IntAct - open source resource for molecular interaction data. - Samuel Kerrien; Yasmin Alam-Faruque; Bruno Aranda; I. Bancarz; Alan J. Bridge; C. Derow; Emily Dimmer; Marc Feuermann; A. Friedrichsen; Rachael P. Huntley; C. Kohler; Jyoti Khadake; et al. (Nucleic Acids Res., 2007)

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. - Pascale Gaudet; Lydie Lane; Petra Fey; Alan J. Bridge; Sylvain Poux; Andrea H. Auchincloss; Kristian B. Axelsen; Silvia Braconi-Quintaje; Emmanuel Boutet; P. Brown; Elisabeth Coudert; Ruchira S. Datta; et al. (Database J. Biol. Databases Curation, 2009)

The IntAct molecular interaction database in 2010. - Bruno Aranda; P. Achuthan; Yasmin Alam-Faruque; Irina M. Armean; Alan J. Bridge; C. Derow; Marc Feuermann; A. T. Ghanbarian; Samuel Kerrien; Jyoti Khadake; Jules Kerssemakers; C. Leroy; et al. (Nucleic Acids Res., 2010)

Rhea - a manually curated resource of biochemical reactions. - Rafael Alcántara; Kristian B. Axelsen; Anne Morgat; Eugeni Belda; Elisabeth Coudert; Alan J. Bridge; Hong Cao; Paula de Matos; Marcus Ennis; Steve Turner; Gareth I. Owen; Lydie Bougueleret; et al. (Nucleic Acids Res., 2012)

The UniProt-GO Annotation database in 2011. - Emily C. Dimmer; Rachael P. Huntley; Yasmin Alam-Faruque; Tony Sawford; Claire O'Donovan; Maria Jesus Martin; Benoit Bely; Paul Browne; Wei Mun Chan; Ruth Y. Eberhardt; Michael Gardner; Kati Laiho; et al. (Nucleic Acids Res., 2012)

The IntAct molecular interaction database in 2012. - Samuel Kerrien; Bruno Aranda; Lionel Breuza; Alan J. Bridge; Fiona Broackes-Carter; Carol Chen; Margaret J. Duesbury; Marine Dumousseau; Marc Feuermann; Ursula Hinz; Christine Jandrasits; Rafael C. Jiménez; et al. (Nucleic Acids Res., 2012)

UniPathway: a resource for the exploration and annotation of metabolic pathways. - Anne Morgat; Eric Coissac; Elisabeth Coudert; Kristian B. Axelsen; Guillaume Keller; Amos Bairoch; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Alain Viari (Nucleic Acids Res., 2012)

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. - Thierry Schüpbach; Marco Pagni; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Lorenzo Cerutti (Bioinform., 2013)

Application of text-mining for updating protein post-translational modification annotation in UniProtKB. - Anne-Lise Veuthey; Alan J. Bridge; Julien Gobeill; Patrick Ruch; Johanna R. McEntyre; Lydie Bougueleret; Ioannis Xenarios (BMC Bioinform., 2013)

HAMAP in 2013, new developments in the protein family classification and annotation system. - 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; et al. (Nucleic Acids Res., 2013)

New and continuing developments at PROSITE. - Christian J. A. Sigrist; Edouard De Castro; Lorenzo Cerutti; Béatrice A. Cuche; Nicolas Hulo; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios (Nucleic Acids Res., 2013)

Reconciliation of metabolites and biochemical reactions for metabolic networks. - Thomas Bernard; Alan J. Bridge; Anne Morgat; Sébastien Moretti; Ioannis Xenarios; Marco Pagni (Briefings Bioinform., 2014)

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. - Sylvain Poux; Michele Magrane; Cecilia N. Arighi; Alan J. Bridge; Claire O'Donovan; Kati Laiho (Database J. Biol. Databases Curation, 2014)

The SwissLipids knowledgebase for lipid biology. - Lucila Aimo; Robin Liechti; Nevila Hyka-Nouspikel; Anne Niknejad; Anne Gleizes; Lou Götz; Dmitry Kuznetsov; Fabrice P. A. David; F. Gisou van der Goot; Howard Riezman; Lydie Bougueleret; Ioannis Xenarios; et al. (Bioinform., 2015)

Updates in Rhea - a manually curated resource of biochemical reactions. - Anne Morgat; Kristian B. Axelsen; Thierry Lombardot; Rafael Alcántara; Lucila Aimo; Mohamed Zerara; Anne Niknejad; Eugeni Belda; Nevila Hyka-Nouspikel; Elisabeth Coudert; Nicole Redaschi; Lydie Bougueleret; et al. (Nucleic Acids Res., 2015)

HAMAP in 2015: updates to the protein family classification and annotation system. - 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; et al. (Nucleic Acids Res., 2015)

The UniProtKB guide to the human proteome. - Lionel Breuza; Sylvain Poux; Anne Estreicher; Maria Livia Famiglietti; Michele Magrane; Michael Tognolli; Alan J. Bridge; Delphine Baratin; Nicole Redaschi (Database J. Biol. Databases Curation, 2016)

MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. - Sébastien Moretti; Olivier Martin 002; T. Van Du Tran; Alan J. Bridge; Anne Morgat; Marco Pagni (Nucleic Acids Res., 2016)

InterPro in 2017 - beyond protein family and domain annotations. - Robert D. Finn; Teresa K. Attwood; Patricia C. Babbitt; Alex Bateman; Peer Bork; Alan J. Bridge; Hsin-Yu Chang; Zsuzsanna Dosztányi; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2017)

Updates in Rhea - an expert curated resource of biochemical reactions. - Anne Morgat; Thierry Lombardot; Kristian B. Axelsen; Lucila Aimo; Anne Niknejad; Nevila Hyka-Nouspikel; Elisabeth Coudert; Monica Pozzato; Marco Pagni; Sébastien Moretti; Steven Rosanoff; Joseph Onwubiko; et al. (Nucleic Acids Res., 2017)

Towards in the Field Fast Pathogens Detection Using FPGAs. - Simone Casale Brunet; Thierry Schüpbach; Nicolas Guex; Christian Iseli; Alan J. Bridge; Dmitry Kuznetsov; Christian J. A. Sigrist; Phillippe Lemercier; Ioannis Xenarios; Endri Bezati (FPL, 2018)

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. - Amel Bekkar; Anne Estreicher; Anne Niknejad; Cristina Casals-Casas; Alan J. Bridge; Ioannis Xenarios; Julien Dorier; Isaac Crespo (Database J. Biol. Databases Curation, 2018)

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. - Kyubum Lee; Maria Livia Famiglietti; Aoife McMahon; Chih-Hsuan Wei; Jacqueline A. L. MacArthur; Sylvain Poux; Lionel Breuza; Alan J. Bridge; Fiona Cunningham; Ioannis Xenarios; Zhiyong Lu (PLoS Comput. Biol., 2018)

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. - Maria Livia Famiglietti; Anne Estreicher; Lionel Breuza; Sylvain Poux; Nicole Redaschi; Ioannis Xenarios; Alan J. Bridge (Database J. Biol. Databases Curation, 2019)

Updates in Rhea: SPARQLing biochemical reaction data. - Thierry Lombardot; Anne Morgat; Kristian B. Axelsen; Lucila Aimo; Nevila Hyka-Nouspikel; Anne Niknejad; Alexandr Ignatchenko; Ioannis Xenarios; Elisabeth Coudert; Nicole Redaschi; Alan J. Bridge (Nucleic Acids Res., 2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations. - Alex L. Mitchell; Teresa K. Attwood; Patricia C. Babbitt; Matthias Blum; Peer Bork; Alan J. Bridge; Shoshana D. Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2019)

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. - Rachel Drysdale; Charles E. Cook; Robert Petryszak; Vivienne Baillie Gerritsen; Mary Barlow; Elisabeth Gasteiger; Franziska Gruhl; Jürgen Haas; Jerry Lanfear; Rodrigo Lopez; Nicole Redaschi; Heinz Stockinger; et al. (Bioinform., 2020)

Enzyme annotation in UniProtKB using Rhea. - Anne Morgat; Thierry Lombardot; Elisabeth Coudert; Kristian B. Axelsen; Teresa Batista Neto; Sebastien Gehant; Parit Bansal; Jerven T. Bolleman; Elisabeth Gasteiger; Edouard De Castro; Delphine Baratin; Monica Pozzato; et al. (Bioinform., 2020)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

The InterPro protein families and domains database: 20 years on. - Matthias Blum; Hsin-Yu Chang; Sara Chuguransky; Tiago Grego; Swaathi Kandasamy; Alex L. Mitchell; Gift Nuka; Typhaine Paysan-Lafosse; Matloob Qureshi; Shriya Raj; Lorna J. Richardson; Gustavo A. Salazar; et al. (Nucleic Acids Res., 2021)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

SwissBioPics - an interactive library of cell images for the visualization of subcellular location data. - Philippe Le Mercier; Jerven T. Bolleman; Edouard De Castro; Elisabeth Gasteiger; Parit Bansal; Andrea H. Auchincloss; Emmanuel Boutet; Lionel Breuza; Cristina Casals-Casas; Anne Estreicher; Marc Feuermann; Damien Lieberherr; et al. (Database J. Biol. Databases Curation, 2022)

Rhea, the reaction knowledgebase in 2022. - Parit Bansal; Anne Morgat; Kristian B. Axelsen; Venkatesh Muthukrishnan; Elisabeth Coudert; Lucila Aimo; Nevila Hyka-Nouspikel; Elisabeth Gasteiger; Arnaud Kerhornou; Teresa Batista Neto; Monica Pozzato; Marie-Claude Blatter; et al. (Nucleic Acids Res., 2022)

Making expert curated knowledge graphs FAIR. - Jerven T. Bolleman; Alan J. Bridge; Nicole Redaschi; UniProt Consortium (SWAT4HCLS, 2023)

UniProt, ChEBI and IDSM Sachem: exploring biologically relevant ligands. - Sebastien Gehant; Elisabeth Coudert; Anne Morgat; Jerven T. Bolleman; Nicole Redaschi; Alan J. Bridge; UniProt Consortium (SWAT4HCLS, 2023)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)

InterPro in 2022. - Typhaine Paysan-Lafosse; Matthias Blum; Sara Chuguransky; Tiago Grego; Beatriz Lázaro Pinto; Gustavo A. Salazar; Maxwell L. Bileschi; Peer Bork; Alan J. Bridge; Lucy J. Colwell; Julian Gough; Daniel H. Haft; et al. (Nucleic Acids Res., 2023)

FAIR Service Descriptions: enriching life science SPARQL endpoints. - Jerven T. Bolleman; Alan J. Bridge; Nicole Redaschi (SWAT4HCLS, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (CoRR, 2024)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. - Jerven T. Bolleman; Vincent Emonet; Adrian M. Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan J. Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-André Michel; Anne Morgat; et al. (CoRR, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (Zenodo, 2024)