GFO Part I Basic Principles
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15.2 Application of GFO to Biomedical Ontologies

Various domain-specific ontologies have been developed within the biomedical domain over the last years. For example, Open Biomedical Ontologies33 (OBO) is an umbrella organization for various ontologies covering domains such as the anatomy of individual species, celltypes (6), or molecular functions of genes and gene products (3).

The rapid growth of biomedical ontologies in size and number leads to the problem of ontology and data integration. How is it possible for different ontologies to interoperate? How can the content of different ontologies be retrieved in a single query?

In contrast to GFO, most biomedical ontologies are represented using a weak formalism. They can be represented as a directed acyclic graph (DAG). In a DAG, the categories are represented as nodes, and the relations between the categories are represented as edges. For example, the relation that ``nucleus'' is part of a ``cell'' is represented by two nodes, ``nucleus'' and ``cell'', which are linked by a directed edge, which is labeled ``part-of''. These graphs are commonly used in conjunction with a minimal set of axioms, such as transitivity or symmetry.

Many of the relationships used in these biomedical ontologies can be defined in GFO. For example, the mereological relations, like part-of, are already present in GFO. It is often the case that the semantics of relations using the same name differ between different biomedical ontologies. Aligning two ontologies that use a relation with the same name in different ways requires a formalism that will allow for a representation of the differences in the two ontologies used. These differences are beyond the expressiveness of DAGs, but can be made precise within first order logic using the conceptualization that is provided by the GFO.

In (14), GFO has already been used to represent knowledge about biological functions in the Gene Ontology(3), the Celltype Ontology (6) and the Chemical Entities of Biological Interest (ChEBI) Ontology (12). As shown in (13,14), the GFO's method for describing functions using requirements, goals and a role universal leads to greater expressiveness, and the possibility for more fine-grained analyses of biological phenomena. In addition, it is possible to use this analysis to re-analyze the so-called annotation relation34.

Furthermore, GFO plays a role in a curation framework for biomedical ontologies, which is currently under development35. This framework is based on a semantic wiki, and it allows for the formal representation of relations between concepts within the wiki. These relations are typed, in the sense that their arguments are restricted to categories, and these are based on GFO. In a sense, a core ontology is derived from the content upon which the semantic wiki is based.

GFO, however, provides the possibility for further uses in biomedical ontologies. In (14), the construction of a domain ontology based on GFO's treatment of functions is proposed. GFO can provide the conceptual means to ease the construction of additional domain-specific ontologies, and provide a common framework that will be compatible with a majority of the biomedical ontologies, in order to assist in the integration of different ontologies, and to make them amenable for automated reasoning.

Robert Hoehndorf 2006-10-18


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