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Database Cover Image for Volume 2025
Volume 2025
2025
(In Progress)
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issue cover
EISSN 1758-0463

Volume 2025, 2025

SEND: a suite of tools for the easy sharing of linked biological data
Rodolfo S Allendes Osorio and others
Database, Volume 2025, 2025, baaf068, https://doi.org/10.1093/database/baaf068
ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0
Silvia Tenorio-Salgado and others
Database, Volume 2025, 2025, baaf071, https://doi.org/10.1093/database/baaf071
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 and Debashree Bandyopadhyay
Database, Volume 2025, 2025, baaf069, https://doi.org/10.1093/database/baaf069
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins
Yanyan Zhu and others
Database, Volume 2025, 2025, baaf070, https://doi.org/10.1093/database/baaf070
Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis
Marziyeh Mousazadeh and others
Database, Volume 2025, 2025, baaf042, https://doi.org/10.1093/database/baaf042
PASS2: update of database of structure-based sequence alignments
Revathy Menon and others
Database, Volume 2025, 2025, baaf072, https://doi.org/10.1093/database/baaf072
Genomic Predicted cross performance: a tool for optimizing parental combinations in breeding programs
Christine Nyaga and others
Database, Volume 2025, 2025, baaf074, https://doi.org/10.1093/database/baaf074
PolED: a manually curated database of functional studies of POLE and POLD1 variants reported in humans
Lev Tsarin and Polina V Shcherbakova
Database, Volume 2025, 2025, baaf076, https://doi.org/10.1093/database/baaf076
Enhancing statistical analysis of real world data
Laha Ale and others
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 and others
Database, Volume 2025, 2025, baaf075, https://doi.org/10.1093/database/baaf075

Original Articles

HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production
Alexander B Rogers and others
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 and others
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 and others
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 and others
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 and others
Database, Volume 2025, 2025, baae132, https://doi.org/10.1093/database/baae132
A change language for ontologies and knowledge graphs
Harshad Hegde and others
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 and others
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 and others
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 and others
Database, Volume 2025, 2025, baae121, https://doi.org/10.1093/database/baae121
LitSumm: large language models for literature summarization of noncoding RNAs
Andrew Green and others
Database, Volume 2025, 2025, baaf006, https://doi.org/10.1093/database/baaf006
Building resource-efficient community databases using open-source software
Sook Jung and others
Database, Volume 2025, 2025, baaf005, https://doi.org/10.1093/database/baaf005
TumorAgDB1.0: tumor neoantigen database platform
Yan Shao and others
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 and others
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 and others
Database, Volume 2025, 2025, baaf013, https://doi.org/10.1093/database/baaf013
MANUDB: database and application to retrieve and visualize mammalian NUMTs
Bálint Biró and others
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 and others
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 and others
Database, Volume 2025, 2025, baaf019, https://doi.org/10.1093/database/baaf019
A comprehensive experimental comparison between federated and centralized learning
Swier Garst and others
Database, Volume 2025, 2025, baaf016, https://doi.org/10.1093/database/baaf016
Post-composing ontology terms for efficient phenotyping in plant breeding
Naama Menda and others
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 and others
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 and others
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 and 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 and others
Database, Volume 2025, 2025, baaf028, https://doi.org/10.1093/database/baaf028
CPDMS: a database system for crop physiological disorder management
Jae-Hyeon Oh and others
Database, Volume 2025, 2025, baaf031, https://doi.org/10.1093/database/baaf031
CancerPPD2: an updated repository of anticancer peptides and proteins
Milind Chauhan and others
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 and others
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 and others
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 and others
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 and others
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 and others
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 and others
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 and others
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 and others
Database, Volume 2025, 2025, baaf043, https://doi.org/10.1093/database/baaf043
The state of the human coding gene catalogues
Miguel Maquedano and others
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 and others
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 and others
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 and others
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 and others
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 and others
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 and others
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 and others
Database, Volume 2025, 2025, baaf057, https://doi.org/10.1093/database/baaf057
StrainInfo—the central database for linked microbial strain identifiers
Artur Lissin and others
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 and others
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 and others
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 and others
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 and 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 and others
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 and others
Database, Volume 2025, 2025, baaf049, https://doi.org/10.1093/database/baaf049

Database tools

BbGSD: Black-boned Sheep Genome SNP Database
Chunjuan He and others
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 and others
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 and others
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 and others
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 and others
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 and Hidemasa Bono
Database, Volume 2025, 2025, baaf022, https://doi.org/10.1093/database/baaf022
VarGuideAtlas: a repository of variant interpretation guidelines
Mireia Costa and others
Database, Volume 2025, 2025, baaf017, https://doi.org/10.1093/database/baaf017
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database
Jiaojiao Zhao and others
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 and others
Database, Volume 2025, 2025, baaf026, https://doi.org/10.1093/database/baaf026
STCDB4ND: a signal transduction classification database for neurological diseases
Boyan Gong and others
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 and others
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 and others
Database, Volume 2025, 2025, baaf056, https://doi.org/10.1093/database/baaf056
Zoonosis: a comprehensive database of zoonotic pathogens
Boyuan Zhang and others
Database, Volume 2025, 2025, baaf062, https://doi.org/10.1093/database/baaf062

Database update

GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database
Sarthak Joshi and others
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 and others
Database, Volume 2025, 2025, baaf044, https://doi.org/10.1093/database/baaf044

Reviews

Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models
Muhammad Nabeel Asim and others
Database, Volume 2025, 2025, baaf027, https://doi.org/10.1093/database/baaf027
A review on Gene Ontology evaluations
Borja Pitarch and others
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 and others
Database, Volume 2025, 2025, baaf067, https://doi.org/10.1093/database/baaf067

Tutorial

A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture
Annarita Marrano and others
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 and others
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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  • Online ISSN 1758-0463
  • Copyright © 2025 Oxford University Press

Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide

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