Merge pull request #10 from uc-cdis/updates

Updates to support the ETL
uc-cdis · Jun 28, 2024 · c9f3221 · c9f3221
2 parents 6ed52e3 + 4ab3ea1
commit c9f3221
Show file tree

Hide file tree

Showing 4 changed files with 14 additions and 21 deletions.
diff --git a/gdcdictionary/schemas/dataset.yaml b/gdcdictionary/schemas/dataset.yaml
@@ -45,6 +45,14 @@ properties:
     description: A unique identifier for the dataset.
     type: string
 
+  commons_name:
+    description: A short ID for the data commons or resource from which the metadata originate.
+    type: string
+
+  commons_long_name:
+    description: The expanded name of the data commons or resource from which the metadata originate.
+    type: string
+
   data_citation:
     description: The citation for the published dataset.
     type: string

diff --git a/gdcdictionary/schemas/imaging_series.yaml b/gdcdictionary/schemas/imaging_series.yaml
@@ -141,15 +141,6 @@ properties:
     description: (0018, 5101) Radiographic view associated with (0018, 5100) Patient Position.
     type: string
 
-
-
-
-
-
-
-
-
-
   # links
   imaging_studies:
     description: The submitter_id or id of the imaging_study this imaging_series belongs to, i.e., a link to a record in the parent node.

diff --git a/gdcdictionary/schemas/imaging_study.yaml b/gdcdictionary/schemas/imaging_study.yaml
@@ -63,9 +63,9 @@ properties:
     items:
       type: string
 
-  # EthnicGroup: # use subject.ethnicity
-  #   description: (0010,2160) The ethnic group to which the patient belongs.
-  #   type: string
+  EthnicGroup: # use subject.ethnicity
+    description: (0010,2160) The ethnic group to which the patient belongs.
+    type: string
 
   study_modality:
     description: The list of modalities in the imaging study; derived from (0008, 0060) Modality.
@@ -80,9 +80,9 @@ properties:
   # PatientBirthYear:
   #   description: (0010,0030) Patient's Birth Date Attribute
 
-  # PatientID: # use subject.submitter_id
-  #   description: (0010,0020) A unique identifier for the patient.
-  #   type: string
+  PatientID: # use subject.submitter_id
+    description: (0010,0020) A unique identifier for the patient.
+    type: string
 
   PatientSex: # use subject.gender as source of truth, but this can store DICOM value
     description: (0010,0040) the patient's sex; the biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic  (internal and external), chromosomal, and hormonal characteristics 

diff --git a/gdcdictionary/schemas/subject.yaml b/gdcdictionary/schemas/subject.yaml
@@ -90,17 +90,11 @@ properties:
     term:
       $ref: "_terms.yaml#/ethnicity"
     type: string
-#   EthnicGroup: # use subject.ethnicity
-#     description: (0010,2160) The ethnic group to which the patient belongs.
-#     type: string
 
   gender:
     term:
       $ref: "_terms.yaml#/gender"
     type: string
-#   PatientSex: # use subject.gender
-#     description: (0010,0040) the patient's sex; the biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic  (internal and external), chromosomal, and hormonal characteristics 
-#     type: string
 
   index_event:
     description: The event used as the anchor or start date for all temporal data elements. This acts as day 0 on a timeline of events relating to the patient.