Database-The Journal of Biological Databases and Curation

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	78
BioKC: a collaborative platform for curation and annotation of molecular interactions	53
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	46
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	40
Building resource-efficient community databases using open-source software	39
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	38
The importance of graph databases and graph learning for clinical applications	38
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	33
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	29
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	27
CCIDB: a manually curated cell–cell interaction database with cell context information	26
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	25
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	23
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	21
Post-composing ontology terms for efficient phenotyping in plant breeding	19
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	18
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training	17
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	17
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	17
DisGeNet: a disease-centric interaction database among diseases and various associated genes	16
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus	16
Integrated data-driven biotechnology research environments	16
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	16
HOFE: an interactive forensic entomological database	16
New approaches in developing medicinal herbs databases	15

ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	15
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)	14
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer	14
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	14
PheNormGPT: a framework for extraction and normalization of key medical findings	14
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	14
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	14
Towards discovery: an end-to-end system for uncovering novel biomedical relations	13
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	13
Interactive tools for functional annotation of bacterial genomes	13
TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines	13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	13
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	13
Localizatome: a database for stress-dependent subcellular localization changes in proteins	13
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	12
KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants	12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	12
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	12
Visualization and exploration of linked data using virtual reality	11
PASS2: update of database of structure-based sequence alignments	11
CardioHotspots: a database of mutational hotspots for cardiac disorders	10
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	10
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	9
scDrugAtlas: an integrative single-cell drug response database for dissecting tumour heterogeneity in therapeutic efficacy	9
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	9
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	9
CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, bioche	9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	9
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	8
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	8
TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol	8
MANUDB: database and application to retrieve and visualize mammalian NUMTs	8
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	8
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	8
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
OzButterflies – a high quality open database of multispectral images and spectra of tropical to temperate Australian butterflies	8
ImmRNA: a database of RNAs associated with tumor immunity	8
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	8
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	8
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
neomerDB: a comprehensive database of neomer biomarkers in cancer	8
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	8

PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	7
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	7
MOKCa-3D database: functional and structural analysis of missense mutations in cancer	7
NbThermo: a new thermostability database for nanobodies	7
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
IBDkb: an AI-enhanced integrative knowledge base for inflammatory bowel disease research and drug discovery	6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	6
SynVectorDB: embedding-based retrieval system for synthetic biology parts	6
The state of the human coding gene catalogues	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
Correction to: The importance of graph databases and graph learning for clinical applications	6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	6
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	6
IsoProDB: an integrated map of human protein isoforms for accelerated research	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
The Portuguese Beacon: sharing genomic variant data safely	6
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities	5
Transformer-based approach for symptom recognition and multilingual linking	5
A review on Gene Ontology evaluations	5
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	5
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	5
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	5
Mapping of EFO terms from the GWAS catalog data to multiple ontologies at the Rat Genome Database	5
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	5
FAD: a comprehensive database merging information about food allergens	5
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	5
scBrainMap: a landscape for cell types and associated genetic markers in the brain	5
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
CPMKG: a condition-based knowledge graph for precision medicine	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
Biomedical literature-based clinical phenotype definition discovery using large language models	5
Autophagy3D: a comprehensive autophagy structure database	5
Standardized naming of microbiome samples in Genomes OnLine Database	5
Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach	4
Quantitative analysis of growth and diversification in venom data using database metrics	4
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease	4
BEDB: a comprehensive binding energy database for molecular docking and dynamics: insights into Human Metapneumovirus (HMPV) Inhibitors	4
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	4
NORG - Nitrogen ORGanizer: a novel web-based system for cryopreservation and freezer management	4
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	4
LitSumm: large language models for literature summarization of noncoding RNAs	4
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome	4
MDDOmics: multi-omics resource of major depressive disorder	4
A comprehensive experimental comparison between federated and centralized learning	4
A database on the historical and current occurrences of snakes in Eswatini	4
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	4
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	4
AgingReG: a curated database of aging regulatory relationships in humans	4
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants	4
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	4
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update	4
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation	4
PDC: a highly compact file format to store protein 3D coordinates	4
CancerPPD2: an updated repository of anticancer peptides and proteins	4
Dataset of xenobiotics human renal clearance values	4
HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses	4
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank	4
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature	4
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	4
GExplore 1.5: a comprehensive Caenorhabditis elegans database for the analysis of gene function with a new user-friendly web interface	4
predicTox: an integrated database of clinical risk frequencies and human gene expression signatures for cardiotoxic drugs	4
MantaID: a machine learning–based tool to automate the identification of biological database IDs	4
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	3
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics	3
FuNGI: Fungal Nucleolar Genomic Inventory—a comprehensive database of fungal proteins with predicted nucleolar localization signals	3
Assessing resource use: a case study with the Human Disease Ontology	3
STCDB4ND: a signal transduction classification database for neurological diseases	3
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape	3
Biomedical relation extraction with knowledge base–refined weak supervision	3
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants	3
MetaCancerDB: a database of site-specific RNA–miRNA correlations in cancer metastasis	3
Assessing the use of supplementary materials to improve genomic variant discovery	3
MACSFeD—a database of mosquito acoustic communication and swarming features	3
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes	3
A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs	3

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	3
nhanesA: achieving transparency and reproducibility in NHANES research	3
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture	3
Automated annotation and validation of human respiratory virus sequences using VADR	3
MineProt: a stand-alone server for structural proteome curation	3
VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness	3
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning	3
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles	3
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies	3
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb	3
Best practices for the manual curation of intrinsically disordered proteins in DisProt	3
The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation	3
The Immunopeptidomics Ontology (ImPO)	3
The landscape of health disparities in the UK Biobank	3
VarGuideAtlas: a repository of variant interpretation guidelines	3
Notes on the data quality of bibliographic records from the MEDLINE database	3
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	3
Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes	3
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	3
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	3
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop	3
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome	3
GIDISdb: a gene expression database for exploring human immune responses in infectious diseases	2
PANGEN: an online platform for the comparison and creation of diagnostic gene panels	2
CIGAF—a database and interactive platform for insect-associated trichomycete fungi	2
Genomic Predicted cross performance: a tool for optimizing parental combinations in breeding programs	2
A comprehensive database for biological data derived from sewage in five European cities	2
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis	2
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond	2
BbGSD: Black-boned Sheep Genome SNP Database	2
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures	2
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress	2
PlantIntronDB: a database for plant introns that host functional elements	2
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	2
From library to landscape: integrative annotation workflows for compound libraries in drug repurposing	2
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database	2
DISPEL: database for ascertaining the best medicinal plants to cure human diseases	2
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen	2
GdbMTB: a manually curated genomic database of magnetotactic bacteria	2
Global Globin Network and adopting genomic variant database requirements for thalassemia	2
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications	2
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications	2
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance	2
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data	2
MyxoPortal: a database of myxobacterial genomic features	2
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	2
MASH-GA: a manually curated cross-species transcriptomic database for metabolic-associated steatohepatitis	2
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations	2
The Microbe Directory: a centralized database for biological interpretation of microbiome data	2
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	2
ePerturbDB: enhancer’s experimental perturbation database	2
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery	2
GMMID: genetically modified mice information database	2
BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme	2
Automated annotation of scientific texts for ML-based keyphrase extraction and validation	2
BDCD: a comprehensive Brain Disease Cell-cell communication Database	2
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	2
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins	2
Enhancing statistical analysis of real world data	2
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	2