Database-The Journal of Biological Databases and Curation

Papers
(The TQCC of Database-The Journal of Biological Databases and Curation is 5. 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 2021-07-01 to 2025-07-01.)
ArticleCitations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR136
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines133
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV86
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science83
The importance of graph databases and graph learning for clinical applications76
CCIDB: a manually curated cell–cell interaction database with cell context information73
BioKC: a collaborative platform for curation and annotation of molecular interactions59
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data54
Building resource-efficient community databases using open-source software51
Multi-omics molecular biomarkers and database of osteoarthritis38
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research37
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes36
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology28
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources27
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles27
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture26
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements26
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII25
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data24
Post-composing ontology terms for efficient phenotyping in plant breeding24
A roadmap for the functional annotation of protein families: a community perspective23
DisGeNet: a disease-centric interaction database among diseases and various associated genes20
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences20
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer19
New approaches in developing medicinal herbs databases19
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins18
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data17
HOFE: an interactive forensic entomological database17
COVIDium: a COVID-19 resource compendium16
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations16
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold15
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies14
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species14
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands13
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production13
PheNormGPT: a framework for extraction and normalization of key medical findings13
Interactive tools for functional annotation of bacterial genomes13
BCEDB: a linear B-cell epitopes database for SARS-CoV-212
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT12
Localizatome: a database for stress-dependent subcellular localization changes in proteins12
Towards discovery: an end-to-end system for uncovering novel biomedical relations12
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database11
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba11
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides11
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database11
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies11
CardioHotspots: a database of mutational hotspots for cardiac disorders10
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
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis10
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation10
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations9
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design9
StopKB: a comprehensive knowledgebase for nonsense suppression therapies9
Visualization and exploration of linked data using virtual reality9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine9
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues9
PharmaKoVariome database for supporting genetic testing9
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics8
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity8
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins8
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules7
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 immunity7
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 47
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence7
Conference report: Biocuration 2021 Virtual Conference7
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature7
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants6
MANUDB: database and application to retrieve and visualize mammalian NUMTs6
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome6
Pipeline to explore information on genome editing using large language models and genome editing meta-database6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology6
Classifying domain-specific text documents containing ambiguous keywords6
GeMI: interactive interface for transformer-based Genomic Metadata Integration6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models6
A review on antimicrobial peptides databases and the computational tools6
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms6
NbThermo: a new thermostability database for nanobodies5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation5
ForestForward: visualizing and accessing integrated world forest data from the last 50 years5
Transformer-based approach for symptom recognition and multilingual linking5
CPMKG: a condition-based knowledge graph for precision medicine5
Standardized naming of microbiome samples in Genomes OnLine Database5
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database5
BCSCdb: a database of biomarkers of cancer stem cells5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer5
LitCovid ensemble learning for COVID-19 multi-label classification5
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database5
Autophagy3D: a comprehensive autophagy structure database5
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data5
LitSumm: large language models for literature summarization of noncoding RNAs5
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase 5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders5
Correction to: The importance of graph databases and graph learning for clinical applications5
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms5
The World Spider Trait database: a centralized global open repository for curated data on spider traits5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives5
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria5
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images5
Emati: a recommender system for biomedical literature based on supervised learning5
cancercelllines.org—a novel resource for genomic variants in cancer cell lines5
ProbResist: a database for drug-resistant probiotic bacteria5
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