https://github.com/ClinicalTrialOntology/CTO

CTO: Core Ontology of Clinical Trials
https://github.com/ClinicalTrialOntology/CTO

clinical-trials obofoundry ontology

Last synced: 3 months ago
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CTO: Core Ontology of Clinical Trials

• Host: GitHub
• URL: https://github.com/ClinicalTrialOntology/CTO
• Owner: ClinicalTrialOntology
• Created: 2020-02-05T13:55:11.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2024-05-31T19:33:48.000Z (8 months ago)
• Last Synced: 2024-06-01T16:34:28.081Z (8 months ago)
• Topics: clinical-trials, obofoundry, ontology
• Language: Jupyter Notebook
• Homepage:
• Size: 2.09 MB
• Stars: 11
• Watchers: 6
• Forks: 2
• Open Issues: 16
• Metadata Files:
  • Readme: README.md

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README

        
# 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](https://github.com/OPMI/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](https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf) selected from [ClinicalTrials.gov](https://www.clinicaltrials.gov/) and [WHO clinical trial terms](https://www.who.int/ictrp/network/trds/en/) 

- [Development weekly meeting notes on google doc](https://docs.google.com/document/d/1VnmFhqFwfH3qcShiZUTO9ALF-3JKCs2oa3MQ2LotH6U/edit)

## Publication

1. **[CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView](http://ceur-ws.org/Vol-2807/paperH.pdf)**. [   [ slides](https://icbo2020.inf.unibz.it/wp-content/uploads/2020/09/icbo-s1700a_15.pdf) (pdf), [talk video](https://www.youtube.com/watch?v=4tmyDN6enuA&list=PLhzFEi0G-n-uom3STXbNSL4lOyCNyGQ5B&index=4) (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