Authors: Chih-Hsuan Wei
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Journal Article

The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop

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Rezarta Islamaj, Chih-Hsuan Wei, Po-Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar, Nicholas Miliaras, Oleg Rodionov, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Zhiyong Lu
Database, Volume 2024, 2024, baae071, https://doi.org/10.1093/database/baae071
Published: 09 August 2024
Journal Article

The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII

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Rezarta Islamaj, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Almeida, Richard A. A Jonker, Sofia I. R Conceição, Diana F Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee … Zhiyong Lu
Database, Volume 2024, 2024, baae069, https://doi.org/10.1093/database/baae069
Published: 08 August 2024
Journal Article

Assigning species information to corresponding genes by a sequence labeling framework

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Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
Database, Volume 2022, 2022, baac090, https://doi.org/10.1093/database/baac090
Published: 13 October 2022
Journal Article

A sequence labeling framework for extracting drug–protein relations from biomedical literature

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Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
Database, Volume 2022, 2022, baac058, https://doi.org/10.1093/database/baac058
Published: 20 July 2022
Journal Article

Using deep learning to identify translational research in genomic medicine beyond bench to bedside

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Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J Khoury, Zhiyong Lu
Database, Volume 2019, 2019, baz010, https://doi.org/10.1093/database/baz010
Published: 08 February 2019
Journal Article

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

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Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang … Zhiyong Lu
Database, Volume 2019, 2019, bay147, https://doi.org/10.1093/database/bay147
Published: 28 January 2019
Journal Article

Overview of the BioCreative VI text-mining services for Kinome Curation Track

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Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
Database, Volume 2018, 2018, bay104, https://doi.org/10.1093/database/bay104
Published: 17 October 2018
Journal Article

Assisting document triage for human kinome curation via machine learning

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Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu
Database, Volume 2018, 2018, bay091, https://doi.org/10.1093/database/bay091
Published: 18 September 2018
Journal Article

Mining chemical patents with an ensemble of open systems

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Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu
Database, Volume 2016, 2016, baw065, https://doi.org/10.1093/database/baw065
Published: 12 May 2016
Journal Article

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

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Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu
Database, Volume 2016, 2016, baw068, https://doi.org/10.1093/database/baw068
Published: 08 May 2016
Journal Article

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

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Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu
Database, Volume 2016, 2016, baw032, https://doi.org/10.1093/database/baw032
Published: 19 March 2016
Journal Article

Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

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John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman
Database, Volume 2014, 2014, bau094, https://doi.org/10.1093/database/bau094
Published: 22 September 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

tmBioC: improving interoperability of text-mining tools with BioC

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Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu
Database, Volume 2014, 2014, bau073, https://doi.org/10.1093/database/bau073
Published: 25 July 2014
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

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

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Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu
Database, Volume 2012, 2012, bas041, https://doi.org/10.1093/database/bas041
Published: 15 November 2012
Journal Article

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

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Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
Database, Volume 2012, 2012, bas042, https://doi.org/10.1093/database/bas042
Published: 15 November 2012