Authors: Rezarta Islamaj
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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

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

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Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura … Zhiyong Lu
Database, Volume 2023, 2023, baad005, https://doi.org/10.1093/database/baad005
Published: 07 March 2023
Journal Article

NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles

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Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu
Database, Volume 2022, 2022, baac102, https://doi.org/10.1093/database/baac102
Published: 01 December 2022
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

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

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Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak … Zhiyong Lu
Database, Volume 2022, 2022, baac069, https://doi.org/10.1093/database/baac069
Published: 31 August 2022
Journal Article

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

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Rezarta Islamaj, W John Wilbur, Natalie Xie, Noreen R Gonzales, Narmada Thanki, Roxanne Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu
Database, Volume 2019, 2019, baz064, https://doi.org/10.1093/database/baz064
Published: 02 July 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

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

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Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers
Database, Volume 2017, 2017, baw147, https://doi.org/10.1093/database/baw147
Published: 10 January 2017
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

Crowdsourcing and curation: perspectives from biology and natural language processing

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Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Doğan, Kevin Bretonnel Cohen
Database, Volume 2016, 2016, baw115, https://doi.org/10.1093/database/baw115
Published: 08 August 2016
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

BioC implementations in Go, Perl, Python and Ruby

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Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau
Database, Volume 2014, 2014, bau059, https://doi.org/10.1093/database/bau059
Published: 23 June 2014
Journal Article

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

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Donald C. Comeau, Haibin Liu, Rezarta Islamaj Doğan, W. John Wilbur
Database, Volume 2014, 2014, bau056, https://doi.org/10.1093/database/bau056
Published: 15 June 2014
Journal Article

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora

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Rezarta Islamaj Doğan, Donald C. Comeau, Lana Yeganova, W. John Wilbur
Database, Volume 2014, 2014, bau044, https://doi.org/10.1093/database/bau044
Published: 09 June 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

Understanding PubMed® user search behavior through log analysis

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Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu
Database, Volume 2009, 2009, bap018, https://doi.org/10.1093/database/bap018
Published: 27 November 2009