Physiomimi Format - nsrr/edf-editor-translator GitHub Wiki

Annotation translator tool converts vendor-specific format to a standardized XML format. Each scored event is one node including EventConcept mapped to concept in ontology, Starttime, Duraton. Notes is optional, depending on column Note in mapping file. If a scored event is not found in mapping file, a node with event concept Technical notes is inserted, and that event is saved in Log file, with event name and path to annotation file.

• Software version

    <PSGAnnotation>
      <SoftwareVersion>Sandman</SoftwareVersion>
    </PSGAnnotation>
  

• Epoch length

    <EpochLength>30</EpochLength>
  

• Scored events

    <ScoredEvents>
      <ScoredEvent>
        <EventConcept>Recording Start Time</EventConcept>
        <Starttime>0</Starttime>
        <Duration>39600</Duration>
        <ClockTime>05.03.03 22.30.00</ClockTime>
      </ScoredEvent>
      <ScoredEvent>
        <EventConcept> SDO:HypopneaSleepEvent</EventConcept>
        <Starttime>84913</Starttime>
        <Duration>12.43</Duration>
        <Notes>Associated with Arousal</Notes>
      </ScoredEvent>
      <ScoredEvent>
        <EventConcept> SDO:RightLegLimpMovement</EventConcept>
        <Starttime>86025</Starttime>
        <Duration>2.00</Duration>
      </ScoredEvent>
    </ScoredEvents>
  

• Sleep stages: are considered events, with duration is computed as time from the start of current stage till the start of next stage in seconds, instead of every 30 second epoch.

  • SDO:WakeState: wake state
  • SDO:NonRapidEyeMovementSleep-N1: sleep stage 1
  • SDO:NonRapidEyeMovementSleep-N2: sleep stage 2
  • SDO:NonRapidEyeMovementSleep-N3: sleep stage 3
  • SDO:NonRapidEyeMovementSleep-N4: sleep stage 4
  • SDO:RapidEyeMovementSleep: REM Sleep

    <ScoredEvent>
      <EventConcept>SDO:WakeState</EventConcept>
      <Starttime>84432</Starttime>
      <Duration>30.00</Duration>
    </ScoredEvent>
    <ScoredEvent>
      <EventConcept>SDO:NonRapidEyeMovementSleep-N2</EventConcept>
      <Starttime>24162</Starttime>
      <Duration>270.00</Duration>
    </ScoredEvent>
    <ScoredEvent>
      <EventConcept>SDO:NonRapidEyeMovementSleep-N3</EventConcept>
      <Starttime>24612</Starttime>
      <Duration>30.00</Duration>
    </ScoredEvent>
    <ScoredEvent>
      <EventConcept>SDO:NonRapidEyeMovementSleep-N2</EventConcept>
      <Starttime>24642</Starttime>
      <Duration>150.00</Duration>
    </ScoredEvent>
    <ScoredEvent>
      <EventConcept>SDO:RapidEyeMovementSleep</EventConcept>
      <Starttime>24792</Starttime>
      <Duration>210.00</Duration>
    </ScoredEvent>
  

Event mapping file in CSV format is used to map laboratory-specific event names to concepts in PhysioMIMI's ontology. Each line is one concept name. Note is optional.

  EventType,Event,Value,Note
  Arousal,Arousal (),SDO:SleepArousalFinding,
  Arousal,Arousal (ASDA),SDO:SleepArousalFinding,ASDA Arousal
  EpochLength,,30,
  Oximetry Artifact,SpO2 artifact,Oximetry Artifact Event,
  Desaturation,SpO2 desaturation,SDO:HemoglobinOxygenDesaturationFinding,
  Respiratory,Central Apnea,SDO:CentralApneaFinding,
  Respiratory,Hypopnea,SDO:HypopneaFinding,
  Respiratory,Mixed Apnea,SDO:MixedApneaFinding,
  Respiratory,Obstructive Apnea,SDO:ObstructiveApneaFinding,
  Sleep Staging,0,SDO:WakeState,
  Sleep Staging,1,SDO:NonRapidEyeMovementSleep-N1,
  Sleep Staging,2,SDO:NonRapidEyeMovementSleep-N2,
  Sleep Staging,3,SDO:NonRapidEyeMovementSleep-N3,
  Sleep Staging,4,SDO:NonRapidEyeMovementSleep-N4,
  Sleep Staging,5,SDO:RapidEyeMovementSleep,