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Zheng J, Li X, Masci AM, Kahn H, Huffman A, Asfaw E, Pan Y, Guo J, He V, Song J, Seleznev AI, Lin AY, He Y. Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. J Biomed Semantics 2024; 15:12. [PMID: 38890666 PMCID: PMC11186274 DOI: 10.1186/s13326-024-00312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND 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 analysis. While CanVaxKB serves as a pioneering database for over 670 manually annotated cancer vaccines, it is important to distinguish that a database, on its own, does not offer the structured relationships and standardized definitions found in an ontology. Recognizing this, we expanded the Vaccine Ontology (VO) to include those cancer vaccines present in CanVaxKB that were not initially covered, enhancing VO's capacity to systematically define and interrelate cancer vaccines. RESULTS An ontology design pattern (ODP) was first developed and applied to semantically represent various cancer vaccines, capturing their associated entities and relations. By applying the ODP, we generated a cancer vaccine template in a tabular format and converted it into the RDF/OWL format for generation of cancer vaccine terms in the VO. '12MP vaccine' was used as an example of cancer vaccines to demonstrate the application of the ODP. VO also reuses reference ontology terms to represent entities such as cancer diseases and vaccine hosts. Description Logic (DL) and SPARQL query scripts were developed and used to query for cancer vaccines based on different vaccine's features and to demonstrate the versatility of the VO representation. Additionally, ontological modeling was applied to illustrate cancer vaccine related concepts and studies for in-depth cancer vaccine analysis. A cancer vaccine-specific VO view, referred to as "CVO," was generated, and it contains 928 classes including 704 cancer vaccines. The CVO OWL file is publicly available on: http://purl.obolibrary.org/obo/vo/cvo.owl , for sharing and applications. CONCLUSION To facilitate the standardization, integration, and analysis of cancer vaccine data, we expanded the Vaccine Ontology (VO) to systematically model and represent cancer vaccines. We also developed a pipeline to automate the inclusion of cancer vaccines and associated terms in the VO. This not only enriches the data's standardization and integration, but also leverages ontological modeling to deepen the analysis of cancer vaccine information, maximizing benefits for researchers and clinicians. AVAILABILITY The VO-cancer GitHub website is: https://github.com/vaccineontology/VO/tree/master/CVO .
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Affiliation(s)
- Jie Zheng
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xingxian Li
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anna Maria Masci
- Data Impact and Governance, Technology Data and Innovation, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hayleigh Kahn
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eliyas Asfaw
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yuanyi Pan
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jinjing Guo
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Virginia He
- The College of Brown University, Brown University, Providence, RI, 02912, USA
| | - Justin Song
- College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrey I Seleznev
- Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Asiyah Yu Lin
- Axle Research and Technology, Rockville, MD, 20852, USA
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Bello RS, Walsh MT, Harper B, Amos CE, Oestman K, Nutt S, Galindez M, Block K, Rechis R, Bednar EM, Tektiridis J, Foxhall L, Moreno M, Shete S, Hawk E. Creating and Activating an Implementation Community to Drive HPV Vaccine Uptake in Texas: The Role of an NCI-Designated Cancer Center. Vaccines (Basel) 2023; 11:1128. [PMID: 37376517 DOI: 10.3390/vaccines11061128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The University of Texas MD Anderson Cancer Center, a comprehensive cancer center designated by the National Cancer Institute (NCI), defines its service population area as the State of Texas (29.1 M), the second most populous state in the country and the state with the greatest number of uninsured residents in the United States. Consistent with a novel and formal commitment to prevention as part of its core mission, alongside clear opportunities in Texas to drive vaccine uptake, MD Anderson assembled a transdisciplinary team to develop an institutional Framework to increase adolescent HPV vaccination and reduce HPV-related cancer burden. The Framework was developed and activated through a four-phase approach aligned with the NCI Cancer Center Support Grant Community Outreach and Engagement component. MD Anderson identified collaborators through data-driven outreach and constructed a portfolio of collaborative multi-sector initiatives through review processes designed to assess readiness, impact and sustainability. The result is an implementation community of 78 institutions collaboratively implementing 12 initiatives within a shared measurement framework impacting 18 counties. This paper describes a structured and rigorous process to set up the implementation of a multi-year investment in evidence-based strategies to increase HPV vaccination that solves challenges preventing implementation of recommended strategies and to encourage similar initiative replication.
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Affiliation(s)
- Rosalind S Bello
- The HPV Vaccination Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Office of Health Policy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T Walsh
- The HPV Vaccination Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Impact Evaluation Core, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Joint Center on Geospatial Analysis & Health, Houston, TX 77030, USA
| | - Blake Harper
- The HPV Vaccination Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Charles E Amos
- The HPV Vaccination Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Office of Health Policy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Katherine Oestman
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie Nutt
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Impact Evaluation Core, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Joint Center on Geospatial Analysis & Health, Houston, TX 77030, USA
| | - Marcita Galindez
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Impact Evaluation Core, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Joint Center on Geospatial Analysis & Health, Houston, TX 77030, USA
| | - Kaitlyn Block
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruth Rechis
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Impact Evaluation Core, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica M Bednar
- Cancer Prevention and Control Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer Tektiridis
- Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lewis Foxhall
- Office of Health Policy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Moreno
- Government Relations, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sanjay Shete
- Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ernest Hawk
- Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Spurgeon ME, Lambert PF. Mus musculus Papillomavirus 1: a New Frontier in Animal Models of Papillomavirus Pathogenesis. J Virol 2020; 94:e00002-20. [PMID: 32051276 PMCID: PMC7163119 DOI: 10.1128/jvi.00002-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Animal models of viral pathogenesis are essential tools in human disease research. Human papillomaviruses (HPVs) are a significant public health issue due to their widespread sexual transmission and oncogenic potential. Infection-based models of papillomavirus pathogenesis have been complicated by their strict species and tissue specificity. In this Gem, we discuss the discovery of a murine papillomavirus, Mus musculus papillomavirus 1 (MmuPV1), and how its experimental use represents a major advancement in models of papillomavirus-induced pathogenesis/carcinogenesis, and their transmission.
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Affiliation(s)
- Megan E Spurgeon
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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