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Repository Signals File Format

  • Lines beginning with # are comments.
  • Each line in the file defines either:
    • A Generic Signal Type
      Use GENERIC_SIGNAL_TYPE prefix to declare a new signal type. The format is:
      GENERIC_SIGNAL_TYPE [type_alias] [GSV_string_spec]
      (Three tab-separated fields)
      • GENERIC_SIGNAL_TYPE: Marks the line as a signal type definition.
      • type_alias: A short name for the signal type.
      • GSV_string_spec: The full specification is a single, comma-separated string. All T() (Time) channels must be listed before all V() (Value) channels. For example: T(i),V(f).
        • Time channels use T(X), where X is a comma-separated list of basic types (see Types).
        • Example: T(i) means one integer time channel; T(i,i) means two integer time channels (can also be written as T(i),T(i)).
        • Value channels follow after time channels with comma separator between. A signal can include no time channels or no value channels.
    • A Signal Definition
      Use SIGNAL to define a signal. Each line should have at least four fields, defaults are used for missing fields.
      • SIGNAL: Marks the line as a signal definition.
      • signal_name: The name of the signal.
      • signal_unique_code: A unique numeric code for the signal within the repository.
      • signal_type: Specify the type directly as a GSV_string_spec (e.g., T(i),V(f) for one integer time channel and one float value channel), or refer to a previously defined type alias using 16:type_alias. The 16 is required for the parser to use Custom types and not old and deprecated data type structured.
      • comment: Free text, ignored by the system. Can be empty. Usually we document the signal group liek demographic,labs,cbc. Sometimes multiple tags are provided.
      • categorical_bitmask: A bitmask written left to right with one digit for each value channel indicating which value channels are categorical. 1=categorical, 0=numeric. (e.g., 10 means the first of two value channels is categorical, the second is numeric). Default is 0 for all value channels.
      • units (optional): Units for the signal, separated by | for multiple channels.

Time/Value Channel Types

Here is a complete list of supported types:

  • u prefix to specify unsigned number and controls the _is_signed
  • c - character, 8 bit integer that can hold 256 unique numbers
  • s - short, 16 bit that can hold 65536 unique numbers
  • i - integer, 32 bits, can hold 4B unique numbers
  • l - long, 64 bits, can hold 1.8*10^19 unique numbers
  • f - float 32 bits
  • d - double float 64 bits
  • D- long double

For source code please refer to MedSignals.h type_enc::encode

Example

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# Tab-delimited format

# Legacy signals definition (Used only for ColonFlag AlgoMarker)
SIGNAL  GENDER      100     0       Male=1,Female=2    1  
SIGNAL  BP          920     8    systolic,diastoloc    00    mmHg|mmHg
SIGNAL  Hemoglobin  1000    1     cbc   0   mg/dL
SIGNAL  RC          2309    1       Med All ReadCodes ^[0-9A-HJ-NP-U] .no I,O,V,W,X,Y    1
SIGNAL  Drug        2400    8       Drugs: date, drug code, duration in days, use proper    10    days

# Newer signals definition:
GENERIC_SIGNAL_TYPE   VInt    V(i)
GENERIC_SIGNAL_TYPE   LabT1V1    T(i),V(f)
GENERIC_SIGNAL_TYPE   CategoricalT1V1    T(i),V(i)
GENERIC_SIGNAL_TYPE   LabT1V2    T(i),V(f,f)
GENERIC_SIGNAL_TYPE   Date2Val_i_f    T(i),V(i,f)

SIGNAL  GENDER      100     16:VInt       Male=1,Female=2    1  
SIGNAL  BP          920     16:LabT1V2    systolic,diastoloc    00    mmHg|mmHg
SIGNAL  Hemoglobin  1000    16:LabT1V1     cbc   0   mg/dL
SIGNAL  RC          2309    16:CategoricalT1V1       Med All ReadCodes ^[0-9A-HJ-NP-U] .no I,O,V,W,X,Y    1
SIGNAL  Drug        2400    16:Date2Val_i_f       Drugs: date, drug code, duration in days, use proper    10    days

A full list of deprecated signal types by numeric code