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 2021-12-01 to 2025-12-01.)

Article	Citations
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	173
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	106
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	105
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	104
Building resource-efficient community databases using open-source software	103
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	72
CCIDB: a manually curated cell–cell interaction database with cell context information	64
Multi-omics molecular biomarkers and database of osteoarthritis	49
The importance of graph databases and graph learning for clinical applications	45
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	45
Empirical substitution models of protein evolution: database, relationships, and modeling considerations	32
BioKC: a collaborative platform for curation and annotation of molecular interactions	31
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	30
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	30
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	30
Post-composing ontology terms for efficient phenotyping in plant breeding	29
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	28
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	27
Integrated data-driven biotechnology research environments	27
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	26
A roadmap for the functional annotation of protein families: a community perspective	25
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	25
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	24
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	23
DisGeNet: a disease-centric interaction database among diseases and various associated genes	22

HOFE: an interactive forensic entomological database	21
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	20
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	20
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	19
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	19
New approaches in developing medicinal herbs databases	17
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	17
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	17
PheNormGPT: a framework for extraction and normalization of key medical findings	16
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	15
Interactive tools for functional annotation of bacterial genomes	14
Localizatome: a database for stress-dependent subcellular localization changes in proteins	14
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production	14
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	14
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini	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
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	13
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	13
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database	13
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	13
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	12
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	12
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	12
PharmaKoVariome database for supporting genetic testing	12
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	11
CardioHotspots: a database of mutational hotspots for cardiac disorders	11
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	11
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	11
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	10
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	10
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	10
Visualization and exploration of linked data using virtual reality	10
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	10
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	10
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
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	10
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	10
PASS2: update of database of structure-based sequence alignments	10
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	9
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	9
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	9
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	9
Conference report: Biocuration 2021 Virtual Conference	9
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
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
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens	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
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	8
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	7
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity	7
LitCovid ensemble learning for COVID-19 multi-label classification	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	7
A review on antimicrobial peptides databases and the computational tools	7
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	7
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	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
Automated extraction of genes associated with antibiotic resistance from the biomedical literature	7
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	7
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	7
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	7
ImmRNA: a database of RNAs associated with tumor immunity	7
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	7
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	6
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	6
ProbResist: a database for drug-resistant probiotic bacteria	6
PLoV: a comprehensive database of genetic variants leading to pregnancy loss	6
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond	6
Pipeline to explore information on genome editing using large language models and genome editing meta-database	6
NbThermo: a new thermostability database for nanobodies	6
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	6
The state of the human coding gene catalogues	6
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	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
Correction to: The importance of graph databases and graph learning for clinical applications	6
BCSCdb: a database of biomarkers of cancer stem cells	6
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	6