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 2022-06-01 to 2026-06-01.)

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	70
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	51
BioKC: a collaborative platform for curation and annotation of molecular interactions	40
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	36
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	36
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	32
The importance of graph databases and graph learning for clinical applications	32
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	32
Building resource-efficient community databases using open-source software	27
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	25
CCIDB: a manually curated cell–cell interaction database with cell context information	23
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	23
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	20
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	18
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	17
Integrated data-driven biotechnology research environments	17
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training	17
Post-composing ontology terms for efficient phenotyping in plant breeding	16
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	16
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	16
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	14
An approach to making life sciences FAIR—FAIR-DS as a tool for Aspergillus fumigatus	13
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)	13
New approaches in developing medicinal herbs databases	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
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer	13
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	13
HOFE: an interactive forensic entomological database	13
Localizatome: a database for stress-dependent subcellular localization changes in proteins	12
Interactive tools for functional annotation of bacterial genomes	12
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	12
PheNormGPT: a framework for extraction and normalization of key medical findings	12
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	12
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	11
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	11
TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines	11
Towards discovery: an end-to-end system for uncovering novel biomedical relations	11
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	11
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	10
Visualization and exploration of linked data using virtual reality	10
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	10
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	10
PASS2: update of database of structure-based sequence alignments	10
CardioHotspots: a database of mutational hotspots for cardiac disorders	9
scDrugAtlas: an integrative single-cell drug response database for dissecting tumour heterogeneity in therapeutic efficacy	9
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	9
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	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	8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	8
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	8
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	8
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
neomerDB: a comprehensive database of neomer biomarkers in cancer	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	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
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	7
MANUDB: database and application to retrieve and visualize mammalian NUMTs	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
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	7
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	7
MOKCa-3D database: functional and structural analysis of missense mutations in cancer	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
SynVectorDB: embedding-based retrieval system for synthetic biology parts	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
ImmRNA: a database of RNAs associated with tumor immunity	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
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
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	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
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
NbThermo: a new thermostability database for nanobodies	5
CPMKG: a condition-based knowledge graph for precision medicine	5
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	5
A review on Gene Ontology evaluations	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
Transformer-based approach for symptom recognition and multilingual linking	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	5
FAD: a comprehensive database merging information about food allergens	5
The state of the human coding gene catalogues	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
Mapping of EFO terms from the GWAS catalog data to multiple ontologies at the Rat Genome Database	5
IsoProDB: an integrated map of human protein isoforms for accelerated research	5