==Using WebProtégé for curation of PGx recommendations==
We suppose that the user has modified the ''Classes'' tab as explained above. We will use the drug voriconazole as an example.
By navigating in the ''Class Hierachy'' view, the curator can e.g. view the class element ''Voriconazole CYP2C19:Decreased function''. The naming is based on ===Curation of the functional status that is provided by PharmGKB's API, and the drug and gene name is added because functional of star alleles===[[File:WebProtege user interface func status is gene specific and possibly drug specific (may be sensible to make functional status independent of drug, cf. Voriconazole Phenotype below). In the definition png|thumb|Inspection of the gene function element ''Voriconazole CYP2C19:Decreased function'', pay attention to in the ''OWL Entity Description EditorClass Hierarchy'' where we see shows which star alleles that the ''Voriconazole CYP2C19:Decreased function'' is equivalent to a gene that has haplotype either CYP2C19*10, CYP2C19*16, CYP2C19*19, CYP2C19*25, CYP2C19*26 or CYP2C19*9:have this functional status]]
[[FileBy navigating in the ''Class Hierachy'' view, the curator can e.g. view the class element ''Voriconazole CYP2C19:WebProtege user interface func Decreased function''. (The naming is based on the functional status that is provided by PharmGKB's API, and the drug and gene name is added because functional statusis gene specific and possibly drug specific.png|frameless|Inspection )In the definition of the element ''Voriconazole CYP2C19: Decreased function'' from , pay attention to the Class Hierarchy describing PGx recommendations for ''OWL Entity Description Editor'' where we see that the drug ''Voriconazole]]CYP2C19:Decreased function'' is equivalent to a gene that has haplotype either CYP2C19*10, CYP2C19*16, CYP2C19*19, CYP2C19*25, CYP2C19*26 or CYP2C19*9.
Although the Functional Status [[File:WebProtege user interface func status discussion.png|thumb|Comments can be manually modified by the curator, we believe that it is better to edit the Functional Status programmatically, based added on the current PharmGKB functional status. By starting a discussion per-element basis to highlighted class elements in the ''Comment'' viewClass Hierarchy, suggestions can be included in and the next version of the ontology:comment is by default sent by email to all curators.]]
[[File:WebProtege user interface func status discussion.png|frameless|Comments Although the Functional Status can be added 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 per-element basis to highlighted class elements discussion in the Class Hierarchy''Comment'' view, and suggestions can be included in the comment is by default sent by email to all curatorsnext version of the ontology.]]
===Curation of the ''Phenotype'' of patient diplotypes===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 reason for modelling phenotypes on a per gene basis is if that 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|framelessthumb|Anticipating inclusion of CPIC definition A model of phenotypes in the PharmGKB API data, we have modelled the CPIC Phenotype by combining combination of pairs of Functional Statuses]]
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. As for the functional status, we suggest that curators start a discussion if definitions of Phenotypes should be changed.
===Curation of the ''Recommendation''===
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:
[[File:WebProtege user interface guideline language.png|framelessthumb|Translating a CPIC recommendation into another language can be achieved by adding a new property Recommendations with a recommendation text and a language (here ''no'')]]
==Using Desktop Protégé for curation of PGx recommendations==
