The mouse pathology ontology, MPATH; structure and applications

Journal of Biomedical Semantics

Georgios V Gkoutos¹  Colin McKerlie³  Beth A Sundberg²  John P Sundberg²  Paul N Schofield² 

[1] Department of Computer Science, University of Aberystwyth, Old College, King Street, SY23 2AX Ceredigion, Wales;The Jackson Laboratory, 600, Main Street, Bar Harbor, ME 04609-1500, USA;Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, M5G 1X8, Toronto, Canada

关键词: Phenotype;    Mouse;    Disease;    Ontology;    Pathology;   

Others  :  807024
DOI  :  10.1186/2041-1480-4-18

 received in 2013-02-04, accepted in 2013-08-19,  发布年份 2013

【 摘 要 】

Background

The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated into data collection platforms (such as computerized medical record-keeping systems) to enable the pathologist to rapidly screen and accurately record observations. The MPATH ontology was originally constructed in 2,000 by a committee of pathologists for the annotation of rodent histopathology images, but is now widely used for coding and analysis of disease and phenotype data for rodents, humans and zebrafish.

Construction and content

MPATH is divided into two main branches describing pathological processes and structures based on traditional histopathological principles. It does not aim to include definitive diagnoses, which would generally be regarded as disease concepts. It contains 888 core pathology terms in an almost exclusively is_a hierarchy nine layers deep. Currently, 86% of the terms have textual definitions and contain relationships as well as logical axioms to other ontologies such the Gene Ontology.

Application and utility

MPATH was originally devised for the annotation of histopathological images from mice but is now being used much more widely in the recording of diagnostic and phenotypic data from both mice and humans, and in the construction of logical definitions for phenotype and disease ontologies. We discuss the use of MPATH to generate cross-products with qualifiers derived from a subset of the Phenotype and Trait Ontology (PATO) and its application to large-scale high-throughput phenotyping studies. MPATH provides a largely species-agnostic ontology for the descriptions of anatomic pathology, which can be applied to most amniotes and is now finding extensive use in species other than mice. It enables investigators to interrogate large datasets at a variety of depths, use semantic analysis to identify the relations between diseases in different species and integrate pathology data with other data types, such as pharmacogenomics.

【 授权许可】

   
2013 Schofield et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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