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
• 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 off

Instantiate ChemoOnto with followed lines

Go to src/ChemoOnto

cd src/ChemoOnto/

python3 instantiatesChemoOntoWithFollowedLines.py -AC on -AA off -S off -R off

ChemoOnto 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