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

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.