Better encoding of multiple dosing

[matthiaskoenig]

Problem: Often multiple dosing with a single substance. Necessary to encode many interventions and timings. This results in a lot of overhead and many curation issues.

• allow simple syntax for storing multiple dosing protocol
• see schema in https://github.com/Open-Systems-Pharmacology/Database-for-observed-data

=> Add timestamp => Add support for multiple dosing

[matthiaskoenig]

• [~] no possibility to encode time of day; Multiple solutions used:

  • additional intervention with time of day; measurement_type circadian status.
  • some time encoded as group characteristica

• [x] absolute and relative timing; outputs are timed relative;

• [x] get rid of time end; -> keep time end; multiple dosings with time_end have to be encoded individually; e.g. multiple constant infusions with break;

• [x] simple repeated dosing schemas

• [x] how to encode different dosing amounts? -> use separate interventions

• 0|12|40|60 : syntax1, give the timepoints; dosing at 0 [time_units], 12 [time_units], 40 [time_units], ...

• S0T24R3 : syntax1, give the start timepoint, interval time and repeats (parse with regular expressions); dosing equivalent to 0 | 24 | 48

• S-48T48R2 | 80 | 90 | S100T12R2 = -48|0|80|90|100|112 (helper function for translation)

• different dosing amounts have to be encoded as separate interventions

• The dosing regime will be stored in the time field. Storage as string field with validation;

Example for encoding absolute times (e.g. for circadian effects):

• [x] qualitative timing: morning, evening, daytime, nighttime
• [x] absolute timing: 8:00, 12.00

      {
        "name": "dex_morning || caf_evening",
        "substance": "dextormethorphan || caffeine",
        "measurement_type": "dosing",
        "application": "multiple dose",
        "form": "tablet",
        "route": "po",
        "value": "30",
        "unit": "mg"
        "time": "S0T24R10 || S12T24R10",
        "time_unit": "hr"
        "timestamp": "8:00 | evening"
      }

Example for multiple dosing:

      {
        "name": "dex_multi1 || dex_multi2",
        "substance": "dextormethorphan",
        "measurement_type": "dosing",
        "application": "multiple dose",
        "form": "tablet",
        "route": "po",
        "value": "30 || 60",
        "unit": "mg"
        "time": "S0T24R10 || S240T48R10",
        "time_unit": "hr"
      }

relative and absolute timings

• At the moment the output times are relative to the intervention times.
• This is up to the curator (results in possible absolute offset)

Example for multiple constant infusions. For now no special handling.

      {
        "name": "gip_infusions",
        "substance": "gip",
        "measurement_type": "dosing",
        "application": "multiple infusion",
        "form": "solution",
        "route": "iv",
        "value": "2",
        "unit": "mg/kg/min"
        "time": "S0E12T24R2",
        "time_unit": "hr"
      }

=> single infusions

      {
        "name": "gip_infusion1 || gip_infusion2",
        "substance": "gip",
        "measurement_type": "dosing",
        "application": "infusion",
        "form": "solution",
        "route": "iv",
        "value": "2",
        "unit": "mg/kg/min"
        "time": "0 || 24",
        "time_end": "12 || 36",
        "time_unit": "hr"
      }