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This tutorial gives an introduction to using [https://www.pgx.no/webprotege WebProtégé ] for curating PGx recommendations.
==User interface of Pharmacoracle's WebProtégé==
[[File:Webprotege main screen.png|thumb|Default ''Classes'' tab with views ''Class Hierarchy'', ''Class'', ''Comments'' and ''Project Feed'' is shown when opening a new OWL file or creating a new OWL ontology]]
When opening an OUS adapted PharmGKB OWL file PGx guideline in WebProtégé for the first time, we are presented to the ''Classes'' tab, containing four so-called views(frames)
* ''Class Hierarchy'' (a tree of all class entities of this ontology)
* ''Class'' (for description and editing of each class entity)
==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]]
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 register a new account at the WebProtégé], and contact us 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).
However, for quality assurance of PGx guideline semantics, we still need to use the desktop version of Protégé<ref>Support for semantic reasoning may be introduced in WebProtege at a later stage</ref>.
[[File:Protege compare guideline structure.png|thumb|By running the reasoner in the Desktop Protégé, we can ensure that the OUS guidelines and the CPIC guidelines are sematnically equivalent]]
