OOIR: Observatory of International Research

Papers

(The TQCC of Database-The Journal of Biological Databases and Curation is 6. 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 2022-01-01 to 2026-01-01.)

Article	Citations
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	181
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	110
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	108
Building resource-efficient community databases using open-source software	106
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	106
CCIDB: a manually curated cell–cell interaction database with cell context information	74
The importance of graph databases and graph learning for clinical applications	68
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	53
BioKC: a collaborative platform for curation and annotation of molecular interactions	49
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	47
Multi-omics molecular biomarkers and database of osteoarthritis	35
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	33
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	32
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	31
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	31
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	31
Integrated data-driven biotechnology research environments	30
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	28
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	27
Post-composing ontology terms for efficient phenotyping in plant breeding	27
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	27
DisGeNet: a disease-centric interaction database among diseases and various associated genes	26
A roadmap for the functional annotation of protein families: a community perspective	25
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	23
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	23

HOFE: an interactive forensic entomological database	22
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	21
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	20
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	20
New approaches in developing medicinal herbs databases	19
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	18
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	17
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	17
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	17
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	17
PheNormGPT: a framework for extraction and normalization of key medical findings	17
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	15
Localizatome: a database for stress-dependent subcellular localization changes in proteins	15
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	14
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	14
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	14
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	14
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	14
Interactive tools for functional annotation of bacterial genomes	14
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	13
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
Towards discovery: an end-to-end system for uncovering novel biomedical relations	13
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	12
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	12
Visualization and exploration of linked data using virtual reality	12
CardioHotspots: a database of mutational hotspots for cardiac disorders	12
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	11
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	11
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	11
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	11
PASS2: update of database of structure-based sequence alignments	11
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	11
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	10
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	10
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	10
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	10
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	10
PharmaKoVariome database for supporting genetic testing	10
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	10
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	10
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	10
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	9
Conference report: Biocuration 2021 Virtual Conference	9
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	9
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	9
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	8

Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	8
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	8
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	8
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	8
ImmRNA: a database of RNAs associated with tumor immunity	8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	8
MANUDB: database and application to retrieve and visualize mammalian NUMTs	8
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	7
LitCovid ensemble learning for COVID-19 multi-label classification	7
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	7
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	7
Pipeline to explore information on genome editing using large language models and genome editing meta-database	7
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	7
NbThermo: a new thermostability database for nanobodies	7
GeMI: interactive interface for transformer-based Genomic Metadata Integration	7
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	7
A review on antimicrobial peptides databases and the computational tools	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	7
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	7
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	7
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	7
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
BCSCdb: a database of biomarkers of cancer stem cells	6
CPMKG: a condition-based knowledge graph for precision medicine	6
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	6
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	6
The state of the human coding gene catalogues	6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	6
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities	6
Transformer-based approach for symptom recognition and multilingual linking	6
Standardized naming of microbiome samples in Genomes OnLine Database	6
ProbResist: a database for drug-resistant probiotic bacteria	6
Correction to: The importance of graph databases and graph learning for clinical applications	6
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	6
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	6
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	6
A review on Gene Ontology evaluations	6