Limits...
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.

Lin Y, Zheng J, He Y - J Biomed Semantics (2016)

Bottom Line: Third, VICO helps manage the complexity of the domain knowledge using logically defined ontological hierarchies and axioms.Fourth, VICO supports efficient query and comparison, e.g., through the Description Language (DL)-Query and SPARQL.Fifth, VICO helps discover new knowledge.

View Article: PubMed Central - PubMed

Affiliation: Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

ABSTRACT

Background: Although signing a vaccination (or immunization) informed consent form is not a federal requirement in the US and Canada, such a practice is required by many states and pharmacies. The content and structures of these informed consent forms vary, which makes it hard to compare and analyze without standardization. To facilitate vaccination informed consent data standardization and integration, it is important to examine various vaccination informed consent forms, patient answers, and consent results. In this study, we report a Vaccination Informed Consent Ontology (VICO) that extends the Informed Consent Ontology and integrates related OBO foundry ontologies, such as the Vaccine Ontology, with a focus on vaccination screening questionnaire in the vaccination informed consent domain.

Results: Current VICO contains 993 terms, including 248 VICO specific terms and 709 terms imported from 17 OBO Foundry ontologies. VICO ontologically represents and integrates 12 vaccination informed consent forms from the Walgreens, Costco pharmacies, Rite AID, University of Maryland College Park, and the government of Manitoba, Canada. VICO extends Informed Consent Ontology (ICO) with vaccination screening questionnaires and questions. Our use cases and examples demonstrate five usages of VICO. First, VICO provides standard, robust and consistent representation and organization of the knowledge in different vaccination informed consent forms, questionnaires, and questions. Second, VICO integrates prior knowledge, e.g., the knowledge of vaccine contraindications imported from the Vaccine Ontology (VO). Third, VICO helps manage the complexity of the domain knowledge using logically defined ontological hierarchies and axioms. VICO glues multiple schemas that represent complex vaccination informed consent contents defined in different organizations. Fourth, VICO supports efficient query and comparison, e.g., through the Description Language (DL)-Query and SPARQL. Fifth, VICO helps discover new knowledge. For instance, by integrating the prior knowledge imported from the VO with a user's answer to informed consent questions (e.g., allergic reaction question) for a specific vaccination, we can infer whether or not the patient can be vaccinated with the vaccine.

Conclusions: The Vaccination Informed Consent Ontology (VICO) represents entities related to vaccination informed consents with a special focus on vaccination informed consent forms, and questionnaires and questions in the forms. Our use cases and examples demonstrated how VICO could support a platform for vaccination informed consent data standardization, data integration, and data queries.

No MeSH data available.


Related in: MedlinePlus

The ontology hierarchy and associated axioms of the Afluria influenza vaccine. The contents are defined in VO and imported to VICO. The figure is a screenshot from Ontobee [16]. The highlighted egg allergen axiom is used for a use case demo detailed later in this paper
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4837519&req=5

Fig4: The ontology hierarchy and associated axioms of the Afluria influenza vaccine. The contents are defined in VO and imported to VICO. The figure is a screenshot from Ontobee [16]. The highlighted egg allergen axiom is used for a use case demo detailed later in this paper

Mentions: As a demonstration of importing prior knowledge from VO, Fig. 4 shows the VO’s representation of a vaccine, Afluria. Afluria is a human influenza viral vaccine licensed for use in the USA. It is an inactivated vaccine against Influenza virus A. It is manufactured by the CSL Limited, and distributed by Merck & Co, Inc. Various characteristics of Afluria were represented using logical axioms in VO. For example, the axiom: ‘has vaccine allergen’ some ‘chicken egg protein allergen’ encodes that the Afluria vaccine contains a trace of chicken egg protein, which is able to induce allergic reaction in certain population. Therefore, the hypersensitivity to chicken egg becomes a contraindication to this vaccine. Another vaccine allergen associated with this vaccine is neomycin. This vaccine is administered via an intramuscular route. The vaccine information has been imported to VICO from VO as detailed in the Methods section. Such importing mechanism provides a valid strategy for VICO to integrate prior knowledge as recorded in VO.Fig. 4


VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.

Lin Y, Zheng J, He Y - J Biomed Semantics (2016)

The ontology hierarchy and associated axioms of the Afluria influenza vaccine. The contents are defined in VO and imported to VICO. The figure is a screenshot from Ontobee [16]. The highlighted egg allergen axiom is used for a use case demo detailed later in this paper
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4837519&req=5

Fig4: The ontology hierarchy and associated axioms of the Afluria influenza vaccine. The contents are defined in VO and imported to VICO. The figure is a screenshot from Ontobee [16]. The highlighted egg allergen axiom is used for a use case demo detailed later in this paper
Mentions: As a demonstration of importing prior knowledge from VO, Fig. 4 shows the VO’s representation of a vaccine, Afluria. Afluria is a human influenza viral vaccine licensed for use in the USA. It is an inactivated vaccine against Influenza virus A. It is manufactured by the CSL Limited, and distributed by Merck & Co, Inc. Various characteristics of Afluria were represented using logical axioms in VO. For example, the axiom: ‘has vaccine allergen’ some ‘chicken egg protein allergen’ encodes that the Afluria vaccine contains a trace of chicken egg protein, which is able to induce allergic reaction in certain population. Therefore, the hypersensitivity to chicken egg becomes a contraindication to this vaccine. Another vaccine allergen associated with this vaccine is neomycin. This vaccine is administered via an intramuscular route. The vaccine information has been imported to VICO from VO as detailed in the Methods section. Such importing mechanism provides a valid strategy for VICO to integrate prior knowledge as recorded in VO.Fig. 4

Bottom Line: Third, VICO helps manage the complexity of the domain knowledge using logically defined ontological hierarchies and axioms.Fourth, VICO supports efficient query and comparison, e.g., through the Description Language (DL)-Query and SPARQL.Fifth, VICO helps discover new knowledge.

View Article: PubMed Central - PubMed

Affiliation: Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

ABSTRACT

Background: Although signing a vaccination (or immunization) informed consent form is not a federal requirement in the US and Canada, such a practice is required by many states and pharmacies. The content and structures of these informed consent forms vary, which makes it hard to compare and analyze without standardization. To facilitate vaccination informed consent data standardization and integration, it is important to examine various vaccination informed consent forms, patient answers, and consent results. In this study, we report a Vaccination Informed Consent Ontology (VICO) that extends the Informed Consent Ontology and integrates related OBO foundry ontologies, such as the Vaccine Ontology, with a focus on vaccination screening questionnaire in the vaccination informed consent domain.

Results: Current VICO contains 993 terms, including 248 VICO specific terms and 709 terms imported from 17 OBO Foundry ontologies. VICO ontologically represents and integrates 12 vaccination informed consent forms from the Walgreens, Costco pharmacies, Rite AID, University of Maryland College Park, and the government of Manitoba, Canada. VICO extends Informed Consent Ontology (ICO) with vaccination screening questionnaires and questions. Our use cases and examples demonstrate five usages of VICO. First, VICO provides standard, robust and consistent representation and organization of the knowledge in different vaccination informed consent forms, questionnaires, and questions. Second, VICO integrates prior knowledge, e.g., the knowledge of vaccine contraindications imported from the Vaccine Ontology (VO). Third, VICO helps manage the complexity of the domain knowledge using logically defined ontological hierarchies and axioms. VICO glues multiple schemas that represent complex vaccination informed consent contents defined in different organizations. Fourth, VICO supports efficient query and comparison, e.g., through the Description Language (DL)-Query and SPARQL. Fifth, VICO helps discover new knowledge. For instance, by integrating the prior knowledge imported from the VO with a user's answer to informed consent questions (e.g., allergic reaction question) for a specific vaccination, we can infer whether or not the patient can be vaccinated with the vaccine.

Conclusions: The Vaccination Informed Consent Ontology (VICO) represents entities related to vaccination informed consents with a special focus on vaccination informed consent forms, and questionnaires and questions in the forms. Our use cases and examples demonstrated how VICO could support a platform for vaccination informed consent data standardization, data integration, and data queries.

No MeSH data available.


Related in: MedlinePlus