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 – ClinicalTrials.gov Cross Reference selected from ClinicalTrials.gov and WHO clinical trial terms

• Development weekly meeting notes on google doc

Publication

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) http://ceur-ws.org/Vol-2807/; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9389640/

Development

• 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