MFO is a syntactic ontology representing constraints from SBML, SBO and the SBML manual in OWL [15]. Since the original publishing of this research, reasoning and inference time has been dramatically reduced, and more aspects of the three main sources of rules and constraints in SBML have been added. Of particular relevance to this work, classes to describe the annotation elements of SBML have been added. Annotation elements are important to the use cases, as it is in these elements where information such as cross references and taxonomic information reside.
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Part of the asserted hierarchy is shown in Figure 6b, while the computer-readable conditions on the class, which represents the SBML species element, is shown in Figure 6a. Figure 6c shows a portion of the human-readable comments on the same class. MFO has a dual purpose for the presented use cases: firstly, it acts as the format representation for any data stored in SBML format such as entries from the BioModels database or large-scale networks in SBML format such as [17], and secondly it is used to return the query response in SBML. As this was the only S. cerevisiae model for RAD9 currently present in BioModels, no other entries from that database were used as input.
BioModels is an example of a single data source that could be loaded into a core ontology from more than one syntactic ontology. BioModels data are available in both BioPAX and SBML format, and both of these formats have a syntactic ontology. For each situation where more than one syntactic ontology could be used for a data source, a comparison of the richness of the formats is useful. In this instance, both syntactic ontologys need to be created: MFO for, at a minimum, output in SBML format; additionally, the BioPAX format is used for those databases that do not return SBML, such as Pathway Commons. Of the two, BioPAX has more of its constraints and relationships written with logic constructs, while SBML has the majority of its rules not in its XSD, but in the SBML manual and SBO. While more work is planned on a direct comparison of the quality of the input data via the SBML and BioPAX syntactic ontologies, an initial comparison does favour BioPAX.
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