A Fourfold Pathogen Reference Ontology Suite

2024-12-31

AI Summary

The Infectious Disease Ontology (IDO) suffers from incomplete coverage, insufficient pathogen specificity, and challenges in cross-pathogen data integration. Method: We propose a “hub-and-spoke” ontology extension paradigm and systematically construct four pathogen-specific reference ontologies—Virus Infectious Disease Ontology (VIDO), Bacterial Infectious Disease Ontology (BIDO), Fungal Infectious Disease Ontology (MIDO), and Parasitic Infectious Disease Ontology (PIDO)—thereby collaboratively extending IDO and the Coronavirus Infectious Disease Ontology (CIDO). All ontologies are formalized in OWL and strictly adhere to OBO Foundry principles, enabling modular, reusable knowledge modeling. Contribution/Results: This suite addresses long-standing gaps in updated ontologies for bacterial, fungal, and parasitic diseases, significantly enhancing semantic consistency, interoperability, and computational analyzability of infectious disease data. It establishes a standardized knowledge infrastructure to support precise epidemiological modeling and cross-pathogen comparative research.

Technology Category

• Knowledge Representation and Reasoning: Ontologies
• Data Mining & Knowledge Management: Linked Open Data, Knowledge Graphs & KB Completion
• Search and Optimization: Mixed Discrete/Continuous Search

Application Category

• Semantics and Knowledge: Scalable techniques for the creation, curation, publication, maintenance, and consumption of large, Web-based, structured, reusable, knowledge graphs and ontologies
• Systems and Infrastructure for Web, Mobile and WoT: Decentralized Web and Fediverse systems
• Security and Privacy: Data transparency and provenance

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.

Problem

• Infectious Disease Ontology
• Data Reusability
• COVID-19 Pandemic

Innovation

• Infectious Disease Ontology
• Data Standardization
• Biomedical Terminology Unification