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 2020-11-01 to 2024-11-01.)

Article	Citations
Post-translational modifications in proteins: resources, tools and prediction methods	405
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	105
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses	90
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	88
A review on antimicrobial peptides databases and the computational tools	60
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration	57
GrainGenes: a data-rich repository for small grains genetics and genomics	45
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	42
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images	40
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions	40
The World Spider Trait database: a centralized global open repository for curated data on spider traits	38
A Simple Standard for Sharing Ontological Mappings (SSSOM)	38
Curation of over 10 000 transcriptomic studies to enable data reuse	29
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	28
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans	28
An overview of graph databases and their applications in the biomedical domain	25
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	24
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	23
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery	23
A roadmap for the functional annotation of protein families: a community perspective	23
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	22
HPVMD-C: a disease-based mutation database of human papillomavirus in China	22
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations	21
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning	21
phytochemdb: a platform for virtual screening and computer-aided drug designing	20

HBFP: a new repository for human body fluid proteome	20
An update of KAIKObase, the silkworm genome database	19
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach	19
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins	18
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research	18
The Progenetix oncogenomic resource in 2021	17
COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome	16
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species	15
CANNUSE, a database of traditional Cannabis uses—an opportunity for new research	14
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations	14
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	14
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	14
NbThermo: a new thermostability database for nanobodies	13
CMBD: a manually curated cancer metabolic biomarker knowledge database	12
BCSCdb: a database of biomarkers of cancer stem cells	11
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition	11
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database	11
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	11
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data	11
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales	11
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature	11
The Breeding Information Management System (BIMS): an online resource for crop breeding	11
GeMI: interactive interface for transformer-based Genomic Metadata Integration	10
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	10
APICURON: a database to credit and acknowledge the work of biocurators	10
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	10
COTTONOMICS: a comprehensive cotton multi-omics database	9
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	9
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students	9
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses	9
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens	9
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	9
TIDB: a comprehensive database of trained immunity	9
emiRIT: a text-mining-based resource for microRNA information	9
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease	9
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	9
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings	8
Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces	8
Tripal MegaSearch: a tool for interactive and customizable query and download of big data	8
Integration of 1:1 orthology maps and updated datasets into Echinobase	8
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	7
PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters	7
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine	7
Extraction of causal relations based on SBEL and BERT model	7
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study	7
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis	7
mPPI: a database extension to visualize structural interactome in a one-to-many manner	7
Review of databases for experimentally validated human microRNA–mRNA interactions	7
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	7
GNIFdb: a neoantigen intrinsic feature database for glioma	7

scBrainMap: a landscape for cell types and associated genetic markers in the brain	6
PSINDB: the postsynaptic protein–protein interaction database	6
Bioinformatics tools developed to support BioCompute Objects	6
PlantGF: an analysis and annotation platform for plant gene families	6
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application	6
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	6
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in dat	6
SalivaDB—a comprehensive database for salivary biomarkers in humans	6
RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome	6
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID	6
Prototheca-ID: a web-based application for molecular identification of Prototheca species	6
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases	6
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences	6
Acinetobase: the comprehensive database and repository of Acinetobacter strains	5
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit	5
COVIDium: a COVID-19 resource compendium	5
New approaches in developing medicinal herbs databases	5
PolyQ Database—an integrated database on polyglutamine diseases	5
CPMCP: a database of Chinese patent medicine and compound prescription	5
Coronavirus Immunotherapeutic Consortium Database	5
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	5
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	5
Multi-omics molecular biomarkers and database of osteoarthritis	5
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	5
dbBIP: a comprehensive bipolar disorder database for genetic research	5
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer	5
Standardization of assay representation in the Ontology for Biomedical Investigations	5
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy	5