changes for csf into DD v1

gdcdictionary/schemas/analyte.yaml

@@ -52,6 +52,11 @@ uniqueKeys:
 properties:
   $ref: "_definitions.yaml#/ubiquitous_properties"
 
+  analyte_absolute_input:
+    description: >
+      Nanograms of nucleic acid (input to assay)
+    type: number
+
   analyte_isolation_method:
     description: >
       The name or general description of the method used to isolate the analyte. Alternatively, if

gdcdictionary/schemas/biospecimen.yaml

@@ -138,6 +138,7 @@ properties:
       - "Dermal"
       - "Descending Colon"
       - "Diaphragm"
+      - "Direct From Prior Resection Cavity"
       - "Duodenum"
       - "Ear"
       - "Ear Canal"
@@ -310,6 +311,7 @@ properties:
       - "Sternum"
       - "Stomach"
       - "Stomach (Mucosa Only)"
+      - "Subarachnoid/Cisternal"
       - "Subcutaneous Tissue"
       - "Synovium"
       - "Temporal Cortex"
@@ -340,6 +342,7 @@ properties:
       - "Vein"
       - "Venous"
       - "Vertebra"
+      - "Ventricular"
       - "Vulva"
       - "White Blood Cells"
       - "Wrist"
@@ -414,6 +417,7 @@ properties:
     enum:
       - "Advanced Adenoma"
       - "Blood Cancer"
+      - "Brain Cancer"
       - "Breast Cancer"
       - "Colorectal Cancer"
       - "Gastric Cancer"
@@ -450,7 +454,10 @@ properties:
     enum:
       - "Biopsy"
       - "Blood Draw"
+      - "Intraoperative"
+      - "Lumbar Puncture"
       - "Not Applicable"
+      - "Ommaya/External Cathete"
       - "Unknown"
 
   primary_site:
@@ -513,6 +520,11 @@ properties:
       The temperature, in centigrade, at which the biospecimen was kept while it was being transported from the procurement site to its processing destination.
     type: number
 
+  storage_tube_type:
+    description: >
+      The kind of receptacle used for shipping/storage. Applicable if specimen transferred from collection tube to a second, e.g. preservative, tube.
+    type: number
+
   tissue_type:
     term:
       $ref: "_terms.yaml#/tissue_type"
@@ -524,6 +536,28 @@ properties:
       - "Peritumoral"
       - "Unknown"
 
+  tube_transfer_indicator:
+    description: >
+      True/False Indicates whether there was a tube transfer for the specimen.
+    type: boolean
+
+  tube_transfer_time_lower:
+    description: >
+      The lower limit on the amount of time, in hours, between
+      initial specimen collection and transfer to new tube (applicable if specimen transferred from collection tube to a second, e.g. preservative, tube)
+    type: number
+
+  tube_transfer_time_upper:
+    description: >
+      The upper limit on the amount of time, in hours, between
+      initial specimen collection and transfer to new tube (applicable if specimen transferred from collection tube to a second, e.g. preservative, tube)
+    type: number
+
+  tube_transfer_temperature:
+    description: "Temperature, in centigrade, the specimen is kept at while awaiting transfer to new tube. (applicable if specimen transferred from collection tube to a second, e.g. preservative, tube)."
+    type: number
+
+
   tumor_code:
     term:
       $ref: "_terms.yaml#/tumor_code"

gdcdictionary/schemas/sample.yaml

@@ -50,6 +50,16 @@ properties:
       if you have provided a detailed protocol, enter its file_name here.
     type: string
 
+  centrifugated_indicator:
+    description: >
+      True/False Indicates whether the specimen was centrifugated.
+    type: boolean
+
+  centrifugation_method:
+    description: >
+      The name or description of the method used to obtain the CSF fraction sample. (e.g., Novartis Protocol #001, 2,000 g centrifuge at 4°C with gentle deceleration). Detailed protocol should be provided as a supplemental file when possible.
+    type: string
+
   composition:
     term:
       $ref: "_terms.yaml#/composition"
@@ -82,6 +92,16 @@ properties:
       - Unknown
       - Whole Bone Marrow
 
+  hours_to_centrifugation_lower:
+    description: >
+      The lower limit on the amount of time, in hours, between the sample collection and the centrifugation into its components. Note this is only required if centrifugation was performed and if the exact time is unknown. If only one time value is known for hours_to_centrifugation then only use `hours_to_centrifugation_lower`
+    type: number
+
+  hours_to_centrifugation_upper:
+    description: >
+      The upper limit on the amount of time, in hours, between the sample collection and the centrifugation into its components. Note this is only required if centrifugation was performed and if the exact time is unknown.  If only one time value is known for hours_to_centrifugation then only use `hours_to_centrifugation_lower`
+    type: string
+
   hours_to_fractionation_lower:
     description: >
       The lower limit on the amount of time, in hours, between the blood draw and the fractionation

gdcdictionary/schemas/sequencing_assay.yaml

@@ -46,6 +46,11 @@ properties:
     enum:
       - Targeted Sequencing
       - Copy Number Analysis
+      - Other
+
+  assay_method_other:
+    description: "General name or description of the method used to characterize the analyte not defined in `assay_method`."
+    type: string
 
   assay_target:
     term: