OOIR: Observatory of International Research

Papers

(The TQCC of Database-The Journal of Biological Databases and Curation is 4. 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 2021-04-01 to 2025-04-01.)

Article	Citations
athisomiRDB: A comprehensive database of Arabidopsis isomiRs	119
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps	115
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish	81
cancercelllines.org—a novel resource for genomic variants in cancer cell lines	70
Conference report: Biocuration 2021 Virtual Conference	64
LitSumm: large language models for literature summarization of noncoding RNAs	58
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	52
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images	48
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	46
Emati: a recommender system for biomedical literature based on supervised learning	35
HBFP: a new repository for human body fluid proteome	30
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development	29
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4	28
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics	26
Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is	24
Improved insights into the SABIO-RK database via visualization	24
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines	23
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV	23
aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation	22
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria	22
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization	19
PolyQ Database—an integrated database on polyglutamine diseases	18
Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases	17
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences	17
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals	17

Autophagy3D: a comprehensive autophagy structure database	17
Standardized naming of microbiome samples in Genomes OnLine Database	16
TEx-MST: tissue expression profiles of MANE select transcripts	15
Multi-omics molecular biomarkers and database of osteoarthritis	15
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants	13
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science	13
DRGKB: a knowledgebase of worldwide diagnosis-related groups’ practices for comparison, evaluation and knowledge-guided application	13
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses	12
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank	12
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer	12
Preproject ‘Swiss Virtual Natural History Collection’	12
Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach	11
HPVMD-C: a disease-based mutation database of human papillomavirus in China	11
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data	10
Best practices for the manual curation of intrinsically disordered proteins in DisProt	10
scBrainMap: a landscape for cell types and associated genetic markers in the brain	10
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata	10
TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques	10
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	9
The Immunopeptidomics Ontology (ImPO)	9
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium	9
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR	9
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research	9
CropGF: a comprehensive visual platform for crop gene family mining and analysis	8
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	8
BioKC: a collaborative platform for curation and annotation of molecular interactions	8
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome	8
SEPDB: a database of secreted proteins	8
Building resource-efficient community databases using open-source software	8
KinMod database: a tool for investigating metabolic regulation	8
The importance of graph databases and graph learning for clinical applications	8
GNIFdb: a neoantigen intrinsic feature database for glioma	8
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy	7
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	7
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	7
CCIDB: a manually curated cell–cell interaction database with cell context information	7
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	7
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence	7
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	7
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications	7
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules	6
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse	6
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity	6
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII	6
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature	6
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait	6
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update	6
Correction to: Standardized naming of microbiome samples in Genomes OnLine Database	6
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis	6
LiqBioer: a manually curated database of cancer biomarkers in body fluid	6

Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome	6
Is metadata of articles about COVID-19 enough for multilabel topic classification task?	6
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients	6
PurificationDB: database of purification conditions for proteins	6
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology	6
A roadmap for the functional annotation of protein families: a community perspective	6
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence	5
FGCD: a database of fungal gene clusters related to secondary metabolism	5
MyxoPortal: a database of myxobacterial genomic features	5
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures	5
AgingReG: a curated database of aging regulatory relationships in humans	5
A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources	5
Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific	5
Influenza sequence validation and annotation using VADR	5
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application	5
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish	5
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	5
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes	5
PlantIntronDB: a database for plant introns that host functional elements	5
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders	5
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants	4
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	4
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype	4
Post-composing ontology terms for efficient phenotyping in plant breeding	4
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID	4
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)	4
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	4
HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae	4
DisGeNet: a disease-centric interaction database among diseases and various associated genes	4
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data	4
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	4
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources	4
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy	4
New reasons for biologists to write with a formal language	4
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank	4
Working in biocuration: contemporary experiences and perspectives	4
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles	4
Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study	4
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements	4
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations	4