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. 2025 Jul 9;16(1):12.
doi: 10.1186/s13326-025-00333-6.

A fourfold pathogen reference ontology suite

John Beverley  1   2 , Shane Babcock  3   4 , Carter Benson  5   6 , Giacomo De Colle  3   5 , Sydney Cohen  3 , Alexander D Diehl  3   5 , Ram A N R Challa  5 , Rachel A Mavrovich  3   5 , Joshua Billig  3   5 , Anthony Huffman  7 , Yongqun He  7
Affiliations

A fourfold pathogen reference ontology suite

John Beverley et al. J Biomed Semantics. .

Abstract

Background: 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.

Methods: The "hub-and-spoke" methodology is adopted 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).

Results: IDO is introduced before reporting on the scopes, major classes and relations, applications and extensions of IDO to VIDO, BIDO, MIDO, and PIDO.

Conclusions: The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease ontologies 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, quality, and analysis.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The structure of the hub-and-spoke model used to develop downwards from IDO
Fig. 2
Fig. 2
Protégé display of a portion of asserted and inferred VIDO hierarchies
Fig. 3
Fig. 3
Virus replication in VIDO
Fig. 4
Fig. 4
Bacteria type vocabulary in BIDO
Fig. 5
Fig. 5
Semantic enrichment of existing bacteria vocabulary in BIDO
Fig. 6
Fig. 6
PIDO design pattern where “type of” relates instances and classes and object properties relate instances
Fig. 7
Fig. 7
Refactorization of IDOMAL and IDOSCHISTO using PIDO. New classes in PIDO enable construction of a unifying data model, where relations used for construction are shown in italics
See this image and copyright information in PMC

Update of

References

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