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Database Cover Image for Volume 2025
Volume 2025
2025
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EISSN 1758-0463

Volume 2025, 2025

Original Articles

HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production
Alexander B Rogers, Varsha Kale, Germana Baldi, Antton Alberdi, M Thomas P Gilbert, Dipayan Gupta, Morten T Limborg, Sen Li, Thomas Payne, Bent Petersen, Jacob A Rasmussen, Lorna Richardson, Robert D Finn
Database, Volume 2025, 2025, baae112, https://doi.org/10.1093/database/baae112
DisGeNet: a disease-centric interaction database among diseases and various associated genes
Yaxuan Hu, Xingli Guo, Yao Yun, Liang Lu, Xiaotai Huang, Songwei Jia
Database, Volume 2025, 2025, baae122, https://doi.org/10.1093/database/baae122
Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach
Wilailack Meesawad, Jen-Chieh Han, Chun-Yu Hsueh, Yu Zhang, Hsi-Chuan Hung, Richard Tzong-Han Tsai
Database, Volume 2025, 2025, baae127, https://doi.org/10.1093/database/baae127
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations
Esmaeil Nourani, Evangelia-Mantelena Makri, Xiqing Mao, Sampo Pyysalo, Søren Brunak, Katerina Nastou, Lars Juhl Jensen
Database, Volume 2025, 2025, baae129, https://doi.org/10.1093/database/baae129
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database
Jennifer R Smith, Marek A Tutaj, Jyothi Thota, Logan Lamers, Adam C Gibson, Akhilanand Kundurthi, Varun Reddy Gollapally, Kent C Brodie, Stacy Zacher, Stanley J F Laulederkind, G Thomas Hayman, Shur-Jen Wang, Monika Tutaj, Mary L Kaldunski, Mahima Vedi, Wendy M Demos, Jeffrey L De Pons, Melinda R Dwinell, Anne E Kwitek
Database, Volume 2025, 2025, baae132, https://doi.org/10.1093/database/baae132
A change language for ontologies and knowledge graphs
Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J Harry Caufield, John B Graybeal, Nomi L Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A Overton, Mark A Musen, Christopher J Mungall
Database, Volume 2025, 2025, baae133, https://doi.org/10.1093/database/baae133
BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis
Naina Kumari, Samir Kumar, Anupama Roy, Princy Saini, Sarika Jaiswal, Mir Asif Iquebal, Ulavappa B Angadi, Dinesh Kumar
Database, Volume 2025, 2025, baae128, https://doi.org/10.1093/database/baae128
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype
Limin Zhang, Julian Starr, Bruce Ford, Anton Reznicek, Yuxuan Zhou, Étienne Léveillé-Bourret, Étienne Lacroix-Carignan, Jacques Cayouette, Tyler W Smith, Donald Sutherland, Paul Catling, Jeffery M Saarela, Hong Cui, James Macklin
Database, Volume 2025, 2025, baae097, https://doi.org/10.1093/database/baae097
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics
Sara Sepehri, Anja Heymans, Dinja De Win, Jan Maushagen, Audrey Sanctorum, Christophe Debruyne, Robim M Rodrigues, Joery De Kock, Vera Rogiers, Olga De Troyer, Tamara Vanhaecke
Database, Volume 2025, 2025, baae121, https://doi.org/10.1093/database/baae121
LitSumm: large language models for literature summarization of noncoding RNAs
Andrew Green, Carlos Eduardo Ribas, Nancy Ontiveros-Palacios, Sam Griffiths-Jones, Anton I Petrov, Alex Bateman, Blake Sweeney
Database, Volume 2025, 2025, baaf006, https://doi.org/10.1093/database/baaf006
Building resource-efficient community databases using open-source software
Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Jodi Humann, Ping Zheng, Jing Yu, Dorrie Main
Database, Volume 2025, 2025, baaf005, https://doi.org/10.1093/database/baaf005
TumorAgDB1.0: tumor neoantigen database platform
Yan Shao, Yang Gao, Ling-Yu Wu, Shu-Guang Ge, Peng-Bo Wen
Database, Volume 2025, 2025, baaf010, https://doi.org/10.1093/database/baaf010
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data
Elly Poretsky, Victoria C Blake, Carson M Andorf, Taner Z Sen
Database, Volume 2025, 2025, baaf011, https://doi.org/10.1093/database/baaf011
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database
Thomas C Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J Mattingly
Database, Volume 2025, 2025, baaf013, https://doi.org/10.1093/database/baaf013
MANUDB: database and application to retrieve and visualize mammalian NUMTs
Bálint Biró, Zoltán Gál, Zsófia Nagy, Juan Francisco Garcia, Tsend-Ayush Batbold, Orsolya Ivett Hoffmann
Database, Volume 2025, 2025, baaf009, https://doi.org/10.1093/database/baaf009
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress
Pingping Huang, Weilin Cao, Zhaojun Li, Qingshuai Chen, Guangchao Wang, Bailing Zhou, Jihua Wang
Database, Volume 2025, 2025, baaf015, https://doi.org/10.1093/database/baaf015
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms
Fernando Mora-Márquez, Mikel Hurtado, Unai López de Heredia
Database, Volume 2025, 2025, baaf019, https://doi.org/10.1093/database/baaf019
A comprehensive experimental comparison between federated and centralized learning
Swier Garst, Julian Dekker, Marcel Reinders
Database, Volume 2025, 2025, baaf016, https://doi.org/10.1093/database/baaf016
Post-composing ontology terms for efficient phenotyping in plant breeding
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
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data
Sharon Wei, Kapeel Chougule, Andrew Olson, Zhenyuan Lu, Marcela K Tello-Ruiz, Vivek Kumar, Sunita Kumari, Lifang Zhang, Audra Olson, Catherine Kim, Nick Gladman, Doreen Ware
Database, Volume 2025, 2025, baaf021, https://doi.org/10.1093/database/baaf021
mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments
Tzu-Hsien Yang, Xiang-Wei Li, Yuan-Han Lee, Shang-Yi Lu, Wei-Sheng Wu, Heng-Chi Lee
Database, Volume 2025, 2025, baaf023, https://doi.org/10.1093/database/baaf023
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling
Brian M Mack, Matthew D Lebar
Database, Volume 2025, 2025, baaf033, https://doi.org/10.1093/database/baaf033
Localizatome: a database for stress-dependent subcellular localization changes in proteins
Takahide Matsushima, Yuki Naito, Tomoki Chiba, Ryota Kurimoto, Keiko Itano, Koji Ochiai, Koichi Takahashi, Naoki Goshima, Hiroshi Asahara
Database, Volume 2025, 2025, baaf028, https://doi.org/10.1093/database/baaf028
CPDMS: a database system for crop physiological disorder management
Jae-Hyeon Oh, Hwang-Weon Jeong, Il Pyung Ahn, Seon-Hwa Bae, Sung Mi Kim, Eunhee Kim, Su Jung Ra, Jinjeong Lee, Hye Yeon Choi, Young-Joo Seol
Database, Volume 2025, 2025, baaf031, https://doi.org/10.1093/database/baaf031
CancerPPD2: an updated repository of anticancer peptides and proteins
Milind Chauhan, Amisha Gupta, Ritu Tomer, Gajendra P S Raghava
Database, Volume 2025, 2025, baaf030, https://doi.org/10.1093/database/baaf030
A longitudinal analysis of function annotations of the human proteome reveals consistently high biases
An Phan, Parnal Joshi, Claus Kadelka, Iddo Friedberg
Database, Volume 2025, 2025, baaf036, https://doi.org/10.1093/database/baaf036
An exploratory study combining Virtual Reality and Semantic Web for life science research using Graph2VR
Alexander J Kellmann, Sander van den Hoek, Max Postema, W T Kars Maassen, Brenda S Hijmans, Marije A van der Geest, K Joeri van der Velde, Esther J van Enckevort, Morris A Swertz
Database, Volume 2025, 2025, baaf008, https://doi.org/10.1093/database/baaf008
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond
Fang-Yi Su, Gia-Han Ngo, Ben Phan, Jung-Hsien Chiang
Database, Volume 2025, 2025, baaf025, https://doi.org/10.1093/database/baaf025
PLoV: a comprehensive database of genetic variants leading to pregnancy loss
Evgeniia M Maksiutenko, Igor V Bezdvornykh, Yury A Barbitoff, Yulia A Nasykhova, Andrey S Glotov
Database, Volume 2025, 2025, baaf037, https://doi.org/10.1093/database/baaf037
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors
Honglian Huang, Danqi Huang, Ziyi Wei, Yanling Qi, M James C Crabbe, Xiaoyan Zhang, Ying Wang
Database, Volume 2025, 2025, baaf038, https://doi.org/10.1093/database/baaf038
BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme
Princy Saini, Ankita Singh, Tilak Chandra, Dheeraj Kumar Chaurasia, Kunal Chaudhary, Priyanka Jain, G Boopalakrishnan, Sarika Jaiswal, Shyam Sunder Dey, Tusar Kanti Behera, Ulavappa Basavanneppa Angadi, Mir Asif Iquebal, Dinesh Kumar
Database, Volume 2025, 2025, baaf039, https://doi.org/10.1093/database/baaf039
A database on the historical and current occurrences of snakes in Eswatini
Ara Monadjem, Richard C Boycott, Thea Litscha-Koen, Adam Kane, Wisdom M Dlamini, Lindelwa Mmema, Katharine L Strutton, Zakhele Hlophe, Sara Padidar
Database, Volume 2025, 2025, baaf040, https://doi.org/10.1093/database/baaf040
DrugCombo: an informatics bridge for anticancer drug combination Phase I trial design
Lei Wang, Shijun Zhang, Lai Wei, Yuxi Zhu, Naleef Fareed, Lijun Cheng, Williams Carson, Dwight Owen, Yong Zang, Suyu Liu, Aditi Shendre, Xiaofu Liu, Lang Li
Database, Volume 2025, 2025, baaf043, https://doi.org/10.1093/database/baaf043
The state of the human coding gene catalogues
Miguel Maquedano, Daniel Cerdán-Vélez, Michael L Tress
Database, Volume 2025, 2025, baaf045, https://doi.org/10.1093/database/baaf045
ScLineageAtlas: a comprehensive single-cell genomics database for characterizing cellular clones in cancer
Jinyang Liu, Rui Hou, Junlin Xu, Tingting Hui, Haotian Tian, Yankun Liu, Meijun Zhang, Geng Tian, Jialiang Yang
Database, Volume 2025, 2025, baaf046, https://doi.org/10.1093/database/baaf046
Biomedical literature-based clinical phenotype definition discovery using large language models
Samar Binkheder, Xiaofu Liu, Michael Wu, Lei Wang, Aditi Shendre, Sara K Quinney, Wei-Qi Wei, Lang Li
Database, Volume 2025, 2025, baaf047, https://doi.org/10.1093/database/baaf047
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community
Peter Selby, Rafael Abbeloos, Anne-Francoise Adam-Blondon, Francisco J Agosto-Pérez, Michael Alaux, Isabelle Alic, Khaled Al-Shamaa, Johan Steven Aparicio, Jan Erik Backlund, Aldrin Batac, Sebastian Beier, Gabriel Besombes, Alice Boizet, Matthijs Brouwer, Terry Casstevens, Arnaud Charleroy, Keo Corak, Chaney Courtney, Mariano Crimi … The BrAPI Consortium
Database, Volume 2025, 2025, baaf048, https://doi.org/10.1093/database/baaf048
Automatic genetic phenotype normalization from dysmorphology physical examinations: an overview of the BioCreative VIII—Task 3 competition
Davy Weissenbacher, Xinwei Zhao, Jessica R C Priestley, Katherine M Szigety, Sarah F Schmidt, Karen O'Connor, Ekin Soysal, Kirk Roberts, Jiewei Qi, Ling Luo, Zhihao Yang, Hongfei Lin, Hajung Kim, Chanhwi Kim, Jiwoong Sohn, Tim Beck, Marek Rei, Sunkyu Kim, T Ian Simpson … Graciela Gonzalez-Hernandez
Database, Volume 2025, 2025, baaf051, https://doi.org/10.1093/database/baaf051
p53motifDB: integration of genomic information and tumour suppressor p53 binding motifs
Gabriele Baniulyte, Sawyer M Hicks, Morgan A Sammons
Database, Volume 2025, 2025, baaf053, https://doi.org/10.1093/database/baaf053
MRdb: a comprehensive database of univariate and multivariate Mendelian randomization with large-scale GWAS summary data
Qian Liu, Yujie Zhang, Houxing Li, Jiatong Li, Mengyu Xin, Rui Sun, Yifan Dai, Xinxin Shan, Yuting He, Borui Xu, Shangwei Ning, Peng Wang, Qiuyan Guo
Database, Volume 2025, 2025, baaf054, https://doi.org/10.1093/database/baaf054
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity
Rubén González-Miguéns, Àlex Gàlvez-Morante, Margarita Skamnelou, Meritxell Antó, Elena Casacuberta, Daniel J Richter, Enrique Lara, Daniel Vaulot, Javier del Campo, Iñaki Ruiz-Trillo
Database, Volume 2025, 2025, baaf057, https://doi.org/10.1093/database/baaf057
StrainInfo—the central database for linked microbial strain identifiers
Artur Lissin, Isabel Schober, Julius F Witte, Helko Lüken, Adam Podstawka, Julia Koblitz, Boyke Bunk, Peter Dawyndt, Peter Vandamme, Paul de Vos, Jörg Overmann, Lorenz C Reimer
Database, Volume 2025, 2025, baaf059, https://doi.org/10.1093/database/baaf059
The Microbe Directory: a centralized database for biological interpretation of microbiome data
Maria A Sierra, Krista Ryon, Mohith R Arikatla, Radwa Elshafey, Hardik Bhaskar, Jacqueline Proszynski, Chandrima Bhattacharya, Heba Shaaban, David C Danko, Pradeep Ambrose, Sarah A Spaulding, Maria Mercedes Zambrano, The Microbe Directory Consortium, Christopher E Mason
Database, Volume 2025, 2025, baaf060, https://doi.org/10.1093/database/baaf060
The impact of curation errors in the PDBBind Database on machine learning predictions of protein–protein binding affinity
Jason D Gans, Justin E Miller, Esen Sokullu, Nileena Velappan, Ramesh K Jha
Database, Volume 2025, 2025, baaf061, https://doi.org/10.1093/database/baaf061
Gene Loss DB: a curated database for gene loss in mammals—the cetacean collection
Gonçalo Espregueira Themudo, Raquel Ruivo, Raul Valente, Nádia Artilheiro, Diogo Oliveira, Inês Amorim, Bernardo Pinto, Luís Filipe C Castro, Sergio Fernandes, Mónica Lopes-Marques
Database, Volume 2025, 2025, baaf065, https://doi.org/10.1093/database/baaf065
VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness
Hongrui Wang, Jason P Londo
Database, Volume 2025, 2025, baaf055, https://doi.org/10.1093/database/baaf055
Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity
Daniela Raciti, Kimberly M Van Auken, Valerio Arnaboldi, Christopher J Tabone, Hans-Michael Muller, Paul W Sternberg
Database, Volume 2025, 2025, baaf063, https://doi.org/10.1093/database/baaf063
CobVar—a comprehensive resource of vitamin B12-associated genomic variants
Neha H Suresh, Chaitra A Kilpady, Akshata A Kamath, Ashikh Ahmed, Tinku Thomas, Anura V Kurpad, Ambily Sivadas
Database, Volume 2025, 2025, baaf049, https://doi.org/10.1093/database/baaf049
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins
Yanyan Zhu, Liya Liu, Yueming Hu, Sida Li, Enyan Liu, Yanshi Hu, Shilong Zhang, Haoyu Chao, Qiuyu Fang, Huan Yu, Ming Chen
Database, Volume 2025, 2025, baaf070, https://doi.org/10.1093/database/baaf070
PolED: a manually curated database of functional studies of POLE and POLD1 variants reported in humans
Lev Tsarin, Polina V Shcherbakova
Database, Volume 2025, 2025, baaf076, https://doi.org/10.1093/database/baaf076
Enhancing statistical analysis of real world data
Laha Ale, Robert Gentleman, Christopher Endres, Sam Pullman, Nathan Palmer, Rafael Goncalves, Deepayan Sarkar
Database, Volume 2025, 2025, baaf073, https://doi.org/10.1093/database/baaf073
CircAI: a comprehensive database of CircRNA associated with A-to-I RNA editing
Yulan Wang, Lingxiao Zou, Jian Zhao, Jing Wu, Meng Zhang, Jingjing Liu, Quan Wang, Xuejiang Guo, Xiaofeng Song, Yixuan Wang
Database, Volume 2025, 2025, baaf075, https://doi.org/10.1093/database/baaf075
Automated annotation and validation of human respiratory virus sequences using VADR
Jeffrey Furlong, Stephanie Goya, Eric P Nawrocki, Vincent Calhoun, Eneida Hatcher, Linda Yankie, Alexander L Greninger
Database, Volume 2025, 2025, baaf078, https://doi.org/10.1093/database/baaf078
HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses
Pan Zhang, Tianxiang Ouyang, Xiaowen Hu, Jie Huang, Biao Xiao, Zhijian Huang, Xingyang Shi, Xinyi Wu, Linying Chen, Yongkang Wu, Hanyue Wang, Ying Zhang, Guangdi Li, Hui Liu, Lei Deng
Database, Volume 2025, 2025, baaf079, https://doi.org/10.1093/database/baaf079
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens
Clémentine Battistel, Jean-Christophe Mouren, Benjamin Morga, Camille Pelletier, Lydie Canier, Céline Garcia, Isabelle Arzul, Yaelle Pihan, Laura Leroi, Germain Chevignon, Patrick Guido Durand, Maude Jacquot
Database, Volume 2025, 2025, baaf080, https://doi.org/10.1093/database/baaf080
From library to landscape: integrative annotation workflows for compound libraries in drug repurposing
Jeanette Reinshagen, Brinton Seashore-Ludlow, Yojana Gadiya, Anna-Lena Gustavsson, Ziaurrehman Tanoli, Tero Aittokallio, Johanna Huchting, Annika Jenmalm-Jensen, Philip Gribbon, Andrea Zaliani, Flavio Ballante
Database, Volume 2025, 2025, baaf081, https://doi.org/10.1093/database/baaf081
The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation
Shao-Yan Pu, Jing-Sheng Lu, Xin-Ling Tao, Zi-Feng Li, Ya-Nan Wang, Hao-Miao Zhang, Xuemei Lu
Database, Volume 2025, 2025, baaf077, https://doi.org/10.1093/database/baaf077
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus
Sibbe Bakker, Mariana Santos-Silva, Johanna Rhodes, Sijmen Schoustra, Bas Zwaan, Anna Fensel
Database, Volume 2025, 2025, baaf082, https://doi.org/10.1093/database/baaf082
CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae fish
Princy Saini, Kunal Chaudhary, Jutan Das, Naina Kumari, Sarika Jaiswal, Kiran D Rasal, U B Angadi, Mir Asif Iquebal, Dinesh Kumar
Database, Volume 2025, 2025, baaf087, https://doi.org/10.1093/database/baaf087

Database tools

BbGSD: Black-boned Sheep Genome SNP Database
Chunjuan He, Lichang Chen, Juntao Cao, Yuqing Zhong, Zhendong Gao, Weidong Deng, Jiajin Zhang
Database, Volume 2025, 2025, baaf004, https://doi.org/10.1093/database/baaf004
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design
Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, ZhaoTing Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang
Database, Volume 2025, 2025, baaf001, https://doi.org/10.1093/database/baaf001
AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein
Xiaomin Zhang, Zhongyi Lei, Jiarong Zhang, Tingting Yang, Xian Liu, Jiguo Xue, Ming Ni
Database, Volume 2025, 2025, baaf002, https://doi.org/10.1093/database/baaf002
TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes
Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei
Database, Volume 2025, 2025, baaf012, https://doi.org/10.1093/database/baaf012
ForestForward: visualizing and accessing integrated world forest data from the last 50 years
E. L Tejada-Gutiérrez, J Mateo Fornés, F Solsona, R Alves
Database, Volume 2025, 2025, baaf018, https://doi.org/10.1093/database/baaf018
Pipeline to explore information on genome editing using large language models and genome editing meta-database
Takayuki Suzuki, Hidemasa Bono
Database, Volume 2025, 2025, baaf022, https://doi.org/10.1093/database/baaf022
VarGuideAtlas: a repository of variant interpretation guidelines
Mireia Costa, Alberto García S., Oscar Pastor
Database, Volume 2025, 2025, baaf017, https://doi.org/10.1093/database/baaf017
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database
Jiaojiao Zhao, Min Wu, Meihua Wan, Xue Li, Jie Li, Qin Liu, Minghao Xiong, Mengjie Tu, Jun Zhou, Shilin Li, Jie Zhang, Jiangping Fu, Yin Zhang, Chungang Zhao, Litong Qin, Xue Yang, Hong Zhao, Yan Zhang, Fanxin Zeng
Database, Volume 2025, 2025, baaf029, https://doi.org/10.1093/database/baaf029
Mapping assays to the key characteristics of carcinogens to support decision-making
Gabrielle Rigutto, Cliona M McHale, Ettayapuram Ramaprasad Azhagiya Singam, Iemaan Rana, Luoping Zhang, Martyn T Smith
Database, Volume 2025, 2025, baaf026, https://doi.org/10.1093/database/baaf026
STCDB4ND: a signal transduction classification database for neurological diseases
Boyan Gong, Sida Li, Yifan Chen, Liya Liu, Ralf Hofestädt, Ming Chen
Database, Volume 2025, 2025, baaf032, https://doi.org/10.1093/database/baaf032
Empirical substitution models of protein evolution: database, relationships, and modeling considerations
Paula Iglesias-Rivas, Roberto Del Amparo, Javier A Cabaleiro, Miguel Arenas
Database, Volume 2025, 2025, baaf052, https://doi.org/10.1093/database/baaf052
A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability
Ivan Fruggiero, Alessandro Maisto, Sara Passaro, Domenico Gentile, Angelina Nunziata, Nunzio D’Agostino
Database, Volume 2025, 2025, baaf056, https://doi.org/10.1093/database/baaf056
Zoonosis: a comprehensive database of zoonotic pathogens
Boyuan Zhang, Dan Liu, Weiwen Wang, Xiaoqiang Li, Yifei Xie, Huitong Li, Hongmei Zhou, Jianshuai Gao, Hui Jiang, Xuezheng Fan, Jiabo Ding, Qingchun Shen, Xizheng Ma
Database, Volume 2025, 2025, baaf062, https://doi.org/10.1093/database/baaf062
SEND: a suite of tools for the easy sharing of linked biological data
Rodolfo S Allendes Osorio, Yi-An Chen, Kenji Mizuguchi
Database, Volume 2025, 2025, baaf068, https://doi.org/10.1093/database/baaf068
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities
Sharayu Ghodeswar, Debashree Bandyopadhyay
Database, Volume 2025, 2025, baaf069, https://doi.org/10.1093/database/baaf069
Genomic Predicted cross performance: a tool for optimizing parental combinations in breeding programs
Christine Nyaga, Marlee R Labroo, Agre Paterne, Asrat Asfaw, Marnin D Wolfe, Isaak Yosief Tecle, Lukas A Mueller
Database, Volume 2025, 2025, baaf074, https://doi.org/10.1093/database/baaf074

Database updates

GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database
Sarthak Joshi, Shailendu Mohapatra, Dhwani Kumar, Adwait Joshi, Meenakshi Iyer, Ramanathan Sowdhamini
Database, Volume 2025, 2025, baaf035, https://doi.org/10.1093/database/baaf035
GExplore 1.5: a comprehensive Caenorhabditis elegans database for the analysis of gene function with a new user-friendly web interface
Harald Hutter, Mehrdad Moosavi, Nelly Mafi
Database, Volume 2025, 2025, baaf044, https://doi.org/10.1093/database/baaf044
ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0
Silvia Tenorio-Salgado, Cinthia Rodríguez Maya, Edgardo Galan-Vasquez, André Borges Farias, Dulce Álvarez-López, Jose Luis Villalpando-Aguilar, Alberto J Martin, Leonardo Ledesma-Dominguez, Ernesto Perez-Rueda
Database, Volume 2025, 2025, baaf071, https://doi.org/10.1093/database/baaf071
PASS2: update of database of structure-based sequence alignments
Revathy Menon, Soumya Nayak, Rama Rajesh, Ramanathan Sowdhamini
Database, Volume 2025, 2025, baaf072, https://doi.org/10.1093/database/baaf072

Reviews

Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models
Muhammad Nabeel Asim, Tayyaba Asif, Faiza Hassan, Andreas Dengel
Database, Volume 2025, 2025, baaf027, https://doi.org/10.1093/database/baaf027
A review on Gene Ontology evaluations
Borja Pitarch, Mónica Chagoyen, Juan A G Ranea, Florencio Pazos
Database, Volume 2025, 2025, baaf058, https://doi.org/10.1093/database/baaf058
Review of autism spectrum disorder databases for the identification of candidate genes
Diana Martínez-Minguet, René Noel, Alberto García S., Mireia Costa, Oscar Pastor
Database, Volume 2025, 2025, baaf067, https://doi.org/10.1093/database/baaf067
Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis
Marziyeh Mousazadeh, Babak Khorsand, Sayed Mostafa Modarres Mousavi, Hooman Mahmoudi Aznaveh, Mohamad Hassan Fouani, Faezeh Mousazadeh, Mehrnaz Rad-Faraji, Arezoo Golestanipour, Soheila Mohammadi, Fateme Zarein, Alireza Dantism, Javad Zahiri, Maryam Nikkhah
Database, Volume 2025, 2025, baaf042, https://doi.org/10.1093/database/baaf042

Tutorial

A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture
Annarita Marrano, Leyla Cabugos, Alenka Hafner, Beant Kapoor, John McNamara, Megan O’Donnell, Leonore Reiser, Marcela Karey Tello-Ruiz, Huiting Zhang, Margaret Staton
Database, Volume 2025, 2025, baaf034, https://doi.org/10.1093/database/baaf034

Perspective/Opinion

Working in biocuration: contemporary experiences and perspectives
Sarah R Davies
Database, Volume 2025, 2025, baaf003, https://doi.org/10.1093/database/baaf003
Integrated data-driven biotechnology research environments
Rosalia Moreddu
Database, Volume 2025, 2025, baaf064, https://doi.org/10.1093/database/baaf064
Navigating open-source waters: the pharmaceutical industry’s role in bioontology development
Shawn Zheng Kai Tan, Joshua Daniel Valdez, Saritha Vettikunnel Kuriakose
Database, Volume 2025, 2025, baaf066, https://doi.org/10.1093/database/baaf066

Expression of concern

Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes
Database, Volume 2025, 2025, baaf007, https://doi.org/10.1093/database/baaf007

Corrections

Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study
Database, Volume 2025, 2025, baae131, https://doi.org/10.1093/database/baae131
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders
Database, Volume 2025, 2025, baaf014, https://doi.org/10.1093/database/baaf014
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders
Database, Volume 2025, 2025, baaf050, https://doi.org/10.1093/database/baaf050
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