MOTIVATION: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. RESULTS: In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. AVAILABILITY AND IMPLEMENTATION: UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.
MOTIVATION: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. RESULTS: In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. AVAILABILITY AND IMPLEMENTATION: UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.
Authors: Chuming Chen; Qinghua Wang; Hongzhan Huang; Cholanayakanahalli R Vinayaka; John S Garavelli; Cecilia N Arighi; Darren A Natale; Cathy H Wu Journal: Database (Oxford) Date: 2019-01-01 Impact factor: 3.451
Authors: Ivo Pedruzzi; Catherine Rivoire; Andrea H Auchincloss; Elisabeth Coudert; Guillaume Keller; Edouard de Castro; Delphine Baratin; Béatrice A Cuche; Lydie Bougueleret; Sylvain Poux; Nicole Redaschi; Ioannis Xenarios; Alan Bridge Journal: Nucleic Acids Res Date: 2014-10-27 Impact factor: 19.160
Authors: Michelle Giglio; Rebecca Tauber; Suvarna Nadendla; James Munro; Dustin Olley; Shoshannah Ball; Elvira Mitraka; Lynn M Schriml; Pascale Gaudet; Elizabeth T Hobbs; Ivan Erill; Deborah A Siegele; James C Hu; Chris Mungall; Marcus C Chibucos Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971
Authors: Alex L Mitchell; Teresa K Attwood; Patricia C Babbitt; Matthias Blum; Peer Bork; Alan Bridge; Shoshana D Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew I Fraser; Julian Gough; David R Haft; Hongzhan Huang; Ivica Letunic; Rodrigo Lopez; Aurélien Luciani; Fabio Madeira; Aron Marchler-Bauer; Huaiyu Mi; Darren A Natale; Marco Necci; Gift Nuka; Christine Orengo; Arun P Pandurangan; Typhaine Paysan-Lafosse; Sebastien Pesseat; Simon C Potter; Matloob A Qureshi; Neil D Rawlings; Nicole Redaschi; Lorna J Richardson; Catherine Rivoire; Gustavo A Salazar; Amaia Sangrador-Vegas; Christian J A Sigrist; Ian Sillitoe; Granger G Sutton; Narmada Thanki; Paul D Thomas; Silvio C E Tosatto; Siew-Yit Yong; Robert D Finn Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971
Authors: Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R Eddy; Aurélien Luciani; Simon C Potter; Matloob Qureshi; Lorna J Richardson; Gustavo A Salazar; Alfredo Smart; Erik L L Sonnhammer; Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto; Robert D Finn Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971
Authors: Philippe Le Mercier; Jerven Bolleman; Edouard de Castro; Elisabeth Gasteiger; Parit Bansal; Andrea H Auchincloss; Emmanuel Boutet; Lionel Breuza; Cristina Casals-Casas; Anne Estreicher; Marc Feuermann; Damien Lieberherr; Catherine Rivoire; Ivo Pedruzzi; Nicole Redaschi; Alan Bridge Journal: Database (Oxford) Date: 2022-04-12 Impact factor: 4.462
Authors: Marc Feuermann; Emmanuel Boutet; Anne Morgat; Kristian B Axelsen; Parit Bansal; Jerven Bolleman; Edouard de Castro; Elisabeth Coudert; Elisabeth Gasteiger; Sébastien Géhant; Damien Lieberherr; Thierry Lombardot; Teresa B Neto; Ivo Pedruzzi; Sylvain Poux; Monica Pozzato; Nicole Redaschi; Alan Bridge Journal: Metabolites Date: 2021-01-12
Authors: Michael Bernhofer; Christian Dallago; Tim Karl; Venkata Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; Yana Bromberg; Tatyana Goldberg; Laszlo Kajan; Sean O'Donoghue; Chris Sander; Andrea Schafferhans; Avner Schlessinger; Gerrit Vriend; Milot Mirdita; Piotr Gawron; Wei Gu; Yohan Jarosz; Christophe Trefois; Martin Steinegger; Reinhard Schneider; Burkhard Rost Journal: Nucleic Acids Res Date: 2021-07-02 Impact factor: 16.971