Neuroanatomical domain of the foundational model of anatomy ontology

Trond T Nilsen,James F Brinkley,Maryann E Martone,B Nichols,Landon T Detwiler,Jessica A Turner,Daniel L Rubin,Jose LV Mejino

doi:10.1186/2041-1480-5-1

Abstract

BackgroundThe diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are expected and valid, no widely adopted approach exists to harmonize different brain labeling protocols and terminologies. Our approach uses the natural organizing framework provided by anatomical structure to correlate terminologies commonly used in neuroimaging.DescriptionThe Foundational Model of Anatomy (FMA) Ontology provides a semantic framework for representing the anatomical entities and relationships that constitute the phenotypic organization of the human body. In this paper we describe recent enhancements to the neuroanatomical content of the FMA that models cytoarchitectural and morphological regions of the cerebral cortex, as well as white matter structure and connectivity. This modeling effort is driven by the need to correlate and reconcile the terms used in neuroanatomical labeling protocols. By providing an ontological framework that harmonizes multiple views of neuroanatomical organization, the FMA provides developers with reusable and computable knowledge for a range of biomedical applications.ConclusionsA requirement for facilitating the integration of basic and clinical neuroscience data from diverse sources is a well-structured ontology that can incorporate, organize, and associate neuroanatomical data. We applied the ontological framework of the FMA to align the vocabularies used by several human brain atlases, and to encode emerging knowledge about structural connectivity in the brain. We highlighted several use cases of these extensions, including ontology reuse, neuroimaging data annotation, and organizing 3D brain models.

Highlights

The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization
We applied the ontological framework of the Foundational Model of Anatomy (FMA) to align the vocabularies used by several human brain atlases, and to encode emerging knowledge about structural connectivity in the brain
Our goal is to provide such a framework for human neuroimaging that will facilitate the integration and harmonization of data registered to standard coordinate systems with labels for structures in human brain atlases

Summary

Introduction

The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. In this paper we describe recent enhancements to the neuroanatomical content of the FMA that models cytoarchitectural and morphological regions of the cerebral cortex, as well as white matter structure and connectivity. This modeling effort is driven by the need to correlate and reconcile the terms used in neuroanatomical labeling protocols. The labeling protocols used to define the boundaries of neuroanatomical regions can vary widely across brain atlases, so collections of anatomical entities from different labeling schemes do not always stand in a relation that allows a one-to-one mapping. Data annotated with labels from different atlases are difficult to compare based on labels alone

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Conclusion