cordDqChecker

CordDqChecker is a Tool for data quality assessment and reporting in CORD-MI.

Acknowledgement: This work was done within the “Collaboration on Rare Diseases” of the Medical Informatics Initiative (CORD-MI) funded by the German Federal Ministry of Education and Research (BMBF), under grant number: FKZ-01ZZ1911R.

Data Quality Metrics

• The following indicators and key numbers are configured by default data quality reports:

  Dimension	Indicator Name
  completeness	missing_item_rate, missing_value_rate, orphaCoding_completeness_rate
  plausibility	outlier_rate, orphaCoding_plausibility_rate
  uniqueness	rdCase_unambiguity_rate, duplication_rate
  concordance	orphaCoding_rel_py_ipt, unambiguous_rdCase_rel_py_ipat, tracerCase_rel_py_ipat

  Key number	Name
  inpatient case number per year	case_no_p_ipat
  case number per year	case_no_py
  patient number per year	patient_no_py
  orpha code number per year	orphaCoding_no_py
  RD case number per year	rdCase_no_py
  Orpha-coded case number per year	orphaCase_no_py
  unambiguous-RD case number per year	unambiguous_rdCase_no_py

• The data quality framework dqLib has been used as an R package for generating specific reports on data quality related issues and metrics.

• The following references are required to assess the quality of orphacoding and can be easily updated with new versions:

  • The standard Alpha-ID-SE terminology [1]

  • A reference for tracer diagnoses such as the list provided in [2].

    [1] BfArM - Alpha-ID-SE [Internet]. [cited 2022 May 23]. Available from: https://www.bfarm.de/EN/Code-systems/Terminologies/Alpha-ID-SE/_node.html

    [2] List of Tracer Diagnoses Extracted from Alpha-ID-SE Terminology [Internet]. 2022 [cited 2022May 24]. Available from: https://doi.org/21.11101/0000-0007-F6DF-9

Distributed Execution

cordDqChecker was successfully tested using Personal Health Train (PHT) and applied on synthetic data stored in multiple FHIR servers. The aggregated results are stored in folder ./PHT/Data/Export. To create a PHT image run ./Dockerfile.

Cross-site Reports

Here are examples of cross-site reports on data quality generated using sythetic data.

Local Execution

To analyse your data quality locally go to folder ./Local and run cordDqChecker.R to genrate data quality reports.

• The script cordDqChecker.R reads data from FHIR server or from supported file formats such as CSV and Excel. The path varialbe specifies which dataset should be imported. For Example you can define your path as following:

  • path="http://141.5.101.1:8080/fhir/" or
  • path="./Data/medData/dqTestData.csv" or
  • path="./Data/medData/dqTestData.xlsx"

• The default values of local variables are set as follows:

  • reportYear=2020
  • max_FHIRbundles=50
  • INPATIENT_CASE_NO=10000
  • path="http://141.5.101.1:8080/fhir/"
  • tracerPath="./Data/refData/CordTracerList_v2.csv"

We use the CSV file "./Local/Data/refData/CordTracerList_v2.csv" as default reference for tracer diagnoses. We also provide the CORD-MI list of tracer diagnoses version 1.0 in the folder for reference data "./Local/Data/refData/Export". Once the source data path and local variables are defined, start the script to check the quality of your data. The genrated repots are saved in folder "./Local/Data/Export".

Local Reports

Here are some examples of data quality reports generated locally using sythetic data.

Note

• Before starting cordDqChecker.R you need to install required libraries using this script installPackages.R

• To avoid local dependency issues go to folder ./Local and just run the command sudo docker-compose up to get cordDqChecker running.

• The missing item rate will be calculated based on FHIR implementation guidlines of the MII core data set. Hence, mandatory items of the basic modules Person, Case and Diagnosis are required.

• To cite cordDqChecker, please use the following BibTeX entry:

  @software{Tahar_cordDqChecker,
  author = {Tahar, Kais},title = {{cordDqChecker}},
  url = {https://github.com/medizininformatik-initiative/cord-dq-checker},
  year = {2021}
  }
  
  

See also: dqLib CORD-MI