NIRS-Ontology: An Ontology for Non-Invasive Respiratory Support in Acute Care

This repository contains the NIRS Ontology, developed to support knowledge representation in acute care settings. It integrates ventilation modalities, therapy parameters, patient characteristics, and clinical outcomes using standardized vocabularies and rule-based reasoning. To explore the interactive class hierarchy with standardized annotations, click here to view the NIRS Ontology Class Hierarchy

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Availability in NCBO BioPortal

This ontology has also been submitted to the NCBO BioPortal and can be accessed here:

• NCBO BioPortal: https://bioportal.bioontology.org/ontologies/NIRS

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📁 Repository Structure

Folder/File	Description
NIRS-Ontology.owl	Core OWL ontology file including classes, properties, annotations, and SWRL rules.
docs/NIRS_Class_Hierarchy.html	Interactive HTML viewer for the ontology class hierarchy with annotations.
docs/NIRS_Class_Hierarchy_with_Annotations.json	Structured JSON file representing the ontology class tree with annotations.
README.md	Project overview, usage instructions, and reproducibility information.

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📦 Getting Started

To explore or extend the ontology:

1. Open in Protégé
   Download Protégé and load NIRS-Ontology.owl.

2. View Class Tree
   Download and Open NIRS_Class_Hierarchy.html in a web browser for an interactive view.

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🧬 Data Source

The ontology was evaluated using data and clinical scenarios derived from the eICU Collaborative Research Database.
Access: https://physionet.org/content/eicu-crd/ (credentialed access required).

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Citation

If you use this work, please cite:

Islam MF, Mosier J, Subbian V (2026) Development and evaluation of an ontology for non-invasive respiratory support in acute care. PLoS One 21(5): e0348199. https://doi.org/10.1371/journal.pone.0348199

BibTeX

@article{10.1371/journal.pone.0348199,
    doi = {10.1371/journal.pone.0348199},
    author = {Islam, Md Fantacher AND Mosier, Jarrod AND Subbian, Vignesh},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Development and evaluation of an ontology for non-invasive respiratory support in acute care},
    year = {2026},
    month = {05},
    volume = {21},
    url = {https://doi.org/10.1371/journal.pone.0348199},
    pages = {1-15},
    number = {5},

}

📬 Contact

For questions or collaboration inquiries, please contact:

Md Fantacher Islam
PhD Student, Systems and Industrial Engineering
University of Arizona
📧 fantacher@arizona.edu