Ontology-supported research on vaccine efficacy, safety and integrative biological networks

He, Yongqun

doi:10.1586/14760584.2014.923762

Cited by 13 publications

(13 citation statements)

References 86 publications

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“…We intend to frequently update our database in the future. In addition to the manual curation method, we will also investigate how computational methods, such as ontology-based literature mining and meta-analysis [19, 47, 48], would improve the database annotations and updates.…”

Section: Discussionmentioning

confidence: 99%

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

Deng

Martin

Patil

et al. 2015

Vaccine

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A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development.

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Section: Discussionmentioning

confidence: 99%

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

Deng

Martin

Patil

et al. 2015

Vaccine

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“…Beside these research-oriented data sources, other relevant vaccinerelated databases collect data from vaccine safety and reports vaccine adverse events (VAE) from many post-licensure vaccines (such as the Vaccine Adverse Event Reporting System available at www.vaers.hhs.gov), and could facilitate the association between particular adverse events and specific vaccinations. Other research databases could help overcome bottlenecks in vaccinology (for review, He, 2014).…”

Section: The Making Of a Vaccinementioning

confidence: 99%

Big Data: Challenge and Opportunity for Translational and Industrial Research in Healthcare

Rossi

Grifantini

2018

Front. Digit. Humanit.

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Research and innovation are constant imperatives for the healthcare sector: medicine, biology and biotechnology support it, and more recently computational and data-driven disciplines gained relevance to handle the massive amount of data this sector is and will be generating. To be effective in translational and healthcare industrial research, big data in the life science domain need to be organized, well annotated, catalogued, correlated and integrated: the biggest the data silos at hand, the stronger the need for organization and tidiness. The degree of such organization marks the transition from data to knowledge for strategic decision making. Medicine is supported by observations and data and for certain aspects medicine is becoming a data science supported by clinicians. While medicine defines itself as personalized, quantified (precision med) or in high-definition, clinicians should be prepared to deal with a world in which Internet of People paraphrases the Internet of Things paradigm. Integrated use of electronic health records (EHRs) and quantitative data (both clinical and molecular) is a key process to develop precision medicine. Health records collection was originally designed for patient care and billing and/or insurance purposes. The digitization of health records facilitates and opens up new possibilities for science and research and they should be now collected and managed with this aim in mind. More data and the ability to efficiently handle them is a significant advantage not only for clinicians and life science researchers, but for drugs producers too. In an industrial sector spending increasing efforts on drug repurposing, attention to efficient methods to unwind the intricacies of the hugely complex reality of human physiology, such as network based methods and physical chemistry computational methods, became of paramount importance. Finally, the main pillars of industrial R&D processes for vaccines, include initial discovery, early-late pre clinics, pre-industrialization, clinical phases and finally registration-commercialization. The passage from one step to another is regulated by stringent pass/fail criteria. Bottlenecks of the R&D process are often represented by animal and human studies, which could be rationalized by surrogate in vitro assays as well as by predictive molecular and cellular signatures and models.

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“…Therefore, there is a desire to generate a more systematical theory that traces the root causes of different types of AEs and associated factors. Based on the Immune Response Gene Network Theory and several other theories including the Evolutionary Synthesis Theory [74], the Cell Theory [75], and the “Immune Network Theory” [76], the author has recently proposed a One Network Theory of the Life of an organism (abbreviated as “OneNet theory”) [34]. As described below, the OneNet theory provides an ideal framework to study the molecular mechanisms of causal AEs induced by vaccinations and drug treatments.…”

Section: Theories Towards Understanding Adverse Event Causality Mechamentioning

confidence: 99%

“…The first three characteristics were defined and discussed in the original paper [34]. The last OneNet characteristic is newly added to provide a mechanism to measure the effect (or outcome) of the complex OneNet process.…”

Section: Theories Towards Understanding Adverse Event Causality Mechamentioning

confidence: 99%

“…For the mechanism studies in pharmacovigilance, there have been two recently proposed theories, i.e. , the “Immune Response Gene Network” theory [32, 33] and the OneNet Theory of Life (abbreviated as “the OneNet theory”) [34]. Ontology and ontology-based Semantic Web technologies may provide a robust platform for reproducible data representation, exchange, sharing, and analysis [35, 36].…”

Section: Introductionmentioning

confidence: 99%

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Ontology-Based Vaccine and Drug Adverse Event Representation and Theory-Guided Systematic Causal Network Analysis Toward Integrative Pharmacovigilance Research

2016

Curr Pharmacol Rep

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Compared with controlled terminologies (e.g., MedDRA, CTCAE, and WHO-ART), the community-based Ontology of AEs (OAE) has many advantages in adverse event (AE) classifications. The OAE-derived Ontology of Vaccine AEs (OVAE) and Ontology of Drug Neuropathy AEs (ODNAE) serve as AE knowledge bases and support data integration and analysis. The Immune Response Gene Network Theory explains molecular mechanisms of vaccine-related AEs. The OneNet Theory of Life treats the whole process of a life of an organism as a single complex and dynamic network (i.e., OneNet). A new “OneNet effectiveness” tenet is proposed here to expand the OneNet theory. Derived from the OneNet theory, the author hypothesizes that one human uses one single genotype-rooted mechanism to respond to different vaccinations and drug treatments, and experimentally identified mechanisms are manifestations of the OneNet blueprint mechanism under specific conditions. The theories and ontologies interact together as semantic frameworks to support integrative pharmacovigilance research.

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Ontology-supported research on vaccine efficacy, safety and integrative biological networks

Cited by 13 publications

References 86 publications

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

Big Data: Challenge and Opportunity for Translational and Industrial Research in Healthcare

Ontology-Based Vaccine and Drug Adverse Event Representation and Theory-Guided Systematic Causal Network Analysis Toward Integrative Pharmacovigilance Research

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