Processes and problems in the formative evaluation of an interface to the Foundational Model of Anatomy knowledge base.

The Digital Anatomist Foundational Model of Anatomy (FMA) is a large semantic network of more than 100,000 terms that refer to the anatomical entities, which together with 1.6 million structural relationships symbolically represent the physical organization of the human body. Evaluation of such a large knowledge base by domain experts is challenging because of the sheer size of the resource and the need to evaluate not just classes but also relationships. To meet this challenge, the authors have developed a relation-centric query interface, called Emily, that is able to query the entire range of classes and relationships in the FMA, yet is simple to use by a domain expert. Formative evaluation of this interface considered the ability of Emily to formulate queries based on standard anatomy examination questions, as well as the processing speed of the query engine. Results show that Emily is able to express 90% of the examination questions submitted to it and that processing time is generally 1 second or less, but can be much longer for complex queries. These results suggest that Emily will be a very useful tool, not only for evaluating the FMA, but also for querying and evaluating other large semantic networks.

Problems and solutions with integrating terminologies into evolving knowledge bases.

We have merged two established anatomical terminologies with an evolving ontology of biological structure: the Foundational Model of Anatomy. We describe the problems we have encountered and the solutions we have developed. We believe that both the problems and solutions generalize to the integration of any legacy terminology with a disciplined ontology within the same domain.

A relation-centric query engine for the Foundational Model of Anatomy.

The Foundational Model of Anatomy (FMA), a detailed representation of the structural organization of the human body, was constructed to support the development of software applications requiring knowledge of anatomy. The FMA's focus on the structural relationships between anatomical entities distinguishes it from other current anatomical knowledge sources. We developed Emily, a query engine for the FMA, to enable users to explore the richness and depth of these relationships. Preliminary analysis suggests that Emily is capable of correctly processing real world anatomical queries provided they have been translated into a constrained form suitable for processing by the query engine.

Representing complexity in part-whole relationships within the Foundational Model of Anatomy.

The Foundational Model of Anatomy (FMA) is a frame-based ontology that represents declarative knowledge about the structural organization of the human body. Part-whole relationships play a particularly important role in this representation. In order to assure that knowledge-based applications relying on the FMA as a resource can reason about anatomy, we have modified and enhanced currently available schemes of meronymic relationships. We have introduced and defined distinct partitions for decomposing anatomical structures and attributed the part relationships in order to eliminate ambiguity and enhance specificity in the richness of meronymic relationships within the FMA.

Proposed classification of cells in the Foundational Model of Anatomy.

A logical and principled representation of cell types and their component parts could serve as a framework for correlating the various ontologies that are emerging in bioinformatics with a focus on cells and subcellular biological entities. In order to address this need we have extended the Foundational Model of Anatomy (FMA)1,2 from macroscopic to cellular and subcellular anatomical entities. The poster will provide a live demonstration of this implementation.

The evolving neuroanatomical component of the Foundational Model of Anatomy.

In order to meet the need for an expressive ontology in neuroinformatics, we have integrated the extensive terminologies of NeuroNames and Terminologia Anatomica into the Foundational Model of Anatomy (FMA). We have enhanced the FMA to accommodate information unique to neuronal structures, such as axonal input/output relationships.