Database-The Journal of Biological Databases and Curation

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	124
The importance of graph databases and graph learning for clinical applications	124
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	86
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	73
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	68
Building resource-efficient community databases using open-source software	63
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	53
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	50
BioKC: a collaborative platform for curation and annotation of molecular interactions	48
CCIDB: a manually curated cell–cell interaction database with cell context information	36
Multi-omics molecular biomarkers and database of osteoarthritis	33
A roadmap for the functional annotation of protein families: a community perspective	33
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	29
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	25
DisGeNet: a disease-centric interaction database among diseases and various associated genes	25
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	24
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	23
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	22
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	22
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	21
New approaches in developing medicinal herbs databases	19
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	19
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	19
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	17

SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	17
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	16
HOFE: an interactive forensic entomological database	16
COVIDium: a COVID-19 resource compendium	16
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	15
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	15
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	13
Interactive tools for functional annotation of bacterial genomes	13
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	13
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	13
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	12
PheNormGPT: a framework for extraction and normalization of key medical findings	12
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	11
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	11
Localizatome: a database for stress-dependent subcellular localization changes in proteins	11
Towards discovery: an end-to-end system for uncovering novel biomedical relations	11
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	10
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	10
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	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
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	9
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	9
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	9
PharmaKoVariome database for supporting genetic testing	9
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	8
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	8
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	8
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
Visualization and exploration of linked data using virtual reality	8
CardioHotspots: a database of mutational hotspots for cardiac disorders	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	8
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	8
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	8
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	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	7
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	7
Conference report: Biocuration 2021 Virtual Conference	7
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 Pacific	7
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	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

Classifying domain-specific text documents containing ambiguous keywords	6
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	6
ImmRNA: a database of RNAs associated with tumor immunity	6
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
MANUDB: database and application to retrieve and visualize mammalian NUMTs	6
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
A review on antimicrobial peptides databases and the computational tools	6
NbThermo: a new thermostability database for nanobodies	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	5
LitCovid ensemble learning for COVID-19 multi-label classification	5
BENviewer: a gene interaction network visualization server based on graph embedding model	5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5
Transformer-based approach for symptom recognition and multilingual linking	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
Pipeline to explore information on genome editing using large language models and genome editing meta-database	5
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	5
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	5
BCSCdb: a database of biomarkers of cancer stem cells	5
CPMKG: a condition-based knowledge graph for precision medicine	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
The World Spider Trait database: a centralized global open repository for curated data on spider traits	5
ProbResist: a database for drug-resistant probiotic bacteria	5
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
Autophagy3D: a comprehensive autophagy structure database	4
Standardized naming of microbiome samples in Genomes OnLine Database	4
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	4
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	4
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	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
scBrainMap: a landscape for cell types and associated genetic markers in the brain	4
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	4
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	4
mPPI: a database extension to visualize structural interactome in a one-to-many manner	4
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	4
Emati: a recommender system for biomedical literature based on supervised learning	4
AgingReG: a curated database of aging regulatory relationships in humans	4
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	4
TEx-MST: tissue expression profiles of MANE select transcripts	4
HPVMD-C: a disease-based mutation database of human papillomavirus in China	4
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	4
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	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
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	4
KinMod database: a tool for investigating metabolic regulation	4
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles	3
Assessing the use of supplementary materials to improve genomic variant discovery	3
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants	3
EfGD: the Erianthus fulvus genome database	3
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells	3
Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains	3
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature	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
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
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?	3
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials	3
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	3
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms	3
MantaID: a machine learning–based tool to automate the identification of biological database IDs	3
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	3
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants	3
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification	3
ImmuneData: an integrated data discovery system for immunology data repositories	3
An open-access data set of pig skin anatomy and physiology for modelling purposes	3
MDDOmics: multi-omics resource of major depressive disorder	3
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	3
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	3
PDC: a highly compact file format to store protein 3D coordinates	3

IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease	3
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	3
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank	3
A comprehensive experimental comparison between federated and centralized learning	3
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	3
OakRootRNADB—a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur)	3
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies	3
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics	2
Best practices for the manual curation of intrinsically disordered proteins in DisProt	2
Notes on the data quality of bibliographic records from the MEDLINE database	2
VarGuideAtlas: a repository of variant interpretation guidelines	2
MineProt: a stand-alone server for structural proteome curation	2
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	2
MACSFeD—a database of mosquito acoustic communication and swarming features	2
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape	2
The landscape of health disparities in the UK Biobank	2
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	2
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	2
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	2
Assessing resource use: a case study with the Human Disease Ontology	2
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop	2
The Immunopeptidomics Ontology (ImPO)	2
Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes	2
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics	2
emiRIT: a text-mining-based resource for microRNA information	2
Biomedical relation extraction with knowledge base–refined weak supervision	2
Acinetobase: the comprehensive database and repository of Acinetobacter strains	2
MyxoPortal: a database of myxobacterial genomic features	2
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome	2
PlantIntronDB: a database for plant introns that host functional elements	2
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses	2
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	2
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	2
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	2
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture	2
nhanesA: achieving transparency and reproducibility in NHANES research	2
Task reformulation and data-centric approach for Twitter medication name extraction	2
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues	2
PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web	2
XePhIR: the zebrafish xenograft phenotype interactive repository	2
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes	2
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb	2
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	2
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	2
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	2
Full-text chemical identification with improved generalizability and tagging consistency	2