1. Principles, Ontological Framework and Implementation of the FMA Ontology
C. Rosse and J.L.V. Mejino. The Foundational Model of Anatomy Ontology. In A. Burger, D. Davidson, and R. Baldock, editors, Anatomy Ontologies for Bioinformatics: Principles and Practice, volume 6, pages 59-117, London, 2007. Springer.
Rosse C, Mejino JVL. 2003. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 36:478-500.
A comprehensive account of the FMA which replaces a concept-based view with a reality-based representation of more than 75,000 multiply located anatomical entities (universals) which exist in the idealized (canonical) instances that they subsume. In addition to the taxonomy component of the FMA, it gives an account of the structural and developmental relationships that exist between anatomical entities.
Rosse, C., M. Ben-Said, K.R. Eno, J.F. Brinkley 1995 Enhancements of Anatomical Information in UMLS Knowledge Sources . In: Gardner RM, editor. Proc 19th Annu Symp Comput Appl Med Care (SCAMC 95). Philadelphia : Hanley & Belfus,1995: 873-877.
The first report on the initial version of the FMA (Digital Anatomist Symbolic Knowledge Base ) and its relation to the anatomical content of National Library of Medicine's Unified Medical Language System (UMLS).
Rosse, C., Shapiro, L.G. and Brinkley, JF. 1998. The Digital Anatomist Foundational Model: Principles for Defining and Structuring its Concept Domain. In Chute EG (ed): A paradigm shift in health care information systems: clinical infrastructures for the 21st century. JAMIA Symposium Supplement. '98: 820-824
A preliminary account of principles for guiding the establishment of an ontology of anatomy.
Rosse C, Mejino JL, Modayur BR, Jakobovits R, Hinshaw KP, Brinkley JF. 1998. Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist Symbolic Knowledge Base. J. Am. Med. Informatics Assoc.5:17-40.
Distinguishes two meanings of the term ‘anatomy': 1. the structural organization of a biological organism; and 2. the scientific discipline that studies this organization, thus separating epistemology and reality. Proposes a comprehensive ontology of the physical entities that constitute a human body based on the structural properties by which anatomical entities can be sorted into classes and distinguished from one another.
Mejino, J.L.V. and Rosse ,C. 1999. Conceptualizations of Anatomical Spatial Entities in the Digital Anatomist Foundational Model. J. Am. Med. Assoc. AMIA '99 Symp. Suppl. '99: 112-116.
The FMA is the only ontology that explicitly distinguishes among physical entities between those that have or do not have mass and treats anatomical spaces, surfaces, lines and points as universals or classes.
Michael J, Mejino JLV, Rosse C. 2001. The role of definitions in biomedical concept representation. JAMIA Symposium Supplement. '01:463-467.
Advocates the need for Aristotelian definitions in biomedical ontologies and illustrates the employment of genus and differentiae for establishing classes of anatomical entities in the FMA
2. Extensions of the FMA Ontology to neuroanatomy and microscopic anatomy
Martin RF, Mejino JLV, Bowden DM, Brinkley JF, Rosse C. 2001. Foundational model of neuroanatomy: its implications for the Human Brain Project. JAMIA Symposium Supplement. '01:438-442.
Martin RF, Rickard K, Mejino JLV, Agoncillo AV, Brinkley JF, Rosse C. The evolving neuroanatomical component of the Foundational Model of Anatomy. In proc, AMIA fall symposium. 2003; 927.
The FMA is the only ontology that fully integrates neuroanatomy from the cellular to the macroscopic levels for both the central and peripheral nervous systems with the anatomy of other parts of the body.
Agoncillo AV, Mejino JLV, Rickard KL, Detwiler LT, Rosse C. Proposed classification of cells in the Foundational Model of Anatomy. Proc AMIA Symp.2003; 775.
The cellular and subcellular entities represented in the FMA compare in number to those in the Gene Ontology. Correlation of these two ontologies is being pursued as illustrated by the next reference.
Gennari, J.H., Silberfein, A., and Wiley, J.C. (2005). Integrating genomic knowledge sources through an anatomy ontology. Proceedings of the Pacific Symposium on Biocomputing 2005, pp. 115-126
Travillian RS, Rosse C, Shapiro LG. An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy. Proc AMIA Symp. 2003; 669-673.
Travillian RS, Gennari JH, Shapiro LG. Of mice and men: design of a comparative anatomy information system. Proc AMIA Symp. 2005.
Extension of the FMA to the anatomy of other mammalian species, particularly to that of the mouse, is being pursued by our own as well as other groups .
Cook DL, Mejino JLV Jr, Rosse C. Rosse C. Evolution of a Foundational Model of Physiology: Symbolic Representation for Functional Bioinformatics . In Proceedings, MedInfo 2004 , pages 336-340, San Francisco , CA .
The FMA furnishes the participants in all physiological and pathological processes.
Kumar A, Yip YL, Smith B, Marwede D, Novotny D. An ontology for carcinoma classification for clinical bioinformatics. Stud Health Technol Inform. 2005;116:635-40.
The FMA is used as a basis for classification schemes of carcinomas, as an example of pathologies.
Smith B, Kumar A, Ceusters W, Rosse C. On carcinomas and other pathological entities. Comparative and Functional Genomics 2005
Presents an ontological framework for the derivation of pathological structures from anatomical entities represented in the FMA.
Rosse C, Kumar A, Mejino JLV, Cook DL, Detwiler LT, Smith B.2005. A strategy for improving and integrating biomedical ontologies. In, Proceedings, American Medical Informatics Association Fall Symposium, Washington.DC.
A high-level or meta-ontology is proposed through the integration of Basic Formal Ontology and the FMA, which encompasses anatomical and pathological continuants as well as physiological and pathological occurrents. The framework of this Ontology of Biomedical Reality (OBR) takes account of organismal entities in the purview of the basic biomedical sciences.
Mejino, Jose L V and Martin, Richard F and Detwiler, Landon T and Brinkley, James F (2007) Challenges in Reconciling Different Views of Neuroanatomy in a Reference Ontology of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, Chicago, IL.
3. Relations in the FMA Ontology and their influence on other ontologies
Neal, P.J., Shapiro, L.G. and Rosse, C. 1998. The Digital Anatomist Spatial Abstraction: a scheme for the spatial description of anatomical entities. In Chute CG (ed): A paradigm shift in health care information systems: clinical infrastructures for the 21st century. JAMIA Symposium Supplement. '98:423-427.
The first publication that adopts for the domain of anatomy distinctions between boundary and part relations from general spatial theory.
Mejino JLV Jr, Agoncillo AV, Rickard KL, Rosse C. Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy. Proc AMIA Symp. 2003;450-454.
The FMA accommodates multiple, overlapping ways to decompose anatomical entities into their parts to accord with the different contexts in which anatomy is applied in biomedicine.
Smith B, Rosse C. The role of foundational relations in the alignment of biomedical ontologies. In Proceedings, MedInfo 2004 , pages 444-448, San Francisco , CA .
The relations IS_A and HAS_PART are formalized for instances and classes of the FMA.
Mejino JLVJ, Rosse C. Symbolic modeling of structural relationships in the Foundational Model of Anatomy. In: Proceedings, First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). Whistler Mountain , Canada ; 2004.
Natural language definitions are provided for a whole suite of structural relationships implemented in the FMA.
Smith B, Mejino Jr. JLV, Schulz S, Kumar A, Rosse C: Anatomical Information Science. In Cohn AG, Mark DM (editors): Spatial Information Theory; Proceedings of International Conference, COSIT 2005, Ellicottville, NY, USA, September 14-18, 2005. p.149.
Formalizes and extends the definitions of the FMA's suite of structural relations.
Smith B , Ceusters W , Klagges B , Köhler J , Kumar A , Lomax J , Mungall C , Neuhaus F , AL Rector , Rosse C.: Relations in biomedical ontologies. Genome Biology 2005, 6: R46 doi:10.1186/gb-2005-6-5-r46
Redefines some of the relations dealt with by the previous two publications in the context of Open Biomedical Ontologies.
Donnelly M, Bittner T, Rosse C. 2005. A formal theory for spatial representation and reasoning in biomedical ontologies. Artif Intell Med.
Evaluates spatial representation of anatomy in the FMA and GALEN and proposes and extension of formal spatial theory to anatomy.
4. Querying the FMA Ontology
Mork P, Brinkley JF, Rosse C. 2003. OQAFMA querying agent for the Foundational Model of anatomy: providing flexible and efficient access to a large semantic network. J Biomed Inform 2003;36:501-517 .
Distelhorst G, Srivastava V, Rosse C, Brinkley JF. A Prototype Natural Language Interface to a Large Complex Knowledge Base, the Foundational Model of Anatomy. Proc AMIA Symp. 2003: 200-204
Detwiler LT, Mejino JLV, Rosse C, Brinkley JF. Efficient web-based navigation of the Foundational Model of Anatomy. Proceedings AMIA Symposium. 2003; 829.
Detwiler LT, Chung E, Li A, Mejino JLV Jr, Agoncillo AV, Brinkley JF, Rosse C. A Relation-Centric Query Engine for the Foundational Model of Anatomy. In Proceedings, MedInfo 2004 , pages 341-345, San Francisco , CA
5. Evaluation of the FMA Ontology
Shapiro LG, Chung E, Detwiler T, Mejino JLV, Agoncillo AV, Brinkley JF, Rosse C. Processes and problems in the formative evaluation of an interface to the Foundational Model of Anatomy knowledge base. J Am Med Inform Assoc. 2005; 12:35 -46.
Describes a software tool for querying the FMA and illustrates the FMA's capability for providing correct answers to multiple-choice exam questions selected from published compendia, even when these answers have to be inferred (reasoned) from existing information in the FMA.
Smith B, Köhler J, Kumar A: On the application of formal principles to life science data: A case study in the Gene Ontology. DILS 2004: Data Integration in the Life Sciences . 2004;:124-139.
Contrasts the FMA's sound ontological structure with shortcomings of the Gene Ontology
Zhang S, Bodenreider O . Law and order: Assessing and enforcing compliance with ontological modeling principles. Computers in Biology and Medicine 2005.
Evaluates the FMA as a case study and finds it compliant with 10 ontological principles.
6. Uses and Selected Applications of the FMA Ontology
6.1. Research in ontologies, informatics and computer science
Mejino, J.L. and Rosse, C. 1998. The Potential of the Digital Anatomist Foundational Model for assuring consistency in UMLS sources. In Chute EG (ed): A paradigm shift in health care information systems: clinical infrastructures for the 21st century. JAMIA Symposium Supplement. '98:825-829
Agoncillo, A., Mejino JLV, 1999. Rosse C. Influence of the Digital Anatomist Foundational Model on Traditional Representations of Anatomical Concepts. J. Am. Med. Assoc. AMIA '99 Symp. Suppl. '99: 2-6.
Noy NF, Mejino JLV Jr., Musen MA, Rosse C. 2004. Pushing the envelope: challenges in frame-based representation of human anatomy. Data & Knowledge Engineering 2004;48:335-359.
Illustrates how the need for representing the richness of anatomical information in the FMA has provided the motivation for enhancing the expressivity of the Protégé knowledge representation system.
Peter Mork, Philip A. Bernstein: Adapting a Generic Match Algorithm to Align Ontologies of Human Anatomy. ICDE 2004: 787-790
The FMA serves as a test-bed for developing a generic model matching algorithm.
Songmao Zhang, Peter Mork, Olivier Bodenreider: Lessons learned from aligning two representations of anatomy. KR-MED 2004: 102-108
A case study in ontology alignment using the anatomy component of GALEN and the FMA
Songmao Zhang,Olivier Bodenreider: Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain. Pacific Symposium on Biocomputing 2004 : 250-261
Zhang S, Bodenreider O . Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. Proc AMIA Symp 2005
Aleksovski Z, ten Kate W, van Harmelen F. (2006). Exploiting the structure of background knowledge used in ontology matching. Ontology Matching Workshop, ISWC, Athens, Georgia, USA.
Rickard, K. L. and Mejino, J. L. V. and Martin, R. F. and Agoncillo, A. V. and Rosse, C. (2004) Problems and Solutions with Integrating Terminologies into Evolving Knowledge Bases. In Proceedings, MedInfo 2004 , pages 420-424, San Francisco, CA.
Conceptual and technical challenges in integrating Terminologia Anatomica, a hard copy terminology with the FMA
Jakobovits RM, Rosse C, Brinkley JF. 2002. WIRM: An Open Source Toolkit for Building Biomedical Web Applications. J. Am. Med. Informatics Assoc;9:557-570.
Detwiler LT, Brinkley, JF. (2006). Custom views of reference ontology. In Proceedings, American Medical Informatics Association Fall Symposium, Bethesda, MD.
Brinkley JF, Detwiler LT, Gennari JH, Rosse C, Suciu D. (2006) A framework for using reference ontologies as a foundation for the semantic web. In Proceedings, American Medical Informatics Association Fall Symposium, Bethesda, MD.
Detwiler LT, Rosse C. (2005) Knowledge base version reintegration. In Proceedings, American Medical Informatics Association Fall Symposium, Washington DC .
6.2. Research in file format conversion
Golbreich C, Zhang S, Bodenreider O. (2006) The foundational model of anatomy in OWL: Experience and perspectives.
Journal of Web Semantics, Web Semantics: Science, Services and Agents on the World Wide Web, Volume 4, Issue 3, Pages 181-195.
Dameron O, Rubin DL, Musen M. (2005). Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. In Proceedings, American Medical Informatics Association Fall Symposium, 181-185, Washington DC .
6.3. Research in biomedical imaging
Brinkley, J.F. and Rosse, C. 1997. The Digital Anatomist distributed framework and its applications to knowledge-based medical imaging. J. Am. Med. Informatics Assoc.4:165-183.
Brinkley JF, Rosse C. 2002. Imaging informatics and the Human Brain Project: the role of structure. Year Book of Medical Informatics. Haux R, Kulikowski C. editors: Year Book of Medical Informatics ‘02. Schattauer and the International Medical Informatics Association. Stutgart. 131-148.
Brinkley JF, Rosse C. 2002. Imaging and the Human Brain Project: a review. Methods of Information in Medicine 41:245-260.
6.4. Design of information systems
Brinkley, J.F., Bradley, S.W., Sundsten, J. W. and Rosse, C. 1997. The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases. Computers in Biomed. Res. 30:472-503.
Brinkley, J.F., Wong, B.A., Hinshaw, K.P. and Rosse, C. 1999 Design of an Anatomy Information System IEEE 19:3 pp 38-48.
Brinkley, J.F. and Rosse, C. 1998. Requirements for an on-line knowledge-based anatomy information system. In Chute EG (ed): A paradigm shift in health care information systems: clinical infrastructures for the 21st century. JAMIA Symposium Supplement. '98:892-896
6.5. Clinical Informatics
Kalet, I.J., Wu, J., Lease, M., Austin-Seymour, M.M., Brinkley, J.F., and Rosse, C. 1999 Anatomical information in radiation treatment planning. J. Am. Med. Assoc. AMIA '99 Symp. Suppl. '99: 291-295.
Jakobovits R, Brinkley JF, Rosse C, Weinberger E. 2001. Enabling clinicians, researchers and educators to build custom web-based biomedical information systems. JAMIA Symposium Supplement. '01:279-283
The Digital Anatomist Interactive Atlases: http://sig.biostr.washington.edu/projects/da/
The Digital Anatomist Interactive Atlases integrate the FMA with 3D graphical models and other images of anatomy enabling knowledge-based navigation and interactivity. The atlases are used in 95 countries and experience an average of 20,000 hits per day.
Wong, B.A., Rosse, C., and Brinkley, J.F. Semi-automatic Scene Generation using the Digital Anatomist Foundational Model. J. Am. Med. Assoc. AMIA '99 Symp. Suppl. 1999: 637-641
Campbell B, Rosse C, Brinkley JF. 2001. The virtual anatomy lab: a hands-on anatomy learning environment. In Westwood JD , Miller Hoffman H, Mogel JT, Stredney D, Robb RA. (editors) Medicine meets virtual reality 2001. IOS Press Amsterdam . pp 85-87.