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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

Basic VICO design pattern
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Fig2: Basic VICO design pattern

Mentions: The basic VICO ontology design pattern is composed of various entities linked by defined relations as illustrated in Fig. 2. Specifically, before a vaccination process, a vaccination informed consent form is documented by an organization/company (e.g., the company Costco). A vaccination screening questionnaire containing a list of questions is provided for a vaccination patient or his/her legal representative to answer. The ‘documented_by’ is a relation defined by VICO as ‘an object property that represents a relation between a document and an entity that writes, maintains and releases the document’. A specific vaccination consent form is often restricted to be used in a specific geographic location (e.g., Manitoba in Canada or South Carolina in USA). The contents of the questions in the form often cover different topics such as the vaccination patient’s current health status, current treatment, allergic reaction history, past vaccination history, and so on. The vaccination patient’s age and biological sex (female or male) are modelled using PATO term ‘has_quality’ linking the age and biological sex to patient. The vaccination process occurs via a specified vaccination route (e.g., intranasal influenza vaccination for FluMist) (Fig. 2). A question, for example, ‘question on serious nasal condition’ (asked for FluMist vaccination only) ‘is about vaccination procedure’ some ‘FluMist vaccination’, which is a live attenuated influenza vaccine. A vaccination related question may also be related to a disease (e.g., cancer) or an adverse event process, which has been expressed in VICO using the relation ‘is about’ (Fig. 2). Details about ontological modeling of vaccine/vaccination can be found in the previous VO paper [5, 6]. Informed consent representation is introduced in previous ICO paper [4]. By integrating VO/ICO representations and including VICO-specific contents, VICO provides a framework to link vaccination patient, vaccinee quality, vaccine, vaccine quality, vaccination, vaccination targets, informed consent process, informed consent forms, questions, questionnaires, and related information.Fig. 2


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

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

Basic VICO design pattern
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Basic VICO design pattern
Mentions: The basic VICO ontology design pattern is composed of various entities linked by defined relations as illustrated in Fig. 2. Specifically, before a vaccination process, a vaccination informed consent form is documented by an organization/company (e.g., the company Costco). A vaccination screening questionnaire containing a list of questions is provided for a vaccination patient or his/her legal representative to answer. The ‘documented_by’ is a relation defined by VICO as ‘an object property that represents a relation between a document and an entity that writes, maintains and releases the document’. A specific vaccination consent form is often restricted to be used in a specific geographic location (e.g., Manitoba in Canada or South Carolina in USA). The contents of the questions in the form often cover different topics such as the vaccination patient’s current health status, current treatment, allergic reaction history, past vaccination history, and so on. The vaccination patient’s age and biological sex (female or male) are modelled using PATO term ‘has_quality’ linking the age and biological sex to patient. The vaccination process occurs via a specified vaccination route (e.g., intranasal influenza vaccination for FluMist) (Fig. 2). A question, for example, ‘question on serious nasal condition’ (asked for FluMist vaccination only) ‘is about vaccination procedure’ some ‘FluMist vaccination’, which is a live attenuated influenza vaccine. A vaccination related question may also be related to a disease (e.g., cancer) or an adverse event process, which has been expressed in VICO using the relation ‘is about’ (Fig. 2). Details about ontological modeling of vaccine/vaccination can be found in the previous VO paper [5, 6]. Informed consent representation is introduced in previous ICO paper [4]. By integrating VO/ICO representations and including VICO-specific contents, VICO provides a framework to link vaccination patient, vaccinee quality, vaccine, vaccine quality, vaccination, vaccination targets, informed consent process, informed consent forms, questions, questionnaires, and related information.Fig. 2

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