• Python packages

  • python == 3.8.5
  • torch == 1.8.1
  • numpy == 1.19.2
  • pandas == 1.0.1
  • tqdm == 4.61.0

• Others

  • groovy == 4.0.0
  • JVM == 1.8.0_333
  • Protégé (https://protege.stanford.edu/)

• Family Ontology

  cd ./code/model

  python family.py

• Pizza Ontology

  cd ./code/model

  python pizza.py

• Human Phenotype Ontology

  cd ./data/HPO/ && unzip BIOGRID-ALL-4.4.211.tab.zip && cd ../../code/model

  sh run_hpo.sh

We elaborate the steps of data preparation to foster further research. This section is unnecessary for running the experiments.

• Human Phenotype Ontology

  • Download datasets

    cd ./data/HPO/

    wget http://purl.obolibrary.org/obo/hp.owl

    wget https://downloads.thebiogrid.org/File/BioGRID/Release-Archive/BIOGRID-4.4.211/BIOGRID-ALL-4.4.211.tab.zip

    unzip ./data/HPO/BIOGRID-ALL-4.4.211.tab.zip

    wget http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt

  • Semantic Entailment (Generating the True Testing Axioms)

    Open hp.owl with the graphical interface of Protégé

    Select ELK as the logical reasoner

    Save the inferred ontology as hpInferred.owl

  • OWL to Axioms

    groovy ./code/ppc/GetTBox.groovy ./data/HPO/hp.owl > ./data/HPO/TBox.txt

    groovy ./code/ppc/GetTBox.groovy ./data/HPO/hpInferred.owl > ./data/HPO/TBoxInferred.txt

• Pizza Ontology

  • Download datasets

    cd ./data/Pizza/

    wget https://protege.stanford.edu/ontologies/pizza/pizza.owl

  • Semantic Entailment (Generating the True Testing Axioms)

    Open pizza.owl with the graphical interface of Protégé

    Select HermiT as the logical reasoner

    Save the inferred ontology as pizzaInferred.owl

  • OWL to Axioms

    groovy ./code/ppc/GetTBox.groovy ./data/Pizza/pizza.owl > ./data/Pizza/pizzaTBox.txt

    groovy ./code/ppc/GetTBox.groovy ./data/Pizza/pizzaInferred.owl > ./data/Pizza/pizzaTBoxInferred.txt