Coordinating virus research: The Virus Infectious Disease Ontology

Area of Science:

• Biomedical Informatics
• Infectious Disease Research
• Ontology Engineering

Background:

• The COVID-19 pandemic necessitated rapid data analysis for SARS-CoV-2 research.
• Consistent data interpretation is crucial to avoid data silos and ensure research reproducibility.
• Ontologies offer structured vocabularies to standardize scientific data.

Purpose of the Study:

• To describe the application of ontologies in COVID-19 research.
• To introduce the Virus Infectious Disease Ontology (VIDO) as an extension of the Infectious Disease Ontology (IDO) Core.
• To demonstrate the integration of VIDO and CIDO with existing ontologies for SARS-CoV-2 data annotation.

Main Methods:

• Development of VIDO following Open Biological and Biomedical Ontology (OBO) Foundry principles.
• Reuse of existing OBO ontologies, including IDO Core.
• Annotation of SARS-CoV-2 research data using terms from VIDO and CIDO.
• Connecting VIDO to CIDO and other relevant ontologies.

Main Results:

• VIDO provides a reference ontology for viral infectious diseases.
• Ontologies with a common upper-level vocabulary can be seamlessly integrated.
• Demonstrated successful annotation of SARS-CoV-2 research data using VIDO and CIDO.
• Highlighted the potential for ontologies in host-pathogen data analytics and EHR annotation.

Conclusions:

• Ontologies, particularly VIDO and CIDO, are vital for consistent data interpretation in infectious disease research.
• The OBO Foundry principles facilitate the development and integration of specialized ontologies.
• Future work includes expanding ontologies to other infectious agents and applications in data analytics and healthcare.