BioGRID stores 24 different types of interactions, and pairs of interacting entities can be retrieved in PSI-MIF 2.5 format [16]. To fulfil the requirements of Use Case 2, the physical PPI data were ultimately used, where both participants were proteins. PSI-MIF can easily be used to generate a simple syntactic ontology. The BioGRID syntactic ontology is shown in Figure 3.2. Figure 3a shows an overview of the classes created for the BioGRID syntactic ontology, while Figure 3b shows the conditions applied to the
class. This syntactic ontology was generated using the XMLTab plugin in Protégé 3.4 RC1 and written in OWL-DL.
[Overview of the PSI-MIF syntactic ontology.]
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Pathway Commons and BioGRID store very similar types of data, and yet have a different underlying representation. This exemplifies the challenges facing the biomedical community that can be answered with semantic data integration: very similar data types are being exported in two different data formats.
Very recently (March 2009), Pathway Commons began importing BioGRID data, after this paper was written. This will make it easier in future to retrieve information. Future work will instead focus on adding interaction information from other interaction databases.
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