{"id":13318259,"url":"https://github.com/ClinicalTrialOntology/CTO","last_synced_at":"2025-03-11T01:31:58.988Z","repository":{"id":73482222,"uuid":"238462209","full_name":"ClinicalTrialOntology/CTO","owner":"ClinicalTrialOntology","description":"CTO: Core Ontology of Clinical Trials","archived":false,"fork":false,"pushed_at":"2024-05-31T19:33:48.000Z","size":2190,"stargazers_count":11,"open_issues_count":16,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-06-01T16:34:28.081Z","etag":null,"topics":["clinical-trials","obofoundry","ontology"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ClinicalTrialOntology.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-02-05T13:55:11.000Z","updated_at":"2024-05-31T19:33:51.000Z","dependencies_parsed_at":"2023-03-02T08:00:17.261Z","dependency_job_id":null,"html_url":"https://github.com/ClinicalTrialOntology/CTO","commit_stats":{"total_commits":91,"total_committers":10,"mean_commits":9.1,"dds":0.7252747252747253,"last_synced_commit":"db123b89e820cad98f47d1f80597b420467ecbec"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ClinicalTrialOntology%2FCTO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ClinicalTrialOntology%2FCTO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ClinicalTrialOntology%2FCTO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ClinicalTrialOntology%2FCTO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ClinicalTrialOntology","download_url":"https://codeload.github.com/ClinicalTrialOntology/CTO/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":221201927,"owners_count":16775442,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clinical-trials","obofoundry","ontology"],"created_at":"2024-07-29T18:29:51.890Z","updated_at":"2024-10-23T13:32:01.923Z","avatar_url":"https://github.com/ClinicalTrialOntology.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CTO: Clinical Trial Ontology\n\n- 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. \n\n- The CTO-core uses Basic Formal Ontology (BFO) as its top level ontology.\n\n- [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.\n\n- 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/) \n\n- [Development weekly meeting notes on google doc](https://docs.google.com/document/d/1VnmFhqFwfH3qcShiZUTO9ALF-3JKCs2oa3MQ2LotH6U/edit)\n\n## Publication\n1. **[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\u0026list=PLhzFEi0G-n-uom3STXbNSL4lOyCNyGQ5B\u0026index=4) (mp4, 10MB) ] \u003cbr/\u003e \n  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 \u003cbr/\u003e\n 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/\n\n## Development \n\n- src/ontology/modules\n  - contains OntoFox input files\n  - manually created \n- src/ontology/modules/\n  - contains OntoFox output files\n  - automatically generated\n- src/ontology/ClinicalTrialOntology.owl\n  -  main devlopement file, imports module\n  - manually created \n- src/ontology/catalog-v001.xml\n  - Protege catalog file that links IRIs from impored modules to relative file paths\n  - manually created \n- cto.owl\n  - most recent release (merged main devlopement file with all imported modules\n  - automatically generated \n  \n \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FClinicalTrialOntology%2FCTO","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FClinicalTrialOntology%2FCTO","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FClinicalTrialOntology%2FCTO/lists"}