ChemoOnto, an ontology to qualify the course of chemotherapies
Chemotherapies are complex treatments that consist in the administration of cytotoxic drugs to patients. Chemotherapies are organized in cycles. Within a cycle, the molecules, their doses and days of administration are determined by standard regimens (i.e., protocols), recommended by scientific societies. But in real life, treatment may not go as planned. Toxicity events, personal arrangements, holidays or other factors may lead to dose reductions or delays in administrations. Indeed, to improve treatment response, while limiting toxicity events physicians frequently interrupt, modify, or combine regimens. To better understand individual chemotherapy response, it is important to be able to precisely represent, measure and compare these adjustments. The availability of Electronic Health Records (EHRs) offer an unprecedented set of observations to generate real-world evidence for oncology. We believe that a common data model that combines representations of both standard and implemented treatment regimens would facilitate comparisons, enabling further studies. To answer this need, we propose ChemoOnto, an ontology designed to represent chemotherapy treatment courses.
What you will find
- ontological structure of ChemoOnto
ChemoOnto_structure.owl[2] - the code to define ChemoOnto structure and to instantiate it with theoretical protocol and actual lines in
src/repository. - examples of csv data tables used to instatiate the graph are in
data/repository:- examples of csv with theoretical protocols in
theroretical_protocols_tables/repository - examples of csv tables with false patients data in
followed_lines/repository
- examples of csv with theoretical protocols in
- external ontologies linked to ChemoOnto are in
external_ontologies/repository. - how to SPARQL query ChemoOnto with GraphDB in
SPARQL_query_ChemoOnto/repository.
Examples of command lines
Instantiate ChemoOnto with theoretical protocols
Go to src/ChemoOnto
cd src/ChemoOnto/python3 instantiatesChemoOntoWithTheoreticalPRC.py -AC on -AA off -S off -R offInstantiate ChemoOnto with followed lines
Go to src/ChemoOnto
cd src/ChemoOnto/python3 instantiatesChemoOntoWithFollowedLines.py -AC on -AA off -S off -R offChemoOnto structure and an example of its instantiation
References
[1] Rogier, A., Rance, B., Coulet, A. (2023). ChemoOnto, an ontology to qualify the course of chemotherapies. Bio-ontologies COSI 2023, Poster.
[2] ChemoOnto on the BioPortal: https://bioportal.bioontology.org/ontologies/CHO
[3] ChemoOnto reuse in ChemoKG: Jong Ho Jhee, Alice Rogier, Dune Giraud, Emma Pinet, Brigitte Sabatier, Bastien Rance and Adrien Coulet. Representation and comparison of chemotherapy protocols with ChemoKG and graph embeddings, submitted to SWAT4HCLS 2024.
[4] ChemoKB on GitHub: https://github.com/TeamHeka/chemokb