-
Article
Open AccessEmpowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis
The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. The heterogeneity of cancer vaccine data significantly impedes effective integration and...
-
Article
Open AccessOntological representation, modeling, and analysis of parasite vaccines
Pathogenic parasites are responsible for multiple diseases, such as malaria and Chagas disease, in humans and livestock. Traditionally, pathogenic parasites have been largely an evasive topic for vaccine desig...
-
Article
Killing tumor-associated bacteria with a liposomal antibiotic generates neoantigens that induce anti-tumor immune responses
Increasing evidence implicates the tumor microbiota as a factor that can influence cancer progression. In patients with colorectal cancer (CRC), we found that pre-resection antibiotics targeting anaerobic bact...
-
Article
Open AccessBig knowledge visualization of the COVID-19 CIDO ontology evolution
The extensive international research for medications and vaccines for the devastating COVID-19 pandemic requires a standard reference ontology. Among the current COVID-19 ontologies, the Coronavirus Infectious...
-
Article
Open AccessA comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of develo** effective and saf...
-
Article
Open AccessIdentification of missing hierarchical relations in the vaccine ontology using acquired term pairs
The Vaccine Ontology (VO) is a biomedical ontology that standardizes vaccine annotation. Errors in VO will affect a multitude of applications that it is being used in. Quality assurance of VO is imperative to ...
-
Article
Open AccessICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
Bacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand an...
-
Protocol
Development and Applications of Interoperable Biomedical Ontologies for Integrative Data and Knowledge Representation and Multiscale Modeling in Systems Medicine
The data FAIR Guiding Principles state that all data should be Findable, Accessible, Interoperable, and Reusable. Ontology is critical to data integration, sharing, and analysis. Given thousands of ontologies ...
-
Protocol
Vaccine Design by Reverse Vaccinology and Machine Learning
Reverse vaccinology (RV) is the state-of-the-art vaccine development strategy that starts with predicting vaccine antigens by bioinformatics analysis of the whole genome of a pathogen of interest. Vaxign is th...
-
Article
Anatomical structures, cell types and biomarkers of the Human Reference Atlas
The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international ...
-
Article
Open AccessDevelopment of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis
The 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for dise...
-
Article
Open AccessCIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature
With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and...
-
Article
Open AccessPotential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2
The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, ...
-
Article
Open AccessIntegrative web-based analysis of omics data for study of drugs against SARS-CoV-2
Research on drugs against SARS-CoV-2 (cause of COVID-19) has been one of the major world concerns at present. There have been abundant research data and findings in this field. The interference of drugs on gen...
-
Article
Open AccessOntological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection
Our systematic literature collection and annotation identified 106 chemical drugs and 31 antibodies effective against the infection of at least one human coronavirus (including SARS-CoV, SAR-CoV-2, and MERS-CoV)
-
Article
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative e...
-
Article
Open AccessCIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis
The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
-
Protocol
Perform Pathway Enrichment Analysis Using ReactomeFIViz
Modern large-scale biological data analysis often generates a set of significant genes, frequently associated with scores. Pathway-based approaches are routinely performed to understand the functional contexts...
-
Article
Open AccessOHMI: the ontology of host-microbiome interactions
Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data. We propose that...
-
Article
Open AccessA 2018 workshop: vaccine and drug ontology studies (VDOS 2018)
This Editorial first introduces the background of the vaccine and drug relations and how biomedical terminologies and ontologies have been used to support their studies. The history of the seven workshops, ini...
