ChemoKG

Welcome on ChemoKG-open

About expand_less

ChemoKG-open is an knowledge graph in RDF (Resource Description Framework) of chemotherapy protocols. It encompasses 513 protocols, which provides the necessary classes and relations to represent the various dimensions of protocols.

The protocols themselves have been extracted from a local database of the Pharmacy Service of the European Georges Pompidou Hospital of the AP-HP, Paris.

A description of ChemoKG-open and its implementation is available in [1]. The full ChemoKG data that support the findings of this study are available upon reasonable request.

Citing ChemoKG expand_less

When citing ChemoKG, please use the following reference:
Jhee, J. H., Rogier, A., Giraud, D., Pinet, E., Sabatier, B., Rance, B., & Coulet, A. (2024). Representation and comparison of chemotherapy protocols with ChemoKG and graph embeddings. SWAT4HCLS, in press. 

							
@article{jheeSWAT4HCLS24,
  author    = {Jong Ho Jhee and
               Alice Rogier and
               Dune Giraud and
               Emma Pinet and
               Brigitte Sabatier and
               Bastien Rance and               
               Adrien Coulet},
  title     = {Representation and comparison of chemotherapy protocols 
	with ChemoKG and graph embeddings},
  conference   = {SWAT4HCLS},  
  year      = {2024},  
}

Integrated datasets expand_less

You can download the main knowledge graph from here (in .ttl format), ChemoKG-open.

The integrated data sets are:

  • ChemoOnto (custom RDFization of chemotherapy protocols) - Github Zenodo [2]
  • DrugBank (from Bio2RDF) - License [3]
  • ChEBI (from ChEBI) - License [4]

    • Examples of SPARQL queries expand_less

    Search the chemotherapy protocols (chemo:PRC)

    PREFIX chem: <http://chemonto.owl#>
SELECT DISTINCT ?PRC ?PRCNAME 
where { 
    ?PRC chem:hasName ?PRCNAME.
}

    Check the graph around protocols

    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX chem: <http://chemonto.owl#>
PREFIX cho: <http://chemonto.owl/#>
PREFIX ns4: <http://www.drugbank.ca/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT distinct ?PRCNAME ?drugAdm ?dayAdmSTR ?drugLabel ?dose ?is_bolus ?bioRoleLabel ?ATC ?HalfLife {
    cho:PRC_27 chem:hasName ?PRCNAME.
    cho:PRC_27 chem:hasCycle ?cycle_theo.
    ?cycle_theo chem:hasAdministration ?drugAdm.
    ?drugAdm chem:hasDrug ?drugInd.
    ?drugInd rdfs:label ?drugLabel.
    ?drugAdm chem:hasDose ?dose.
    ?drugAdm chem:hasDayDrugAdm ?dayAdmSTR.
    ?drugAdm chem:isBolus ?is_bolus.
    ?drugInd cho:hasBiologicalRole ?bioRole.
    ?bioRole rdfs:label ?bioRoleLabel.
    ?drugInd owl:sameAs ?drugBank.
    ?drugBank ns4:hasATC ?ATC.
    ?drugBank ns4:hasHalfLife ?DBHL.
    ?DBHL ns4:description ?HalfLife.
    filter(xsd:double(?HalfLife))
    } limit 100

    References expand_less

    1. Jhee, J. H., Rogier, A., Giraud, D., Pinet, E., Sabatier, B., Rance, B., & Coulet, A. (2024). Representation and comparison of chemotherapy protocols with ChemoKG and graph embeddings. SWAT4HCLS, in press.
    2. ROGIER, A., Rance, B., & Coulet, A. (2024, January 22). ChemoOnto, an ontology to qualify the course of chemotherapies. ISMB-ECCB, 2023, Lyon. Zenodo.
    3. Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., ... & Wilson, M. (2018). DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic acids research, 46(D1), D1074-D1082.
    4. Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., ... & Steinbeck, C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic acids research, 44(D1), D1214-D1219.

    Privacy policy expand_less

    Who we are

    We are a group of researchers part of the HEKA Team which is a research team in Inria Paris, France. ChemoKG is supported by Inria Paris and the CombO project.

    This website is hosted by the Inria Paris.

    What personal data we collect on this site and why we collect them

    Cookies

    We do not use cookies.

    Analytics

    We keep the connection logs (including the user IP address, the visited URL which may contain the SPARQL query from the SPARQL endpoint or the URL of the described entity from the Faceted Browser) for approximately 13 months (including backups).

    We need to keep this information for legal and security reasons and we want to measure usage statistics for this service.

    Who we share your data with

    We do not share your data with others.

    How long we retain your data

    Connection logs are kept for approximately 13 months.

    What rights you have over your data

    Users of this site do not have an account.

    We cannot remove your connections out of our system due to legal and security reasons. They disappear completely after approximately 13 months.

    Acknowledgement expand_less

    Much appreciation is extended to Pierre Monnin for his invaluable assistance in the development of this website.

    Third-party tools expand_less

    This website uses the following third-party tools: