Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase
BackgroundViral vaccines have been proven significant in protecting us against viral diseases such as COVID-19. To better understand and design viral vaccines, it is critical to systematically collect, annotate, and analyse various viral vaccines and identify enriched patterns from these viral vacci...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1509226/full |
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| author | Anthony Huffman Mehul Gautam Arya Gandhi Priscilla Du Lauren Austin Kallan Roan Jie Zheng Yongqun He Yongqun He |
| author_facet | Anthony Huffman Mehul Gautam Arya Gandhi Priscilla Du Lauren Austin Kallan Roan Jie Zheng Yongqun He Yongqun He |
| author_sort | Anthony Huffman |
| collection | DOAJ |
| description | BackgroundViral vaccines have been proven significant in protecting us against viral diseases such as COVID-19. To better understand and design viral vaccines, it is critical to systematically collect, annotate, and analyse various viral vaccines and identify enriched patterns from these viral vaccines. MethodsWe systematically collected experimentally verified viral vaccines from the literature, manually annotated, and stored the information in the VIOLIN vaccine database. The annotated information included basic vaccine names, pathogens and diseases, vaccine components, vaccine formulations, and their induced host responses. Enriched patterns were identified from our systematical analysis of the viral vaccines and vaccine antigens. ResultsA total of 2,847 viral vaccines against 95 viral species (including 72 RNA viral species and 23 DNA viral species) were collected, manually annotated, and stored in the VIOLIN vaccine database. These viral vaccines used 542 vaccine antigens. A taxonomical analysis found various DNA and RNA viruses covered by the viral vaccines. These vaccines target different viral life cycle stages (e.g., viral entry, assembly, exit, and immune evasion) as identified in top ranked human, animal vaccines, and HPV vaccines. The vaccine antigen proteins also show up in different virion locations in viruses such as HRSV vaccines. Both structural and non-structural viral proteins have been used for viral vaccine development. Protective vaccine antigens tend to have a protegenicity score of >85% based on the Vaxign-ML calculation, which measures predicted suitability for vaccine use. While predicted adhesins still have significantly higher chances of being protective antigens, only 21.42% of protective viral vaccine antigens were predicted to be adhesins. Furthermore, our Gene Ontology (GO) enrichment analysis using a customized Fisher’s exact test identified many enriched patterns such as viral entry into the host cell, DNA/RNA/ATP/ion binding, and suppression of host type 1 interferon-mediated signaling pathway. The viral vaccines and their associated entities and relations are ontologically modeled and represented in the Vaccine Ontology (VO). A VIOLIN web interface was developed to support user friendly queries of viral vaccines. DiscussionViral vaccines were systematically collected and annotated in the VIOLIN vaccine knowledgebase, and the analysis of these viral vaccines identified many insightful patterns. |
| format | Article |
| id | doaj-art-8a0eec40554f44d2b514ded58f8b0fb7 |
| institution | Kabale University |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-8a0eec40554f44d2b514ded58f8b0fb72025-02-07T06:49:29ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-02-011510.3389/fcimb.2025.15092261509226Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebaseAnthony Huffman0Mehul Gautam1Arya Gandhi2Priscilla Du3Lauren Austin4Kallan Roan5Jie Zheng6Yongqun He7Yongqun He8Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United StatesCollege of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United StatesCollege of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United StatesCollege of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United StatesCollege of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United StatesCollege of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United StatesUnit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United StatesDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United StatesUnit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United StatesBackgroundViral vaccines have been proven significant in protecting us against viral diseases such as COVID-19. To better understand and design viral vaccines, it is critical to systematically collect, annotate, and analyse various viral vaccines and identify enriched patterns from these viral vaccines. MethodsWe systematically collected experimentally verified viral vaccines from the literature, manually annotated, and stored the information in the VIOLIN vaccine database. The annotated information included basic vaccine names, pathogens and diseases, vaccine components, vaccine formulations, and their induced host responses. Enriched patterns were identified from our systematical analysis of the viral vaccines and vaccine antigens. ResultsA total of 2,847 viral vaccines against 95 viral species (including 72 RNA viral species and 23 DNA viral species) were collected, manually annotated, and stored in the VIOLIN vaccine database. These viral vaccines used 542 vaccine antigens. A taxonomical analysis found various DNA and RNA viruses covered by the viral vaccines. These vaccines target different viral life cycle stages (e.g., viral entry, assembly, exit, and immune evasion) as identified in top ranked human, animal vaccines, and HPV vaccines. The vaccine antigen proteins also show up in different virion locations in viruses such as HRSV vaccines. Both structural and non-structural viral proteins have been used for viral vaccine development. Protective vaccine antigens tend to have a protegenicity score of >85% based on the Vaxign-ML calculation, which measures predicted suitability for vaccine use. While predicted adhesins still have significantly higher chances of being protective antigens, only 21.42% of protective viral vaccine antigens were predicted to be adhesins. Furthermore, our Gene Ontology (GO) enrichment analysis using a customized Fisher’s exact test identified many enriched patterns such as viral entry into the host cell, DNA/RNA/ATP/ion binding, and suppression of host type 1 interferon-mediated signaling pathway. The viral vaccines and their associated entities and relations are ontologically modeled and represented in the Vaccine Ontology (VO). A VIOLIN web interface was developed to support user friendly queries of viral vaccines. DiscussionViral vaccines were systematically collected and annotated in the VIOLIN vaccine knowledgebase, and the analysis of these viral vaccines identified many insightful patterns.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1509226/fullvirusontologygene enrichmentreverse vaccinologyantigensadhesin |
| spellingShingle | Anthony Huffman Mehul Gautam Arya Gandhi Priscilla Du Lauren Austin Kallan Roan Jie Zheng Yongqun He Yongqun He Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase Frontiers in Cellular and Infection Microbiology virus ontology gene enrichment reverse vaccinology antigens adhesin |
| title | Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase |
| title_full | Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase |
| title_fullStr | Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase |
| title_full_unstemmed | Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase |
| title_short | Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase |
| title_sort | systematic collection annotation and pattern analysis of viral vaccines in the violin vaccine knowledgebase |
| topic | virus ontology gene enrichment reverse vaccinology antigens adhesin |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1509226/full |
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