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==User interface of Pharmacoracle's WebProtégé==
==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. We have downloaded the CPIC guideline from the PharmGKB API and converted the PharmGKB JSON-LD file to the OWL format that can be edited in WebProtégé. ===Curation of the functional status of star alleles===[[File:WebProtege user interface func status.png|thumb|Inspection of the gene function element ''Voriconazole CYP2C19: Decreased function'' in the ''Class Hierarchy'' shows which star alleles that have this functional status]] 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 the functional status that is provided by PharmGKB's API, and the drug and gene name is added because functional 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 of the ''Voriconazole CYP2C19:Decreased function'', pay attention to the ''OWL Entity Description Editor'' where we see 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. [[File:WebProtege user interface func status discussion.png|thumb|Comments can be added on a per-element basis to highlighted class elements in the Class Hierarchy, and the comment is by default sent by email to all curators.]] 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. ===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 reason for modelling phenotypes on a per gene basis is 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. [[File:WebProtege user interface phen.png|thumb|A model of the CPIC Phenotype by 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 appropriate language.[[File:WebProtege user interface guideline language.png|thumb|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'')]] ===Downloading the guideline in OWL format===[[File:WebProtege download owl ontology.png|thumb|A new revision of the OWL PGx guideline can be downloded from the ''History'' tab]] One way to download a new revision of the guideline, is to go to the ''History'' tab, click on the revision number that you want to download, and download this as a .zip-file. ===Try the Pharmacoracle WebProtégé yourself===Either contact us to [https://www.pgx.no/webprotege register a new account at the WebProtégé], and for access to test ontologies or try the Tutorial account: user: Tutorial password: Tutorial2018 The Tutorial account contains definitions of PGx alleles, PGx variants, functional status, phenotype and recommendations for the drug azathioprine. ==Using Desktop Protégé for curation of PGx recommendations==Collaborative curation of PGx recommendations can quite easily be performed in WebProtégé, as explained above (of course, as with any tool, curators have to get used to it).