Database-The Journal of Biological Databases and Curation

Article	Citations
athisomiRDB: A comprehensive database of Arabidopsis isomiRs	119
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	115
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish	81
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	70
Conference report: Biocuration 2021 Virtual Conference	64
LitSumm: large language models for literature summarization of noncoding RNAs	58
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	52
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	48
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	46
Emati: a recommender system for biomedical literature based on supervised learning	35
HBFP: a new repository for human body fluid proteome	30
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development	29
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	28
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	26
Improved insights into the SABIO-RK database via visualization	24
Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is	24
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	23
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	23
aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation	22
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	22
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	19
PolyQ Database—an integrated database on polyglutamine diseases	18
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences	17
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals	17
Autophagy3D: a comprehensive autophagy structure database	17

Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	17
Standardized naming of microbiome samples in Genomes OnLine Database	16
Multi-omics molecular biomarkers and database of osteoarthritis	15
TEx-MST: tissue expression profiles of MANE select transcripts	15
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	13
DRGKB: a knowledgebase of worldwide diagnosis-related groups’ practices for comparison, evaluation and knowledge-guided application	13
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	13
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	12
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	12
Preproject ‘Swiss Virtual Natural History Collection’	12
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses	12
HPVMD-C: a disease-based mutation database of human papillomavirus in China	11
Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach	11
Best practices for the manual curation of intrinsically disordered proteins in DisProt	10
scBrainMap: a landscape for cell types and associated genetic markers in the brain	10
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	10
TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques	10
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	10
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	9
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	9
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	9
The Immunopeptidomics Ontology (ImPO)	9
CropGF: a comprehensive visual platform for crop gene family mining and analysis	8
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	8
BioKC: a collaborative platform for curation and annotation of molecular interactions	8
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	8
SEPDB: a database of secreted proteins	8
Building resource-efficient community databases using open-source software	8
KinMod database: a tool for investigating metabolic regulation	8
The importance of graph databases and graph learning for clinical applications	8
GNIFdb: a neoantigen intrinsic feature database for glioma	8
CCIDB: a manually curated cell–cell interaction database with cell context information	7
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	7
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	7
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	7
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications	7
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy	7
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	7
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	7
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	6
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update	6
Correction to: Standardized naming of microbiome samples in Genomes OnLine Database	6
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis	6
LiqBioer: a manually curated database of cancer biomarkers in body fluid	6
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome	6
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	6
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	6
PurificationDB: database of purification conditions for proteins	6
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	6

A roadmap for the functional annotation of protein families: a community perspective	6
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	6
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	6
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	6
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	6
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature	6
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures	5
AgingReG: a curated database of aging regulatory relationships in humans	5
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish	5
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	5
Influenza sequence validation and annotation using VADR	5
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application	5
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	5
FGCD: a database of fungal gene clusters related to secondary metabolism	5
MyxoPortal: a database of myxobacterial genomic features	5
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	5
PlantIntronDB: a database for plant introns that host functional elements	5
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders	5
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	5
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	5
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy	4
New reasons for biologists to write with a formal language	4
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank	4
Working in biocuration: contemporary experiences and perspectives	4
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	4
Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	4
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	4
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	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
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	4
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	4
Post-composing ontology terms for efficient phenotyping in plant breeding	4
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID	4
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	4
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	4
HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae	4
DisGeNet: a disease-centric interaction database among diseases and various associated genes	4
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	4
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	4
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	4
MantaID: a machine learning–based tool to automate the identification of biological database IDs	3
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	3
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature	3
RegEl corpus: identifying DNA regulatory elements in the scientific literature	3
HOFE: an interactive forensic entomological database	3
EfGD: the Erianthus fulvus genome database	3
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	3
iCAZyGFADB: an insect CAZyme and gene function annotation database	3
WASP: the World Archives of Species Perception	3
Classifying domain-specific text documents containing ambiguous keywords	3
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens	3
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms	3
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data	3
A Simple Standard for Sharing Ontological Mappings (SSSOM)	3
HumanMine: advanced data searching, analysis and cross-species comparison	3
MEDFORD: A human- and machine-readable metadata markup language	3
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease	3
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases	3
Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes	3
LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases	3
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification	3
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data	3
COVIDium: a COVID-19 resource compendium	3
Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains	3
GrainGenes: a data-rich repository for small grains genetics and genomics	3
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	3
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations	3
PDC: a highly compact file format to store protein 3D coordinates	3
GMMID: genetically modified mice information database	3
Recognition and normalization of multilingual symptom entities using in-domain-adapted BERT models and classification layers	3
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications	3
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India	3
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	3
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes	3
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	3
Global Globin Network and adopting genomic variant database requirements for thalassemia	2
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	2
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	2
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	2
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations	2

TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes	2
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank	2
MANUDB: database and application to retrieve and visualize mammalian NUMTs	2
A terpenoids database with the chemical content as a novel agronomic trait	2
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	2
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	2
A change language for ontologies and knowledge graphs	2
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond	2
PlagueKD: a knowledge graph–based plague knowledge database	2
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	2
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	2
Correction to: SEPDB: a database of secreted proteins	2
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	2
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen	2
Automated annotation of scientific texts for ML-based keyphrase extraction and validation	2
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides	2
A comprehensive experimental comparison between federated and centralized learning	2
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	2
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase	2
PlantGF: an analysis and annotation platform for plant gene families	2
Automatic Extraction of Medication Mentions from Tweets—Overview of the BioCreative VII Shared Task 3 Competition	2
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation	2
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	2
SC2sepsis: sepsis single-cell whole gene expression database	2
A review on antimicrobial peptides databases and the computational tools	2
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation	2
BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis	2
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis	2
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress	2
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells	2
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	2
ImmRNA: a database of RNAs associated with tumor immunity	2
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling	2
New approaches in developing medicinal herbs databases	2
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance	2
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning	1
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market	1
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials	1
ImmuneData: an integrated data discovery system for immunology data repositories	1
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species	1
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles	1
ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database	1
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	1
Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	1
CIGAF—a database and interactive platform for insect-associated trichomycete fungi	1
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions	1
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	1
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery	1
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)	1
AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein	1
DAPredict: a database for drug action phenotype prediction	1
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	1
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	1
PheNormGPT: a framework for extraction and normalization of key medical findings	1
Translational drug–interaction corpus	1
The World Spider Trait database: a centralized global open repository for curated data on spider traits	1
collectNET: a web server for integrated inference of cell–cell communication network	1
Pipeline to explore information on genome editing using large language models and genome editing meta-database	1
MDDOmics: multi-omics resource of major depressive disorder	1
PMBC: a manually curated database for prognostic markers of breast cancer	1
NbThermo: a new thermostability database for nanobodies	1
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII	1
Correction to: RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	1
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	1
Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization	1
Assessing the use of supplementary materials to improve genomic variant discovery	1
COTTONOMICS: a comprehensive cotton multi-omics database	1
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain	1
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications	1
TumorAgDB1.0: tumor neoantigen database platform	1
LitCovid ensemble learning for COVID-19 multi-label classification	1
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	1
SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis	1
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis	1
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	1
DISPEL: database for ascertaining the best medicinal plants to cure human diseases	1
A sequence labeling framework for extracting drug–protein relations from biomedical literature	1
AGODB: a comprehensive domain annotation database of argonaute proteins	1
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants	1
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	1
GeMI: interactive interface for transformer-based Genomic Metadata Integration	1
Interactive tools for functional annotation of bacterial genomes	1
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	1
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	1
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	1
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings	1
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	1
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	1
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome	1
The MetaGens algorithm for metagenomic database lossy compression and subject alignment	1
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification	1