The UniProt website API: facilitating programmatic access to protein knowledge

Shadab Ahmad(European Bioinformatics Institute), Leonardo Jose da Costa Gonzales(European Bioinformatics Institute), Emily Bowler-Barnett(European Bioinformatics Institute), Daniel L Rice(European Bioinformatics Institute), Minjoon Kim(European Bioinformatics Institute), Supun Wijerathne(European Bioinformatics Institute), Aurélien Luciani(European Bioinformatics Institute), Swaathi Kandasaamy(European Bioinformatics Institute), Jie Luo(European Bioinformatics Institute), Xavier Watkins(European Bioinformatics Institute), Edd Turner(European Bioinformatics Institute), María Martin(European Bioinformatics Institute), Alex Bateman, María Martin(European Bioinformatics Institute), Sandra Orchard, Michele Magrane, Shiqi Ye, Aduragbemi S. Adesina, Shadab Ahmad(European Bioinformatics Institute), Emily Bowler-Barnett(European Bioinformatics Institute), David C. J. Carpentier, Paul Denny, Jun Fan, Leonardo Jose da Costa Gonzales(European Bioinformatics Institute), Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy(European Bioinformatics Institute), Antonia Lock, Aurélien Luciani(European Bioinformatics Institute), Jie Luo(European Bioinformatics Institute), Yvonne Lussi, Juan Marín, Pedro Raposo, Daniel L Rice(European Bioinformatics Institute), James Stephenson, Prabhat Totoo, Nadya Urakova, Preethi Vasudev, Supun Wijerathne(European Bioinformatics Institute), Khawaja Talal Ibrahim, Minjoon Kim(European Bioinformatics Institute), C. Yu, Alan Bridge, Lucila Aimo, Ghislaine Argoud‐Puy, Andrea H Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, 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, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J A Sigrist, Karin Sonesson, Shyamala Sundaram, Anastasia Sveshnikova, Cathy Wu, Chuming Chen, Hongzhan Huang, Kati Laiho, Minna Lehväslaiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C R Vinayaka, Yuqi Wang, Raja Mazumber, Vijay Shanker, Jian Zhang
Nucleic Acids Research
May 7, 2025
10.1093/nar/gkaf394
Cited by 121Open Access
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Abstract

The UniProt REST API is a freely available, open-access resource that powers the UniProt.org website and gives users flexible programmatic interaction with protein knowledge data. It provides access to UniProtKB, UniRef, UniParc, Proteomes, GeneCentric, ARBA, UniRule, and the ID Mapping tool, along with supporting data and controlled vocabularies. Users can access the API with their favorite programming language and generate example code snippets to access the UniProt databases using the API documentation page (https://www.uniprot.org/api-documentation) in various languages. API results can be returned and downloaded in various formats. With an average of 303 million requests per month over the last year, the API enables structured search queries using logical operators and parentheses, allows users to specify fields of interest within results, and customize downloads for direct integration into workflows. The API is a powerful tool that empowers users to fully utilize UniProt data across multiple datasets, enabling download, analysis, and extraction of valuable research insights. This website is free and open to all users, and there is no login requirement.

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