Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework

Authors: Luo, Ling, Wei, Chih-Hsuan, Lai, Po-Ting, Chen, Qingyu, Doğan, Rezarta Islamaj, Lu, Zhiyong

Source: Database, Volume 2022, 2022, baac090

Subject Terms: Computer Science - Computation and Language, Computer Science - Information Retrieval, Computer Science - Machine Learning, Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2205.03853

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

Authors: Chen, Qingyu, Allot, Alexis, Leaman, Robert, Doğan, Rezarta Islamaj, Du, Jingcheng, Fang, Li, Wang, Kai, Xu, Shuo, Zhang, Yuefu, Bagherzadeh, Parsa, Bergler, Sabine, Bhatnagar, Aakash, Bhavsar, Nidhir, Chang, Yung-Chun, Lin, Sheng-Jie, Tang, Wentai, Zhang, Hongtong, Tavchioski, Ilija, Pollak, Senja, Tian, Shubo, Zhang, Jinfeng, Otmakhova, Yulia, Yepes, Antonio Jimeno, Dong, Hang, Wu, Honghan, Dufour, Richard, Labrak, Yanis, Chatterjee, Niladri, Tandon, Kushagri, Laleye, Fréjus, Rakotoson, Loïc, Chersoni, Emmanuele, Gu, Jinghang, Friedrich, Annemarie, Pujari, Subhash Chandra, Chizhikova, Mariia, Sivadasan, Naveen, Lu, Zhiyong

Subject Terms: Computer Science - Digital Libraries, Computer Science - Computation and Language, Computer Science - Information Retrieval, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2204.09781

PMC text mining subset in BioC: 2.3 million full text articles and growing

Authors: Comeau, Donald C., Wei, Chih-Hsuan, Doğan, Rezarta Islamaj, Lu, Zhiyong

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/1804.05957

NCBI disease corpus: A resource for disease name recognition and concept normalization

Authors: Doğan, Rezarta Islamaj, Leaman, Robert, Lu, Zhiyong

Source: In Journal of Biomedical Informatics February 2014 47:1-10

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

Authors: Doğan, Rezarta Islamaj¹ Rezarta.Islamaj@nih.gov, Sun Kim¹, Chatr-aryamontri, Andrew², Chang, Christie S.³, Oughtred, Rose³, Rust, Jennifer³, Wilbur, W. John¹, Comeau, Donald C.¹, Dolinski, Kara¹, Tyers, Mike^2,4

Source: Database: The Journal of Biological Databases & Curation. 2017, Vol. 2017 Issue 1, p1-11. 11p.

Subject Terms: *PROTEIN-protein interactions, *MOLECULAR genetics, *MOLECULAR biology, *DATA mining, *MOLECULAR interactions

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

Authors: Sun Kim¹, Doğan, Rezarta Islamaj¹, Chatr-Aryamontri, Andrew², Chang, Christie S.³, Oughtred, Rose³, Rust, Jennifer³, Batista-Navarro, Riza⁴, Carter, Jacob⁴, Ananiadou, Sophia⁴, Matos, Sérgio⁵, Santos, André⁵, Campos, David⁶, Oliveira, José Luís⁵, Singh, Onkar⁷, Jonnagaddala, Jitendra^8,9, Hong-Jie Dai¹⁰, Su, Emily Chia-Yu⁷, Yung-Chun Chang^11,12, Yu-Chen Su¹³, Chun-Han Chu¹¹

Source: Database: The Journal of Biological Databases & Curation. 2016, Vol. 2016, p1-13. 13p.

Subject Terms: *INTERNETWORKING, *DATA curation, *XML (Extensible Markup Language), *MACHINE learning, *BIOLOGICAL databases

BioC implementations in Go, Perl, Python and Ruby.

Authors: Wanli Liu¹ (AUTHOR), Doğan, Rezarta Islamaj¹ (AUTHOR), Dongseop Kwon² (AUTHOR), Marques, Hernani³ (AUTHOR), Rinaldi, Fabio³ (AUTHOR), Wilbur, W. John¹ (AUTHOR), Comeau, Donald C.¹ (AUTHOR) comeau@ncbi.nlm.nih.gov

Source: Database: The Journal of Biological Databases & Curation. 2014, Vol. 2014, p1-9. 9p. 1 Color Photograph, 7 Black and White Photographs.

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

Authors: Doğan, Rezarta Islamaj¹ (AUTHOR) Rezarta.Islamaj@nih.gov, Comeau, Donald C.¹ (AUTHOR), Yeganova, Lana¹ (AUTHOR), Wilbur, W. John¹ (AUTHOR)

Source: Database: The Journal of Biological Databases & Curation. 2014, Vol. 2014, p1-7. 7p. 1 Color Photograph, 1 Black and White Photograph, 1 Diagram, 3 Charts.

BioC: a minimalist approach to interoperability for biomedical text processing.

Authors: Comeau, Donald C.¹, Doğan, Rezarta Islamaj¹ Rezarta.Islamaj@nih.gov, Ciccarese, Paolo^2,3, Cohen, Kevin Bretonnel⁴, Krallinger, Martin⁵, Leitner, Florian⁵, Zhiyong Lu¹, Yifan Peng⁶, Rinaldi, Fabio⁷, Torii, Manabu⁶, Valencia, Alfonso⁵, Verspoor, Karin⁸, Wiegers, Thomas C.⁹, Wu, Cathy H.⁶, Wilbur, W. John¹

Source: Database: The Journal of Biological Databases & Curation. 2013, Vol. 2013, p1-15. 15p.

Subject Terms: *ELECTRONIC data processing, *DATABASE management, *NATURAL language processing, *TEXT mining, *ARTIFICIAL intelligence, *HUMAN-computer interaction

A context-blocks model for identifying clinical relationships in patient records.

Authors: Doğan, Rezarta Islamaj¹ Rezarta.Islamaj@nih.gov, Névéol, Aurélie¹, Zhiyong Lu¹

Source: BMC Bioinformatics. Jan2011 Supplement 3, Vol. 12, p1-11. 11p. 3 Diagrams, 9 Charts.

Subject Terms: *COMPUTERS in medicine, *ARTIFICIAL intelligence in medicine, *MEDICAL informatics, *HUMAN-computer interaction, *USER interfaces, *MEDICAL care

Click-words: learning to predict document keywords from a user perspective.

Authors: Doğan, Rezarta Islamaj, Lu, Zhiyong

Source: Bioinformatics; November 1 2010, Vol. 26 Issue 21, p2767-2775, 9p

Author Name Disambiguation for PubMed.

Authors: Wanli Liu (AUTHOR), Doğan, Rezarta Islamaj (AUTHOR), Kim, Sun (AUTHOR), Comeau, Donald C. (AUTHOR), Won Kim (AUTHOR), Yeganova, Lana (AUTHOR), Zhiyong Lu (AUTHOR), Wilbur, W. John (AUTHOR)

Source: Journal of the Association for Information Science & Technology. Apr2014, Vol. 65 Issue 4, p765-781. 17p.

Subject Terms: *Information retrieval, *Algorithms, *Online information services, *Research funding, *Statistical sampling, Authors, Comparative studies, MEDLINE, Evaluation research

URL: 94969746

Topics in machine learning for biomedical literature analysis and text retrieval.

Authors: Doğan, Rezarta Islamaj¹, Yeganova, Lana¹ Yeganova@mail.nih.gov

Source: BMC Bioinformatics. Jan2011 Supplement 3, Vol. 12, p1-3. 3p.

Subject Terms: *MEDICAL literature, *LIFE sciences literature

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PMC text mining subset in BioC: about three million full-text articles and growing.

Authors: Comeau, Donald C¹, Wei, Chih-Hsuan¹, Doğan, Rezarta Islamaj¹, Lu, Zhiyong¹, zhiyong.lu@nih.gov

Source: Bioinformatics; Sep2019, Vol. 35 Issue 18, p3533-3535, 3p

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

Authors: Doğan, Rezarta Islamaj¹ (AUTHOR), Kim, Sun¹ (AUTHOR), Chatr-aryamontri, Andrew² (AUTHOR), Wei, Chih-Hsuan¹ (AUTHOR), Comeau, Donald C¹ (AUTHOR), Antunes, Rui³ (AUTHOR), Matos, Sérgio³ (AUTHOR), Chen, Qingyu⁴ (AUTHOR), Elangovan, Aparna⁴ (AUTHOR), Panyam, Nagesh C⁴ (AUTHOR), Verspoor, Karin⁴ (AUTHOR), Liu, Hongfang⁵ (AUTHOR), Wang, Yanshan⁵ (AUTHOR), Liu, Zhuang⁶ (AUTHOR), Altınel, Berna⁷ (AUTHOR), Hüsünbeyi, Zehra Melce⁸ (AUTHOR), Özgür, Arzucan (AUTHOR), Fergadis, Aris⁹ (AUTHOR), Wang, Chen-Kai¹⁰ (AUTHOR), Dai, Hong-Jie¹¹ (AUTHOR)

Source: Database: The Journal of Biological Databases & Curation. 2019, Vol. 2019, pN.PAG-N.PAG. 1p.

Subject Terms: *KNOWLEDGE base, *INDIVIDUALIZED medicine, *PROTEIN-protein interactions, *SCIENTIFIC literature, *ELECTRONIC health records, *STATISTICAL learning

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