ArticleJournal of biomedical semantics2014
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches.Frontiers in pharmacology · 2019Pooled it
- Immune Response and Molecular Mechanisms of Cardiovascular Adverse Effects of Spike Proteins from SARS-CoV-2 and mRNA Vaccines.Biomedicines · 2023Review
- Genetic Risk Factors for Neurological Disorders in Children with Adverse Events Following Immunization: A Descriptive Study of a Polish Case Series.International journal of molecular sciences · 2023Article
- COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.Briefings in bioinformatics · 2022Article
- IL-4 gene polymorphisms and their association with nematodes infection in Pakistani population.African health sciences · 2022Article
- Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development.Current pharmaceutical design · 2021Review
- Causality assessment of adverse events following immunization: the problem of multifactorial pathology.F1000Research · 2020Article
- A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).BMC bioinformatics · 2019Article
- Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.Journal of biomedical informatics · 2018Review
- Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.Drug safety · 2016Article
- Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research.Current pharmacology reports · 2016Article
- Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2016Article
- Adversomics: a new paradigm for vaccine safety and design.Expert review of vaccines · 2015Review
- A 2013 workshop: vaccine and drug ontology studies (VDOS 2013).Journal of biomedical semantics · 2014Article
- OAE: The Ontology of Adverse Events.Journal of biomedical semantics · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDue to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to disease, we developed an Ontology of Genetic Susceptibility Factors (OGSF), a biomedical ontology in the domain of genetic susceptibility and genetic susceptibility factors. The OGSF framework was then applied in the area of vaccine adverse events (VAEs).
resultsOGSF aligns with the Basic Formal Ontology (BFO). OGSF defines 'genetic susceptibility' as a subclass of BFO:disposition and has a material basis 'genetic susceptibility factor'. The 'genetic susceptibility to pathological bodily process' is a subclasses of 'genetic susceptibility'. A VAE is a type of pathological bodily process. OGSF represents different types of genetic susceptibility factors including various susceptibility alleles (e.g., SNP and gene). A general OGSF design pattern was developed to represent genetic susceptibility to VAE and associated genetic susceptibility factors using experimental results in genetic association studies. To test and validate the design pattern, two case studies were populated in OGSF. In the first case study, human gene allele DBR*15:01 is susceptible to influenza vaccine Pandemrix-induced Multiple Sclerosis. The second case study reports genetic susceptibility polymorphisms associated with systemic smallpox VAEs. After the data of the Case Study 2 were represented using OGSF-based axioms, SPARQL was successfully developed to retrieve the susceptibility factors stored in the populated OGSF. A network of data from the Case Study 2 was constructed by using ontology terms and individuals as nodes and ontology relations as edges. Different social network analys is (SNA) methods were then applied to verify core OGSF terms. Interestingly, a SNA hub analysis verified all susceptibility alleles of SNPs and a SNA closeness analysis verified the susceptibility genes in Case Study 2. These results validated the proper OGSF structure identified different ontology aspects with SNA methods.
conclusionsOGSF provides a verified and robust framework for representing various genetic susceptibility types and genetic susceptibility factors annotated from experimental VAE genetic association studies. The RDF/OWL formulated ontology data can be queried using SPARQL and analyzed using centrality-based network analysis methods.
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