Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Rabie Saidi https://orcid.org/0000-0002-0449-5253 https://www.wikidata.org/entity/Q50728636

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 Kristian B. Axelsen Parit Bansal Marie-Claude Blatter Jerven T. Bolleman Emmanuel Boutet Lionel Breuza Blanca Cabrera Gil Cristina Casals-Casas Kamal Chikh Echioukh Béatrice A. Cuche Anne Estreicher Maria Livia Famiglietti Marc Feuermann Elisabeth Gasteiger Pascale Gaudet Vivienne Baillie Gerritsen Arnaud Gos Nadine Gruaz-Gumowski Chantal Hulo Nevila Hyka-Nouspikel Florence Jungo Arnaud Kerhornou Philippe Le Mercier Damien Lieberherr Patrick Masson Anne Morgat Venkatesh Muthukrishnan Salvo Paesano Ivo Pedruzzi Sandrine Pilbout Lucille Pourcel Sylvain Poux Manuela Pruess Catherine Rivoire Karin Sonesson Shyamala Sundaram Alex Bateman Maria Jesus Martin Sandra E. Orchard Michele Magrane Shadab Ahmad Emanuele Alpi Emily H. Bowler-Barnett Ramona Britto Hema Bye-A-Jee Austra Cukura Paul Denny 0002 Tunca Dogan Thankgod Ebenezer Jun Fan Penelope Garmiri Leonardo Jose da Costa Gonzales Emma Hatton-Ellis Abdulrahman Hussein Alexandr Ignatchenko Giuseppe Insana Rizwan Ishtiaq Vishal Joshi Dushyanth Jyothi Swaathi Kandasamy Antonia Lock Aurelien Luciani Marija Lugaric Jie Luo Yvonne Lussi Alistair MacDougall Fábio Madeira Mahdi Mahmoudy Alok Mishra 0004 Katie Moulang Andrew Nightingale Sangya Pundir Guoying Qi Shriya Raj Pedro Raposo Daniel Rice Rabie Saidi Rafael Santos Elena Speretta James D. Stephenson Prabhat Totoo Edward Turner Nidhi Tyagi Preethi Vasudev Kate Warner Xavier Watkins Rossana Zaru Hermann Zellner Cathy H. Wu Cecilia N. Arighi Leslie Arminski Chuming Chen Yongxing Chen Hongzhan Huang Kati Laiho Peter B. McGarvey Darren A. Natale Karen Ross C. R. Vinayaka Qinghua Wang 0003 Yuqi Wang Annotation of biologically relevant ligands in UniProtKB using ChEBI. 2023 January 39 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btac793 https://www.wikidata.org/entity/Q125822472 db/journals/bioinformatics/bioinformatics39.html#CoudertGCPBNSRBBAAAABBNB23

Gabriela Alejandra Merino Rabie Saidi Diego H. Milone Georgina Stegmayer Maria Jesus Martin Hierarchical deep learning for predicting GO annotations by integrating protein knowledge. 4488-4496 2022 38 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btac536 db/journals/bioinformatics/bioinformatics38.html#MerinoSMSM22

Alistair MacDougall Vladimir Volynkin Rabie Saidi Diego Poggioli Hermann Zellner Emma Hatton-Ellis Vishal Joshi Claire O'Donovan Sandra E. Orchard Andrea H. Auchincloss Delphine Baratin Jerven T. Bolleman Elisabeth Coudert Edouard De Castro Chantal Hulo Patrick Masson Ivo Pedruzzi Catherine Rivoire Cecilia N. Arighi Qinghua Wang 0003 Chuming Chen Hongzhan Huang John S. Garavelli C. R. Vinayaka Lai-Su Yeh Darren A. Natale Kati Laiho Maria Jesus Martin Alexandre Renaux Klemens Pichler UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. 5562 2021 36 Bioinform. 22-23 https://doi.org/10.1093/bioinformatics/btaa663 https://www.wikidata.org/entity/Q130682028 db/journals/bioinformatics/bioinformatics36.html#MacDougallVSPZH21

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 Austra Cukura Alan W. Sousa da Silva Paul Denny 0002 Tunca Dogan Thankgod Ebenezer Jun Fan Leyla Jael García Castro Penelope Garmiri George E. Georghiou Leonardo Gonzales Emma Hatton-Ellis Abdulrahman Hussein Alexandr Ignatchenko Giuseppe Insana Rizwan Ishtiaq Petteri Jokinen Vishal Joshi Dushyanth Jyothi Antonia Lock Rodrigo Lopez Aurelien Luciani Jie Luo Yvonne Lussi Alistair MacDougall Fábio Madeira Mahdi Mahmoudy Manuela Menchi Alok Mishra 0004 Katie Moulang Andrew Nightingale Carla Susana Oliveira Sangya Pundir Guoying Qi Shriya Raj Daniel Rice Milagros Rodríguez-López Rabie Saidi Joseph Sampson Tony Sawford Elena Speretta Edward Turner Nidhi Tyagi Preethi Vasudev Vladimir Volynkin Kate Warner Xavier Watkins Rossana Zaru Hermann Zellner Alan J. Bridge Sylvain Poux Nicole Redaschi Lucila Aimo Ghislaine Argoud-Puy Andrea H. Auchincloss Kristian B. Axelsen Parit Bansal Delphine Baratin Marie-Claude Blatter Jerven T. Bolleman Emmanuel Boutet Lionel Breuza Cristina Casals-Casas Edouard De Castro Kamal Chikh Echioukh Elisabeth Coudert Béatrice A. Cuche Mikael Doche Dolnide Dornevil Anne Estreicher Maria Livia Famiglietti Marc Feuermann Elisabeth Gasteiger Sebastien Gehant Vivienne Baillie Gerritsen Arnaud Gos Nadine Gruaz-Gumowski Ursula Hinz Chantal Hulo Nevila Hyka-Nouspikel Florence Jungo Guillaume Keller Arnaud Kerhornou Vicente Lara Philippe Le Mercier Damien Lieberherr Thierry Lombardot Xavier Martin Patrick Masson Anne Morgat Teresa Batista Neto Salvo Paesano Ivo Pedruzzi Sandrine Pilbout Lucille Pourcel Monica Pozzato Manuela Pruess Catherine Rivoire Christian J. A. Sigrist Karin Sonesson Andre Stutz Shyamala Sundaram Michael Tognolli Laure Verbregue Cathy H. Wu Cecilia N. Arighi Leslie Arminski Chuming Chen Yongxing Chen John S. Garavelli Hongzhan Huang Kati Laiho Peter B. McGarvey Darren A. Natale Karen Ross C. R. Vinayaka Qinghua Wang 0003 Yuqi Wang Lai-Su Yeh Jian Zhang 0051 Patrick Ruch Douglas Teodoro UniProt: the universal protein knowledgebase in 2021. D480-D489 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa1100 https://www.wikidata.org/entity/Q102383737 db/journals/nar/nar49.html#BatemanMOMAAABB21

Alistair MacDougall Vladimir Volynkin Rabie Saidi Diego Poggioli Hermann Zellner Emma Hatton-Ellis Vishal Joshi Claire O'Donovan Sandra E. Orchard Andrea H. Auchincloss Delphine Baratin Jerven T. Bolleman Elisabeth Coudert Edouard De Castro Chantal Hulo Patrick Masson Ivo Pedruzzi Catherine Rivoire Cecilia N. Arighi Qinghua Wang 0003 Chuming Chen Hongzhan Huang John S. Garavelli C. R. Vinayaka Lai-Su Yeh Darren A. Natale Kati Laiho Maria Jesus Martin Alexandre Renaux Klemens Pichler UniProt Consortium UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. 4643-4648 2020 36 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btaa485 db/journals/bioinformatics/bioinformatics36.html#MacDougallVSPZH20

Rabie Saidi Wajdi Dhifli Mondher Maddouri Engelbert Mephu Nguifo Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs. 561-571 2019 26 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2018.0171 https://www.wikidata.org/entity/Q62610094 db/journals/jcb/jcb26.html#SaidiDMN19

Tunca Dogan Alistair MacDougall Rabie Saidi Diego Poggioli Alex Bateman Claire O'Donovan Maria Jesus Martin UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. 2264-2271 2016 32 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btw114 https://www.wikidata.org/entity/Q38447701 db/journals/bioinformatics/bioinformatics32.html#DoganMSPBOM16

Jon C. Ison Kristoffer Rapacki Hervé Ménager Matús Kalas Emil Rydza Piotr Chmura Christian Anthon Niall Beard Karel Berka Dan M. Bolser Tim Booth Anthony Bretaudeau Jan Brezovsky Rita Casadio Gianni Cesareni Frederik Coppens Michael Cornell Gianmauro Cuccuru Kristian Davidsen Gianluca Della Vedova Tunca Dogan Olivia Doppelt-Azeroual Laura Emery Elisabeth Gasteiger Thomas Gatter Tatyana Goldberg Marie Grosjean Björn A. Grüning Manuela Helmer-Citterich Hans Ienasescu Vassilios Ioannidis Martin Closter Jespersen Rafael C. Jiménez Nick S. Juty Peter Juvan Maximilian Koch Camille Laibe Jing-Woei Li Luana Licata Fabien Mareuil Ivan Micetic Rune Møllegaard Friborg Sébastien Moretti Chris Morris Steffen Möller Aleksandra Nenadic Hedi Peterson Giuseppe Profiti Peter M. Rice Paolo Romano 0001 Paola Roncaglia Rabie Saidi Andrea Schafferhans Veit Schwämmle Callum Smith Maria Maddalena Sperotto Heinz Stockinger Radka Svobodová Vareková Silvio C. E. Tosatto Victor de la Torre Paolo Uva Allegra Via Guy Yachdav Federico Zambelli Gert Vriend Burkhard Rost Helen E. Parkinson Peter Løngreen Søren Brunak Tools and data services registry: a community effort to document bioinformatics resources. 38-47 2016 44 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkv1116 https://www.wikidata.org/entity/Q26759572 db/journals/nar/nar44.html#IsonRMKRCABBBBB16

Slim Bouker Rabie Saidi Sadok Ben Yahia Engelbert Mephu Nguifo Mining Undominated Association Rules Through Interestingness Measures. 2014 23 Int. J. Artif. Intell. Tools 4 https://doi.org/10.1142/S0218213014600112 https://www.wikidata.org/entity/Q62610108 db/journals/ijait/ijait23.html#BoukerSYN14

Wajdi Dhifli Rabie Saidi Engelbert Mephu Nguifo Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities. 162-172 2014 21 J. Comput. Biol. 2 https://doi.org/10.1089/cmb.2013.0092 https://www.wikidata.org/entity/Q30354395 db/journals/jcb/jcb21.html#DhifliSN14

Wajdi Dhifli Rabie Saidi Engelbert Mephu Nguifo Mining Representative Unsubstituted Graph Patterns Using Prior Similarity Matrix http://arxiv.org/abs/1303.2054 2013 CoRR abs/1303.2054 db/journals/corr/corr1303.html#abs-1303-2054

Slim Bouker Rabie Saidi Sadok Ben Yahia Engelbert Mephu Nguifo Towards a semantic and statistical selection of association rules http://arxiv.org/abs/1305.5824 2013 CoRR abs/1305.5824 db/journals/corr/corr1305.html#abs-1305-5824

Wajdi Dhifli Mohamed Moussaoui Rabie Saidi Engelbert Mephu Nguifo Towards an Efficient Discovery of the Topological Representative Subgraphs. 2013 CoRR http://arxiv.org/abs/1307.7411 abs/1307.7411 db/journals/corr/corr1307.html#DhifliMSN13

Rabie Saidi Motif extraction from complex data: case of protein classification. (Extraction de motifs des données complexes: cas de la classification des protéines). 2012 Blaise Pascal University, Clermont-Ferrand, France https://tel.archives-ouvertes.fr/tel-02063250 Wajdi Dhifli Rabie Saidi Engelbert Mephu Nguifo A novel approach for mining representative spatial motifs of proteins. 506-508 2012 BCB https://doi.org/10.1145/2382936.2383001 https://www.wikidata.org/entity/Q62610117 conf/bcb/2012 db/conf/bcb/bcb2012.html#DhifliSN12 Rabie Saidi Sabeur Aridhi Engelbert Mephu Nguifo Mondher Maddouri Feature extraction in protein sequences classification: a new stability measure. 683-689 2012 BCB https://doi.org/10.1145/2382936.2383060 https://www.wikidata.org/entity/Q62610119 conf/bcb/2012 db/conf/bcb/bcb2012.html#SaidiANM12 Slim Bouker Rabie Saidi Sadok Ben Yahia Engelbert Mephu Nguifo Ranking and Selecting Association Rules Based on Dominance Relationship. 658-665 2012 conf/ictai/2012 ICTAI https://doi.org/10.1109/ICTAI.2012.94 https://doi.ieeecomputersociety.org/10.1109/ICTAI.2012.94 https://www.wikidata.org/entity/Q62610122 db/conf/ictai/ictai2012.html#BoukerSYN12

Rabie Saidi Mondher Maddouri Engelbert Mephu Nguifo Protein sequences classification by means of feature extraction with substitution matrices. 175 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-175 https://www.wikidata.org/entity/Q33551028 db/journals/bmcbi/bmcbi11.html#SaidiMN10

Wajdi Dhifli Rabie Saidi Protein graph repository. 641-642 2010 EGC conf/f-egc/2010 db/conf/f-egc/egc2010.html#DhifliS10 https://editions-rnti.fr/?inprocid=1001403 Rabie Saidi Sabeur Aridhi Mondher Maddouri Engelbert Mephu Nguifo Etude de stabilité de méthodes d'extraction de motifs à partir des séquences protéiques. 703-704 2010 EGC conf/f-egc/2010 db/conf/f-egc/egc2010.html#SaidiAMN10 https://editions-rnti.fr/?inprocid=1001454 Rabie Saidi Mondher Maddouri Engelbert Mephu Nguifo Comparing graph-based representations of protein for mining purposes. 35-38 2009 KDD Workshop on Statistical and Relational Learning in Bioinformatics https://doi.org/10.1145/1562090.1562098 https://www.wikidata.org/entity/Q62610137 conf/kdd/2009srb db/conf/kdd/srb2009.html#SaidiMN09 Rabie Saidi Mondher Maddouri Engelbert Mephu Nguifo Biological Sequences Encoding for Supervised Classification. 224-238 2007 conf/bird/2007 BIRD https://doi.org/10.1007/978-3-540-71233-6_18 https://www.wikidata.org/entity/Q62610175 db/conf/bird/bird2007.html#SaidiMN07 Rabie Saidi Mondher Maddouri Engelbert Mephu Nguifo Classification supervisée de séquences biologiques basée sur les motifs et les matrices de substitution. 409-420 2007 conf/f-egc/2007 EGC db/conf/f-egc/egc2007.html#SaidiMN07 https://editions-rnti.fr/?inprocid=1001409 Rahat Agivetova Shadab Ahmad Lucila Aimo Emanuele Alpi Christian Anthon Ghislaine Argoud-Puy Sabeur Aridhi Cecilia N. Arighi Leslie Arminski Andrea H. Auchincloss Kristian B. Axelsen Parit Bansal Delphine Baratin Alex Bateman Niall Beard Karel Berka Marie-Claude Blatter Jerven T. Bolleman Dan M. Bolser Tim Booth Slim Bouker Emmanuel Boutet Emily H. Bowler-Barnett Anthony Bretaudeau Lionel Breuza Jan Brezovsky Alan J. Bridge Ramona Britto Søren Brunak Borisas Bursteinas Hema Bye-A-Jee Rita Casadio Cristina Casals-Casas Edouard De Castro Leyla Jael CastroLeyla Jael García Castro Gianni Cesareni Chuming Chen Yongxing Chen Piotr Chmura Ray Coetzee UniProt Consortium Frederik Coppens Michael Cornell Elisabeth Coudert Gianmauro Cuccuru Béatrice A. Cuche Austra Cukura Kristian Davidsen Paul Denny 0002 Wajdi Dhifli Mikael Doche Tunca Dogan Olivia Doppelt-Azeroual Dolnide Dornevil Thankgod Ebenezer Kamal Chikh Echioukh Laura Emery Anne Estreicher Maria Livia Famiglietti Jun Fan Marc Feuermann Rune Møllegaard Friborg John S. Garavelli Penelope Garmiri Elisabeth Gasteiger Thomas Gatter Pascale Gaudet Sebastien Gehant George E. Georghiou Vivienne Baillie Gerritsen Blanca Cabrera Gil Tatyana Goldberg Leonardo Gonzales Leonardo Jose da Costa Gonzales Arnaud Gos Marie Grosjean Nadine Gruaz-Gumowski Björn A. Grüning Emma Hatton-Ellis Manuela Helmer-Citterich Ursula Hinz Hongzhan Huang Chantal Hulo Abdulrahman Hussein Nevila Hyka-Nouspikel Hans Ienasescu Alexandr Ignatchenko Giuseppe Insana Vassilios Ioannidis Rizwan Ishtiaq Jon C. Ison Martin Closter Jespersen Rafael C. Jiménez Petteri Jokinen Vishal Joshi Florence Jungo Nick S. Juty Peter Juvan Dushyanth Jyothi Matús Kalas Swaathi Kandasamy Guillaume Keller Arnaud Kerhornou Maximilian Koch Camille Laibe Kati Laiho Vicente Lara Jing-Woei Li Luana Licata Damien Lieberherr Antonia Lock Thierry Lombardot Peter Løngreen Rodrigo Lopez Aurelien Luciani Marija Lugaric Jie Luo Yvonne Lussi Alistair MacDougall Mondher Maddouri Fábio Madeira Michele Magrane Mahdi Mahmoudy Fabien Mareuil Maria Jesus Martin Xavier Martin Patrick Masson Peter B. McGarvey Hervé Ménager Manuela Menchi Philippe Le Mercier Gabriela Alejandra Merino Ivan Micetic Diego H. Milone Alok Mishra 0004 Steffen Möller Sébastien Moretti Anne Morgat Chris Morris Katie Moulang Mohamed Moussaoui Venkatesh Muthukrishnan Darren A. Natale Aleksandra Nenadic Teresa Batista Neto Engelbert Mephu Nguifo Andrew Nightingale Claire O'Donovan Carla Susana Oliveira Sandra E. Orchard Salvo Paesano Helen E. Parkinson Ivo Pedruzzi Hedi Peterson Klemens Pichler Sandrine Pilbout Diego Poggioli Lucille Pourcel Sylvain Poux Monica Pozzato Giuseppe Profiti Manuela Pruess Sangya Pundir Guoying Qi Shriya Raj Kristoffer Rapacki Pedro Raposo Nicole Redaschi Alexandre Renaux Daniel Rice Peter M. Rice Catherine Rivoire Milagros Rodríguez-López Paolo Romano 0001 Paola Roncaglia Karen E. RossKaren Ross Burkhard Rost Patrick Ruch Emil Rydza Joseph Sampson Rafael Santos Tony Sawford Andrea Schafferhans Veit Schwämmle Christian J. A. Sigrist Alan W. Sousa da Silva Callum Smith Karin Sonesson Elena Speretta Maria SperottoMaria Maddalena Sperotto Georgina Stegmayer James D. Stephenson Heinz Stockinger Andre Stutz Shyamala Sundaram Douglas Teodoro Michael Tognolli Victor de la Torre Silvio C. E. Tosatto Prabhat Totoo Edward Turner Nidhi Tyagi Paolo Uva Radka Svobodová Vareková Preethi Vasudev Gianluca Della Vedova Laure Verbregue Allegra Via C. R. Vinayaka Vladimir Volynkin Gert Vriend Qinghua Wang 0003 Yuqi Wang Kate Warner Xavier Watkins Cathy H. Wu Guy Yachdav Sadok Ben Yahia Lai-Su Yeh Federico Zambelli Rossana Zaru Hermann Zellner Jian Zhang 0051