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 2020-05-01 to 2024-05-01.)

Article	Citations
Post-translational modifications in proteins: resources, tools and prediction methods	298
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies	81
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses	76
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation	60
A review on antimicrobial peptides databases and the computational tools	40
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration	35
The World Spider Trait database: a centralized global open repository for curated data on spider traits	30
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions	28
A Simple Standard for Sharing Ontological Mappings (SSSOM)	28
GrainGenes: a data-rich repository for small grains genetics and genomics	28
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species	26
An overview of graph databases and their applications in the biomedical domain	23
Curation of over 10 000 transcriptomic studies to enable data reuse	22
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images	22
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies	22
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans	22
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning	20
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses	18
HPVMD-C: a disease-based mutation database of human papillomavirus in China	18
An update of KAIKObase, the silkworm genome database	17
COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome	16
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins	16
A roadmap for the functional annotation of protein families: a community perspective	16
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery	16
HBFP: a new repository for human body fluid proteome	16

The Progenetix oncogenomic resource in 2021	15
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research	15
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach	15
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations	14
phytochemdb: a platform for virtual screening and computer-aided drug designing	14
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species	13
CANNUSE, a database of traditional Cannabis uses—an opportunity for new research	13
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins	13
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database	13
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins	12
PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins	12
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales	11
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition	11
The Breeding Information Management System (BIMS): an online resource for crop breeding	11
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database	10
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade	10
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba	9
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature	9
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease	9
APICURON: a database to credit and acknowledge the work of biocurators	9
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data	9
emiRIT: a text-mining-based resource for microRNA information	9
CMBD: a manually curated cancer metabolic biomarker knowledge database	9
Integration of 1:1 orthology maps and updated datasets into Echinobase	8
BCSCdb: a database of biomarkers of cancer stem cells	8
TIDB: a comprehensive database of trained immunity	8
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes	8
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students	8
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses	7
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings	7
Tripal MegaSearch: a tool for interactive and customizable query and download of big data	7
NbThermo: a new thermostability database for nanobodies	7
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research	7
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers	7
COTTONOMICS: a comprehensive cotton multi-omics database	7
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences	7
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species	7
mPPI: a database extension to visualize structural interactome in a one-to-many manner	6
GeMI: interactive interface for transformer-based Genomic Metadata Integration	6
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases	6
Bioinformatics tools developed to support BioCompute Objects	6
EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature	6
COVIDium: a COVID-19 resource compendium	6
Extraction of causal relations based on SBEL and BERT model	6
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis	6
Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces	6
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models	5
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine	5
New approaches in developing medicinal herbs databases	5
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs	5

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	5
PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters	5
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics	5
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data	5
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)	5
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation	5
Coronavirus Immunotherapeutic Consortium Database	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
Multi-omics molecular biomarkers and database of osteoarthritis	5
Prototheca-ID: a web-based application for molecular identification of Prototheca species	5