Database-The Journal of Biological Databases and Curation

Article	Citations
Post-translational modifications in proteins: resources, tools and prediction methods	405
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	105
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses	90
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	88
A review on antimicrobial peptides databases and the computational tools	60
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration	57
GrainGenes: a data-rich repository for small grains genetics and genomics	45
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	42
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions	40
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images	40
The World Spider Trait database: a centralized global open repository for curated data on spider traits	38
A Simple Standard for Sharing Ontological Mappings (SSSOM)	38
Curation of over 10 000 transcriptomic studies to enable data reuse	29
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	28
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans	28
An overview of graph databases and their applications in the biomedical domain	25
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	24
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	23
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery	23
A roadmap for the functional annotation of protein families: a community perspective	23
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	22
HPVMD-C: a disease-based mutation database of human papillomavirus in China	22
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning	21
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations	21
phytochemdb: a platform for virtual screening and computer-aided drug designing	20

HBFP: a new repository for human body fluid proteome	20
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach	19
An update of KAIKObase, the silkworm genome database	19
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research	18
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins	18
The Progenetix oncogenomic resource in 2021	17
COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome	16
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species	15
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations	14
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	14
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	14
CANNUSE, a database of traditional Cannabis uses—an opportunity for new research	14
NbThermo: a new thermostability database for nanobodies	13
CMBD: a manually curated cancer metabolic biomarker knowledge database	12
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database	11
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	11
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data	11
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales	11
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature	11
The Breeding Information Management System (BIMS): an online resource for crop breeding	11
BCSCdb: a database of biomarkers of cancer stem cells	11
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition	11
GeMI: interactive interface for transformer-based Genomic Metadata Integration	10
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	10
APICURON: a database to credit and acknowledge the work of biocurators	10
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	10
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students	9
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses	9
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens	9
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	9
TIDB: a comprehensive database of trained immunity	9
emiRIT: a text-mining-based resource for microRNA information	9
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease	9
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	9
COTTONOMICS: a comprehensive cotton multi-omics database	9
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	9
Tripal MegaSearch: a tool for interactive and customizable query and download of big data	8
Integration of 1:1 orthology maps and updated datasets into Echinobase	8
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings	8
Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces	8
Extraction of causal relations based on SBEL and BERT model	7
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	7
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis	7
mPPI: a database extension to visualize structural interactome in a one-to-many manner	7
Review of databases for experimentally validated human microRNA–mRNA interactions	7
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	7
GNIFdb: a neoantigen intrinsic feature database for glioma	7
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	7
PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters	7
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine	7

Bioinformatics tools developed to support BioCompute Objects	6
PlantGF: an analysis and annotation platform for plant gene families	6
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application	6
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	6
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in dat	6
SalivaDB—a comprehensive database for salivary biomarkers in humans	6
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	6
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID	6
Prototheca-ID: a web-based application for molecular identification of Prototheca species	6
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases	6
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	6
scBrainMap: a landscape for cell types and associated genetic markers in the brain	6
PSINDB: the postsynaptic protein–protein interaction database	6
Multi-omics molecular biomarkers and database of osteoarthritis	5
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	5
dbBIP: a comprehensive bipolar disorder database for genetic research	5
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer	5
Standardization of assay representation in the Ontology for Biomedical Investigations	5
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy	5
Acinetobase: the comprehensive database and repository of Acinetobacter strains	5
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit	5
COVIDium: a COVID-19 resource compendium	5
New approaches in developing medicinal herbs databases	5
PolyQ Database—an integrated database on polyglutamine diseases	5
CPMCP: a database of Chinese patent medicine and compound prescription	5
Coronavirus Immunotherapeutic Consortium Database	5
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	5
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	5
SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis	4
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	4
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase	4
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies	4
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	4
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	4
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	4
DGPD: a knowledge database of dense granule proteins of the Apicomplexa	4
JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types	4
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market	4
QSDB—a graphical Quorum Sensing Database	4
Automatic Extraction of Medication Mentions from Tweets—Overview of the BioCreative VII Shared Task 3 Competition	4
Classifying domain-specific text documents containing ambiguous keywords	4
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	4
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences	4
Standardized naming of microbiome samples in Genomes OnLine Database	4
A transcriptome atlas and interactive analysis platform for autoimmune disease	4
A nomenclature for echinoderm genes	4
ProbResist: a database for drug-resistant probiotic bacteria	4
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials	4
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India	4
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	4
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects	4
circExp database: an online transcriptome platform for human circRNA expressions in cancers	4
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	4
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	4
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1	4
Mining drug–target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships	4
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery	4
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions	3
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII	3
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification	3
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	3
EfGD: the Erianthus fulvus genome database	3
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	3
CropGF: a comprehensive visual platform for crop gene family mining and analysis	3
A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles	3
LeishMANIAdb: a comparative resource for Leishmania proteins	3
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis	3
ImmuneData: an integrated data discovery system for immunology data repositories	3
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	3
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells	3
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	3
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data	3
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	3
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	3
dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins	3
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics	3
XePhIR: the zebrafish xenograft phenotype interactive repository	3
A sequence labeling framework for extracting drug–protein relations from biomedical literature	3
Translational drug–interaction corpus	3
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	3

Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization	3
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	3
LiqBioer: a manually curated database of cancer biomarkers in body fluid	3
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses	3
BC-TFdb: a database of transcription factor drivers in breast cancer	3
nhanesA: achieving transparency and reproducibility in NHANES research	3
OUP accepted manuscript	3
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2	3
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data	2
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII	2
Large-scale regulatory and signaling network assembly through linked open data	2
LINPS: a database for cancer-cell-specific perturbations of biological networks	2
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants	2
Emati: a recommender system for biomedical literature based on supervised learning	2
An open-access data set of pig skin anatomy and physiology for modelling purposes	2
TEx-MST: tissue expression profiles of MANE select transcripts	2
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences	2
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications	2
MEDFORD: A human- and machine-readable metadata markup language	2
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	2
SC2sepsis: sepsis single-cell whole gene expression database	2
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature	2
HCDT: an integrated highly confident drug–target resource	2
Biomedical relation extraction with knowledge base–refined weak supervision	2
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	2
https://www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan	2
Notes on the data quality of bibliographic records from the MEDLINE database	2
CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole	2
HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae	2
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	2
LitCovid ensemble learning for COVID-19 multi-label classification	2
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish	2
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation	2
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure	2
Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes	2
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms	2
Assigning species information to corresponding genes by a sequence labeling framework	2
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	2
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study	2
SmartWoodID—an image collection of large end-grain surfaces to support wood identification systems	2
OUP accepted manuscript	2
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata	2
LBD: a manually curated database of experimentally validated lymphoma biomarkers	2
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	2
Development of a biomarker database toward performing disease classification and finding disease interrelations	2
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator	2
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	2
HGFDB: a collective database of helmeted guinea fowl genomics	2
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications	2
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	2
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	2
HumanMine: advanced data searching, analysis and cross-species comparison	2
CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database	2
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	2
An online database for einkorn wheat to aid in gene discovery and functional genomics studies	2