Annotation of biologically relevant ligands in UniProtKB using ChEBI

Elisabeth Coudert(SIB Swiss Institute of Bioinformatics), Sébastien Géhant(SIB Swiss Institute of Bioinformatics), Edouard de Castro(SIB Swiss Institute of Bioinformatics), Monica Pozzato(SIB Swiss Institute of Bioinformatics), Delphine Baratin(SIB Swiss Institute of Bioinformatics), Teresa Batista Neto(SIB Swiss Institute of Bioinformatics), Christian J A Sigrist(SIB Swiss Institute of Bioinformatics), Nicole Redaschi(SIB Swiss Institute of Bioinformatics), Alan Bridge(SIB Swiss Institute of Bioinformatics), Alan Bridge(SIB Swiss Institute of Bioinformatics), Lucila Aimo, Ghislaine Argoud‐Puy, Andrea H Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin(SIB Swiss Institute of Bioinformatics), Teresa M Batista Neto(SIB Swiss Institute of Bioinformatics), Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals‐Casas, Kamal Chikh Echioukh, Elisabeth Coudert(SIB Swiss Institute of Bioinformatics), Beatrice Cuche, Edouard de Castro(SIB Swiss Institute of Bioinformatics), Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger(SIB Swiss Institute of Bioinformatics), Pascale Gaudet, Sébastien Géhant(SIB Swiss Institute of Bioinformatics), Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka‐Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato(SIB Swiss Institute of Bioinformatics), Manuela Pruess, Nicole Redaschi(SIB Swiss Institute of Bioinformatics), Catherine Rivoire, Christian J A Sigrist(SIB Swiss Institute of Bioinformatics), Karin Sonesson, Shyamala Sundaram, Alex Bateman, María Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily Bowler-Barnett, Ramona Britto, Hema Bye- A-Jee, Austra Cukura, Paul Denny, Tunca Doğan, ThankGod E. Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurélien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel L Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, E. B. Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho(European Bioinformatics Institute), Peter B. McGarvey, Darren A. Natale, Karen Ross, C R Vinayaka, Qinghua Wang(SIB Swiss Institute of Bioinformatics), Yuqi Wang(SIB Swiss Institute of Bioinformatics)
Bioinformatics
December 9, 2022
10.1093/bioinformatics/btac793
Cited by 313Open Access
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Abstract

MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant interactions between protein sequences and structures and small molecule ligands. RESULTS: We structured the data model for cognate ligand binding site annotations in UniProtKB and performed a complete reannotation of all cognate ligand binding sites using stable unique identifiers from ChEBI, which we now use as the reference vocabulary for all such annotations. We developed improved search and query facilities for cognate ligands in the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that ChEBI provides. AVAILABILITY AND IMPLEMENTATION: Binding site annotations for cognate ligands described using ChEBI are available for UniProtKB protein sequence records in several formats (text, XML and RDF) and are freely available to query and download through the UniProt website (www.uniprot.org), REST API (www.uniprot.org/help/api), SPARQL endpoint (sparql.uniprot.org/) and FTP site (https://ftp.uniprot.org/pub/databases/uniprot/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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