The following ontologies were used in experiments involving a real classical part (the following ontologies) and a generated probabilistic part.

1. The NCI Anatomy Ontology (NCI) (from the Ontology Alignment Evaluation contest 2009):  http://oaei.ontologymatching.org/2009/results/anatomy/
2. The Subcellular Anatomy Ontology (SAO): http://ccdb.ucsd.edu/CCDBWebSite/sao.html
3. The SWEET-JPL Process Ontology: http://sweet.jpl.nasa.gov/ontology/
4. The Sequence Ontology with Composite Terms (SO-XP): http://wiki.geneontology.org/index.php/SO:Composite_Terms
5. The Teleost Anatomy Ontology (TAO): https://www.nescent.org/phenoscape/Teleost_Anatomy_Ontology
6. The Cell Type ontology: http://obolibrary.org/cgi-bin/detail.cgi?id=cell

The versions of these ontologies used in the experiments can be downloaded here.