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→Using WebProtégé for curation of PGx recommendations
Although the Functional Status can be manually modified by the curator, we believe that it is better to edit the Functional Status programmatically, based on the current PharmGKB functional status. By starting a discussion in the ''Comment'' view, suggestions can be included in the next version of the ontology:
[[File:WebProtege user interface func status discussion.png|frameless|Comments can be addedon a per-element basis to highlighted class elements in the Class Hierarchy, and the comment is by default sent by email to all curators.]] CPIC has recommended to use the term Phenotype for the metabolization status, transportation function or presence of a particular trait. Currently, this Phenotype is not a independent entity in the PharmGKB API. This means that for a drug that is affected by two genes, the Phenotype is aggregated for the two genes. We suggest to make a phenotype per gene, and make a recommendation for the combination of phenotypes. If more genes are added later, then it may be easier to expand the guideline. Another usecase is if we want to make a guideline that is not drug-dependent, but rather made for families of drugs for Psychopharmaca or Cancer, and involving very many different genes. As an example, we see that the phenotype ''Voriconazole CYP2C19:Intermediate Metabolizer'' is either a heterozygote Voriconazole CYP2C19:Increased function/No function or a Voriconazole CYP2C19:No function/Normal function:[[File:WebProtege user interface phen.png|frameless|Anticipating inclusion of CPIC definition of phenotypes in the PharmGKB API data, we have modelled the CPIC Phenotype by combining Functional Statuses]] As for the funtional status, we suggest that curators start a discussion if definitions of Phenotypes should be changed. Finally, the WebProtégé can be used for writing the actual prose of the recommendations. For instance, if the curator wants to translate the CPIC recommendations into another language, in the ''Class'' view, she can enter a property ''Recommendations'', a recommendation text and tagging it with the language:
