Qualification plan: enhancements/simplifications

[Yuri05]

tbd.

[PavelBal]

Allow to match multiple observed data to a simulation ouput in one "OutputMappings"-block.

Old:

      {
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": "Cho2002.Mean Ompz.20mg.po.EM",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": "#2166ac",
            "Caption": "Control (without Moclobemide)",
            "Symbol": "Circle"
          },
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM moclobemide 300mg po",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": "Cho2002.Mean Ompz+Moc.20mg.po.EM",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": "#b2182b",
            "Caption": "Treatment with Moclobemide",
            "Symbol": "Square"
          }
        ]
      }

New:

      {
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": {"Cho2002.Mean Ompz.20mg.po.EM", "Cho2002.Mean Ompz+Moc.20mg.po.EM"},
            "StartTime": {0, 0},
            "TimeUnit": {"h", "h"},
            "Color": {"#2166ac", "#b2182b"},
            "Caption": {"Control (without Moclobemide)", "Treatment with Moclobemide"},
            "Symbol": {"Circle", "Square"}
          }
        ]
      }

[Yuri05]

I support the idea of multiple observed data sets per simulated output. However I see some problems/TODOs with the proposed solution.

In the current setting the inputs are used as following:

• StartTime and TimeUnit are used to define the time shift on both simulated and observed data
• Color is used for both simulated and observed data
• Symbol is used for observed data only

"OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": "Cho2002.Mean Ompz.20mg.po.EM",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": "#2166ac",
            "Caption": "Control (without Moclobemide)",
            "Symbol": "Circle"
          }

Questions:

1. Do we really need different time shifts for different observed data sets?
2. Do we really need different captions/colors/symbols for different observed data sets?

If in the most cases we can live with the same time shift and the same caption/color I would vote for the simpler solution:

{
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": ["Cho2002.Mean Ompz.20mg.po.EM", "Cho2002.Mean Ompz+Moc.20mg.po.EM"],
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": "#b2182b",
            "Caption": "Observed data",
            "Symbol": "Square"
          }
        ]
}

And in those (rare) cases where time shift and/or caption/color differ we still could add additional OutputMappings.

However if time shift and/or caption/color between observed data sets differ more often, then we could do something like below

{
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": "#b2182b",
            "ObservedData": [
             {
               "Name": "Cho2002.Mean Ompz.20mg.po.EM", 
               "StartTime": 1,
               "TimeUnit": "h",
               "Color": "#b2182b",
               "Symbol": "Circle"
             },
             {
               "Name": "Cho2002.Mean Ompz+Moc.20mg.po.EM"
               "StartTime": 2,
               "TimeUnit": "h",
               "Color": "#2166ac",
               "Symbol": "Square"
             }
        ]
}

[PavelBal]

Offer a pre-defined set of colors and symbols

that will be used in plot definitions. E.g., the template json has two entries

"Colors" : ["#2166ac", "#b2182b", "#5666ac", "#a3682c"]
"Symbols" : ["Circle", "Square", "Cross"]

In the plot definition it is used with an index:

      {
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": "Cho2002.Mean Ompz.20mg.po.EM",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": 1,
            "Caption": "Control (without Moclobemide)",
            "Symbol": 1
          },
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM moclobemide 300mg po",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "ObservedData": "Cho2002.Mean Ompz+Moc.20mg.po.EM",
            "StartTime": 0,
            "TimeUnit": "h",
            "Color": 2,
            "Caption": "Treatment with Moclobemide",
            "Symbol": 2
          }
        ]
      }

[Yuri05]

I would go even further and define named styles. E.g.

"LineStyles" : [
  {
    "Name:" "Simulated_Blue",
    "Color": "#0000ff",
    "Symbol": "None", 
    "LineStyle": "Solid",
    "LineWidth": 1
  },
  {
    "Name:" "Observed_Blue",
    "Color": "#0000ff",
    "Symbol": "Circle", 
    "LineStyle": "None",
    "LineWidth": 1
  },
  {
    "Name:" "Observed_Red",
    "Color": "#ff0000",
    "Symbol": "Circle", 
    "LineStyle": "None",
    "LineWidth": 1
  }
]

And then e.g.

{
        "SectionId": 301,
        "Title": "Cho 2002 (Omeprazole 40 mg po) Asian EM",
        "SimulationDuration": 12,
        "TimeUnit": "h",
        "OutputMappings": [
          {
            "Project": "Omeprazole-Moclobemide-DDI",
            "Simulation": "omeprazole 40mg po asian EM",
            "Output": "Organism|PeripheralVenousBlood|Esomeprazole|Omeprazole Plasma (Peripheral Venous Blood)",
            "StartTime": 0,
            "TimeUnit": "h",
            "Style": "Simulated_Blue",
            "ObservedData": [
             {
               "Name": "Cho2002.Mean Ompz.20mg.po.EM", 
               "StartTime": 1,
               "TimeUnit": "h",
               "Style": "Observed_Blue"
             },
             {
               "Name": "Cho2002.Mean Ompz+Moc.20mg.po.EM"
               "StartTime": 2,
               "TimeUnit": "h",
               "Style": "Observed_Red"
             }
        ]
}