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CTO: Clinical Trial Ontology

  • This is a collaborative effort undertaken by Fraunhofer SCAI group(Stepan Gebel, Alpha Tom Kodamullil, Sumit Madan, Johannes Darms), University of Michigan(Yongqun "Oliver" He), NIH PubChem (Qingliang "Leon" Li), and NIH/NHGRI (Asiyah Lin) to develop an ontology to represent clinical trials using a small set of core terms.

  • The CTO-core uses Basic Formal Ontology (BFO) as its top level ontology.

  • OPMI led by University of Michigan and other OBO foundry ontologies serve as the pool of existing terms to import into CTO core.

  • The small set of terms were primarily based on the WHO/ICMJE – Cross Reference selected from and WHO clinical trial terms

  • Development weekly meeting notes on google doc


  1. CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView. [ slides (pdf), talk video (mp4, 10MB) ]
    Authors: Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann- Apitius, Yongqun Oliver He, Alpha Tom Kodamullil
    Journal: Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO);


  • src/ontology/modules
    • contains OntoFox input files
    • manually created
  • src/ontology/modules/
    • contains OntoFox output files
    • automatically generated
  • src/ontology/ClinicalTrialOntology.owl
    • main devlopement file, imports module
    • manually created
  • src/ontology/catalog-v001.xml
    • Protege catalog file that links IRIs from impored modules to relative file paths
    • manually created
  • cto.owl
    • most recent release (merged main devlopement file with all imported modules
    • automatically generated