Database-The Journal of Biological Databases and Curation

Article	Citations
Multi-omics molecular biomarkers and database of osteoarthritis	144
Building resource-efficient community databases using open-source software	137
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	87
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	87
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	80
BioKC: a collaborative platform for curation and annotation of molecular interactions	78
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	61
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	55
CCIDB: a manually curated cell–cell interaction database with cell context information	52
The importance of graph databases and graph learning for clinical applications	38
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	38
A roadmap for the functional annotation of protein families: a community perspective	37
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	29
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	28
DisGeNet: a disease-centric interaction database among diseases and various associated genes	27
Post-composing ontology terms for efficient phenotyping in plant breeding	26
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	26
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	26
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	25
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	24
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	23
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	21
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	20
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	20
HOFE: an interactive forensic entomological database	19

COVIDium: a COVID-19 resource compendium	19
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	18
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	18
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	17
New approaches in developing medicinal herbs databases	17
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	16
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	16
Localizatome: a database for stress-dependent subcellular localization changes in proteins	15
Interactive tools for functional annotation of bacterial genomes	15
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	15
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	14
PheNormGPT: a framework for extraction and normalization of key medical findings	14
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	13
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	13
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	12
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	12
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	12
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	12
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	11
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	11
Towards discovery: an end-to-end system for uncovering novel biomedical relations	11
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	11
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	11
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
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	10
PharmaKoVariome database for supporting genetic testing	10
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	10
Conference report: Biocuration 2021 Virtual Conference	9
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	9
CardioHotspots: a database of mutational hotspots for cardiac disorders	9
Visualization and exploration of linked data using virtual reality	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	9
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	9
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	8
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	8
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	8
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	8
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	8
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	8
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	7
Classifying domain-specific text documents containing ambiguous keywords	7

MANUDB: database and application to retrieve and visualize mammalian NUMTs	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
A review on antimicrobial peptides databases and the computational tools	7
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	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
ImmRNA: a database of RNAs associated with tumor immunity	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
The World Spider Trait database: a centralized global open repository for curated data on spider traits	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
LitCovid ensemble learning for COVID-19 multi-label classification	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	6
NbThermo: a new thermostability database for nanobodies	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
BCSCdb: a database of biomarkers of cancer stem cells	5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	5
HPVMD-C: a disease-based mutation database of human papillomavirus in China	5
TEx-MST: tissue expression profiles of MANE select transcripts	5
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	5
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
ProbResist: a database for drug-resistant probiotic bacteria	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
Autophagy3D: a comprehensive autophagy structure database	5
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	5
Emati: a recommender system for biomedical literature based on supervised learning	5
Standardized naming of microbiome samples in Genomes OnLine Database	5
CPMKG: a condition-based knowledge graph for precision medicine	5
Transformer-based approach for symptom recognition and multilingual linking	5
KinMod database: a tool for investigating metabolic regulation	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	5
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	5
scBrainMap: a landscape for cell types and associated genetic markers in the brain	5
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	5
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	5
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification	4
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation	4
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells	4
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	4
AgingReG: a curated database of aging regulatory relationships in humans	4
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	4
CancerPPD2: an updated repository of anticancer peptides and proteins	4
MantaID: a machine learning–based tool to automate the identification of biological database IDs	4
ImmuneData: an integrated data discovery system for immunology data repositories	4
Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains	4
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms	4
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	4
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	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
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants	4
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	4
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	4
A comprehensive experimental comparison between federated and centralized learning	4
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants	4
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease	4
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update	4
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	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
EfGD: the Erianthus fulvus genome database	4
MDDOmics: multi-omics resource of major depressive disorder	4
PDC: a highly compact file format to store protein 3D coordinates	4
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues	3
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes	3
Biomedical relation extraction with knowledge base–refined weak supervision	3

Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach	3
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration	3
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	3
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles	3
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	3
MACSFeD—a database of mosquito acoustic communication and swarming features	3
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics	3
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop	3
Notes on the data quality of bibliographic records from the MEDLINE database	3
OakRootRNADB—a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur)	3
Task reformulation and data-centric approach for Twitter medication name extraction	3
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies	3
Assessing the use of supplementary materials to improve genomic variant discovery	3
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?	3
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	3
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome	3
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture	3
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb	3
XePhIR: the zebrafish xenograft phenotype interactive repository	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
PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web	3
An open-access data set of pig skin anatomy and physiology for modelling purposes	3
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning	3
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape	3
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	3
Acinetobase: the comprehensive database and repository of Acinetobacter strains	3
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
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	2
Global Globin Network and adopting genomic variant database requirements for thalassemia	2
Full-text chemical identification with improved generalizability and tagging consistency	2
PlantGF: an analysis and annotation platform for plant gene families	2
nhanesA: achieving transparency and reproducibility in NHANES research	2
The Immunopeptidomics Ontology (ImPO)	2
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance	2
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database	2
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery	2
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	2
PlantIntronDB: a database for plant introns that host functional elements	2
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	2
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	2
A sequence labeling framework for extracting drug–protein relations from biomedical literature	2
LiqBioer: a manually curated database of cancer biomarkers in body fluid	2
CIGAF—a database and interactive platform for insect-associated trichomycete fungi	2
Best practices for the manual curation of intrinsically disordered proteins in DisProt	2
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen	2
VarGuideAtlas: a repository of variant interpretation guidelines	2
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank	2
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics	2
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond	2
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	2
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	2
Building a large gene expression-cancer knowledge base with limited human annotations	2
mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments	2
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	2
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data	2
BbGSD: Black-boned Sheep Genome SNP Database	2
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	2
AGODB: a comprehensive domain annotation database of argonaute proteins	2
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	2
DISPEL: database for ascertaining the best medicinal plants to cure human diseases	2
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	2
Automated annotation of scientific texts for ML-based keyphrase extraction and validation	2
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses	2
PlagueKD: a knowledge graph–based plague knowledge database	2
Assessing resource use: a case study with the Human Disease Ontology	2
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens	2
The landscape of health disparities in the UK Biobank	2
GMMID: genetically modified mice information database	2
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications	2
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures	2
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images	2
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market	2
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	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
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis	2
MyxoPortal: a database of myxobacterial genomic features	2
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions	2
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders	2
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications	2