From 3ccb2b077de355bd416e12a812bd8e4731c1ac60 Mon Sep 17 00:00:00 2001 From: urvi-occ Date: Wed, 27 Aug 2025 14:47:34 -0500 Subject: [PATCH 1/2] changes for csf into DD v1 --- gdcdictionary/schemas/analyte.yaml | 5 +++ gdcdictionary/schemas/biospecimen.yaml | 34 +++++++++++++++++++++ gdcdictionary/schemas/sample.yaml | 20 ++++++++++++ gdcdictionary/schemas/sequencing_assay.yaml | 5 +++ 4 files changed, 64 insertions(+) diff --git a/gdcdictionary/schemas/analyte.yaml b/gdcdictionary/schemas/analyte.yaml index 0270ede51..fbf01a106 100644 --- a/gdcdictionary/schemas/analyte.yaml +++ b/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 diff --git a/gdcdictionary/schemas/biospecimen.yaml b/gdcdictionary/schemas/biospecimen.yaml index 4f3952ea9..30871e7d2 100644 --- a/gdcdictionary/schemas/biospecimen.yaml +++ b/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" diff --git a/gdcdictionary/schemas/sample.yaml b/gdcdictionary/schemas/sample.yaml index 8d094dff0..b420f762d 100644 --- a/gdcdictionary/schemas/sample.yaml +++ b/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: + description: > + The number of hours between the sample collection and the centrifugation into its components. + type: number + + hours_to_centrifugation_limits: + description: > + The lower and 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. + type: string + hours_to_fractionation_lower: description: > The lower limit on the amount of time, in hours, between the blood draw and the fractionation diff --git a/gdcdictionary/schemas/sequencing_assay.yaml b/gdcdictionary/schemas/sequencing_assay.yaml index 1bfc5f237..474750477 100644 --- a/gdcdictionary/schemas/sequencing_assay.yaml +++ b/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: From bd175b2b4b7ac6f11bfb386e3c3a8a101a3bc20d Mon Sep 17 00:00:00 2001 From: urvi-occ Date: Thu, 28 Aug 2025 14:46:58 -0500 Subject: [PATCH 2/2] changes for hours_to_centrifugation_lower and hours_to_centrifugation_upper --- gdcdictionary/schemas/sample.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gdcdictionary/schemas/sample.yaml b/gdcdictionary/schemas/sample.yaml index b420f762d..18befc071 100644 --- a/gdcdictionary/schemas/sample.yaml +++ b/gdcdictionary/schemas/sample.yaml @@ -92,14 +92,14 @@ properties: - Unknown - Whole Bone Marrow - hours_to_centrifugation: + hours_to_centrifugation_lower: description: > - The number of hours between the sample collection and the centrifugation into its components. + 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_limits: + hours_to_centrifugation_upper: description: > - The lower and 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. + 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: