A Fourfold Pathogen Reference Ontology Suite

TL;DR

This paper introduces a suite of pathogen-specific reference ontologies derived from the Infectious Disease Ontology to improve data organization and sharing for various infectious diseases, including viruses, bacteria, fungi, and parasites.

Contribution

It presents a novel 'hub and spoke' methodology for creating modular, reusable pathogen-specific extensions of the IDO, enhancing standardization and data integration.

Findings

Developed VIDO, BIDO, MIDO, and PIDO ontologies

Enhances modularization and reusability of infectious disease data

Supports future ontology refinement and application development

Abstract

Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases. We adopt the "hub and spoke" methodology to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO). The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease data within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing and analysis.