taking into account their synonyms, their charges and their hierarchical classification. Rhea is a resource which describes biochemical reactions in a computationally tractable manner. It is developed by the Swiss-Prot Group at SIB.

Access Rhea: https://www.rhea-db.org/

Target audience: biologists (wet-lab scientists, clinicians), bioinformaticians, data scientists, biocurators, cheminformaticians, chemoinformaticians

Click to access specific sections of the talk: 
00:09  Rhea and ChEBI
00:26  Search for ‘palmitate’
00:40  Synonyms
01:31  Charge, and major microspecies at pH 7.3
03:27  Hierarchical classification of chemical compounds

Reference papers
Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A.
Updates in Rhea: SPARQLing biochemical reaction data.
Nucleic Acids Res. 47:D596-D600 (2019).
PMID:30272209 
DOI: 10.1093/nar/gky876 

Other resources mentioned in this talk: 
• ChEBI, Chemical Entities of Biological Interest, a dictionary of ‘small’ chemical compounds https://www.ebi.ac.uk/chebi/

Any question about this talk? Contact rhea-db(at)sib.swiss

This video is available under the creative commons license CC-BY-4.0 
https://creativecommons.org/licenses/by/4.0/