The Digital Anatomist
Foundational Model of Anatomy (FMA)

Project site: http://fma.biostr.washington.edu
Express Licensing is available for the FMA.

Description

The Digital Anatomist Foundational Model of Anatomy (FMA) is an evolving computer-based knowledge source of anatomical information developed and maintained by the Structural Informatics Group at the University of Washington. Fundamental to medical science, knowledge of anatomy must be consistent across disciplines, educational resources, and computer applications. The FMA was developed not only to contribute to the use of standardized language in the medical field, but also to build computer-based inference into biomedical applications.

Currently containing nearly 70,000 concepts (more than 110,000 terms), the FMA represents anatomical entities ranging from biological macromolecules to cells, tissues, organs, organ systems, and major body parts, including the entire body. It improves upon the currently available computable anatomical resources in both detail and scope of represented knowledge. The FMA contains anatomical concepts and relationships necessary to model the structure of the entire human body. This knowledge is structured in a form readable not only by humans but by software applications as well. In summary, the FMA serves as a reference ontology for biomedical informatics and provides the template for 1) representing the structure of other non-human vertebrate species used as experimental models of human diseases, and 2) developing ontologies of embryonic development, physiological functions, and disease processes.

To learn more about the FMA, please visit the project website:
http://fma.biostr.washington.edu

Technological Benefits

The Digital Anatomist Foundational Model of Anatomy (FMA) differs greatly from traditional, “hard copy” sources of anatomical information such as atlases, text books, dictionaries, thesauri or term lists while incorporating the most appropriate concepts from such sources. Although the content of hard copy sources may be transferred to electronic media, they will not lend themselves to the kinds of information navigation afforded by a dynamic system, such as this ontology based on formal semantics; nor will they support the processing of queries. Rather than aiming to standardize terminology, the FMA’s goal is to provide a logical and coherent representation of the physical organization of the body (i.e., its anatomy) through specifying component parts of the body and the structural relationships that exist between these anatomical entities. The FMA accommodates all naming conventions, enabling users to navigate and query the knowledge base, regardless of the terms they use (provided these terms are current in professional biomedical discourse).

As a knowledge source, the FMA can furnish anatomical knowledge to be included in any ‘smart’ application in the biomedical field that aims to operate at a level that requires inference (i.e., reasoning). There is an emerging need for the development of such applications in a number of fields, including anatomy education, the planning of chemo- and radiation therapy, endoscopic surgery, and many other computer-assisted tasks. Adoption of the FMA will improve communication among biomedical applications by standardizing terminology and by providing a common anatomical reference model. The FMA’s ontological framework also provides the foundation upon which intelligent software applications can rely for reasoning about the structure of the human body.

The FMA is a resource for developers of:

• Biomedical ontologies in the basic and clinical sciences
• Experiment management systems in bioinformatics and clinical informatics
• Educational software
• Systems for the management of clinical information
• Biomedical research applications
• Many others, visit the project website to learn more

Development Background

The FMA grew from the research and teaching experience of Cornelius Rosse, Professor Emeritus of Biological Structure and Biomedical Informatics at the University of Washington. In the early 1980s, Dr. Rosse redirected his scholarly activities from biological bench research to the representation of anatomical knowledge in computer-processable form. Based on pioneering work by Drs. John Prothero, John Sundsten and David Conley, which resulted in the in the first realistic reconstructions of parts of the human body through 3D computer graphics, Dr. Rosse established the Digital Anatomist project. To complement graphical representations of anatomy with symbolic knowledge, Dr. Rosse developed the Foundational Model of Anatomy to serve as a resource for knowledge-based applications in biomedical research, education and clinical practice, which have a need for machine-based knowledge about the structure of the body. The representation and integration of image and text-based knowledge has provided a fertile field for research in a number of areas of computer science and informatics, which are pursued by the Structural Informatics Group directed by James F. Brinkley, M.D., Ph.D.

Future Goals

Scaling the FMA to Major Initiatives

Although the Digital Anatomist Foundational Model of Anatomy was released for general use only in November 2003, there are a number of initiatives in various stages of development in which the FMA is playing a seminal role:

• In identifying the development of an ontology for neuroanatomy as a major goal, The Human Brain Project, spearheaded by the National Institutes of Mental Health, has selected the FMA as a prototype for such an ontology. Preliminary work demonstrates the scalability of the FMA’s semantic structure and implementation schema to the neuroanatomy domain. Read the report, Foundational Model of Neuroanatomy, to learn more.
• Under the title "Digital Human," the Federation of American Scientists is spearheading an initiative for “unifying” biomedical ontologies in order to support the modeling of cellular and higher level physiological processes. This initiative has singled out the FMA as the candidate ontology to serve as a bridge and reference for aligning existing and evolving ontologies, recognizing that the structural context and scope of the FMA make it the best candidate for this role.
• DARPA, under the aegis of the Department of Defense, has selected the FMA to provide the global conceptual architecture for the Virtual Soldier project, a multi-institution national initiative for establishing the computational and information exchange infrastructure required for simulating the health consequences of battlefield injuries and predicting a soldier’s physiological status.
• A critical requirement for the validation of animal models of human disease is the verification of anatomical equivalences ranging from genes to cells, tissues, organs, organ systems, and body parts. In response to a need by the National Cancer Institute’s Consortium for Mouse Models of Human Cancer (MMHCC), the FMA has begun to develop, as a demonstration project, symbolic representations of the anatomy of the mouse, mirroring human anatomy in the FMA.

Current Uses and Applications

A number of projects have made use of the FMA even before its official release. These projects fall into the following classes:

Research in Knowledge Modeling

Several intramural research projects at the National Library of Medicine, National Institutes of Health, used the FMA or its UW Digital Anatomist component. For example:

• L. Zhang and Bodenreider used the FMA as one of two large ontologies for the development of lexical methods to map large ontologies to one another, taking into account their semantic structure as well as their terms.
• Bodenreider and Burgun used the FMA to characterize definitions of anatomical concepts and compare these definitions with those in other large ontologies, including WordNet.
• Bean, Rindflesch and Sneiderman made use of the FMA in their research for developing methods for the automatic semantic interpretation of anatomical spatial relationships.
• L. Zhang, Perl, Halper, and Geller at the New Jersey Institute of Technology made use of the classes defined in the FAM for proposing enhancements of UMLS semantic types.
• Beck and Schulz, Freiburg University, Germany, developed methods for transcribing frame based system to Description Logic using the FMA as the substrate.
• Smith and his associates at Institute for Formal Ontologies, Leipzig Germany, reference the FMA in their research as a prototype domain ontology that conforms to ontological principles.
• At Microsoft® Research, Bernstein and Mork used the FMA for developing automated methods for model matching and comparing it with GALEN’s common reference model (CRM), a different approach to the same problem pursued by S. Zhang and Bodenreider at NLM.

Clinical Research

Three clinically-related terminology projects were based on the FMA at the NLM:

• Rindfleasch and associates used it for representing arterial branching, information needed for cardiac catherisation;
• Sneiderman and associates based identification of terminology in medical texts on the FMA;
• Tringali and Hole based the standardization GI endoscopy terminology on the FMA.

Other clinical applications using the FMA include:

• At the UW, Teng and Kalet used the FMA for delineation of the head and neck lymph node region for radiation treatment planning;
• Brinkley, Ojeman and colleagues rely on the neuroanatomy component of FMA for neurosurgery;
• At the University of Rennes, France, Dameron and associates correlate their brain ontology for neurosurgery with the FMA.

Grants

The FMA has been an important component of a large number of grant applications at the UW and elsewhere, including the following:

• Human Brain Project: cortical language mapping (UW)
• Embryology and developmental biology (UW)
• Foundational Model of Physiology (UW)
• Planning grant for Center for Structural Informatics (UW)
• Virtual Soldier Contract funded by DARPA (UW and Stanford University)
• Diagnostic standards for craniofacial disorders (UW)
• Web service for prostate cancer diagnosis (Johns Hopkins)
• Annotated anthropological osteology databases (Universities of Arizona and Nebraska)
• Editing UMLS vocabularies (New Jersey Institute of Technology)

National and International Organizations

The FMA is playing a seminal role in national and international projects, such as the following:

• Standard Ontologies for Functional Genomics (England)
• Digital Human Project coordinated by the Federal Association of Scientists
• Virtual Soldier multi-institution national project, sponsored by DARPA

Digital Ventures' Role

Digital Ventures will license portions or all of the FMA to groups interested in building ontologies from the FMA, or using the FMA as a base. Digital Ventures will also manage rights and revenue of the project as well. Licensing revenue will be used to maintain and support the FMA.

Contact

Email: fma@sig.biostr.washington.edu

Jose L.V. Mejino Jr., MD
or
Landon T. Detwiler
Structural Informatics Group (SIG)
Dept. of Biological Structure
University of Washington School of Medicine
Box 357420
Seattle, WA 98195
Phone: 206-543-7118; 206-616-2336
Fax: 206-543-1524
Email: fma@sig.biostr.washington.edu
Website: http://fma.biostr.washington.edu

Published News

For a better understanding of the FMA, we recommend the following papers:

1. Rosse C., Mejino J.L.V. Jr. 2003. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J Biomed Inform. (In press).
http://sigpubs.biostr.washington.edu/archive/00000135/

2. Michael J., Mejino J.L.V., Rosse C. 2001. The role of definitions in biomedical concept representation. JAMIA Symposium Supplement. '01:463-467.
http://sigpubs.biostr.washington.edu/archive/00000147/

3. Rosse C., Mejino J.L., Modayur B.R., Jakobovits R., Hinshaw K.P., Brinkley J.F. 1998. Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist Symbolic Knowledge Base. J. Am. Med. Informatics Assoc.5:17-40.
http://sigpubs.biostr.washington.edu/archive/00000096/

4. Mejino, J. L. V. and Agoncillo, A. V. and Rickard, K. L. and Rosse, C. (2003). Representing complexity in part-whole relationships within the Foundational Model of Anatomy. JAMIA Symposium Supplement. ’03: (In press). http://sigpubs.biostr.washington.edu/archive/00000140/

There is also a variety of publications about the FMA available at the project website: http://sig.biostr.washington.edu/%7Eonard/SIGPub/AMIAPub.html