Authors: Cathy H. Wu
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Journal Article

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

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Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross, Cecilia Arighi, Cathy H Wu
Database, Volume 2020, 2020, baz157, https://doi.org/10.1093/database/baz157
Published: 12 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

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature

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Jia Ren, Gang Li, Karen Ross, Cecilia Arighi, Peter McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K Vijay-Shanker, Cathy H Wu
Database, Volume 2018, 2018, bay128, https://doi.org/10.1093/database/bay128
Published: 14 December 2018
Journal Article

DEXTER: Disease-Expression Relation Extraction from Text

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Samir Gupta, Hayley Dingerdissen, Karen E Ross, Yu Hu, Cathy H Wu, Raja Mazumder, K Vijay-Shanker
Database, Volume 2018, 2018, bay045, https://doi.org/10.1093/database/bay045
Published: 30 May 2018
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

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

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Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su … Donald C. Comeau
Database, Volume 2016, 2016, baw121, https://doi.org/10.1093/database/baw121
Published: 01 September 2016
Journal Article

BioC-compatible full-text passage detection for protein–protein interactions using extended dependency graph

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Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker
Database, Volume 2016, 2016, baw072, https://doi.org/10.1093/database/baw072
Published: 11 May 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

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

BioC interoperability track overview

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Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Doğan, Antonio Jimeno Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
Database, Volume 2014, 2014, bau053, https://doi.org/10.1093/database/bau053
Published: 28 June 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

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system

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Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
Database, Volume 2014, 2014, bau038, https://doi.org/10.1093/database/bau038
Published: 21 May 2014
Journal Article

BioC: a minimalist approach to interoperability for biomedical text processing

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Donald C. Comeau, Rezarta Islamaj Doğan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
Database, Volume 2013, 2013, bat064, https://doi.org/10.1093/database/bat064
Published: 18 September 2013
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

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

Text mining for the biocuration workflow

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Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, Andrew G. Winter
Database, Volume 2012, 2012, bas020, https://doi.org/10.1093/database/bas020
Published: 18 April 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