Ontology:Foundational Model of Anatomy (FMA)

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Ontology Overview

Name: Foundational Model of Anatomy (FMA)
Description: The FMA is a reference ontology for the domain of anatomy. It represents the canonical, phenotypic structure of the human body, spatial-structure and relations that characterize the physical organization of the body at all salient levels of granularity.
Purpose: To make anatomical information in symbolic form available to knowledge modelers and other developers of applications for education, clinical medicine, electronic health record, biomedical research and all areas of health care delivery and management.
Organization(s): University of Washington
Author(s): Cornelius Rosse (M.D.; D.Sc.), Jose Leonardo (Onard) V. Mejino Jr. (M.D.), Augusto V. Agoncillo (M.D.), Richard F. Martin (Ph.D.), Salvacion Nance Quimosing-Madarang (M.D.)
Justification Built in a very structured and principled way.
Recommended by: Barry Smith
Submitted by: MichaelUschold
Competency Questions:
Domains:
Scenario:
Known issues: The OWL version has significant limitations, compared to the full version. See FMA in OWL
OntologyURI:

http://www.bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl (364)

Licensing: Available without charge under special license. See: FMA™ Ontology License Agreement
Web references:
Other references:

Long Description

What is the FMA Ontology?The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species.

The Foundational Model of Anatomy ontology is one of the information resources integrated in the distributed framework of the Anatomy Information System developed and maintained by the Structural Informatics Group[1]at the University of Washington.

PurposeThe Foundational Model of Anatomy ontology makes available anatomical information in symbolic (non-graphical) form to knowledge modelers and other developers of applications for education, clinical medicine, electronic health record, biomedical research and all areas of health care delivery and management. The intent is to assure - through the FMA - consistency, and ultimately standards, in anatomical class representation. Thus, the FMA is a biomedical informatics resource for developing the anatomy content of applications that target specific user groups; the FMA as such, is not designed as an end-user application for anatomy students, teachers or any other particular user group.

ComponentsThe Foundational Model of Anatomy ontology has four interrelated components:

1. Anatomy taxonomy (At),classifies anatomical entities according to the characteristics they share (genus) and by which they can be distinguished from one another (differentia)-designated in previous publications as the Anatomy ontology or Ao;

2. Anatomical Structural Abstraction (ASA),specifies the part-whole and spatial relationships that exist between the entities represented in At;

3. Anatomical Transformation Abstraction (ATA), specifies the morphological transformation of the entities represented in At during prenatal development and the postnatal life cycle;

4. Metaknowledge (Mk),specifies the principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.

Thus, the Foundational Model of Anatomy ontology may be represented by the abstraction:

FMA = (At, ASA, ATA, Mk)

ContentsThe Foundational Model of Anatomy ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA’s classes into a coherent symbolic model. The FMA is one of the largest computer-based knowledge sources in the biomedical sciences.

The most comprehensive component of the FMA is the Anatomy taxonomy (At). The dominant class in the At is Anatomical Structure. Anatomical structures include all material objects generated by the coordinated expression of groups of the organism’s own structural genes. Thus, they include biological macromolecules, cells and their parts, portions of tissues, organs and their parts, as well as organ systems and body parts (body regions).

Macroscopic anatomical structures are most comprehensively represented, whereas biological molecules have been entered mainly to illustrate the structural continuum from major body parts, such as the thorax, to biological macromolecules, such as myosin.

Portions of body substances, such as blood, CSF, intercellular matrix, and cytoplasm, are defined in terms of their relationship to anatomical structures, and so are spaces, surfaces, lines and points that are associated with anatomical structures.

An objective of Foundational Model Explorer/Conducted Tour is to give an appreciation of the classes that subsume all these diverse classes within a continuous taxonomy.

Traditional sources do not include such a comprehensive taxonomy and do not explicitly define classes or types. Therefore we had to propose and define a number of classesor types of anatomical entities in the FMA for which there is no precedence in the traditional literature. There is an increasing correspondence between the FMA and traditional sources as one proceeds from the root of the At (Anatomical entity) toward the leaf classes of the FMA (e.g., heart, hepatocyte). For example, the FMA contains essentially all the terms of Terminologia Anatomica with an appropriate record of their derivation from this source.

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