Yaml terminology updates (#313)

* added terminology note meta tags, fixed terminology links

* fixed column name mismatch in readmissions yaml, produced full docs

models/ccsr/ccsr_models.yml

@@ -100,6 +100,9 @@ models:
         description: Unique identifier for each patient.
       - name: normalized_code
         description: "The ICD-10-CM code for the diagnosis."
+        meta:
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__icd_10_cm.csv
+          terminology_note: "**Note: this terminology set is too large to be loaded as a seed and is instead loaded from public cloud storage for supported adapters."
       - name: code_description
         description: "The ICD-10-CM code description provided in the CCSR CSV seed file."
       - name: condition_rank
@@ -195,6 +198,9 @@ models:
         description: Unique identifier for each patient.
       - name: normalized_code
         description: The ICD-10-PCS code for the procedure.
+        meta:
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__icd_10_pcs.csv
+          terminology_note: "**Note: this terminology set is too large to be loaded as a seed and is instead loaded from public cloud storage for supported adapters."
       - name: code_description
         description: "The ICD-10-PCS code description provided in the CCSR CSV seed file."
       - name: ccsr_parent_category

models/chronic_conditions/cms_chronic_conditions_models.yml

@@ -284,18 +284,18 @@ models:
             The type of chronic condition as defined by CMS. 
             ('Common' or 'Other chronic or potentially disabling conditions')
           meta:
-            terminology: /value-sets/chronic-conditions/cms-chronic-conditions
+            terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/chronic_conditions/chronic_conditions__cms_chronic_conditions_hierarchy.csv
         - name: condition_category
           description: >
             The category of the condition (e.g. Cardiovascular Disease).
           meta:
-            terminology: /value-sets/chronic-conditions/cms-chronic-conditions
+            terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/chronic_conditions/chronic_conditions__cms_chronic_conditions_hierarchy.csv
         - name: condition
           description: The name of the chronic condition.
           tests:
             - not_null
           meta:
-            terminology: /value-sets/chronic-conditions/cms-chronic-conditions
+            terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/chronic_conditions/chronic_conditions__cms_chronic_conditions_hierarchy.csv
         - name: data_source
           description: >
             Indicates the name of the source dataset (e.g. Medicare Claims).

models/chronic_conditions/tuva_chronic_conditions_models.yml

@@ -29,12 +29,12 @@ models:
             A higher level rollup grouping of conditions from the condition 
             column
           meta:
-            terminology: /value-sets/chronic-conditions/tuva-chronic-conditions
+            terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/chronic_conditions/chronic_conditions__tuva_chronic_conditions_hierarchy.csv
         - name: condition
           description: >
             The name of the condition that each diagnosis code rolls up to
           meta:
-            terminology: /value-sets/chronic-conditions/tuva-chronic-conditions
+            terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/chronic_conditions/chronic_conditions__tuva_chronic_conditions_hierarchy.csv
         - name: first_diagnosis_date
           description: >
             The first date when a diagnosis code that rolls up to this condition 

models/claims_preprocessing/claims_preprocessing_models.yml

@@ -30,11 +30,11 @@ models:
       - name: gender
         description: The gender of the patient.
         meta:
-          terminology: /terminology/demographics/gender
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__gender.csv
       - name: race
         description: The race of the patient.
         meta:
-          terminology: /terminology/demographics/race
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__race.csv
       - name: facility_npi
         description: The NPI for the facility where the encounter occurred.
       - name: provider_first_name
@@ -44,55 +44,45 @@ models:
       - name: ms_drg_code
         description: The MS-DRG code associted with the inpatient visit
         meta:
-          terminology: /terminology/conditions-and-procedures/ms-drg
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__ms_drg.csv
       - name: ms_drg_description
         description: The MS-DRG description associted with the inpatient visit
-        meta:
-          terminology: /terminology/conditions-and-procedures/ms-drg
       - name: medical_surgical
         description: Indicates whether the MS-DRG is medical or surgical in nature.
         meta:
-          terminology: /terminology/conditions-and-procedures/ms-drg
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__ms_drg.csv
       - name: apr_drg_code
         description: The APR-DRG code associted with the inpatient visit
         meta:
-          terminology: /terminology/conditions-and-procedures/apr-drg
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__apr_drg.csv
       - name: apr_drg_description
         description: The APR-DRG description associted with the inpatient visit
-        meta:
-          terminology: /terminology/conditions-and-procedures/apr-drg
       - name: admit_source_code
         description: Admission source code for the encounter.
         meta:
-          terminology: /terminology/administrative-codes/admit-source
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__admit_source.csv
       - name: admit_source_description
         description: Admission source description for the encounter.
-        meta:
-          terminology: /terminology/administrative-codes/admit-source
       - name: admit_type_code
         description: Admission type code for the encounter.
         meta:
-          terminology: /terminology/administrative-codes/admit-type
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__admit_type.csv
       - name: admit_type_description
         description: Admission type description for the encounter.
-        meta:
-          terminology: /terminology/administrative-codes/admit-type
       - name: discharge_disposition_code
         description: Discharge disposition code for the encounter.
         meta:
-          terminology: /terminology/administrative-codes/discharge-disposition
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/terminology/terminology__discharge_disposition.csv
       - name: discharge_disposition_description
         description: Discharge disposition description for the encounter.
-        meta:
-          terminology: /terminology/administrative-codes/discharge-disposition
       - name: total_paid_amount
         description: The total paid amount across all claims for the encounter.
       - name: total_allowed_amount
         description: The total allowed amount across all claims for the encounter.
       - name: total_charge_amount
         description: The total charge amount across all claims for the encounter.
       - name: length_of_stay
-        description: The length of stay for the encoujnter.
+        description: The length of stay for the encounter.
       - name: mortality_flag
         description: 1 if a patient died during the encounter, 0 otherwise.
       - name: data_source

models/cms_hcc/cms_hcc_models.yml

@@ -21,9 +21,13 @@ models:
         description: The type of condition.
       - name: icd_10_cm_code
         description: The ICD-10-CM condition code.
+        meta:
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/cms_hcc/cms_hcc__icd_10_cm_mappings.csv
       - name: hcc_code
         description: >
           HCC code from the latest CMS HCC model available in the mart.
+        meta:
+          terminology: https://github.com/tuva-health/the_tuva_project/blob/main/seeds/value_sets/cms_hcc/cms_hcc__icd_10_cm_mappings.csv
       - name: hcc_description
         description: >
           HCC description from the latest CMS HCC model available in the mart.