diff --git a/gdcdictionary/schemas/_terms.yaml b/gdcdictionary/schemas/_terms.yaml index f3c8c742f..91308c7b5 100644 --- a/gdcdictionary/schemas/_terms.yaml +++ b/gdcdictionary/schemas/_terms.yaml @@ -794,13 +794,11 @@ freezing_method: cde_version: 1.0 term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" -gender: +sex: description: > - Text designations that identify gender. Gender is described as the assemblage of properties that - distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification - of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] + The sex or gender of the participant assigned at birth termDef: - term: Person Gender Text Type + term: Person Sex Text Type source: caDSR cde_id: 2200604 cde_version: 3.0 @@ -1750,17 +1748,6 @@ treatment_type: cde_version: 1.0 term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" -tumor_grade: - description: > - Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation - and aggressiveness. - termDef: - term: Neoplasm Histologic Grade - source: caDSR - cde_id: 2785839 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" - tumor_code: # TOREVIEW description: > A specification of a cancer through cellular origin and localization. diff --git a/gdcdictionary/schemas/case.yaml b/gdcdictionary/schemas/case.yaml index a5df323e6..f58bd008c 100644 --- a/gdcdictionary/schemas/case.yaml +++ b/gdcdictionary/schemas/case.yaml @@ -48,10 +48,10 @@ properties: the patient. Work with your collaborators to decide on the patient's id. type: string - index_date: + index_event: description: > - The reference or anchor date used during date obfuscation, where a single date is obscured by - creating one or more date ranges in relation to this date. + Specifies the clinical or study-related event that serves as the anchor date for date + obfuscation. All derived or shifted dates are calculated relative to the selected event. enum: - Diagnosis - First Patient Visit @@ -70,27 +70,32 @@ properties: description: > The number of days between the date used for index and the date the patient was lost to follow-up. type: integer + + days_to_sample_collection: + description: > + The number of days Duration from Sample Collection + type: integer - promtheus_id: + prometheus_id: description: > - Id for promethus record + Id for prometheus record type: string apollo_id: description: > - Apollo id for promethus record + Apollo id for prometheus record type: string metabolomic_data_available: description: > - Apollo id for promethus record + A yes/no indicator related to whether metabolomic data is available for the patient enum: - "Yes" - "No" exposure_data_available: description: > - Apollo id for promethus record + A yes/no indicator related to whether exposure data is available for the patient enum: - "Yes" - "No" diff --git a/gdcdictionary/schemas/demographic.yaml b/gdcdictionary/schemas/demographic.yaml index a776c94d8..6b2e39bb5 100644 --- a/gdcdictionary/schemas/demographic.yaml +++ b/gdcdictionary/schemas/demographic.yaml @@ -76,9 +76,9 @@ properties: - "Not Hispanic or Latino" - "Unknown" - gender: + sex: term: - $ref: "_terms.yaml#/gender" + $ref: "_terms.yaml#/sex" enum: - "Female" - "Male" @@ -98,7 +98,7 @@ properties: - "Other" - "Unknown" - self_identified_gender: + self_identified_sex: description: > The sex or gender assignment preferred by the participant. enum: diff --git a/gdcdictionary/schemas/diagnosis.yaml b/gdcdictionary/schemas/diagnosis.yaml index e07c7f107..bd0da42b1 100644 --- a/gdcdictionary/schemas/diagnosis.yaml +++ b/gdcdictionary/schemas/diagnosis.yaml @@ -37,7 +37,7 @@ required: - morphology - primary_diagnosis - tissue_or_organ_of_origin - - tumor_grade + - cancer_grade uniqueKeys: @@ -3949,16 +3949,6 @@ properties: $ref: "_terms.yaml#/tissue_or_organ_of_origin" type: string - tumor_grade: - term: - $ref: "_terms.yaml#/tumor_grade" - enum: - - "GX Grade cannot be assessed (undetermined grade)" - - "G1 Well differentiated (low grade)" - - "G2 Moderately differentiated (intermediate grade)" - - "G3 Poorly differentiated (high grade)" - - "G4 Undifferentiated (high grade)" - - "Unknown" # Fields for prometheus-3a days_to_metastatic_diagnosis: @@ -3986,7 +3976,7 @@ properties: type: string cancer_grade: - description: "Associated cancer grade (e.g. 0, 1, 2, 3, 4)." + description: "Associated cancer grade (e.g. 0, 1, 2, 3, 4). The values represents, Grade 0 - Grade cannot be assessed (undetermined grade), Grade 1 - Well differentiated (low grade), Grade 2 - Moderately differentiated (intermediate grade), Grade 3 - Poorly differentiated (high grade), Grade 4 - Undifferentiated (high grade)" enum: - Grade 0 - Grade 1 diff --git a/gdcdictionary/schemas/exposure.yaml b/gdcdictionary/schemas/exposure.yaml index 7fafab8a9..4053872c0 100644 --- a/gdcdictionary/schemas/exposure.yaml +++ b/gdcdictionary/schemas/exposure.yaml @@ -76,14 +76,14 @@ properties: term: $ref: "_terms.yaml#/tobacco_smoking_status" enum: - - "1" - - "2" - - "3" - - "4" - - "5" - - "6" - - "7" - - Unknown + - "Lifelong Non-Smoker" + - "Current Smoker" + - "Current Reformed Smoker, Duration Not Specified" + - "Current Reformed Smoker for ≤ 15 years" + - "Current Reformed Smoker for > 15 years" + - "Smoker at Diagnosis" + - "Smoking History Not Documented" + - "Unknown" years_smoked: term: $ref: "_terms.yaml#/years_smoked" diff --git a/gdcdictionary/schemas/family_history.yaml b/gdcdictionary/schemas/family_history.yaml index 1c2e68bb3..aec035068 100644 --- a/gdcdictionary/schemas/family_history.yaml +++ b/gdcdictionary/schemas/family_history.yaml @@ -54,9 +54,9 @@ properties: $ref: "_terms.yaml#/relationship_type" type: string - relationship_gender: + relationship_sex: term: - $ref: "_terms.yaml#/gender" + $ref: "_terms.yaml#/sex" enum: - female - male diff --git a/gdcdictionary/schemas/treatment.yaml b/gdcdictionary/schemas/treatment.yaml index 1cf79e933..3fc6af909 100644 --- a/gdcdictionary/schemas/treatment.yaml +++ b/gdcdictionary/schemas/treatment.yaml @@ -216,7 +216,7 @@ properties: description: "The total number of unique systemic medical interventions, including the current intervention, in treating metastatic disease." type: integer - complete_resection_no_clear_margins: + complete_resection_clear_margins: description: "Was there a complete surgical resection with clear margins?" enum: - "Yes" diff --git a/sandbox/case/__schema.yaml b/sandbox/case/__schema.yaml index b6d314fcf..be986546c 100644 --- a/sandbox/case/__schema.yaml +++ b/sandbox/case/__schema.yaml @@ -45,10 +45,10 @@ schema: constraints: unique: false # local overriding for uniqueness - - name: gender + name: sex type: string - title: Gender # use title for nice display label - description: "Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc" + title: Sex # use title for nice display label + description: "The sex or gender of the participant assigned at birth" cde_id: 2200604 search: terms_facet constraints: diff --git a/sandbox/diagnosis/__schema.yaml b/sandbox/diagnosis/__schema.yaml index a6f71bc99..868a7428e 100644 --- a/sandbox/diagnosis/__schema.yaml +++ b/sandbox/diagnosis/__schema.yaml @@ -132,14 +132,6 @@ schema: - Gleason scoring system - Nottingham grading system - Glioblastoma pathology nuclear grade - - - name: tumor_grade # don't we need this? - title: Tumor grade - description: "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness." - type: string - constraints: - required: false - allowed: [ GX, G1, G2, G3, G4 ] - name: vital_status # do we need this? title: Vital status diff --git a/sandbox/family_history/__schema.yaml b/sandbox/family_history/__schema.yaml index 69be2f9cc..516d82b15 100644 --- a/sandbox/family_history/__schema.yaml +++ b/sandbox/family_history/__schema.yaml @@ -46,8 +46,8 @@ schema: required: false unique: false allowed: [ parent, sibling, offspring, grandparent ] - - name: relationship_gender - description: "Provide the patient's relationship gender using the defined categories." + - name: relationship_sex + description: "Provide the patient's relationship sex or gender assigned at birth using the defined categories." type: string constraints: required: false