hsolbrig / BDP-Ontology

BDP-Ontology

Refer to Approach.md for detailed information.

Background

Ontology and OWL Tutorial:

https://www.cs.cornell.edu/courses/cs431/2008sp/Lectures/public/lecture-4-09-08.pdf

Where to Download Protegé:

https://protege.stanford.edu/

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/

https://www.cs.man.ac.uk/~rector/papers/Terminology-binding-final-revision-embedded-single-rector%20copy.pdf

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

TODO (6/18/2021 ~ 6/27/2021)

1. Download

Copy of NCIT https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/
A: "Thesaurus.OWL.zip"
AND
B: "ThesaurusInf_21.05d.OWL.zip"

2. Load B into Protege and examine structures, be familiar with Protege.

Load A and run reasoner. It should give same thing as B.

3. Download

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.

4. Download

https://github.com/IHTSDO/classification-service

Then, use this to convert rf2 to owl format.

5. Get reasoner plugin ELK and Snorocket

ELK can be downloaded by File>Check for plugin

Snorocket install

https://aehrc.com/snorocket/

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

6. Change Memory Setting

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.

7. Read

Mondo Paper

8. Read

through background stuff more to familarize with concepts like equivalent class, subclass, protege...

9. Read

through BlendingFHIRandRDF tutorial.

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Stanford Existential Elimination Tutorial

http://logic.stanford.edu/intrologic/notes/chapter_08.html