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 2021-08-01 to 2025-08-01.)
ArticleCitations
Multi-omics molecular biomarkers and database of osteoarthritis144
Building resource-efficient community databases using open-source software137
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research87
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science87
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data80
BioKC: a collaborative platform for curation and annotation of molecular interactions78
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR61
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV55
CCIDB: a manually curated cell–cell interaction database with cell context information52
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines38
The importance of graph databases and graph learning for clinical applications38
A roadmap for the functional annotation of protein families: a community perspective37
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes29
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture28
DisGeNet: a disease-centric interaction database among diseases and various associated genes27
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data26
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII26
Post-composing ontology terms for efficient phenotyping in plant breeding26
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources25
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology24
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements23
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles21
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data20
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences20
HOFE: an interactive forensic entomological database19
COVIDium: a COVID-19 resource compendium19
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer18
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins18
New approaches in developing medicinal herbs databases17
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations17
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold16
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species16
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies15
Localizatome: a database for stress-dependent subcellular localization changes in proteins15
Interactive tools for functional annotation of bacterial genomes15
PheNormGPT: a framework for extraction and normalization of key medical findings14
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 production13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis13
BCEDB: a linear B-cell epitopes database for SARS-CoV-213
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database12
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT12
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini12
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies11
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation11
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database11
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine11
Towards discovery: an end-to-end system for uncovering novel biomedical relations11
PharmaKoVariome database for supporting genetic testing10
StopKB: a comprehensive knowledgebase for nonsense suppression therapies10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes10
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII10
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues10
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases9
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins9
Conference report: Biocuration 2021 Virtual Conference9
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity9
CardioHotspots: a database of mutational hotspots for cardiac disorders9
Visualization and exploration of linked data using virtual reality9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium8
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific8
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling8
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps8
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 48
Is metadata of articles about COVID-19 enough for multilabel topic classification task?8
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines7
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
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature7
Classifying domain-specific text documents containing ambiguous keywords7
MANUDB: database and application to retrieve and visualize mammalian NUMTs7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology7
LitCovid ensemble learning for COVID-19 multi-label classification6
GeMI: interactive interface for transformer-based Genomic Metadata Integration6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms6
NbThermo: a new thermostability database for nanobodies6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years6
Pipeline to explore information on genome editing using large language models and genome editing meta-database6
ImmRNA: a database of RNAs associated with tumor immunity6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond6
The World Spider Trait database: a centralized global open repository for curated data on spider traits6
ProbResist: a database for drug-resistant probiotic bacteria5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders5
Autophagy3D: a comprehensive autophagy structure database5
cancercelllines.org—a novel resource for genomic variants in cancer cell lines5
Emati: a recommender system for biomedical literature based on supervised learning5
Standardized naming of microbiome samples in Genomes OnLine Database5
CPMKG: a condition-based knowledge graph for precision medicine5
Transformer-based approach for symptom recognition and multilingual linking5
KinMod database: a tool for investigating metabolic regulation5
Correction to: The importance of graph databases and graph learning for clinical applications5
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria5
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data5
scBrainMap: a landscape for cell types and associated genetic markers in the brain5
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer5
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins5
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 Database5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database5
BCSCdb: a database of biomarkers of cancer stem cells5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation5
HPVMD-C: a disease-based mutation database of human papillomavirus in China5
TEx-MST: tissue expression profiles of MANE select transcripts5
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study5
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives5
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