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The webprotege code base
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A way to import Jason files? #630

Open kokyriakidis opened 5 years ago

kokyriakidis commented 5 years ago

Is there any way to import jason files or convert it to supported schema?

matthewhorridge commented 5 years ago

@kokyriakidis do you mean JSON-LD? Or what?

kokyriakidis commented 5 years ago

Hmm sorry for my ignorance on the topic. I have plain JASON files downloaded from the "Clinical Guideline Annotations" with the name "DosingGuidlines.jason.zip" from here:

https://www.pharmgkb.org/downloads

I am actually following a guide on how to use webprotege for Pharmacogenomics and it states:

"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".

The problem is that I do not now how to download these files using the REST API and there are only the JASON files available to download

matthewhorridge commented 5 years ago

Can you post a link to the complete tutorial?

kokyriakidis commented 5 years ago

https://www.pgx.no/wiki/index.php/WebProtege

matthewhorridge commented 5 years ago

Thanks for the link. I was wondering how they converted this JSON to OWL, but it doesn't say. Im having trouble running it through the JSON-LD validator at the moment.

kokyriakidis commented 5 years ago 
https://www.pgx.no/wiki/index.php/Pharmacoracle

Pharmacoracle version 1 The first version of the Pharmacoracle is based on the OWLAPI Queries to Pharmacoracle have to be written in the Manchester syntax in the same way as for the DL Query Tab of Stanford's desktop Protégé. The choice of technology was inspired by the Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care of the UPGx project. The ontology of Mathias Samwald is at the core of this system. They use the TrOWL reasoner instead of the HermIT reasoner that is at the core of Pharmacoracle.

The Pharmacoracle infrastructure is written in Python, and the OWLAPI is invoked from Python via Pexpect. For curation, a link between OWL classes and Python is provided by Jean Baptiste Lamy's Owlready2, which we use to translate PharmGKB's JSON-LD to OWL.

Maybe that helps

kokyriakidis commented 5 years ago

Because I have so many unknown words, If I manually make entries to webprotege, is there an API that I can make queries? Or is it possible to make an API?

I want to adapt it on the clinical/hospital environment. Let's say I have a database including patient variants. I want to query the webprotege the variants and get back dosing recommendations based on these variants