Volume 2025

2025

(In Progress)

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EISSN 1758-0463

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IN PROGRESS

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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VarGuideAtlas: a repository of variant interpretation guidelines

Mireia Costa and others

Database, Volume 2025, 2025, baaf017, https://doi.org/10.1093/database/baaf017

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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

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Zoonosis: a comprehensive database of zoonotic pathogens

Boyuan Zhang and others

Database, Volume 2025, 2025, baaf062, https://doi.org/10.1093/database/baaf062

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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

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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

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A review on Gene Ontology evaluations

Borja Pitarch and others

Database, Volume 2025, 2025, baaf058, https://doi.org/10.1093/database/baaf058

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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

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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

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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

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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

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Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders

Database, Volume 2025, 2025, baaf014, https://doi.org/10.1093/database/baaf014

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