Fixed linking of subject to study and updated namespace to PDP produc…

gdcdictionary/schemas/aligned_reads_file.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "aligned_reads_file"
 title: Aligned Reads File
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/aligned_reads_index_file.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "aligned_reads_index_file"
 title: Aligned Reads Index File
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/aliquot.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "aliquot"
 title: Aliquot
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: biospecimen
 program: '*'
 project: '*'

gdcdictionary/schemas/clinical_file.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "clinical_file"
 title: Clinical File
 type: object
-namespace: https://data.midrc.org
+namespace: https://prometheus.data-commons.org/
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/condition.yaml

@@ -4,7 +4,7 @@ id: "condition"
 title: Condition
 type: object
 nodeTerms: null
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'
@@ -70,16 +70,16 @@ properties:
       description: The code for a specific codition, assigned by the code system.
       type: string
 
-  condition_concept_id: 
-      description: The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a condition The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of “Condition” should go in this table. Accepted Concepts. 
+  condition_concept_id:
+      description: The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a condition The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of “Condition” should go in this table. Accepted Concepts.
       type: string
 
-  condition_source_concept_id: 
-      description: This is the concept representing the condition source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Condition necessary for a given analytic use case. Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. 
+  condition_source_concept_id:
+      description: This is the concept representing the condition source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Condition necessary for a given analytic use case. Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.
       type: string
 
-  condition_source_value: 
-      description: This field houses the verbatim value from the source data representing the condition that occurred. For example, this could be an ICD10 or Read code. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. 
+  condition_source_value:
+      description: This field houses the verbatim value from the source data representing the condition that occurred. For example, this could be an ICD10 or Read code. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.
       type: string
 
   condition_code_system:
@@ -110,19 +110,19 @@ properties:
     description: The number of days from the index date to the date the subject was diagnosed with or began experiencing the condition.
     type: integer
 
-  provider_id: 
+  provider_id:
     description: The provider associated with condition record, e.g. the provider who made the diagnosis or the provider who recorded the symptom. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record.
     type: string
 
   site_id:
-    description: The site ID. 
+    description: The site ID.
     type: string
 
-  stop_reason: 
+  stop_reason:
     description: The Stop Reason indicates why a Condition is no longer valid with respect to the purpose within the source data. Note that a Stop Reason does not necessarily imply that the condition is no longer occurring. This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist.
     type: string
 
-  visit_id: 
+  visit_id:
     description: The visit ID.
     type: string
 
@@ -272,7 +272,7 @@ properties:
     description: >
       age at measurement of cac_score (years) (HARMONIZED)
     type: number
-  
+
   age_at_carotid_plaque: ### From BioData Catalyst "medical_history" node
     description: >
       age at measurement of carotid_plaque (years) (HARMONIZED)
@@ -541,8 +541,8 @@ properties:
     description: >
       An indicator of whether a subject had a venous thromboembolism (VTE)event prior to the start of the medical review process (includingself-reported events). (HARMONIZED)
     type: boolean
-  
-  
+
+
   unit_vte_followup_start_age: ### From BioData Catalyst "medical_history" node
     description: >
       harmonization unit for vte_followup_start_age (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)

gdcdictionary/schemas/core_metadata_collection.yaml

@@ -4,7 +4,7 @@ id: "core_metadata_collection"
 title: Core Metadata Collection
 type: object
 nodeTerms: null
-namespace: https://data.midrc.org
+namespace: https://prometheus.data-commons.org/
 category: administrative
 program: '*'
 project: '*'

gdcdictionary/schemas/dataset.yaml

@@ -4,7 +4,7 @@ id: "dataset"
 title: Dataset
 type: object
 nodeTerms: null
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: administrative
 program: '*'
 project: '*'

gdcdictionary/schemas/device_exposure.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "device_exposure"
 title: Device Exposure
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'
@@ -74,7 +74,7 @@ properties:
     type: string
 
   site_id:
-    description: The site ID. 
+    description: The site ID.
     type: string
 
   unique_device_id:

gdcdictionary/schemas/drug_exposure.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "drug_exposure"
 title: Drug Exposure
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'
@@ -110,7 +110,7 @@ properties:
   quantity:
     description: The quantity of drug as recorded in the original prescription or dispensing record.
     type: number
-    
+
   refills:
     description: The number of refills after the initial prescription. The initial prescription is not counted, values start with 0.
     type: integer
@@ -177,11 +177,10 @@ properties:
 #   unit_fasting_lipids:
 #     description: Harmonization unit for fasting_lipids. A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.
 #     type: string
-  
+
 #   unit_lipid_lowering_medication:
 #     description: Harmonization unit for unit_lipid1c. A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.
 #     type: string
 
   subjects:
     $ref: "_definitions.yaml#/to_one"
-

gdcdictionary/schemas/exposure.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "exposure"
 title: Exposure
 type: object
-namespace: http://dcp.bionimbus.org/
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'

gdcdictionary/schemas/image_annotation.yaml

@@ -4,7 +4,7 @@ id: "image_annotation"
 title: Image Annotation
 type: object
 nodeTerms: null
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/image_file.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "image_file"
 title: Image File
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/imaging_series.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "imaging_series"
 title: Imaging Series
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: medical_imaging
 program: '*'
 project: '*'
@@ -167,7 +167,3 @@ properties:
   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"
-
-
-
-

gdcdictionary/schemas/imaging_study.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "imaging_study"
 title: Imaging Study
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: medical_imaging
 program: '*'
 project: '*'
@@ -85,7 +85,7 @@ properties:
     type: string
 
   PatientSex: # use subject.gender as source of truth, but this can store DICOM value
-    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 
+    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
 
   StudyDescription:
@@ -102,4 +102,4 @@ properties:
 
   datasets:
     description: The submitter_id or id of the dataset this subject belongs to, i.e., a link to a record in the parent node.
-    $ref: "_definitions.yaml#/to_many"
+    $ref: "_definitions.yaml#/to_many"

gdcdictionary/schemas/measurement.yaml

@@ -4,7 +4,7 @@ id: "measurement"
 title: Measurement
 type: object
 nodeTerms: null
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'
@@ -78,7 +78,7 @@ properties:
       type: string
 
   site_id:
-    description: The care site ID. 
+    description: The care site ID.
     type: string
 
   unit_concept_id:
@@ -119,7 +119,7 @@ properties:
     description: >
       Resting systolic blood pressure from the upper arm in a clinical setting. (mmHg)
     type: number
-  
+
   age_at_bp_systolic: # from BDC "blood_pressure_test" node
     description: >
       age at measurement of bp_systolic (years)
@@ -192,7 +192,7 @@ properties:
     description: >
       age at measurement of hemoglobin_mcnc_bld. (years) (HARMONIZED)
     type: number
-  
+
   age_at_hematocrit_vfr_bld: ### From BDC "lab_result" node
     description: >
       Measurement of hematocrit, the fraction of volume (vfr) of blood (bld) that is composed of red blood cells. (years) (HARMONIZED)
@@ -332,7 +332,7 @@ properties:
     description: >
       Count by volume, or number concentration (ncnc), of platelets in the blood (bld). (thousands / microliter) (HARMONIZED)
     type: number
-  
+
   pmv_entvol_bld: ### From BDC "lab_result" node
     description: >
       Measurement of the mean volume (entvol) of platelets in the blood (bld), known as mean platelet volume (MPV or PMV). (fL = femtoliter) (HARMONIZED)
@@ -432,10 +432,10 @@ properties:
     description: >
       harmonization unit for rbc_ncnc_bld (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)
     type: string
-  
+
   unit_rdw_ratio_rbc: ### From BDC "lab_result" node
     description: >
-      harmonization unit for rdw_ratio_rbc (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) 
+      harmonization unit for rdw_ratio_rbc (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)
     type: string
 
   unit_total_cholesterol: ### From BDC "lab_result" node
@@ -543,7 +543,7 @@ properties:
     description: >
       Indicate the composition or type of biological sample used for the test (e.g., blood, urine, solid tissue, saliva, etc.)
     type: string
- 
+
   test_type: ### From BloodPAC "diagnostic_test" node
     description: >
       The general type or category of the laboratory or diagnostic test.
@@ -558,5 +558,3 @@ properties:
     description: >
       The numerical value representing the laboratory or diagnostic test measurement of the 'analyte_name'; also indicate the 'test_units'.
     type: number
-
-

gdcdictionary/schemas/metabolomic.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "metabolomic"
 title: Metabolomic
 type: object
-namespace: https://dcp.bionimbus.org/
+namespace: https://prometheus.data-commons.org/
 category: biospecimen
 program: '*'
 project: '*'

gdcdictionary/schemas/observation.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "observation"
 title: Observation
 type: object
-namespace: https://imaging-hub.data-commons.org
+namespace: https://prometheus.data-commons.org/
 category: clinical
 program: '*'
 project: '*'
@@ -62,29 +62,29 @@ properties:
   observation_source_concept_id:
     description: This is the concept representing the OBSERVATION_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Observation necessary for a given analytic use case. Consider using OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the OBSERVATION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.
     type: string
-  
+
   observation_source_value:
     description: This field houses the verbatim value from the source data representing the Observation that occurred. For example, this could be an ICD10 or Read code. This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.
     type: string
-  
+
   observation_type_concept_id:
     description: This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. Accepted Concepts. A more detailed explanation of each Type Concept can be found on the OMOP vocabulary wiki.
     type: string
-  
+
   provider_id:
     description: The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record.
     type: string
 
   qualifier_concept_id:
     description: This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. Use your best judgement as to what Concepts to use here and if they are necessary to accurately represent the clinical record. There is no restriction on the domain of these Concepts, they just need to be Standard.
     type: string
-    
+
   qualifier_source_value:
     description: This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.
     type: string
 
   site_id:
-    description: The care site ID. 
+    description: The care site ID.
     type: string
 
   unit_concept_id:
@@ -102,12 +102,12 @@ properties:
   value_as_number:
     description: This is the numerical value of the Result of the Observation, if applicable and available. It is not expected that all Observations will have numeric results, rather, this field is here to house values should they exist.
     type: number
-  
+
   value_as_string:
     description: This is the textual, categorical value of the Result of the Observation, if applicable and available.
     type: string
 
-  value_source_value: 
+  value_source_value:
     description: This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source. If the observation_source_value was a question, for example, or an observation that requires a result then this field is the answer/ result from the source data. Store the verbatim value that represents the result of the observation_source_value.
     type: string
 
@@ -256,7 +256,7 @@ properties:
   disease_response: ### From BloodPAC "followup" node
     description: "The observed improvement achieved at a certain point in time during a patient's treatment protocol."
     type: string
- 
+
   ecog_performance_status: ### From BloodPAC "followup" node
     description: "The ECOG functional performance status of the patient/participant."
     enum: