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→Pharmacoracle - a REST API based on the OWLAPI
The Pharmacoracle contains OWL ontologies that are based on CPIC recommendations provided by the [https://api.pharmgkb.org PharmGKB API], and which have been further curated to satisfy the [http://www.anx.no needs of the Department of Pharmacology at Oslo University Hospital].
The Pharmacoracle was implemented as an attempt to understand the field of pharmacogenomics, based on data from PharmGKB, and solving the same problem as PharmGKB's (discontinued?) PharmCAT software (previously accessible [https://github.com/PharmGKB/PharmCAT/wiki PharmGKBs PharmCAT softwarehere]), but in the context of the technology and clinical recommendations of our clinic. It may, however, be sensible to integrate PharmCAT in the Pharmacoracle, as soon as PharmCAT becomes the gold standard for VCF to PGx recommendations.
Queries to Pharmacoracle are written in the [https://www.w3.org/TR/owl2-manchester-syntax/ Manchester syntax] in the same way as for the [https://protegewiki.stanford.edu/wiki/DLQueryTab DL Query Tab] of [https://protege.stanford.edu/ Stanford's desktop Protégé]. An advantage of this approach is that it replaces the need of a separate rules engine (rules are to some extent built into the OWL semantics). A disadvantage is that the performance in a production environment may be suboptimal (slow). I believe that the standard way to use OWL is to make a triplet store database (RDF database, e.g. JENA) based on the OWL ontology. The rules can then be written as SPARQL queries to this database. It is possible that there are more lessons to be learned from the PGx clinical decision support [https://bioportal.bioontology.org/ontologies/GENE-CDS ontology of Mathias Samwald], which is at the core of the [https://doi.org/10.1371/journal.pone.0093769 Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care] of the [http://upgx.eu UPGx] project. They use the [http://trowl.org/ TrOWL reasoner] instead of the [http://www.hermit-reasoner.com/ HermIT] reasoner that is at the core of Pharmacoracle.
