OOIR: Observatory of International Research

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 2021-06-01 to 2025-06-01.)

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	131
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	130
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	86
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	78
BioKC: a collaborative platform for curation and annotation of molecular interactions	71
CCIDB: a manually curated cell–cell interaction database with cell context information	70
Multi-omics molecular biomarkers and database of osteoarthritis	57
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	54
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	49
The importance of graph databases and graph learning for clinical applications	38
Building resource-efficient community databases using open-source software	35
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	34
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	29
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	26
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	26
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	25
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	25
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	25
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	23
A roadmap for the functional annotation of protein families: a community perspective	23
DisGeNet: a disease-centric interaction database among diseases and various associated genes	22
Post-composing ontology terms for efficient phenotyping in plant breeding	22
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	19
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	19
New approaches in developing medicinal herbs databases	19

DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	19
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	18
HOFE: an interactive forensic entomological database	17
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	16
COVIDium: a COVID-19 resource compendium	16
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	14
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	13
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	13
Interactive tools for functional annotation of bacterial genomes	13
PheNormGPT: a framework for extraction and normalization of key medical findings	12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	12
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	12
Localizatome: a database for stress-dependent subcellular localization changes in proteins	12
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	12
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	11
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	11
Towards discovery: an end-to-end system for uncovering novel biomedical relations	11
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	10
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	10
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	10
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	10
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	10
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	9
PharmaKoVariome database for supporting genetic testing	9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	9
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	9
CardioHotspots: a database of mutational hotspots for cardiac disorders	9
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	9
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	9
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
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	8
Visualization and exploration of linked data using virtual reality	8
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	8
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	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	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	7
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	7
Conference report: Biocuration 2021 Virtual Conference	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	7
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	6

Classifying domain-specific text documents containing ambiguous keywords	6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	6
ImmRNA: a database of RNAs associated with tumor immunity	6
A review on antimicrobial peptides databases and the computational tools	6
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	6
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	6
MANUDB: database and application to retrieve and visualize mammalian NUMTs	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
The World Spider Trait database: a centralized global open repository for curated data on spider traits	5
NbThermo: a new thermostability database for nanobodies	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	5
CPMKG: a condition-based knowledge graph for precision medicine	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
ProbResist: a database for drug-resistant probiotic bacteria	5
GeMI: interactive interface for transformer-based Genomic Metadata Integration	5
Pipeline to explore information on genome editing using large language models and genome editing meta-database	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
LitCovid ensemble learning for COVID-19 multi-label classification	5
Standardized naming of microbiome samples in Genomes OnLine Database	5
mPPI: a database extension to visualize structural interactome in a one-to-many manner	5
Transformer-based approach for symptom recognition and multilingual linking	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	5
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	5
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	5
BCSCdb: a database of biomarkers of cancer stem cells	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	5
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	5