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 2021-05-01 to 2025-05-01.)

Article	Citations
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	124
The importance of graph databases and graph learning for clinical applications	124
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	86
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	73
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	68
Building resource-efficient community databases using open-source software	63
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data	53
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	50
BioKC: a collaborative platform for curation and annotation of molecular interactions	48
CCIDB: a manually curated cell–cell interaction database with cell context information	36
Multi-omics molecular biomarkers and database of osteoarthritis	33
A roadmap for the functional annotation of protein families: a community perspective	33
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	29
Post-composing ontology terms for efficient phenotyping in plant breeding	26
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	25
DisGeNet: a disease-centric interaction database among diseases and various associated genes	25
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	24
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	23
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	22
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	22
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	21
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	19
New approaches in developing medicinal herbs databases	19
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture	19
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data	17

ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer	17
COVIDium: a COVID-19 resource compendium	16
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations	16
HOFE: an interactive forensic entomological database	16
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins	15
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold	15
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	13
Interactive tools for functional annotation of bacterial genomes	13
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	13
BCEDB: a linear B-cell epitopes database for SARS-CoV-2	13
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands	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
Localizatome: a database for stress-dependent subcellular localization changes in proteins	11
Towards discovery: an end-to-end system for uncovering novel biomedical relations	11
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis	10
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database	10
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides	9
PharmaKoVariome database for supporting genetic testing	9
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	9
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	9
StopKB: a comprehensive knowledgebase for nonsense suppression therapies	9
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	9
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes	9
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine	8
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations	8
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
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	8
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues	8
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	8
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	8
Visualization and exploration of linked data using virtual reality	8
CardioHotspots: a database of mutational hotspots for cardiac disorders	8
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design	8
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	8
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	8
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	8
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	7
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	7
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	7
Conference report: Biocuration 2021 Virtual Conference	7
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	7
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	7
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling	7
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	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

Automated extraction of genes associated with antibiotic resistance from the biomedical literature	6
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines	6
A review on antimicrobial peptides databases and the computational tools	6
NbThermo: a new thermostability database for nanobodies	6
Classifying domain-specific text documents containing ambiguous keywords	6
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters	6
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants	6
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome	6
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology	6
ImmRNA: a database of RNAs associated with tumor immunity	6
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe	6
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect	6
MANUDB: database and application to retrieve and visualize mammalian NUMTs	6
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms	5
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms	5
BCSCdb: a database of biomarkers of cancer stem cells	5
CPMKG: a condition-based knowledge graph for precision medicine	5
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer	5
The World Spider Trait database: a centralized global open repository for curated data on spider traits	5
ProbResist: a database for drug-resistant probiotic bacteria	5
ForestForward: visualizing and accessing integrated world forest data from the last 50 years	5
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database	5
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	5
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives	5
GeMI: interactive interface for transformer-based Genomic Metadata Integration	5
LitCovid ensemble learning for COVID-19 multi-label classification	5
BENviewer: a gene interaction network visualization server based on graph embedding model	5
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders	5
Transformer-based approach for symptom recognition and multilingual linking	5
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database	5
Correction to: The importance of graph databases and graph learning for clinical applications	5
Pipeline to explore information on genome editing using large language models and genome editing meta-database	5