Refer to Approach.md for detailed information.
Ontology and OWL Tutorial:
https://www.cs.cornell.edu/courses/cs431/2008sp/Lectures/public/lecture-4-09-08.pdf
Where to Download Protegé:
Intro to RDF:
https://www.w3.org/TR/rdf11-primer/
3 Papers related to our project:
Previous approaches:
https://www.w3.org/TR/swbp-specified-values/
Most recent approach (we're trying to enhance this):
https://www.cs.man.ac.uk/~rector/papers/Whats-in-a-code/Whats-in-a-code-rector-corrected.pdf
Interesting paper that relates to Chute's presentation AIM: a personal view of where I have been and where we might be going (Alan Rector)
One possible link if you have University access: https://www.sciencedirect.com/science/article/pii/S0933365701000781
Not directly related to this project but great background.
Blending RDF and OWL
Github: https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF
Paper: https://jhu.pure.elsevier.com/en/publications/blending-fhir-rdf-and-owl
Using Z: Specification, Refinement and Proof
PDF: http://www.usingz.com/usingz.pdf
See section 4.4 Definite description
Copy of NCIT
https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/
A: "Thesaurus.OWL.zip"
AND
B: "ThesaurusInf_21.05d.OWL.zip"
Load A and run reasoner. It should give same thing as B.
Copy of SNOMED-CT
https://www.nlm.nih.gov/healthit/snomedct/index.html
To do this, you have to sign-up, get license (if needed), and download international release in rf2 format.
https://github.com/IHTSDO/classification-service
Then, use this to convert rf2 to owl format.
ELK can be downloaded by File>Check for plugin
Snorocket install
Go to the Maven Central Repository and download the latest as snorocket-protege-4.0.1-jar-with-dependencies.jar and then copy it into Protege-5.5.0/Protege.app/Contents/Java/plugins
Update: Protege5.5.0 is not compatible either the snorocket 3.2.0 release nor snorocket 4.0.1. We have to switch back to Protege 5.2 and snorocket 3.2:
- Download Protege 5.2.0 from the bottom of page: https://github.com/protegeproject/protege-distribution/releases/tag/v5.2.0, then unzip and (optionally) move Protege-5.2.0/Protégé.app to /Applications. (Mac OSX Only)
- Download Snorocket from https://search.maven.org/remotecontent?filepath=au/csiro/snorocket-protege/3.2.0/snorocket-protege-3.2.0-jar-with-dependencies.jar and copy it into Protégé.app/Contents/Java/plugins
edit Protege-5.5.0/Protégé.app/Contents/Info.plist
edit Protege-5.2.0/Protégé.app/Contents/Info.plist
<array>
<string>-Dapple.laf.useScreenMenuBar=true</string>
<string>-Xss16M</string>
<string>-Xmx8G</string>
<string>-Xdock:name=Protégé</string>
<string>-DentityExpansionLimit=100000000</string>
<string>-Dlogback.configurationFile=conf/logback.xml</string>
<string>-Dfile.encoding=UTF-8</string>
<string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
</array>
The element with "-Xmx" in it - change the current setting to "-Xmx8G" -- this is assuming that your machine has at least 8GB of memory.
Mondo Paper
through background stuff more to familarize with concepts like equivalent class, subclass, protege...
through BlendingFHIRandRDF tutorial.
Stanford Existential Elimination Tutorial