Unintended consequences of existential quantifications in biomedical ontologies

Area of Science:

• Biomedical Informatics
• Semantic Web Technologies
• Ontology Engineering

Background:

• The Open Biomedical Ontologies (OBO) Foundry provides structured vocabularies for biomedicine.
• OBO ontologies are often released in OBO Flatfile and Web Ontology Language (OWL) formats.
• OWL utilizes formal logic, specifically description logics (OWL-DL), for semantic interpretation.

Purpose of the Study:

• To evaluate the logical consistency of OWL-DL releases of OBO ontologies.
• To determine if logical axioms in OBO ontologies accurately reflect intended meanings.
• To identify common modeling issues and propose solutions.

Main Methods:

• Analysis of OBO Foundry ontologies and cross-products for existential restrictions (someValuesFrom).
• Random sampling of 2,836 clauses for expert review.
• Assessment of inter-rater reliability using Cohen's kappa statistic.

Main Results:

• 23% of existential restrictions in OBO Foundry candidate ontologies were rated as suspicious by experts (Cohen's κ = 0.78).
• A lower, but difficult to quantify, proportion of suspicious restrictions were found in OBO Foundry cross-products (κ = 0.07).
• Identified common modeling problems and usability issues, including lack of ontological commitment and excessive domain-specific relations.

Conclusions:

• Current OWL releases of OBO Foundry ontologies contain logical inaccuracies and ambiguities.
• These issues hinder the accurate representation of biological reality.
• Recommendations include better integration with upper ontologies and limiting relation types with defined domains and ranges.