Ontology-based Categorization of Clinical Studies by Their Conditions

Data, source code, and result for the Journal of Biomedical Informatics paper "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.

Citation

If you found this code helpful, please consider citing:

@article{LIU2022104235,
title = {Ontology-based categorization of clinical studies by their conditions},
journal = {Journal of Biomedical Informatics},
volume = {135},
pages = {104235},
year = {2022},
issn = {1532-0464},
doi = {https://doi.org/10.1016/j.jbi.2022.104235},
url = {https://www.sciencedirect.com/science/article/pii/S1532046422002404},
author = {Hao Liu and Simona Carini and Zhehuan Chen and Spencer {Phillips Hey} and Ida Sim and Chunhua Weng},
keywords = {Ontology, Clinical Study, SNOMED CT, Data Visualization, Categorization},
}