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Journal Article

neomerDB: a comprehensive database of neomer biomarkers in cancer

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Kimonas Provatas, Candace S Y Chan, Ioannis Kerasiotis, Eleftherios Bochalis, Akshatha Nayak, Brad E Zacharia, Georgios A Pavlopoulos, Wei Li, Ilias Georgakopoulos-Soares
Database, Volume 2026, 2026, baag006, https://doi.org/10.1093/database/baag006
Published: 12 February 2026
Journal Article

Tear fluid database: a reference website for tear fluid proteomics

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Drew Mayernik, Saleh Ahmed, Eliza Williams, Tae Jin Lee, Amy Estes, Pamela Martin, Wenbo Zhi, Vishal Jhanji, Shruti Sharma, Ashok Sharma
Database, Volume 2026, 2026, baaf091, https://doi.org/10.1093/database/baaf091
Published: 16 January 2026
Journal Article

Post-composing ontology terms for efficient phenotyping in plant breeding

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Naama Menda, Bryan J Ellerbrock, Christiano C Simoes, Srikanth Kumar Karaikal, Christine Nyaga, Mirella Flores-Gonzalez, Isaak Y Tecle, David Lyon, Afolabi Agbona, Paterne A Agre, Prasad Peteti, Violet Akech, Amos Asiimwe, Eglantine Fauvelle, Karima Meghar, Thierry Tran, Dominique Dufour, Laurel Cooper, Marie-Angélique Laporte … Lukas A Mueller
Database, Volume 2025, 2025, baaf020, https://doi.org/10.1093/database/baaf020
Published: 21 March 2025
Journal Article

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

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Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Arighi, Kristian B Axelsen, Evan Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, Ten Feizi, Catherine Hayes, Callum M Ives, Hiren J Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frederique Lisacek, Yan Liu, Thomas Lütteke … Raja Mazumder
Database, Volume 2024, 2024, baae073, https://doi.org/10.1093/database/baae073
Published: 13 August 2024
Journal Article

SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population

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José M Moreno-Cabrera, Lidia Feliubadaló, Marta Pineda, Patricia Prada-Dacasa, Mireia Ramos-Muntada, Jesús Del Valle, Joan Brunet, Bernat Gel, María Currás-Freixes, Bruna Calsina, Milton E Salazar-Hidalgo, Marta Rodríguez-Balada, Bàrbara Roig, Sara Fernández-Castillejo, Mercedes Durán Domínguez, Mónica Arranz Ledo, Mar Infante Sanz, Adela Castillejo, Estela Dámaso … Conxi Lázaro
Database, Volume 2024, 2024, baae055, https://doi.org/10.1093/database/baae055
Published: 04 July 2024
Journal Article

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank

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Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D Westbrook, Jasmine Y Young, Ardan Patwardhan, Kyle L Morris, Jeffrey C Hoch, Genji Kurisu, Sameer Velankar, Stephen K Burley
Database, Volume 2024, 2024, baae041, https://doi.org/10.1093/database/baae041
Published: 27 May 2024
Journal Article

AHP DB: a reference database of proteins in the human aqueous humor

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Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma
Database, Volume 2024, 2024, baae001, https://doi.org/10.1093/database/baae001
Published: 29 January 2024
Journal Article

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

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Liskin Swint-Kruse, Larissa L Dougherty, Braelyn Page, Tiffany Wu, Pierce T O’Neil, Charulata B Prasannan, Cody Timmons, Qingling Tang, Daniel J Parente, Shwetha Sreenivasan, Todd Holyoak, Aron W Fenton
Database, Volume 2023, 2023, baad030, https://doi.org/10.1093/database/baad030
Published: 03 May 2023
Journal Article

RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome

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G K Ryabykh, S V Kuznetsov, Y D Korostelev, A I Sigorskikh, A A Zharikova, A A Mironov
Database, Volume 2023, 2023, baad025, https://doi.org/10.1093/database/baad025
Published: 24 April 2023
Journal Article

LiqBioer: a manually curated database of cancer biomarkers in body fluid

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Yiding Geng, Lu Jin, Guangjue Tang, Zhangxiang Zhao, Yunyan Gu, Dan Yang
Database, Volume 2022, 2022, baac077, https://doi.org/10.1093/database/baac077
Published: 02 September 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

Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?

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Anfu Tang, Louise Deléger, Robert Bossy, Pierre Zweigenbaum, Claire Nédellec
Database, Volume 2022, 2022, baac070, https://doi.org/10.1093/database/baac070
Published: 25 August 2022
Journal Article

CPMCP: a database of Chinese patent medicine and compound prescription

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Chang Sun, Jipeng Huang, Rong Tang, Minglei Li, Haili Yuan, Yuxiang Wang, Jin-Mao Wei, Jian Liu
Database, Volume 2022, 2022, baac073, https://doi.org/10.1093/database/baac073
Published: 25 August 2022
Journal Article

TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4

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Amy L Olex, Evan French, Peter Burdette, Srilakshmi Sagiraju, Thomas Neumann, Tamas S Gal, Bridget T McInnes
Database, Volume 2022, 2022, baac063, https://doi.org/10.1093/database/baac063
Published: 11 August 2022
Journal Article

A transcriptome atlas and interactive analysis platform for autoimmune disease

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Zhuoqiao Shen, Minghao Fang, Wujianan Sun, Meifang Tang, Nianping Liu, Lin Zhu, Qian Liu, Bin Li, Ruoming Sun, Yu Shi, Chuang Guo, Jun Lin, Kun Qu
Database, Volume 2022, 2022, baac050, https://doi.org/10.1093/database/baac050
Published: 27 June 2022
Journal Article

PlantGF: an analysis and annotation platform for plant gene families

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Jiaxuan Li, Shuai Yang, Xiaojie Yang, Hui Wu, Heng Tang, Long Yang
Database, Volume 2022, 2022, baab088, https://doi.org/10.1093/database/baab088
Published: 17 January 2022
Journal Article

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1

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Fang Huang, Xia Tang, Bo Ye, Songfeng Wu, Keyue Ding
Database, Volume 2022, 2022, baab087, https://doi.org/10.1093/database/baab087
Published: 17 January 2022
Journal Article

CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer

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Amrita Chattopadhyay, Zi Han Teoh, Chi-Yun Wu, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Chia-Hsin Wu, Tzu-Pin Lu, Eric Y Chuang
Database, Volume 2021, 2021, baab044, https://doi.org/10.1093/database/baab044
Published: 14 July 2021
Journal Article

Standardization of assay representation in the Ontology for Biomedical Investigations

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Randi Vita, Jie Zheng, Rebecca Jackson, Damion Dooley, James A Overton, Mark A Miller, Daniel C Berrios, Richard H Scheuermann, Yongqun He, Hande Küçük McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B Jain, Marcus C Chibucos, John Judkins, Michelle G Giglio, Irene Y Feng, Gully Burns, Matthew H Brush … Christian J Stoeckert Jr
Database, Volume 2021, 2021, baab040, https://doi.org/10.1093/database/baab040
Published: 09 July 2021
Journal Article

Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition

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Adam Klie, Brian Y Tsui, Shamim Mollah, Dylan Skola, Michelle Dow, Chun-Nan Hsu, Hannah Carter
Database, Volume 2021, 2021, baab021, https://doi.org/10.1093/database/baab021
Published: 29 April 2021