Rule Set for Telomere Ontology to MFO

Figure 11: The description of MFO, as shown in SWRLTab. Data sources such as BioModels could make use of this representation. Additionally, output of the query response occurs via this syntactic ontology, allowing output formatted in SBML. Filters on the mappings are displayed in the SWRLTab representation as constraints within the rules themselves. This is not a complete rule set for the entirety of MFO, merely a complete set of rules for describing the use cases.
Image mfo-rules-swrltab

Unlike the other syntactic ontologies, MFO is used for output of the query response. While all syntactic ontologiesin rule-based mediation are capable of being used as both inputs and outputs, the use cases presented here specify that in this instance, MFO is used for output. Therefore, the mappings presented in Figure 11 are from telomere ontology to MFO. Please note that all of the rules described in Table 2 have not yet been loaded into the SWRLTab implementation shown in Figure 11. These are imminent, and the image above will change shortly to reflect the implementation of the DL rules.


Table 2: The description of the SBML syntactic ontology, MFO. Read across, each row is a single rule which, when taken together, form the complete description of MFO. The first column contains mappings, where the left-hand side is a class or relation from MFO and the right-hand side is its equivalent in telomere ontology. The second column contains any filters on the syntactic ontology to further restrict what instances are allowed into telomere ontology. Data sources such as BioModels make use of this representation. The dots at the end of the table indicate that this is not a complete rule set for the entirety of SBML, merely a complete set of rules for describing the use cases.
$ Descr(MFO)$
Mappings (MFO $ \rightarrow$ Telomere Ontology) Filters
$ Species(X) \Rightarrow PhysicalEntity(X)$
$ Annotation(X) \Rightarrow Taxon(X)$
$ SpeciesReference(X) \Rightarrow Participant(X)$
$ Reaction(X) \Rightarrow DirectedReaction(X)$
$ Compartment(X) \Rightarrow BiologicalLocalization(X)$
$ hasNestedSbmlPart(X,Y) \Rightarrow hasParticipant(X,Y)$ $ X \sqsubseteq Reaction$
$ (^{-}hasNestedSbmlPart \circ ^{-}hasNestedSbmlPart \circ hasAnnotation)(X,Y) \Rightarrow hasTaxon(X,Y)$ X $ \sqsubseteq Species \sqcap Y \sqsubseteq startsWith(\lq\lq uri:miriam:taxonomy:'')$
$ (hasCompartmentId \circ ^{-}hasId)(X,Y)\Rightarrow located(X,Y)$
$ (hasSpeciesId \circ ^{-}hasId)(X,Y) \Rightarrow hasPhysicalEntity(X,Y)$
...


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