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 2021-11-01 to 2025-11-01.)

Article	Citations
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	169
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	101
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	100
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	99
CCIDB: a manually curated cell–cell interaction database with cell context information	95
BioKC: a collaborative platform for curation and annotation of molecular interactions	69
Building resource-efficient community databases using open-source software	62
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	47
The importance of graph databases and graph learning for clinical applications	44
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	42
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	32
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	30
Multi-omics molecular biomarkers and database of osteoarthritis	30
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	29
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	27
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	27
Post-composing ontology terms for efficient phenotyping in plant breeding	26
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	26
Integrated data-driven biotechnology research environments	25
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	24
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	23
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	23
DisGeNet: a disease-centric interaction database among diseases and various associated genes	22
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	21
A roadmap for the functional annotation of protein families: a community perspective	21

HOFE: an interactive forensic entomological database	20
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	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	19
New approaches in developing medicinal herbs databases	17
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	17
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	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
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	14
Interactive tools for functional annotation of bacterial genomes	14
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	14
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	13
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	13
Localizatome: a database for stress-dependent subcellular localization changes in proteins	13
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT	13
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	13
CobVar—a comprehensive resource of vitamin B12-associated genomic variants	13
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	12
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	12
Towards discovery: an end-to-end system for uncovering novel biomedical relations	12
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	12
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	11
Visualization and exploration of linked data using virtual reality	11
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	11
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	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
CardioHotspots: a database of mutational hotspots for cardiac disorders	10
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	10
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	10
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	10
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	10
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	10
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	10
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	10
PharmaKoVariome database for supporting genetic testing	10
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	9
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	9
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	9
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	9
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	9
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	8
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	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
Conference report: Biocuration 2021 Virtual Conference	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
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors	7

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	7
A review on antimicrobial peptides databases and the computational tools	7
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
MANUDB: database and application to retrieve and visualize mammalian NUMTs	7
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	7
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	7
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	7
ImmRNA: a database of RNAs associated with tumor immunity	7
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	7
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
LitCovid ensemble learning for COVID-19 multi-label classification	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	6
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	6
NbThermo: a new thermostability database for nanobodies	6
Correction to: The importance of graph databases and graph learning for clinical applications	6
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	6
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	5
The state of the human coding gene catalogues	5
Standardized naming of microbiome samples in Genomes OnLine Database	5
LitSumm: large language models for literature summarization of noncoding RNAs	5
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	5
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	5
Autophagy3D: a comprehensive autophagy structure database	5
Transformer-based approach for symptom recognition and multilingual linking	5
A review on Gene Ontology evaluations	5
ProbResist: a database for drug-resistant probiotic bacteria	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
scBrainMap: a landscape for cell types and associated genetic markers in the brain	5
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	5
Biomedical literature-based clinical phenotype definition discovery using large language models	5
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase	5
BCSCdb: a database of biomarkers of cancer stem cells	5
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	5
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	5
Emati: a recommender system for biomedical literature based on supervised learning	5
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	5
TEx-MST: tissue expression profiles of MANE select transcripts	5
HPVMD-C: a disease-based mutation database of human papillomavirus in China	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
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5