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 2021-09-01 to 2025-09-01.)

Article	Citations
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	151
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	140
Multi-omics molecular biomarkers and database of osteoarthritis	89
Building resource-efficient community databases using open-source software	88
The importance of graph databases and graph learning for clinical applications	85
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	85
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	63
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	56
CCIDB: a manually curated cell–cell interaction database with cell context information	53
BioKC: a collaborative platform for curation and annotation of molecular interactions	39
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	38
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	38
A roadmap for the functional annotation of protein families: a community perspective	28
DisGeNet: a disease-centric interaction database among diseases and various associated genes	28
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	27
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	27
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	26
Post-composing ontology terms for efficient phenotyping in plant breeding	26
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	26
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	25
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	25
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	21
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	21
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	21
COVIDium: a COVID-19 resource compendium	20

HOFE: an interactive forensic entomological database	19
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	19
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	18
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	17
New approaches in developing medicinal herbs databases	17
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	17
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	17
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	16
PheNormGPT: a framework for extraction and normalization of key medical findings	15
Localizatome: a database for stress-dependent subcellular localization changes in proteins	15
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	14
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	14
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	14
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	13
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	13
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	13
Interactive tools for functional annotation of bacterial genomes	13
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	12
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	12
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	12
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	12
Towards discovery: an end-to-end system for uncovering novel biomedical relations	12
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	11
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	11
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	11
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	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	10
PharmaKoVariome database for supporting genetic testing	10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
Visualization and exploration of linked data using virtual reality	9
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	9
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	9
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	9
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	9
CardioHotspots: a database of mutational hotspots for cardiac disorders	9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	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	8
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	8
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	8
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	8
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
Conference report: Biocuration 2021 Virtual Conference	8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	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
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	7
A review on antimicrobial peptides databases and the computational tools	7

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	7
ImmRNA: a database of RNAs associated with tumor immunity	7
GeMI: interactive interface for transformer-based Genomic Metadata Integration	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
MANUDB: database and application to retrieve and visualize mammalian NUMTs	7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	7
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	7
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	7
Classifying domain-specific text documents containing ambiguous keywords	7
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
LitCovid ensemble learning for COVID-19 multi-label classification	6
Correction to: The importance of graph databases and graph learning for clinical applications	6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	6
NbThermo: a new thermostability database for nanobodies	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
BCSCdb: a database of biomarkers of cancer stem cells	6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	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
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	6
The World Spider Trait database: a centralized global open repository for curated data on spider traits	6
ProbResist: a database for drug-resistant probiotic bacteria	6
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	6