Database-The Journal of Biological Databases and Curation

Article	Citations
Post-translational modifications in proteins: resources, tools and prediction methods	278
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	78
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses	74
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	53
A review on antimicrobial peptides databases and the computational tools	37
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration	31
The World Spider Trait database: a centralized global open repository for curated data on spider traits	29
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions	27
A Simple Standard for Sharing Ontological Mappings (SSSOM)	25
GrainGenes: a data-rich repository for small grains genetics and genomics	24
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	23
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images	22
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	22
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans	21
An overview of graph databases and their applications in the biomedical domain	20
Curation of over 10 000 transcriptomic studies to enable data reuse	20
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning	19
HPVMD-C: a disease-based mutation database of human papillomavirus in China	18
An update of KAIKObase, the silkworm genome database	17
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	17
HBFP: a new repository for human body fluid proteome	16
COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome	16
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research	15
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	15
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations	14

SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery	14
The Progenetix oncogenomic resource in 2021	14
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach	14
A roadmap for the functional annotation of protein families: a community perspective	14
CANNUSE, a database of traditional Cannabis uses—an opportunity for new research	13
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	13
phytochemdb: a platform for virtual screening and computer-aided drug designing	13
PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins	12
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales	11
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition	11
The Breeding Information Management System (BIMS): an online resource for crop breeding	11
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins	10
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	10
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database	10
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	10
emiRIT: a text-mining-based resource for microRNA information	9
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data	9
APICURON: a database to credit and acknowledge the work of biocurators	9
CMBD: a manually curated cancer metabolic biomarker knowledge database	9
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	9
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species	8
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students	8
BCSCdb: a database of biomarkers of cancer stem cells	8
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease	8
Integration of 1:1 orthology maps and updated datasets into Echinobase	8
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature	8
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	8
COTTONOMICS: a comprehensive cotton multi-omics database	7
Tripal MegaSearch: a tool for interactive and customizable query and download of big data	7
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	7
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings	7
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	7
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	7
TIDB: a comprehensive database of trained immunity	7
Bioinformatics tools developed to support BioCompute Objects	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	6
COVIDium: a COVID-19 resource compendium	6
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses	6
Extraction of causal relations based on SBEL and BERT model	6
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases	6
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	6
mPPI: a database extension to visualize structural interactome in a one-to-many manner	6
EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature	6
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis	6
Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces	6
PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters	5
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer	5
Multi-omics molecular biomarkers and database of osteoarthritis	5
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	5
NbThermo: a new thermostability database for nanobodies	5

Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	5
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	5
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	5
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine	5
Standardization of assay representation in the Ontology for Biomedical Investigations	5
Prototheca-ID: a web-based application for molecular identification of Prototheca species	5
QSDB—a graphical Quorum Sensing Database	4
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens	4
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	4
A nomenclature for echinoderm genes	4
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID	4
DGPD: a knowledge database of dense granule proteins of the Apicomplexa	4
GNIFdb: a neoantigen intrinsic feature database for glioma	4
Coronavirus Immunotherapeutic Consortium Database	4
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	4
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	4
Classifying domain-specific text documents containing ambiguous keywords	4
dbBIP: a comprehensive bipolar disorder database for genetic research	4
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	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
New approaches in developing medicinal herbs databases	4
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1	4
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies	4
Acinetobase: the comprehensive database and repository of Acinetobacter strains	4
circExp database: an online transcriptome platform for human circRNA expressions in cancers	4
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials	4
LeishMANIAdb: a comparative resource for Leishmania proteins	3
A transcriptome atlas and interactive analysis platform for autoimmune disease	3
SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis	3
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects	3
EfGD: the Erianthus fulvus genome database	3
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	3
Standardized naming of microbiome samples in Genomes OnLine Database	3
OUP accepted manuscript	3
ProbResist: a database for drug-resistant probiotic bacteria	3
SalivaDB—a comprehensive database for salivary biomarkers in humans	3
Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization	3
PlantGF: an analysis and annotation platform for plant gene families	3
scBrainMap: a landscape for cell types and associated genetic markers in the brain	3
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	3
PSINDB: the postsynaptic protein–protein interaction database	3
Mining drug–target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships	3
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells	3
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	3
LiqBioer: a manually curated database of cancer biomarkers in body fluid	3
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy	3
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	2
ImmuneData: an integrated data discovery system for immunology data repositories	2
LitCovid ensemble learning for COVID-19 multi-label classification	2
Development of a biomarker database toward performing disease classification and finding disease interrelations	2
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	2
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	2
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	2
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations	2
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics	2
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	2
HCDT: an integrated highly confident drug–target resource	2
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	2
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII	2
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure	2
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	2
XePhIR: the zebrafish xenograft phenotype interactive repository	2
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator	2
A sequence labeling framework for extracting drug–protein relations from biomedical literature	2
Translational drug–interaction corpus	2
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis	2
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation	2
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms	2
Automatic Extraction of Medication Mentions from Tweets—Overview of the BioCreative VII Shared Task 3 Competition	2
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	2
dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins	2
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	2
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study	2
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications	2
Review of databases for experimentally validated human microRNA–mRNA interactions	2
HGFDB: a collective database of helmeted guinea fowl genomics	2
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	2
https://www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan	2
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	2

AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine	2
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	2
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences	2
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase	2
HumanMine: advanced data searching, analysis and cross-species comparison	2
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	2
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	2
HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae	2
CPMCP: a database of Chinese patent medicine and compound prescription	2
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	2
LINPS: a database for cancer-cell-specific perturbations of biological networks	2
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	2
BC-TFdb: a database of transcription factor drivers in breast cancer	2
CaviDB: a database of cavities and their features in the structural and conformational space of proteins	2