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Processed ICD Data

Documentation for CGHR's processed International Classification of Diseases (ICD) data from the World Health Organization (WHO).

Last Updated: July 11, 2023

About

ICD-related codes and mappings used at CGHR.

"The International Classification of Diseases (ICD) is a tool for recording, reporting and grouping conditions and factors that influence health. It contains categories for diseases and disorders, health related conditions, external causes of illness or death, anatomy, sites, activities, medicines, vaccines and more.

The purpose of the ICD is to allow the systematic recording, analysis, interpretation and comparison of mortality and morbidity data collected in different countries or regions and at different times."

- World Health Organization (2022)

The following codes related to ICD are included:

For more information, refer to WHO's ICD Website.

Note: Data files are also available for open access on Github.

Citation

To cite the data, please cite the following depending on the codes and versions used:

ICD-10

  • World Health Organization. (2011). ICD-10: International statistical classification of diseases and related health problems (10th revision) (5th ed., Vol. 2).
@manual{
  who2011,
  title={ICD-10: International statistical classification of diseases and related health problems (10th revision)},
  author={{World Health Organization}},
  year={2011},
  volume={2},
  edition={5}
}

ICD-11

  • World Health Organization. (2022). ICD-11: International Classification of Diseases for Mortality and Morbidity Statistics (11th revision).
@manual{
  who2022,
  title={ICD-11: International Classifcation of Diseases for Mortality and Morbidity Statistics (11th revision)},
  author={{World Health Organization}},
  year={2022}
}

WVA-2016

  • World Health Organization. (2016). Verbal autopsy standards: The 2016 WHO verbal autopsy instrument v1.5.3.
@manual{
  who2016va,
  title={Verbal autopsy standards: The 2016 WHO verbal autopsy instrument v1.5.3},
  author={{World Health Organization}},
  year={2016}
}

WVA-2022

  • World Health Organization. (2017). Verbal autopsy standards: The 2022 WHO verbal autopsy instrument v1.
@manual{
  who2017va,
  title={Verbal autopsy standards: The 2022 WHO verbal autopsy instrument v1},
  author={{World Health Organization}},
  year={2017}
}

WBD-10 and CMEA-10

  • Aleksandrowicz, L., Malhotra, V., Dikshit, R., Gupta, P. C., Kumar, R., Sheth, J., Rathi, K., Suraweera, W., Miasnikof, P., Jotkar, R., Sinha, D., Awasthi, S., Bhatia, P., & Jha, P. (2014). Performance criteria for verbal autopsy-based systems to estimate national causes of death: development and application to the Indian Million Death Study. BMC medicine, 12(1), 1-14. doi:10.1186/1741-7015-12-21.
@article{
  aleksandrowiczetal2014,
  title={Performance criteria for verbal autopsy-based systems to estimate national causes of death: development and application to the Indian Million Death Study},
  author={Aleksandrowicz, Lukasz and Malhotra, Varun and Dikshit, Rajesh and Gupta, Prakash C and Kumar, Rajesh and Sheth, Jay and Rathi, Suresh Kumar and Suraweera, Wilson and Miasnikof, Pierre and Jotkar, Raju and others},
  journal={BMC medicine},
  volume={12},
  number={1},
  pages={1--14},
  year={2014},
  DOI={10.1186/1741-7015-12-21},
  publisher={BioMed Central}
}

CGHR-10

  • Jha, P., Kumar, D., Dikshit, R., Budukh, A., Begum, R., Sati, P., Kolpak, P., Wen, R., Raithatha, S.J., Shah, U., Li, Z.R., Aleksandrowicz, L., Shah, P., Piyasena, K., McCormick, T. H., Gelband, H., and Clark, S. J. (2019). Automated versus physician assignment of cause of death for verbal autopsies: randomized trial of 9374 deaths in 117 villages in India. BMC medicine, 17(1), 1-11. doi:10.1186/s12916-019-1353-2.
@article{
    jha2019,
    title={Automated versus physician assignment of cause of death for verbal autopsies: randomized trial of 9374 deaths in 117 villages in India},
    author={Jha, Prabhat and Kumar, Dinesh and Dikshit, Rajesh and Budukh, Atul and Begum, Rehana and Sati, Prabha and Kolpak, Patrycja and Wen, Richard and Raithatha, Shyamsundar J and Shah, Utkarsh, Li, Zehang Richard and Aleksandrowicz, Lukasz and Shah, Prakash and Piyasena, Kapila and McCormick, Tyler H and Gelband, Hellen and Clark, Samuel J},
    journal={BMC medicine},
    volume={17},
    number={1},
    pages={1--11},
    year={2019},
    publisher={BioMed Central}
}

Contact

Name Email Role
Richard Wen [email protected] Primary contact for code and data access in this repo
Peter Rodriguez [email protected] Contact for database access, CGHR staff only
Wilson Suraweera [email protected] Contact for WBD code inquiries
Rajeev Kamadod [email protected] Contact for ICD-10 equivalency codes for CMEA
Bryan Gascon [email protected] Contact for WHO VA and CGHR 2019 code processing
Patrycja Kolpak [email protected] Contact for details on AVP raw data and CGHR 2019 codes

icd's People

Contributors

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Stargazers

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Watchers

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icd's Issues

WBD Data

Compile ICD to WBD mappings for ICD-10 from Wilson's table (already provided from Peter).

ICD Data

Create ICD datasets to get code labels for RAPID as VA data does not include labels.

Typo in ICD10 to WBD10

data/icd10towbd10.csv

Road trafic accidents -> Road traffic accidents

We are using it to create standardized mortality maps for SL, please let me know when fixed!

CMEA Data

Include ICD code agreement/equivalence list from Rajeev.

Notes

  • This is the Central Medical Evaluation Agreement (CMEA) list used to check agreement between two ICD codes assigned for verbal autopsy records
  • Prabhat is more concerned with the groupings so the most recently assigned code can be used when two codes agree
  • Catherine uses physician 1's code when two codes agree
  • Wilson mentioned a trumping algorithm, but no response since then

WHO VA Codes

There are set of WHO VA codes used to code verbal autopsy records and produce standardized outputs for VA models.

Bryan will compile a list of these and add it to the icd repo.

The cghrCodes package might be helpful in expanding and collapsing ICD-10 codes.

Data: Are BMC Med and CGHR 2019 Codes the same?

Check if the CGHR 2019 codes correspond to the COD categories in the appendix of the Automated vs Physician Study.

Also check if the WBD codes correspond to the CGHR 2019 codes and the AVP appendix COD codes.

There seems to be confusion with the CGHR, AVP study, and WBD codes.

Data

Data: Missing ICD-10 to WBD 10 codes

Some ICD codes were found in Version 10 - Final CGHR-GBD list 18 April 2013 RW (original Wilson).xls, but not found in icd10towbd10.csv.

For example, Child-G03 code is found in Wilson's, but only Neo-G03 and Adult-G03 were found in icd10towbd10.csv. Furthermore, there are 2 duplicates of Neo-G03.
image

The list of ICD codes missing from icd10towbd10.csv are here:
missing_icd_2023-02-28.csv

Data: WVA-2016 to ICD-10 Mapping

@git-cheryl Cheryl compiled a mapping of WHO VA (WVA) codes to ICD-10 codes from Sam's InterVA and InSilicoVA neonate and child outputs provided by Leslie @lanewcombe.

Files

Note: There is an updated version 1.5.3 of the manual, but it does not have ICD-10 mappings as opposed to v1.5 of the manual

Mappings were compiled by Cheryl with the following files from Leslie:

map1.pdf
map2.pdf
map3.pdf
map4.pdf
map5.pdf

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