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 2022-08-01 to 2026-08-01.)

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	78
BioKC: a collaborative platform for curation and annotation of molecular interactions	53
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	46
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	40
Building resource-efficient community databases using open-source software	39
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	38
The importance of graph databases and graph learning for clinical applications	38
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	33
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	29
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	27
CCIDB: a manually curated cell–cell interaction database with cell context information	26
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	25
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	23
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	21
Post-composing ontology terms for efficient phenotyping in plant breeding	19
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	18
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	17
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	17
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training	17
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus	16
Integrated data-driven biotechnology research environments	16
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	16
HOFE: an interactive forensic entomological database	16
DisGeNet: a disease-centric interaction database among diseases and various associated genes	16
New approaches in developing medicinal herbs databases	15

ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	15
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)	14
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer	14
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	14
PheNormGPT: a framework for extraction and normalization of key medical findings	14
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	14
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	14
Towards discovery: an end-to-end system for uncovering novel biomedical relations	13
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	13
Interactive tools for functional annotation of bacterial genomes	13
TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines	13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	13
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	13
Localizatome: a database for stress-dependent subcellular localization changes in proteins	13
KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants	12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	12
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	12
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	12
PASS2: update of database of structure-based sequence alignments	11
Visualization and exploration of linked data using virtual reality	11
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	10
CardioHotspots: a database of mutational hotspots for cardiac disorders	10
scDrugAtlas: an integrative single-cell drug response database for dissecting tumour heterogeneity in therapeutic efficacy	9
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	9
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	9
CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, bioche	9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	9
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	9
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
TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol	8
MANUDB: database and application to retrieve and visualize mammalian NUMTs	8
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	8
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	8
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	8
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
OzButterflies – a high quality open database of multispectral images and spectra of tropical to temperate Australian butterflies	8
ImmRNA: a database of RNAs associated with tumor immunity	8
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
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
neomerDB: a comprehensive database of neomer biomarkers in cancer	8
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	8

Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	7
MOKCa-3D database: functional and structural analysis of missense mutations in cancer	7
NbThermo: a new thermostability database for nanobodies	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	7
SynVectorDB: embedding-based retrieval system for synthetic biology parts	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	6
The state of the human coding gene catalogues	6
Correction to: The importance of graph databases and graph learning for clinical applications	6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	6
IsoProDB: an integrated map of human protein isoforms for accelerated research	6
The Portuguese Beacon: sharing genomic variant data safely	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	6
IBDkb: an AI-enhanced integrative knowledge base for inflammatory bowel disease research and drug discovery	6