List of Figures

  1. An overview of the rule-based mediation.
  2. Rule-based mediation in the context of SBML model annotation.
  3. The syntactic ontology used for BioGRID as created by the Protégé XMLTab plugin using a PSI-MIF XML file.
  4. The UniProtKB syntactic ontology. As with the other syntactic ontologies, instances represent the data itself, while classes represent the structure.
  5. The BioPAX ontology, filled with instances from Pathway Commons describing the near neighbours of RAD9. As with the other syntactic ontologies, instances represent the data itself, while classes represent the structure.
  6. MFO, the already-published OWL file used as the syntactic ontology for SBML.
  7. The telomere ontology, the core ontology for the use cases.
  8. The description of the PSI-MIF syntactic ontology, as shown in SWRLTab. Data sources such as BioGRID make use of this representation. 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 PSI-MIF, merely a complete set of rules for describing the use cases.
  9. The description of the UniProtKB syntactic ontology, as shown in SWRLTab. 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 UniProtKB, merely a complete set of rules for describing the use cases.
  10. The description of BioPAX, as shown in SWRLTab. Data sources such as Pathway Commons make use of this representation. 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 BioPAX, merely a complete set of rules for describing the use cases.
  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.
  12. SWRL Rule TUO_00001
  13. SWRL Rule TUO_00002.
  14. SQWRL Rule TUO_SQWRL_00003. TUO_SQWRL_00002 (not shown here) is a version of TUO_SQWRL_00003, but with UniProt as the database name rather than SGD.
  15. SQWRL Rule TUO_SQWRL_00001.
  16. SQWRL Rule TUO_SQWRL_00004.


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