ontologies | Never manage a namespace object map | Dataset library

I have built a small ontology in Protege to test punning with a SPARQL query. The Ontology is:

I'm developing a Java application using owl-api. For testing I want to use a TestDataProvider to provide test data for unit-testing.

I'm using version 5.0.0 because the tutorial I read is using this version too. I plan to update later.

I need to develop an ontology in computational biochemistry and molecular dynamics. For this, I have collected the terms that is going to be used and attempted to reuse ontologies by searching the terms on ontology search service, such as EBI-OLS. Some terms are very relevant to import/reuse, however, the ontology itself is intended for a more specific domain, such as National Cancer Institute Thesaurus (which has 171,081 classes). Other than that, there are other 10 source ontologies that I could potentially reuse. Some of them are also huge, such as EDAM ontology.

1. Is it okay to reuse ontology that seemingly intended for a more specific domain, such as cancer? We will use the ontology for a more generic use in life science, not only cancer-related domain.

2. Is there any general rule of thumb on which of those 10-ish ontologies that are suitable for reuse? (e.g., the paper describing that ontology should be cited by at least n number of papers, or it should be compatible with Open Biological and Biomedical Ontology (OBO) Foundry principles, or it should be backed by a well-known institution and still maintained).

3. How to decide the sweet spot on the number of ontology sources one can based on? While we can reuse as much available terms as we can (from many ontology sources, especially in life science domain), there is a concern that it would make the resulting knowledge graph representation much more complex.

Thank you for your answers.

How would I decode this json file with JSONDecoder().decode

I want to programmatically get explanations for inferred axioms in consistent ontologies, in a similar manner that one can do in the Protégé UI. I cannot find any straightforward way. I have found the owlexplanation repo, but I cannot for the life of me solve the dependency issues to set up the owlexplanation environment. I have also browsed the javadoc of owlapi regarding explanations (to avoid the other repo altogether), but I don't see anything useful beyond what I can already see browsing the Java source code.

I have thought of simply negating the inferred axiom, to get explanations through inconsistencies, but I would prefer something cleaner, and I am not sure this approach is correct anyway.

Other (possibly) useful context:

• I had used some Java years ago, but I now primarily use Python (I try to use OWL API with JPype and OWL in general with Owlready2).
• I am using HermiT reasoner (again through JPype) (according to build.xml file, latest stable version 1.3.8).
• I have managed to get explanations for unsatisfiability and inconsistency in my setup, without owlexplanation, following this example from the HermiT source code.
• I fell in the rabbit hole wanting to make a usable .jar file for owlexplanation, in order to add it in my JPype classpath. My plan went sideways when I couldn't get the Java project to build in the first place.
• I am using Intellij IDE.

I would appreciate any insight or tips.

UPDATE Jan 6, 2022:

I decided to try once more with the owlexplanation code with a clean head so here is where I am at:

• Downloaded the source code from github and extracted the zip.
• Started IntelliJ and instead from "Creating a project from Existing sources", I clicked "Open" and selected the extracted directory.
• I built the project and it did successfully.
• From Maven tools, I run clean, validate, compile and test succesfully.
• If I run "package" Maven action, it throws as error that "The environment variable JAVA_HOME is not correctly set". The thing is that if I go File>Project Structure, I see that SDK is set to 11, it's not empty.
• Additionally, from the pom.xml file I get these problems:
  • Plugin 'org.apache.maven.plugins:maven-gpg-plugin:1.5' not found
  • Plugin 'org.sonatype.plugins:nexus-staging-maven-plugin:1.6.6' not found

UPDATE Jan 8, 2022: (Trying @Ignazio's answer)

I created a new IntelliJ project, and added the Maven dependencies @Ignazio mentioned (plus some others like slf4j etc) and I got a working example (I think). Moving to my main project (using JPype), I had to manually download some .jars to include in the classpath (as maven can't be used here). These are the ones downloaded so far:

I'm using wordcloud==1.8.1 to render a plot with multiple wordclouds,
each one beeing a bar in a bar chart.

Basically just adding some subplots like this:

my goal is to work on a project using docker without having to constantly rebuild my whole project each time I modify a file a little bit:
The file bellow (not complete) has 2 state, an already updated version that I will call Version_0 which looks like this :

I've had some issues at implementing built-in jena-fuseki reasoner, I could make it work but it would not prevent me from adding incorrect triples. So I wanted to add Openllet reasoner to my jena-fuseki server.

But I can't figure how to add openllet jar to my Docker image and make it work, I've run into many java dependances issues. To add context, my docker-compose looks like that :

I embedded the ontology and now I have the URI with the embedded number. So I could not find a solution. Here is my data on how it looks.