Digital anatomist foundational model of anatomy ontology
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Digital Anatomist Foundational Model of Anatomy Ontology . Development . Todd Detwiler SIG (Structural Informatics Group) at the University of Washington. Development Goals. Methods for representing spatial and symbolic information about the physical organization of the body.

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Development l.jpg
Development

  • Todd Detwiler

  • SIG (Structural Informatics Group) at the University of Washington


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Development Goals

  • Methods for representing spatial and symbolic information about the physical organization of the body.

  • To develop methods for using these structural representations as a basis for organizing non-structural information, under the hypothesis that structure is a logical foundation for organizing and inter-relating most information in biomedicine.

  • To develop web-accessible computer programs which utilize these representations to solve practical problems in clinical medicine, research and education.

  • To initially apply these methods to the domains of biological structure and neuroscience, including macroscopic, microscopic, cellular and subcellular anatomy, the structure of biological macromolecules, and the relationship of these structures to functional properties of the brain.


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FMA Description

  • Computer Based Knowledge System

  • Different from other traditional sources

    • Non-graphical symbols

    • ‘Pure’ Anatomy – No clinical cases, pathological lesions, physiologic functions

    • Class or type oriented vs. Term oriented


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Purpose of FMA

  • To provide consistency

  • To develop the anatomy content of applications, as opposed to being an end-user application

  • To serve as a ‘foundation’ for other non-anatomical ontologies


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Components

  • Anatomy taxonomy (At)

    • classifies anatomical entities according to the characteristics they share and by which they can be distinguished from one another

  • Anatomical Structural Abstraction (ASA)

    • specifies the part-whole and spatial relationships that exist between the entities represented in At

  • Anatomical Transformation Abstraction (ATA)

    • specifies the morphological transformation of the entities represented in At during prenatal development and the postnatal life cycle

  • Metaknowledge (Mk)

    • specifies the principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.


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Contents

  • 75,000 classes

  • 120,000 terms

  • 2.1 million relationship instances

  • 168 relationship types

  • Includes biological macromolecules, cells and their parts, tissues, organs and their parts, as well as organ systems and body parts (body regions)


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Contents

  • Macroscopic anatomical structures most comprehensively represented

  • Body substances defined in terms of relationships to structures

    • Blood, CSF, intracellular matrix, cytoplasm


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Anatomy Taxonomy (At)

  • Prerequisite for ASA and ATA components

  • Classes defined by ‘explicitly stated foundational principles’(http://www1.biostr.washington.edu/%7Eonard/AMIApapers/D005094.pdf)

  • Canonical Types are leaf classes of At

    • Head, heart, right ventricle, etc.

  • Must be assigned a semantic class by the ‘is-a’ relationship before entry into ASA or ATA

  • Most complete of the four parts


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Anatomical Structural Abstraction (ASA)

  • Currently under development

  • Four parts:

    • Dimensional Ontology (Do)

    • Boundary Network (Bn)

    • Part-of Network (Pn)

    • Spatial Association Network (SAn)

  • Part/whole relationships have been populated extensively, but not comprehensively (yet)

  • ‘Part-of’ relationships complete for most organs

  • Spatial relationships of location, containment and orientation are still being entered

    • Developing a tool to provide semi-automatic entry for adjacency relationships


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Anatomical Transformation Abstraction (ATA)

  • Very little data

  • Models embryonic and postnatal development


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Future Developments

  • Mayo Clinic

    • Clinical indexing and indexing output of biomedical experiments

  • Human Brain Project

    • Develop ontology for neuroanatomy

  • ATA phase of development





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