Mining enzyme data in UniProtKB using Rhea

The video of the lecture can be found in the SIB YouTube channel.

Overview

Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest and the standard for enzyme and transporter annotation in UniProtKB. Rhea uses the chemical dictionary ChEBI (Chemical Entities of Biological Interest) to describe reaction participants. Rhea provides computationally tractable enzyme annotations in UniProtKB that support chemical ontology and structure based searches in the UniProt website, REST API, and SPARQL endpoint. Rhea also provides reaction data for a host of other resources including ChEBI, MetaboLights, Reactome, and The Gene Ontology, which now bases enzyme molecular functions on Rhea. Rhea and UniProtKB are SIB resources; they are listed in Expasy, the Swiss Bioinformatics Portal.

The goal of this course is to provide basic theoretical and practical knowledge that will enable participants to mine enzyme data in UniProtKB using chemical structure data and chemical classifications from Rhea and ChEBI.

Audience

This course is addressed to biologists, bioinformaticians, cheminformaticians, programmers and data scientists working with enzyme and small molecule data, including those working with metabolomics data and metabolic networks.

Learning outcomes

At the end of the course, the participants are expected to:

• have acquired a good understanding of the structure and design of the chemical ontology ChEBI and the reaction knowledgebase Rhea, and how they are used in UniProtKB annotation
• be able to search UniProtKB and Rhea using chemical ontology terms and chemical structures - including exact chemical structure searches, as well as substructure and similarity searches, using interactive and programmatic means (REST API and SPARQL).
• have acquired a basic understanding of how to use RDF and SPARQL for integration of chemical and biological data in UniProt with other key knowledgebases and data repositories providing RDF and SPARQL endpoints.

Prerequisites

Knowledge / competencies

This course is designed for beginners with a basic knowledge of biology and chemistry.

Technical

This course will be streamed, you are thus required to have your own computer with an Internet connection.

Registration

Attendance is free-of-charge, however registration is mandatory (see the Apply button below). To attend the practical session on March 3, 2022, register here.

There is no limit on the number of participants. All registered participants will receive one day before, by email the information for remotely connecting to the online meeting room.

Venue and Time

This course will be streamed using Zoom.

The course will start at 15:00 CET and end around 18:00 CET. Precise information will be provided to the participants in due time.

Schedule (CET)

15h00 - 16h45: Introduction : main concepts and resources

• Small molecules / ChEBI
• Biochemical and transport reactions / Rhea
• Enzyme classification / ENZYME (EC numbers)
• Enzyme and transporter sequences / UniProtKB

16h45-17h00 Break

17h00-17h20 Search in UniProt (web and REST API)
17h20-17h40 Search in Rhea (web and REST API)

17h40-18h00: Semantic web : RDF/SPARQL (short introduction + query examples)

Additional information

Coordination: Monique Zahn, SIB Training Group.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.