The mouse pathology ontology, MPATH; structure and applications

Area of Science:

• Anatomic pathology
• Bioinformatics
• Ontology development

Background:

• Accurate capture of disease-related anatomic pathology data is crucial for model organism phenotyping and human clinical practice.
• A simplified nomenclature and coding system is needed for integration into data collection platforms, enabling efficient pathologist observation recording.
• The MPATH ontology, initially for rodent histopathology, now supports coding and analysis of disease and phenotype data across species.

Purpose of the Study:

• To describe the structure and content of the MPATH ontology.
• To highlight the broad applicability and utility of MPATH in various research and clinical contexts.
• To demonstrate MPATH's role in large-scale phenotyping and cross-species disease analysis.

Main Methods:

• MPATH is structured into two main branches for pathological processes and structures, based on histopathological principles.
• It comprises 888 core terms in an is_a hierarchy, with 86% containing definitions and logical axioms linking to other ontologies like Gene Ontology.
• MPATH is utilized to generate cross-products with qualifiers from the Phenotype and Trait Ontology (PATO) for phenotyping studies.

Main Results:

• MPATH provides a species-agnostic framework for describing anatomic pathology applicable to most amniotes.
• Its use extends beyond mice to humans and zebrafish, facilitating recording of diagnostic and phenotypic data.
• MPATH enables interrogation of large datasets, semantic analysis of inter-species disease relations, and integration with pharmacogenomics data.

Conclusions:

• MPATH serves as a versatile, species-agnostic ontology for anatomic pathology.
• It significantly enhances the ability to analyze and integrate diverse pathology and phenotype data.
• MPATH is valuable for high-throughput phenotyping, cross-species disease research, and clinical data management.