Ontology-based Categorization of Clinical Studies by Their Conditions

Data, source code, and result for manuscript Ontology-based Categorization of Clinical Studies by Their Conditions

The demonstration is available at http://cliver.chunhualab.org:8090/

Example input NCTID: NCT00000558, NCT04359095, NCT05440305

Requirement:

• Java 8
• Usagi 1.1.5
• SNOMED CT RF2 release file
• or MeSH ASCII release file (e.g., d2022.bin)

Default categorization:

• SNOMED: Subhierarchy of Disease (disorder) SCTID: 64572001 (131 concepts)
• MeSH: Subhierarchy of Diseases (C01, C04-C26) + Mental Disorder F03

Custom categorization: User can define their own concepts (index terms) for customized categorizations. Format template

Instructions:

1. Run TestTrialFetcher.java to extract clinical studies from ClinicalTrials.GOV ;
2. Run TestConceptSearch.java to perform concept normalizaiton with Usagi ;
3. Run TestClassifyTrialConditionsWithSNOMED.java to get classification results;
4. Run TestClassifyTrialConditionsWithMeSH.java to get classification results.