Merge pull request #4 from uc-cdis/updates

Updates

gdcdictionary/schemas/_definitions.yaml

@@ -231,11 +231,6 @@ ubiquitous_properties:
   submitter_id:
     description: "A human-readable, unique identifier for a record in the metadata database. It can be used in place of the UUID for identifying or recalling a record (e.g., in data queries or uploads/exports)."
     type: string
-  case_ids:
-    description: "A list of one or more case submitter_ids associated with this data."
-    type: array
-    items:
-      type: string
   state:
     $ref: "#/state"
   project_id:

gdcdictionary/schemas/case.yaml

@@ -41,99 +41,25 @@ properties:
 
   $ref: "_definitions.yaml#/ubiquitous_properties"
 
-  age_at_index:
-    description: The study participant's age, in years, at the index event. The index event is determined by the data submitter and used as an anchor date for all temporal variables. Note that an age of 0 indicates a participant who is younger than 1 year old. For participants with ages greater than 89 years, please use the property 'age_at_index_gt89'.
+  PatientAge:
+    description: (0010,1010) the patient's age at imaging.
     type: number
-    maximum: 89
-    minimum: 0
-
-  age_at_index_gt89:
-    description: Indicates whether the subject's age at the time of the study was greater than 89 years.
-    enum:
-      - "Yes"
-      - "No"
-
-  covid19_positive:
-    description: "An indicator of whether the patient has ever had a positive COVID-19 test or been diagnosed with one of the following ICD-10 COVID-19 conditions: COVID-19 (U07. 1), Influenza due to unidentified influenza virus with other manifestations (J11.8), Post COVID-19 condition (U09.9), Myalgic encephalomyelitis/chronic fatigue syndrome (G93.32), or Sequelae of other specified infectious and parasitic diseases (B94.8). For more information about a patient's specific COVID-19 diagnosis, details can be found under Condition."
-    enum:
-      - "Yes"
-      - "No"
-      - "Indeterminate"
-      - "Not Reported"
-
-  country_of_residence:
-    description: The country where the subject resides.
+
+  PatientID:
+    description: (0010,0020) A unique identifier for the patient.
     type: string
 
-  ethnicity:
-    term:
-      $ref: "_terms.yaml#/ethnicity"
-    enum:
-      - Hispanic or Latino
-      - Not Hispanic or Latino
-      - Not Reported
-
-  gen3_linked_subjects_available:
-    description: Indicates whether there is data available for the subject in other data resources.
-    type: boolean
-
-  icu_indicator:
-    description: Indicates whether the subject has been admitted to the ICU.
-    type: boolean
-
-  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.
+  PatientSex:
+    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
 
-  linked_external_data:
-    description: A list of all external data resources that are confirmed to have data for the case.
-    type: array
-    items:
-      type: string
-
-  long_covid_diagnosis:
-    description: "An indicator of whether the patient has ever been diagnosed with one of the following ICD-10 long COVID-19 conditions: U09.9 (Post COVID-19 condition, unspecified), G93.32 (Myalgic encephalomyelitis/chronic fatigue syndrome), and B94.8 (Sequelae of other specified infectious and parasitic diseases).  'Positive' means the patient was diagnosed with a long COVID condition, while 'Not Reported' means the patient has never been diagnosed with a long COVID condition."
-    enum:
-      - Positive
-      - Not Reported
+  EthnicGroup:
+    description: (0010,2160) The ethnic group to which the patient belongs.
+    type: string
 
   race:
     term:
       $ref: "_terms.yaml#/race"
-    enum:
-      - American Indian or Alaska Native
-      - Asian
-      - Black or African American
-      - Native Hawaiian or other Pacific Islander
-      - Other
-      - White
-      - Not Reported
-
-  sex:
-    description: 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.
-    enum:
-      - Female
-      - Male
-      - Not Reported
-
-  site_id:
-    description: A de-identified code used to classify a case as part of a specific data submission.
-    type: string
-
-  token_record_id:
-    description: An ID used to link a de-identified case in MIDRC to the same case in an external data resource.
-    type: string
-
-  treatment_info:
-    description: Indicates whether detailed treatment information is available for the subject.
-    type: boolean
-
-  ventilator_indicator:
-    description: Indicates whether the subject has been on a ventilator.
-    type: boolean
-
-  zip:
-    description: The three-digit United States zip code of residence for any population greater than 20,000. For zip codes where the three digit number represents a population less than 20,000 "000" will be provided.
     type: string
 
   datasets:

gdcdictionary/schemas/dataset.yaml

@@ -31,53 +31,24 @@ links:
 required:
   - submitter_id
   - type
-  - data_description
   - projects
+  - collection_id
 
 uniqueKeys:
   - [id]
   - [project_id, submitter_id]
 
 properties:
+  $ref: "_definitions.yaml#/ubiquitous_properties"
 
-  #system properties, do not change or remove:
-  created_datetime:
-    $ref: "_definitions.yaml#/datetime"
-
-  id:
-    $ref: "_definitions.yaml#/UUID"
-
-  project_id:
-    $ref: "_definitions.yaml#/project_id"
-
-  state:
-    $ref: "_definitions.yaml#/state"
-
-  submitter_id:
-    description: A human-readable identifier for the study's record in the database. It can be used in place of the UUID for identifying or recalling a record.
-    type: string
-
-  type:
-    description: The name of the node in the database to be used in queries. In this case "dataset".
-    enum:
-      - dataset
-
-  updated_datetime:
-    $ref: "_definitions.yaml#/datetime"
-
-  # additional properties to describe the dataset
-  acknowledgement:
-    description: Publication acknowledgement(s) for the published dataset.
+  collection_id:
+    description: A unique identifier for the dataset.
     type: string
 
   data_citation:
     description: The citation for the published dataset.
     type: string
 
-  data_contributor:
-    description: The name of the organization or individual that the contributed dataset belongs to.
-    type: string
-
   data_description:
     description: A brief, free-text description of the data files and associated metadata provided for this dataset.
     type: string
@@ -106,26 +77,6 @@ properties:
     description: The primary body site studied in this dataset.
     type: string
 
-  publication_citation:
-    description: The major or main publication(s) associated with the data itself or with the publication that published the dataset.
-    type: string
-
-  research_description:
-    description: If the dataset is related to a research study, provide a brief, free-text description or abstract of the study being performed, for example, the hypothesis being tested and a very brief description of the materials, methods and results.
-    type: string
-
-  research_design:
-    description: A summary of the goals of the research or a general description of the research's relationship to a clinical application.
-    type: string
-
-  research_objective:
-    description: The general objective of the research; what the researchers hope to discover or determine.
-    type: string
-
-  research_setup:
-    description: A high level description of the setup used to achieve the research objectives.
-    type: string
-
   projects:
     description: The code of the project that this dataset belongs to, i.e., a link to the parent node.
     $ref: "_definitions.yaml#/to_one_project"

gdcdictionary/schemas/imaging_series.yaml

@@ -18,24 +18,29 @@ systemProperties:
   - state
   - created_datetime
   - updated_datetime
-  - file_state
-  - error_type
+
 
 links:
   - exclusive: false
     required: true
     subgroup:
-      - name: core_metadata_collections
+      - name: datasets
+        backref: imaging_series
+        label: member_of
+        target_type: dataset
+        multiplicity: many_to_many
+        required: false
+      - name: cases
         backref: imaging_series
-        label: data_from
-        target_type: core_metadata_collection
+        label: related_to
+        target_type: case
         multiplicity: many_to_one
         required: false
       - name: imaging_studies
         backref: imaging_series
-        label: related_to
+        label: member_of
         target_type: imaging_study
-        multiplicity: many_to_one
+        multiplicity: many_to_many
         required: false
 
 required:
@@ -50,24 +55,8 @@ properties:
 
   $ref: "_definitions.yaml#/ubiquitous_properties"
 
-  manufacturer:
-    description: (0008, 0070) Manufacturer
-    type: string
-
-  manufacturer_model_name:
-    description: (0008, 1090) Manufacturer's Model Name
-    type: string
-
-  modality:
-    description: (0008, 0060) Modality
-    type: string
-
-  series_description:
-    description: (0008, 103e) Series Description
-    type: string
-
-  series_uid:
-    description: (0020, 000e) Series Instance UID
+  BodyPartExamined:
+    description: (0018, 0015) Body Part Examined.
     type: string
 
   data_category:
@@ -85,10 +74,49 @@ properties:
       $ref: "_terms.yaml#/data_type"
     type: string
 
-  core_metadata_collections:
-    description: The submitter_id or id of the core_metadata_collection to which the imaging_series belongs, i.e., a link to a record in the parent node.
-    $ref: "_definitions.yaml#/to_one"
+  dicom_viewer_url:
+    description: A URL where the imaging series can be viewed.
+    type: string
 
+  object_ids:
+    description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the imaging series, if applicable.
+    type: array
+    items:
+      type: string
+
+  Manufacturer:
+    description: (0008, 0070) Manufacturer
+    type: string
+
+  ManufacturerModelName:
+    description: (0008, 1090) Manufacturer's Model Name
+    type: string
+
+  Modality:
+    description: (0008, 0060) Modality
+    type: string
+
+  SeriesDescription:
+    description: (0008, 103e) Series Description
+    type: string
+
+  SeriesInstanceUID:
+    description: (0020, 000e) Series Instance UID
+    type: string
+
+  ViewPosition:
+    description: (0018,5101) Radiographic view associated with Patient Position (0018,5100).
+    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.
     $ref: "_definitions.yaml#/to_one"
+
+  cases:
+    description: The submitter_id or id of the case observed in this imaging_series, i.e., a link to a record in the parent node.
+    $ref: "_definitions.yaml#/to_one"
+
+  datasets:
+    description: The submitter_id or id of the dataset this imaging_series belongs to, i.e., a link to a record in the parent node.
+    $ref: "_definitions.yaml#/to_many"