revamp

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-- '2.7'
+- '3.6'
 before_script:
 - yes | python setup.py install
 - git clone https://github.com/uc-cdis/dictionaryutils; cd dictionaryutils

gdcdictionary/schemas/_terms.yaml

@@ -46,7 +46,7 @@ adverse_event:
 
 age_at_event_days:
   description: >
-    Age at the time of diagnosis expressed.
+    Participant’s age in days of the Outcome event
 
 age_at_diagnosis_days:
   description: >

gdcdictionary/schemas/diagnosis.yaml

@@ -43,69 +43,66 @@ uniqueKeys:
 properties:
   $ref_ubiq: "_definitions.yaml#/ubiquitous_properties"
 
-  age_at_event_days:
-    term:
-      $ref: "_terms.yaml#/age_at_event_days"
-    type:
-      - integer
-      - "null"
-    maximum: 32872
-    minimum: 0
+  external_id:
+    description: "external id used by contributor"
+    type: string
 
+  diagnosis:
+    description: |
+      A calculated rollup of a participant’s diagnoses. If the participant has only Cancer diagnoses, the participant’s value is Cancer. If the participant has only Structural Birth Defect diagnoses, the value is Structural Birth Defects.
+    type: string
+
+  diagnosis_source_text:
+    description: |
+      Analysis, and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such a study/investigation.
+    type: string
+
   diagnosis_category:
-    description: "High level diagnosis categorization."
+    description: |
+      An overarching classification based on the Diagnosis Source Text to aide in quick searching over Cancer and Structural Birth Defects.
     enum:
       - Structural Birth Defect
       - Cancer
-      - Other
-
-  tumor_location:
-    description: "Location of the tumor."
-    type: string
+      - Not Reported
 
-  primary_diagnosis:
-    term:
-      $ref: "_terms.yaml#/primary_diagnosis"
+  icd_id_diagnosis:
+    description: |
+      ICD10 code for the diagnosis.
     type: string
 
-  external_id:
-    description: "external id used by contributor"
+  mondo_id_diagnosis:
+    description: |
+      The Mondo ID associated with the Diagnosis (Source Text) value. Derived by matching the Diagnosis Source Text value with Mondo ID lookups.
     type: string
-
-  source_text_diagnosis:
-    description: "Pathological diagnosis"
+
+  ncit_id_diagnosis:
+    description: |
+      The National Cancer Institute Thesaurus (NCIt) ID associated with the Diagnosis (Source Text) value. Derived by matching the Diagnosis Source Text value with NCIt lookups.
     type: string
 
-  source_text_tumor_location:
-    description: "Location of the tumor"
+  spatial_descriptor:
+    description: |
+      Term to indicate precise, relative anatomical position from where the biospecimen was obtained.
     type: string
 
-  mondo_id_diagnosis:
+  tumor_location_source_text:
     description: |
-      The ID of the term from the Monary Disease Ontology
-      which represents a harmonized diagnosis
+      Text term from the investigator that describes the anatomic site of the tumor.
     type: string
 
-  icd_id_diagnosis:
+  source_text_tumor_location:
     description: |
-      The ID of the term from the International Classification of Diseases
-      which represents harmonized diagnosis
+      TBD
     type: string
 
   uberon_id_tumor_location:
-    term:
-      $ref: "_terms.yaml#/age_at_event_days"
-    type: string
-
-  ncit_id_diagnosis:
     description: |
-      The ID term from the National Cancer Institute Thesaurus which represents a
-      harmonized diagnosis
+      TBD
     type: string
 
   spatial_descriptor:
     description: |
-      Ontology term that harmonizes the spatial concepts from Biological Spatial Ontology
+      TBD
     type: string
 
   participants:

gdcdictionary/schemas/family.yaml

@@ -45,5 +45,14 @@ properties:
     description: "Name given to the family by contributor"
     type: string
 
+  family_composition:
+    description: "A calculated value based on the family members present with genomic data within a participant’s pedigree."
+    enum:
+      - "proband_only"
+      - "duo"
+      - "duo_plus"
+      - "trio" 
+      - "trio_plus"
+
   projects:
     $ref: "_definitions.yaml#/to_one_project"

gdcdictionary/schemas/family_relationship.yaml

@@ -43,10 +43,108 @@ properties:
 
   relative_to_participant_relation:
     description: "Text describing the nature of the relationship (i.e. father, mother, sister, brother)"
-    type: string
+    enum:
+      - Aunt
+      - Brother
+      - Brother-in-law
+      - Brother-Monozygotic Twin
+      - Child
+      - Cousin
+      - Daughter
+      - Father
+      - First cousin once removed
+      - Grandfather
+      - Grandmother
+      - Married in aunt
+      - Married in Husband
+      - Married in-Spouse
+      - Maternal aunt
+      - Maternal cousin
+      - Maternal grandfather
+      - Maternal grandmother
+      - Maternal Great Grandmother
+      - Maternal Great Uncle
+      - Maternal half-sister
+      - Maternal uncle
+      - Mother
+      - Nephew
+      - Other
+      - Paternal aunt
+      - Paternal cousin
+      - Paternal grandfather
+      - Paternal grandmother
+      - Paternal uncle
+      - Sibling
+      - Sister
+      - Son
+      - Spouse
+      - Twin Brother
+      - Twin Sister
+      - Uncle
+      - Uncle-married in
+      - Wife 
+      - Proband
+      - Maternal Granddaughter
 
   participant_to_relative_relation:
     description: "Text describing the nature of the relationship (i.e. father, mother, sister, brother)"
+    enum:
+      - Aunt
+      - Brother
+      - Brother-in-law
+      - Brother-Monozygotic Twin
+      - Child
+      - Cousin
+      - Daughter
+      - Father
+      - First cousin once removed
+      - Grandfather
+      - Grandmother
+      - Married in aunt
+      - Married in Husband
+      - Married in-Spouse
+      - Maternal aunt
+      - Maternal cousin
+      - Maternal grandfather
+      - Maternal grandmother
+      - Maternal Great Grandmother
+      - Maternal Great Uncle
+      - Maternal half-sister
+      - Maternal uncle
+      - Mother
+      - Nephew
+      - Other
+      - Paternal aunt
+      - Paternal cousin
+      - Paternal grandfather
+      - Paternal grandmother
+      - Paternal uncle
+      - Sibling
+      - Sister
+      - Son
+      - Spouse
+      - Twin Brother
+      - Twin Sister
+      - Uncle
+      - Uncle-married in
+      - Wife 
+      - Proband
+      - Maternal Granddaughter
+
+  participant1_id:
+    description: "Participant1 ID"
+    type: string
+
+  participant2_id: 
+    description: "Participant2 ID"
+    type: string
+
+  participant1_to_participant2_relation:
+    description: "Participant1 to Participant2 Relation"
+    type: string
+
+  participant2_to_participant1_relation:
+    description: "Participant2 to Participant1 Relation"
     type: string
 
   participants:

gdcdictionary/schemas/outcome.yaml

@@ -52,22 +52,22 @@ properties:
 
   disease_related:
     description: |
-      Whether Dead and cause of death was disease related (Yes)
-      or Dead and cause of death was not disease related (No)
-      or Not Reported
+      Text value describing whether or not the participant’s outcome is related to their disease. For example, whether their deceased status was due to their disease.
     enum:
       - "Yes"
       - "No"
-      - Not Reported
-      - Reported Unknown
-      - Not Applicable
+      - "Not Reported"
+      - "Reported Unknown"
+      - "Not Applicable"
 
   vital_status:
     term:
       $ref: "_terms.yaml#/age_at_event_days"
     enum:
-      - Dead
-      - Alive
+      - "Deceased"
+      - "Alive"
+      - "Reported Unknown"
+      - "Not Reported"
 
   participants:
     $ref: "_definitions.yaml#/to_one"