Database-The Journal of Biological Databases and Curation

Papers
(The TQCC of Database-The Journal of Biological Databases and Curation is 6. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-09-01 to 2025-09-01.)
ArticleCitations
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data151
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science140
Multi-omics molecular biomarkers and database of osteoarthritis89
Building resource-efficient community databases using open-source software88
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines85
The importance of graph databases and graph learning for clinical applications85
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR63
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV56
CCIDB: a manually curated cell–cell interaction database with cell context information53
BioKC: a collaborative platform for curation and annotation of molecular interactions39
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research38
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data38
A roadmap for the functional annotation of protein families: a community perspective28
DisGeNet: a disease-centric interaction database among diseases and various associated genes28
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture27
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes27
Post-composing ontology terms for efficient phenotyping in plant breeding26
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources26
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII26
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology25
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements25
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences21
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles21
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer21
COVIDium: a COVID-19 resource compendium20
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data19
HOFE: an interactive forensic entomological database19
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations18
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins17
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold17
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies17
New approaches in developing medicinal herbs databases17
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species16
Localizatome: a database for stress-dependent subcellular localization changes in proteins15
PheNormGPT: a framework for extraction and normalization of key medical findings15
BCEDB: a linear B-cell epitopes database for SARS-CoV-214
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands14
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production14
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis13
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides13
Interactive tools for functional annotation of bacterial genomes13
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database12
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database12
Towards discovery: an end-to-end system for uncovering novel biomedical relations12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT12
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies12
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues11
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine11
StopKB: a comprehensive knowledgebase for nonsense suppression therapies11
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations11
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII10
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins10
PharmaKoVariome database for supporting genetic testing10
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases9
CardioHotspots: a database of mutational hotspots for cardiac disorders9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity9
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank9
Visualization and exploration of linked data using virtual reality9
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics9
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata9
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation9
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling8
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity8
Conference report: Biocuration 2021 Virtual Conference8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 48
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)8
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps8
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines7
MANUDB: database and application to retrieve and visualize mammalian NUMTs7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters7
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology7
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants7
Classifying domain-specific text documents containing ambiguous keywords7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?7
A review on antimicrobial peptides databases and the computational tools7
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe7
ImmRNA: a database of RNAs associated with tumor immunity7
GeMI: interactive interface for transformer-based Genomic Metadata Integration7
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect6
Pipeline to explore information on genome editing using large language models and genome editing meta-database6
LitCovid ensemble learning for COVID-19 multi-label classification6
Correction to: The importance of graph databases and graph learning for clinical applications6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders6
NbThermo: a new thermostability database for nanobodies6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome6
BCSCdb: a database of biomarkers of cancer stem cells6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years6
The World Spider Trait database: a centralized global open repository for curated data on spider traits6
ProbResist: a database for drug-resistant probiotic bacteria6
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database6
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