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 2022-05-01 to 2026-05-01.)

Article	Citations
CCIDB: a manually curated cell–cell interaction database with cell context information	65
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	50
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	37
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	35
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	34
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	30
The importance of graph databases and graph learning for clinical applications	28
BioKC: a collaborative platform for curation and annotation of molecular interactions	27
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	25
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	24
Building resource-efficient community databases using open-source software	23
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	23
Post-composing ontology terms for efficient phenotyping in plant breeding	20
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	17
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training	16
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	16
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	16
Integrated data-driven biotechnology research environments	16
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	15
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	15
DisGeNet: a disease-centric interaction database among diseases and various associated genes	14
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	13
HOFE: an interactive forensic entomological database	13
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus	13
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	13

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	13
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	12
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer	12
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	12
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)	12
Interactive tools for functional annotation of bacterial genomes	12
New approaches in developing medicinal herbs databases	12
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	11
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	11
PheNormGPT: a framework for extraction and normalization of key medical findings	11
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	11
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	11
Localizatome: a database for stress-dependent subcellular localization changes in proteins	11
TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines	11
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	10
CardioHotspots: a database of mutational hotspots for cardiac disorders	10
Towards discovery: an end-to-end system for uncovering novel biomedical relations	10
Visualization and exploration of linked data using virtual reality	9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	9
PASS2: update of database of structure-based sequence alignments	9
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
scDrugAtlas: an integrative single-cell drug response database for dissecting tumour heterogeneity in therapeutic efficacy	8
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	7
CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, bioche	7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	7
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	7
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	7
neomerDB: a comprehensive database of neomer biomarkers in cancer	7
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	7
The Portuguese Beacon: sharing genomic variant data safely	6
MANUDB: database and application to retrieve and visualize mammalian NUMTs	6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
SynVectorDB: embedding-based retrieval system for synthetic biology parts	6
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	6
ImmRNA: a database of RNAs associated with tumor immunity	6
MOKCa-3D database: functional and structural analysis of missense mutations in cancer	6

Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
IsoProDB: an integrated map of human protein isoforms for accelerated research	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
CPMKG: a condition-based knowledge graph for precision medicine	5
The state of the human coding gene catalogues	5
NbThermo: a new thermostability database for nanobodies	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	5
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
Transformer-based approach for symptom recognition and multilingual linking	5