Authors: Cecilia N. Arighi
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Journal Article

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII

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Andrew Chatr-aryamontri, Lynette Hirschman, Karen E Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N Arighi
Database, Volume 2022, 2022, baac084, https://doi.org/10.1093/database/baac084
Published: 05 October 2022
Journal Article

emiRIT: a text-mining-based resource for microRNA information

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Debarati Roychowdhury, Samir Gupta, Xihan Qin, Cecilia N Arighi, K Vijay-Shanker
Database, Volume 2021, 2021, baab031, https://doi.org/10.1093/database/baab031
Published: 28 May 2021
Journal Article

UPCLASS: a deep learning-based classifier for UniProtKB entry publications

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Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N Arighi, Patrick Ruch
Database, Volume 2020, 2020, baaa026, https://doi.org/10.1093/database/baaa026
Published: 04 May 2020
Journal Article

PIRSitePredict for protein functional site prediction using position-specific rules

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Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R Vinayaka, John S Garavelli, Cecilia N Arighi, Darren A Natale, Cathy H Wu
Database, Volume 2019, 2019, baz026, https://doi.org/10.1093/database/baz026
Published: 26 February 2019
Journal Article

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality

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Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H Wu, K Vijay-Shanker, Cecilia N Arighi
Database, Volume 2017, 2017, bax081, https://doi.org/10.1093/database/bax081
Published: 13 November 2017
Journal Article

Overview of the interactive task in BioCreative V

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Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen … Cecilia N. Arighi
Database, Volume 2016, 2016, baw119, https://doi.org/10.1093/database/baw119
Published: 01 September 2016
Journal Article

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system

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Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi
Database, Volume 2015, 2015, bav020, https://doi.org/10.1093/database/bav020
Published: 31 March 2015
Journal Article

Overview of the gene ontology task at BioCreative IV

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Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu … Zhiyong Lu
Database, Volume 2014, 2014, bau086, https://doi.org/10.1093/database/bau086
Published: 25 August 2014
Journal Article

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

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Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
Database, Volume 2014, 2014, bau081, https://doi.org/10.1093/database/bau081
Published: 13 August 2014
Journal Article

BC4GO: a full-text corpus for the BioCreative IV GO task

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Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu
Database, Volume 2014, 2014, bau074, https://doi.org/10.1093/database/bau074
Published: 28 July 2014
Journal Article

BioCreative-IV virtual issue

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Cecilia N. Arighi, Cathy H. Wu, Kevin B. Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, John W. Wilbur, Thomas C. Wiegers
Database, Volume 2014, 2014, bau039, https://doi.org/10.1093/database/bau039
Published: 22 May 2014
Journal Article

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

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Sylvain Poux, Michele Magrane, Cecilia N. Arighi, Alan Bridge, Claire O’Donovan, Kati Laiho, The UniProt Consortium
Database, Volume 2014, 2014, bau016, https://doi.org/10.1093/database/bau016
Published: 12 March 2014
Journal Article

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

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Karen E. Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu
Database, Volume 2013, 2013, bat038, https://doi.org/10.1093/database/bat038
Published: 06 June 2013
Journal Article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

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Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila Dahdul, Paula Mabee, Donghui Li, Bethany Harris, Marc Gillespie, Silvia Jimenez, Phoebe Roberts, Lisa Matthews, Kevin Becker, Harold Drabkin … Cathy Wu
Database, Volume 2013, 2013, bas056, https://doi.org/10.1093/database/bas056
Published: 16 January 2013
Journal Article

BioCreative-2012 Virtual Issue

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Cathy H. Wu, Cecilia N. Arighi, Kevin B. Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur
Database, Volume 2012, 2012, bas049, https://doi.org/10.1093/database/bas049
Published: 05 December 2012
Journal Article

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

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Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
Database, Volume 2012, 2012, bas044, https://doi.org/10.1093/database/bas044
Published: 05 December 2012
Journal Article

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

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Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnum Rendino, William Kelley Thomas, Daniel W. Udwary, Cathy H. Wu, the North East Bioinformatics Collaborative Curation Team
Database, Volume 2012, 2012, bar064, https://doi.org/10.1093/database/bar064
Published: 13 February 2012