Feature Request: Submit each comorbidity as new entry instead of list of values in one field

[hknahal]

This issue is related to the Extended (Optional) Comorbidity clinical table which has not yet been implemented (currently being reviewed by TCA Working Group)

Issue:

A patient can have more than one comorbidity, so we can expect a list of comorbidities in the comorbidity field. Similarly, each comorbidity would have its own age_at_comorbidity_diagnosis. This would mean we would need to accept a list of values where order matters (since comorbidity and age values need to correspond) and values don't need to be unique (for example, a patient could have been diagnosed with two comorbidities at the same age (example: comorbidity: [E10, K85] and age_of_comorbidity_diagnosis: [32, 32]). This is similar to the issue described in https://github.com/icgc-argo/argo-dictionary/issues/153.

Possible Implementation:

Instead of accepting a list of values and determining how to ensure the order of the non-unique values, we can require each comorbidity to be submitted as a new entry (on a new line). See here for example submission of comorbidity data. We can also amalgamate/move some of the optional fields in the Donor table since they can be covered in the Comorbidity table. This would eliminate the need to resolve https://github.com/icgc-argo/argo-dictionary/issues/153 and would require the following changes:

• Move prior_malignancy field from Donor table to Comorbidity table since a prior cancer malignancy is a comorbidity.
• Remove cancer_type_prior_malignancy field from Donor table since the comorbidity field in the Comorbidity table covers this (if prior_malignancy is Yes, then the ICD-10 code of the prior cancer would be entered in the comorbidity field).
• Remove age_at_prior_malignancy from Donor table since age_at_comorbidity_diagnosis in Comorbidity table would cover this.
• a genetic disorder (genetic_disorder field in Comorbidity table) would not require age_at_comorbidity_diagnosis since the patient would have been born with the genetic disorder (unlike diabetes which can start later in life for example).
• In the case of multiple comorbidities, we would require the data submitter to submit each comorbidity as a new entry. Fields that are not applicable would be left blank.

[rosibaj]

@rosibaj

• confirm validation rules; does this make any changes within?
• run a test migration with the new dictionary in dev and see how it goes first

[rosibaj]

Removed:

    {
      "description": "Prior malignancy affecting donor.",
      "name": "prior_malignancy",
      "restrictions": {
        "codeList": "#/list/yes_no"
      },
      "valueType": "string",
      "meta": {
        "displayName": "Prior Malignancy",
        "examples": "C41.1, C16.9, C00.5, D46.9"
      }
    },
    {
      "description": "The code to represent the cancer type of a prior malignancy using the WHO ICD-10 code (https://icd.who.int/browse10/2019/en) classification.",
      "name": "cancer_type_prior_malignancy",
      "restrictions": {
        "regex": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$"
      },
      "valueType": "string",
      "meta": {
        "displayName": "Cancer Type Prior Malignancy"
      }
    },
    {
      "description": "If donor has history of prior malignancy, indicate age at previous diagnosis, in years.",
      "name": "age_at_prior_malignancy",
      "valueType": "integer",
      "meta": {
        "displayName": "Age at Prior Malignancy"
      }
    },
    {
      "description": "If donor has history of prior malignancy, indicate laterality of previous diagnosis. (Codelist reference: NCI CDE: 4122391)",
      "name": "laterality_of_prior_malignancy",
      "valueType": "string",
      "restrictions": {
        "codeList": ["Bilateral", "Left", "Midline", "Not applicable", "Right", "Unilateral", "Unilateral, side not specified", "Unknown"]
      },
      "meta": {
        "displayName": "Laterality at Prior Malignancy"
      }
    },

[rosibaj]

Deployed dictionary version 1.7: https://docs.icgc-argo.org/dictionary