ga4gh / ga4gh/phenopacket-schema

Start/end date on treatment object

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Java
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Description

Further to discussion today at GA4GH meeting after OMOP->phenopackets presentation

I mentioned that we couldn't find a good place to put start/end dates for a specific drug_treatment. It was suggested we use the `doseIntervals` object to do this. In our case we do not have specific information about the dose, like the individual dose quantity and schedule frequency which are required for this object. We only have the cumulative dose. As such our treatment object would look something like this:

```json
"treatment": {
"agent": {
"id": "RxNorm:3390",
"label": "diethylstilbestrol"
},
"route_of_administration": {
"id": "SNOMED:261665006",
"label": "Unknown"
},
"drug_type": "PRESCRIPTION",
"cumulative_dose": {
"unit": {
"id": "SNOMED:404216004",
"label": "mg/m2"
},
"value": 25.7
},
"dose_intervals": [{
"quantity":
"unit":
"id": "SNOMED:261665006"
"label": "Unknown"
"value": -99
"scheduleFrequency":
"id": "SNOMED:261665006"
"label": "Unknown"
"interval":
"start": "2020-03-15T13:00:00Z"
"end": "2020-03-25T09:00:00Z"
}]

```

This seems a little clunky, but works. Not sure if it would make sense to add some fields on to the base treatment object or change the `quantity` and `schedule_frequency` fields to non-required so someone could just specify the known start and end dates for the drug exposure

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the treatment object definition in the phenopacket schema and reviewing how doseIntervals, cumulativeDose, and interval dates are currently modeled. Confirm the intended representation with the project maintainers; done means an agreed schema change that supports known start and end dates without requiring unavailable dose details.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
28/100

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