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Annotation of biologically relevant ligands in UniProtKB using ChEBI

2022; Oxford University Press; Volume: 39; Issue: 1 Linguagem: Inglês

10.1093/bioinformatics/btac793

1367-4811

Elisabeth Coudert, Sébastien Géhant, Edouard de Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian Sigrist, Nicole Redaschi, Alan Bridge, Alan Bridge, Lucila Aimo, Ghislaine Argoud‐Puy, Andrea Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals‐Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sébastien Géhant, 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, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian Sigrist, 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 Arighi, Leslie Arminski, Chuming Chen, Chuming Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C R Vinayaka, Qinghua Wang, Yuqi Wang,

Bioinformatics and Genomic Networks

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.