[ENH] Move PET DICOM correspondences into term definitions

src/schema/objects/metadata.yaml

@@ -229,6 +229,8 @@ AttenuationCorrection:
   display_name: Attenuation Correction
   description: |
     Short description of the attenuation correction method used.
+    Corresponds to [DICOM Tag 0054, 1101](https://dicomlookup.com/dicomtags/(0054,1101))
+    `Attenuation Correction Method`.
   type: string
 AttenuationCorrectionMethodReference:
   name: AttenuationCorrectionMethodReference
@@ -355,6 +357,7 @@ BodyPart:
   display_name: Body Part
   description: |
     Body part of the organ / body region scanned.
+    Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`.
   type: string
 BodyPartDetails:
   name: BodyPartDetails
@@ -731,6 +734,7 @@ DecayCorrectionFactor:
   display_name: Decay Correction Factor
   description: |
     Decay correction factor for each frame.
+    Corresponds to [DICOM Tag 0054, 1321](https://dicomlookup.com/dicomtags/(0054,1321)) `Decay Factor`.
   type: array
   items:
     type: number
@@ -1895,16 +1899,16 @@ InjectionEnd:
   name: InjectionEnd
   display_name: Injection End
   description: |
-    Time of end of injection with respect to `"TimeZero"` in the default unit
-    seconds.
+    Time of end of injection with respect to `"TimeZero"`, in seconds.
+    Corresponds to [DICOM Tag 0018, 1073](https://dicomlookup.com/dicomtags/(0018,1073))
+    `Radiopharmaceutical Stop Time` converted to seconds relative to TimeZero.
   type: number
   unit: s
 InjectionStart:
   name: InjectionStart
   display_name: Injection Start
   description: |
-    Time of start of injection with respect to `"TimeZero"` in the default unit
-    seconds.
+    Time of start of injection with respect to `"TimeZero"`, in seconds.
     This corresponds to [DICOM Tag 0018, 1072](https://dicomlookup.com/dicomtags/(0018,1072))
     `Contrast/Bolus Start Time` converted to seconds relative to `"TimeZero"`.
   type: number
@@ -2843,6 +2847,7 @@ PharmaceuticalDoseAmount:
   display_name: Pharmaceutical Dose Amount
   description: |
     Dose amount of administered pharmaceutical.
+    Corresponds to [DICOM Tag 0018, 0028](https://dicomlookup.com/dicomtags/(0018,0028)) `Intervention Drug Dose`.
   anyOf:
     - type: number
     - type: array
@@ -2866,6 +2871,9 @@ PharmaceuticalDoseTime:
     the regimen description should be complete enough to enable unambiguous
     interpretation of `"PharmaceuticalDoseTime"`.
     Unit format of the specified pharmaceutical dose time MUST be seconds.
+    Corresponds to a combination of DICOM Tags
+    [0018, 0027](https://dicomlookup.com/dicomtags/(0018,0027)) `Intervention Drug Stop Time` and
+    [0018, 0035](https://dicomlookup.com/dicomtags/(0018,0035)) `Intervention Drug Start Time`.
   anyOf:
     - type: number
       unit: s
@@ -2885,7 +2893,9 @@ PharmaceuticalName:
   name: PharmaceuticalName
   display_name: Pharmaceutical Name
   description: |
-    Name of pharmaceutical.
+    Name of administered pharmaceutical.
+    Note that this is distinct from any radiotracer or contrast agent used in the scan protocol.
+    This partly matches [DICOM Tag 0018, 0034](https://dicomlookup.com/dicomtags/(0018,0034)) `Intervention Drug Name`.
   type: string
 PhaseEncodingDirection:
   name: PhaseEncodingDirection
@@ -3145,6 +3155,8 @@ ReconFilterSize:
   display_name: Recon Filter Size
   description: |
     Kernel size of post-recon filter (FWHM) in default units `"mm"`.
+    This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210))
+    `Convolution Kernel`.
   anyOf:
     - type: number
       unit: mm
@@ -3157,6 +3169,8 @@ ReconFilterType:
   display_name: Recon Filter Type
   description: |
     Type of post-recon smoothing (for example, `["Shepp"]`).
+    This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210))
+    `Convolution Kernel`.
   anyOf:
     - type: string
     - type: array
@@ -3173,12 +3187,16 @@ ReconMethodName:
   display_name: Recon Method Name
   description: |
     Reconstruction method or algorithm (for example, `"3d-op-osem"`).
+    This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
+    `Reconstruction Method`.
   type: string
 ReconMethodParameterLabels:
   name: ReconMethodParameterLabels
   display_name: Recon Method Parameter Labels
   description: |
     Names of reconstruction parameters (for example, `["subsets", "iterations"]`).
+    This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
+    `Reconstruction Method`.
   type: array
   items:
     type: string
@@ -3187,6 +3205,8 @@ ReconMethodParameterUnits:
   display_name: Recon Method Parameter Units
   description: |
     Unit of reconstruction parameters (for example, `["none", "none"]`).
+    This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
+    `Reconstruction Method`.
   type: array
   items:
     type: string
@@ -3196,6 +3216,8 @@ ReconMethodParameterValues:
   display_name: Recon Method Parameter Values
   description: |
     Values of reconstruction parameters (for example, `[21, 3]`).
+    This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
+    `Reconstruction Method`.
   type: array
   items:
     type: number
@@ -3511,6 +3533,7 @@ ScanDate:
   display_name: Scan Date
   description: |
     Date of scan in the format `"YYYY-MM-DD[Z]"`.
+    Corresponds to [DICOM Tag 0008, 0022](https://dicomlookup.com/dicomtags/(0008,0022)) `Acquisition Date`.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the `acq_time` column of the
     corresponding [Scans file](SPEC_ROOT/modality-agnostic-files/data-summary-files.md#scans-file).
   type: string
@@ -3559,6 +3582,8 @@ ScatterFraction:
   display_name: Scatter Fraction
   description: |
     Scatter fraction for each frame (Units: 0-100%).
+    Corresponds to [DICOM Tag 0054, 1323](https://dicomlookup.com/dicomtags/(0054,1323))
+    `Scatter Fraction Factor`.
   type: array
   items:
     type: number
@@ -4130,6 +4155,9 @@ TracerName:
   display_name: Tracer Name
   description: |
     Name of the tracer compound used (for example, `"CIMBI-36"`)
+    Corresponds to [DICOM Tag 0054, 0300](https://dicomlookup.com/dicomtags/(0054,0300)) `Radionuclide Code Sequence`,
+    extracted from the fields [0008, 0122](https://dicomlookup.com/dicomtags/(0008,0122)) `Mapping Resource Name`
+    and/or [0008, 0105](https://dicomlookup.com/dicomtags/(0008,0105)) `Mapping Resource`.
   type: string
 TracerRadLex:
   name: TracerRadLex
@@ -4142,6 +4170,9 @@ TracerRadionuclide:
   display_name: Tracer Radionuclide
   description: |
     Radioisotope labeling tracer (for example, `"C11"`).
+    Corresponds to [DICOM Tag 0054, 0300](https://dicomlookup.com/dicomtags/(0054,0300)) `Radionuclide Code Sequence`,
+    extracted from the fields [0008, 0100](https://dicomlookup.com/dicomtags/(0008,0100)) `Code Value`
+    and/or [0008, 0104](https://dicomlookup.com/dicomtags/(0008,0104)) `Code Meaning`.
   type: string
 TracerSNOMED:
   name: TracerSNOMED

src/schema/rules/sidecars/pet.yaml

@@ -18,10 +18,6 @@ PETHardware:
       description_addendum: |
         SI unit for radioactivity (Becquerel) should be used (for example, "Bq/mL").
         Corresponds to [DICOM Tag 0054, 1001](https://dicomlookup.com/dicomtags/(0054,1001)) `Units`.
-    BodyPart:
-      level: recommended
-      description_addendum: |
-        Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`.
 
 PETInstitutionInformation:
   selectors:
@@ -47,10 +43,7 @@ PETSample:
     - modality == "pet"
     - suffix == "pet"
   fields:
-    BodyPart:
-      level: optional
-      description_addendum: |
-        Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`.
+    BodyPart: optional
     BodyPartDetails: optional
     BodyPartDetailsOntology: optional
 
@@ -59,15 +52,8 @@ PETRadioChemistry:
     - datatype == "pet"
     - suffix == "pet"
   fields:
-    TracerName:
-      level: required
-      description_addendum: |
-        Corresponds to DICOM Tags (0008,0105) `Mapping Resource` and
-        (0008,0122) `Mapping Resource Name`.
-    TracerRadionuclide:
-      level: required
-      description_addendum: |
-        Corresponds to DICOM Tags (0008,0104) `CodeValue` and (0008,0104) `CodeMeaning`.
+    TracerName: required
+    TracerRadionuclide: required
     InjectedRadioactivity: required
     InjectedRadioactivityUnits: required
     InjectedMass: required
@@ -120,24 +106,11 @@ PETPharmaceuticals:
     - datatype == "pet"
     - suffix == "pet"
   fields:
-    PharmaceuticalName:
-      level: recommended
-      description_addendum: |
-        For pharmaceutical co-administered with tracer.
-        Corresponds to [DICOM Tag 0018, 0034](https://dicomlookup.com/dicomtags/(0018,0034)) `Intervention Drug Name`.
-    PharmaceuticalDoseAmount:
-      level: recommended
-      description_addendum: |
-        For pharmaceutical co-administered with tracer.
-        Corresponds to [DICOM Tag 0018, 0028](https://dicomlookup.com/dicomtags/(0018,0028)) `Intervention Drug Dose`.
+    PharmaceuticalName: recommended
+    PharmaceuticalDoseAmount: recommended
     PharmaceuticalDoseUnits: recommended
     PharmaceuticalDoseRegimen: recommended
-    PharmaceuticalDoseTime:
-      level: recommended
-      description_addendum: |
-        Corresponds to a combination of DICOM Tags
-        [0018, 0027](https://dicomlookup.com/dicomtags/(0018,0027)) `Intervention Drug Stop Time` and
-        [0018, 0035](https://dicomlookup.com/dicomtags/(0018,0035)) `Intervention Drug Start Time`.
+    PharmaceuticalDoseTime: recommended
     Anaesthesia: optional
 
 PETTime:
@@ -147,22 +120,11 @@ PETTime:
   fields:
     TimeZero: required
     ScanStart: required
-    InjectionStart:
-      level: required
-      description_addendum: |
-        Corresponds to [DICOM Tag 0018, 1072](https://dicomlookup.com/dicomtags/(0018,1072))
-        `Radiopharmaceutical Start Time`.
+    InjectionStart: required
     FrameTimesStart: required
     FrameDuration: required
-    InjectionEnd:
-      level: recommended
-      description_addendum: |
-        Corresponds to [DICOM Tag 0018, 1073](https://dicomlookup.com/dicomtags/(0018,1073))
-        `Radiopharmaceutical Stop Time` converted to seconds relative to TimeZero.
-    ScanDate:
-      level: deprecated
-      description_addendum: |
-        Corresponds to [DICOM Tag 0008, 0022](https://dicomlookup.com/dicomtags/(0008,0022)) `Acquisition Date`.
+    InjectionEnd: recommended
+    ScanDate: deprecated
 
 PETReconstruction:
   selectors:
@@ -172,59 +134,25 @@ PETReconstruction:
     AcquisitionMode: required
     ImageDecayCorrected: required
     ImageDecayCorrectionTime: required
-    ReconMethodName:
-      level: required
-      description_addendum: |
-        This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
-        `Reconstruction Method`.
-    ReconMethodParameterLabels:
-      level: required
-      description_addendum: |
-        This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
-        `Reconstruction Method`.
+    ReconMethodName: required
+    ReconMethodParameterLabels: required
     ReconMethodParameterUnits:
       level: recommended
       level_addendum: required if `ReconMethodParameterLabels` does not contain `"none"`
-      description_addendum: |
-        This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
-        `Reconstruction Method`.
     ReconMethodParameterValues:
       level: recommended
       level_addendum: required if `ReconMethodParameterLabels` does not contain `"none"`
-      description_addendum: |
-        This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103))
-        `Reconstruction Method`.
-    ReconFilterType:
-      level: required
-      description_addendum: |
-        This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210))
-        `Convolution Kernel`.
+    ReconFilterType: required
     ReconFilterSize:
       level: recommended
       level_addendum: required if `ReconFilterType` is not `"none"`
-      description_addendum: |
-        This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210))
-        `Convolution Kernel`.
-    AttenuationCorrection:
-      level: required
-      description_addendum: |
-        This corresponds to [DICOM Tag 0054, 1101](https://dicomlookup.com/dicomtags/(0054,1101))
-        `Attenuation Correction Method`.
+    AttenuationCorrection: required
     ReconMethodImplementationVersion: recommended
     AttenuationCorrectionMethodReference: recommended
     ScaleFactor: recommended
-    ScatterFraction:
-      level: recommended
-      description_addendum: |
-        Corresponds to [DICOM Tag 0054, 1323](https://dicomlookup.com/dicomtags/(0054,1323)) `Scatter Fraction Factor`.
-    DecayCorrectionFactor:
-      level: recommended
-      description_addendum: |
-        Corresponds to [DICOM Tag 0054, 1321](https://dicomlookup.com/dicomtags/(0054,1321)) `Decay Factor`.
-    DoseCalibrationFactor:
-      level: recommended
-      description_addendum: |
-        Corresponds to [DICOM Tag 0054, 1322](https://dicomlookup.com/dicomtags/(0054,1322)) `Dose Calibration Factor`.
+    ScatterFraction: recommended
+    DecayCorrectionFactor: recommended
+    DoseCalibrationFactor: recommended
     PromptRate: recommended
     SinglesRate: recommended
     RandomRate: recommended