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Disjunctive shared information between ontology concepts: application to Gene Ontology.

Francisco M Couto¹, Mário J Silva

¹Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Lisboa, 1749-016, Portugal. fcouto@di.fc.ul.pt.

Journal of Biomedical Semantics

|September 3, 2011

Summary

This study introduces DiShIn, a novel method for comparing biomedical ontology concepts by analyzing shared information content among disjunctive ancestors. DiShIn improves semantic similarity measures and can reduce execution time in applications utilizing multiple inheritance.

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Area of Science:

Biomedical Informatics
Computational Biology
Ontology Engineering

Background:

Biomedical ontologies are crucial for comparing concepts and entities.
Current semantic similarity measures often overlook disjunctive ancestors.
This limitation impacts the accuracy of ontology-based comparisons.

Purpose of the Study:

To propose a novel method, DiShIn, for calculating semantic similarity.
To effectively utilize multiple inheritance relationships in biomedical ontologies.
To address the limitations of existing semantic similarity measures regarding disjunctive ancestors.

Main Methods:

DiShIn calculates shared information content based on disjunctive common ancestors.
It identifies these ancestors by analyzing distinct paths from concepts to common ancestors.
The method exploits multiple inheritance structures inherent in many ontologies.

Main Results:

DiShIn demonstrated a statistically significant higher correlation between semantic and sequence similarity when applied to the Gene Ontology.
Performance was evaluated using the CESSM platform, comparing against state-of-the-art measures.
The method effectively incorporates disjunctive common ancestors into similarity calculations.

Conclusions:

DiShIn offers an improved approach to semantic similarity in biomedical ontologies.
Its integration can enhance the accuracy of entity and concept comparisons.
Incorporating DiShIn may also lead to reduced execution times in relevant applications.