Database-The Journal of Biological Databases and Curation

Article	Citations
CCIDB: a manually curated cell–cell interaction database with cell context information	65
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	50
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	37
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	35
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	34
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	30
The importance of graph databases and graph learning for clinical applications	28
BioKC: a collaborative platform for curation and annotation of molecular interactions	27
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	25
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	24
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	23
Building resource-efficient community databases using open-source software	23
Post-composing ontology terms for efficient phenotyping in plant breeding	20
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	17
Integrated data-driven biotechnology research environments	16
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training	16
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	16
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	16
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	15
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	15
DisGeNet: a disease-centric interaction database among diseases and various associated genes	14
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	13
HOFE: an interactive forensic entomological database	13
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus	13
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	13

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	13
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	12
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer	12
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	12
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)	12
Interactive tools for functional annotation of bacterial genomes	12
New approaches in developing medicinal herbs databases	12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	11
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	11
PheNormGPT: a framework for extraction and normalization of key medical findings	11
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	11
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	11
Localizatome: a database for stress-dependent subcellular localization changes in proteins	11
TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines	11
CardioHotspots: a database of mutational hotspots for cardiac disorders	10
Towards discovery: an end-to-end system for uncovering novel biomedical relations	10
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	9
Visualization and exploration of linked data using virtual reality	9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	9
PASS2: update of database of structure-based sequence alignments	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
scDrugAtlas: an integrative single-cell drug response database for dissecting tumour heterogeneity in therapeutic efficacy	8
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	7
CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, bioche	7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	7
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	7
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	7
neomerDB: a comprehensive database of neomer biomarkers in cancer	7
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
The Portuguese Beacon: sharing genomic variant data safely	6
MANUDB: database and application to retrieve and visualize mammalian NUMTs	6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6

SynVectorDB: embedding-based retrieval system for synthetic biology parts	6
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	6
ImmRNA: a database of RNAs associated with tumor immunity	6
MOKCa-3D database: functional and structural analysis of missense mutations in cancer	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
Correction to: The importance of graph databases and graph learning for clinical applications	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
CPMKG: a condition-based knowledge graph for precision medicine	5
NbThermo: a new thermostability database for nanobodies	5
The state of the human coding gene catalogues	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	5
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
IsoProDB: an integrated map of human protein isoforms for accelerated research	5
Transformer-based approach for symptom recognition and multilingual linking	5
Autophagy3D: a comprehensive autophagy structure database	4
scBrainMap: a landscape for cell types and associated genetic markers in the brain	4
Biomedical literature-based clinical phenotype definition discovery using large language models	4
Standardized naming of microbiome samples in Genomes OnLine Database	4
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	4
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	4
GExplore 1.5: a comprehensive Caenorhabditis elegans database for the analysis of gene function with a new user-friendly web interface	4
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	4
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	4
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update	4
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	4
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	4
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	4
A review on Gene Ontology evaluations	4
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	4
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease	4
PDC: a highly compact file format to store protein 3D coordinates	4
MantaID: a machine learning–based tool to automate the identification of biological database IDs	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
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank	4
LitSumm: large language models for literature summarization of noncoding RNAs	4
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	4
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	4
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	4
Mapping of EFO terms from the GWAS catalog data to multiple ontologies at the Rat Genome Database	4
predicTox: an integrated database of clinical risk frequencies and human gene expression signatures for cardiotoxic drugs	4
HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses	4
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature	4
AgingReG: a curated database of aging regulatory relationships in humans	4
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome	4
Assessing the use of supplementary materials to improve genomic variant discovery	3
Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach	3
A comprehensive experimental comparison between federated and centralized learning	3
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies	3
A database on the historical and current occurrences of snakes in Eswatini	3
Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes	3
MineProt: a stand-alone server for structural proteome curation	3
Biomedical relation extraction with knowledge base–refined weak supervision	3
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	3
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles	3
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	3
BEDB: a comprehensive binding energy database for molecular docking and dynamics: insights into Human Metapneumovirus (HMPV) Inhibitors	3
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation	3
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning	3
Notes on the data quality of bibliographic records from the MEDLINE database	3
MACSFeD—a database of mosquito acoustic communication and swarming features	3
VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness	3
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	3
MDDOmics: multi-omics resource of major depressive disorder	3
Dataset of xenobiotics human renal clearance values	3
CancerPPD2: an updated repository of anticancer peptides and proteins	3
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants	3
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop	3
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape	3
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	3
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes	3
Global Globin Network and adopting genomic variant database requirements for thalassemia	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
MASH-GA: a manually curated cross-species transcriptomic database for metabolic-associated steatohepatitis	2

PlantIntronDB: a database for plant introns that host functional elements	2
The Immunopeptidomics Ontology (ImPO)	2
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis	2
Assessing resource use: a case study with the Human Disease Ontology	2
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	2
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome	2
BDCD: a comprehensive Brain Disease Cell-cell communication Database	2
BbGSD: Black-boned Sheep Genome SNP Database	2
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics	2
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen	2
STCDB4ND: a signal transduction classification database for neurological diseases	2
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress	2
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data	2
Automated annotation of scientific texts for ML-based keyphrase extraction and validation	2
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance	2
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	2
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	2
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	2
MyxoPortal: a database of myxobacterial genomic features	2
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	2
DISPEL: database for ascertaining the best medicinal plants to cure human diseases	2
The landscape of health disparities in the UK Biobank	2
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications	2
ePerturbDB: enhancer’s experimental perturbation database	2
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb	2
From library to landscape: integrative annotation workflows for compound libraries in drug repurposing	2
Automated annotation and validation of human respiratory virus sequences using VADR	2
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications	2
Enhancing statistical analysis of real world data	2
GMMID: genetically modified mice information database	2
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	2
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	2
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures	2
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins	2
A comprehensive database for biological data derived from sewage in five European cities	2
Best practices for the manual curation of intrinsically disordered proteins in DisProt	2
CIGAF—a database and interactive platform for insect-associated trichomycete fungi	2
nhanesA: achieving transparency and reproducibility in NHANES research	2
GdbMTB: a manually curated genomic database of magnetotactic bacteria	2
BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme	2
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture	2
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery	2
VarGuideAtlas: a repository of variant interpretation guidelines	2
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond	2
The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation	2