UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

• DOI: 10.1093/bioinformatics/btaa485
• Publication Date: 2020-05-05T19:19:51Z
• Authors: Alistair MacDougall; Vladimir Volynkin; Rabie Saidi; Diego Poggioli; Hermann Zellner; Emma Hatton-Ellis; Vishal Joshi; Claire O’Donovan; Sandra Orchard; Andrea H Auchincloss; Delphine Baratin; Jerven Bolleman; Elisabeth Coudert; Edouard de Castro; Chantal Hulo; Patrick Masson; Ivo Pedruzzi; Catherine Rivoire; Cecilia Arighi; Qinghua Wang; Chuming Chen; Hongzhan Huang; John Garavelli; C R Vinayaka; Lai-Su Yeh; Darren A Natale; Kati Laiho; Maria-Jesus Martin; Alexandre Renaux; Klemens Pichler; ; Alex Bateman; Alan Bridge; Cathy Wu; Cecilia Arighi; Lionel Breuza; Elisabeth Coudert; Hongzhan Huang; Damien Lieberherr; Michele Magrane; Maria J Martin; Peter McGarvey; Darren Natale; Sandra Orchard; Ivo Pedruzzi; Sylvain Poux; Manuela Pruess; Shriya Raj; Nicole Redaschi; Lucila Aimo; Ghislaine Argoud-Puy; Andrea Auchincloss; Kristian Axelsen; Emmanuel Boutet; Emily Bowler; Ramona Britto; Hema Bye-A-Jee; Cristina Casals-C...; Paul Denny; Anne Estreicher; Maria Livia Famig...; Marc Feuermann; John S Garavelli; Penelope Garmiri; Arnaud Gos; Nadine Gruaz; Emma Hatton-Ellis; Chantal Hulo; Nevila Hyka-Nousp...; Florence Jungo; Kati Laiho; Philippe Le Mercier; Antonia Lock; Yvonne Lussi; Alistair MacDougall; Patrick Masson; Anne Morgat; Sandrine Pilbout; Lucille Pourcel; Catherine Rivoire; Karen Ross; Christian Sigrist; Elena Speretta; Shyamala Sundaram; Nidhi Tyagi; C R Vinayaka; Qinghua Wang; Kate Warner; Lai-Su Yeh; Rossana Zaru; Shadab Ahmed; Emanuele Alpi; Leslie Arminski; Parit Bansal; Delphine Baratin; Teresa Batista Neto; Jerven Bolleman; Chuming Chen; Yongxing Chen; Beatrice Cuche; Austra Cukura; Edouard De Castro; ThankGod Ebenezer; Elisabeth Gasteiger; Sebastien Gehant; Leonardo Gonzales; Abdulrahman Hussein; Alexandr Ignatchenko; Giuseppe Insana; Rizwan Ishtiaq; Vishal Joshi; Dushyanth Jyothi; Arnaud Kerhornou; Thierry Lombardot; Aurelian Luciani; Jie Luo; Mahdi Mahmoudy; Alok Mishra; Katie Moulang; Andrew Nightingale; Joseph Onwubiko; Monica Pozzato; Sangya Pundir; Guoying Qi; Daniel Rice; Rabie Saidi; Edward Turner; Preethi Vasudev; Yuqi Wang; Xavier Watkins; Hermann Zellner; Jian Zhang
• Keywords: UniProt

Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result genome sequencing and prediction protein-coding genes. Providing functional annotation for these proteins presents significant continuing challenge. Results In response this challenge, has developed method annotation, known UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) by members consortium. UniRule uses family signatures from InterPro, combined with taxonomic other constraints, select sets reviewed have common properties supported experimental evidence. This is propagated unreviewed UniProtKB that meet same selection criteria, most do not (and are never likely have) experimentally verified annotation. Release 2020_01 contains 6496 rules provide 53 million proteins, accounting 30% 178 UniProtKB. provides scalable enrichment Availability implementation integrated into can be viewed at https://www.uniprot.org/unirule/. code required run publicly available researchers who wish annotate their own sequences. used UniFIRE https://gitlab.ebi.ac.uk/uniprot-public/unifire.