From fa23fbc85a8a53120e22f1831429e8bea29223d4 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Tue, 14 Sep 2021 17:33:11 -0400
Subject: [PATCH 1/9] Regenerated artifacts.

---
 crdch_model/graphql/crdch_model.graphql |  6 +++---
 crdch_model/shex/crdch_model.shex       |  8 ++++----
 crdch_model/shex/crdch_model.shexj      | 16 ++++++++--------
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/crdch_model/graphql/crdch_model.graphql b/crdch_model/graphql/crdch_model.graphql
index bab6eface..3874584a7 100644
--- a/crdch_model/graphql/crdch_model.graphql
+++ b/crdch_model/graphql/crdch_model.graphql
@@ -82,10 +82,10 @@ type CodeableConcept
 type Coding
   {
     code: CrdchString!
+    label: CrdchString
     system: CrdchString!
-    systemURL: CrdchString
+    systemUrl: CrdchString
     systemVersion: CrdchString
-    label: CrdchString
   }
 
 type Diagnosis
@@ -94,7 +94,7 @@ type Diagnosis
     identifier: [Identifier]
     subject: Subject
     ageAtDiagnosis: Quantity
-    yearAtDiagnosis: CrdchInteger
+    diagnosisDate: TimePoint
     condition: EnumCRDCHDiagnosisCondition
     primarySite: [BodySite]
     metastaticSite: [BodySite]
diff --git a/crdch_model/shex/crdch_model.shex b/crdch_model/shex/crdch_model.shex
index 2b166e40f..b96ac27e8 100644
--- a/crdch_model/shex/crdch_model.shex
+++ b/crdch_model/shex/crdch_model.shex
@@ -163,10 +163,10 @@ linkml:Nodeidentifier NONLITERAL
     (  $<Coding_tes> (  &<Entity_tes> ;
           rdf:type [ <Entity> ] ? ;
           <code> @<CrdchString> ;
+          <label> @<CrdchString> ? ;
           <system> @<CrdchString> ;
-          <systemURL> @<CrdchString> ? ;
-          <systemVersion> @<CrdchString> ? ;
-          <label> @<CrdchString> ?
+          <system_url> @<CrdchString> ? ;
+          <system_version> @<CrdchString> ?
        ) ;
        rdf:type [ <Coding> ] ?
     )
@@ -179,7 +179,7 @@ linkml:Nodeidentifier NONLITERAL
           <identifier> @<Identifier> * ;
           <subject> @<Subject> ? ;
           <age_at_diagnosis> @<Quantity> ? ;
-          <year_at_diagnosis> @<CrdchInteger> ? ;
+          <diagnosis_date> @<TimePoint> ? ;
           <condition> @<EnumCRDCHDiagnosisCondition> ? ;
           <primary_site> @<BodySite> * ;
           <metastatic_site> @<BodySite> * ;
diff --git a/crdch_model/shex/crdch_model.shexj b/crdch_model/shex/crdch_model.shexj
index a1f83f549..d46f14b17 100644
--- a/crdch_model/shex/crdch_model.shexj
+++ b/crdch_model/shex/crdch_model.shexj
@@ -799,28 +799,28 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/system",
+                        "predicate": "https://example.org/crdch/label",
                         "valueExpr": "https://example.org/crdch/CrdchString",
-                        "min": 1,
+                        "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/systemURL",
+                        "predicate": "https://example.org/crdch/system",
                         "valueExpr": "https://example.org/crdch/CrdchString",
-                        "min": 0,
+                        "min": 1,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/systemVersion",
+                        "predicate": "https://example.org/crdch/system_url",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/label",
+                        "predicate": "https://example.org/crdch/system_version",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
@@ -894,8 +894,8 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/year_at_diagnosis",
-                        "valueExpr": "https://example.org/crdch/CrdchInteger",
+                        "predicate": "https://example.org/crdch/diagnosis_date",
+                        "valueExpr": "https://example.org/crdch/TimePoint",
                         "min": 0,
                         "max": 1
                      },

From ab5714723a145e6f9758f3a05a49ca4ca8747da3 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 16 Sep 2021 17:27:19 -0400
Subject: [PATCH 2/9] Added basic test for validating artifacts.

---
 Pipfile                          |  6 +-----
 tests/test_validate_artifacts.py | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 5 deletions(-)
 create mode 100644 tests/test_validate_artifacts.py

diff --git a/Pipfile b/Pipfile
index aee974e41..d551c8212 100644
--- a/Pipfile
+++ b/Pipfile
@@ -7,32 +7,28 @@ name = "pypi"
 # For LinkML, we use the `ccdh-dev` branch, which we manually keep in sync with LinkML's main branch
 # as well as some additional changes required for CRDCH generation.
 linkml = {editable = true, ref = "ccdh-dev", git = "https://github.com/cancerDHC/linkml.git"}
-
 # Since we use the development version of LinkML, we also use the development version of linkml-runtime.
 # This may sometimes cause issues between this and LinkML.
 linkml-runtime = {editable = true, git = "https://github.com/linkml/linkml-runtime.git"}
-
 pyparsing = "<=2.4.7"
 rdflib-pyld-compat = "*" # resinstating after removal by migration to linkml model template
 
 [dev-packages]
 pyyaml = "*"            # For reading and writing YAML files.
-
 # Packages needed for testing.
 pytest = "~=6.2.4"
 tox = "*"
 typing_extensions = "*" # This is a tox prereq for Python 3.7, but not installed by Pipenv.
 twine = "*" # should this go in make-venv/Pipfile ?
-
 # Packages needed by sheet2linkml.
 black = "==v21.5b1"     # Used for code linting.
 requests = "*"          # For making HTTP requests.
 pygsheets = "*"         # For accessing Google Sheets.
 python-dotenv = "*"     # For reading .env files.
-
 # Packages needed for building and publishing documentation.
 mike = "*"
 mkdocs-material = "*"
+assertpy = "*"
 
 [pipenv]
 allow_prereleases = true # added by migration to linkml model template
diff --git a/tests/test_validate_artifacts.py b/tests/test_validate_artifacts.py
new file mode 100644
index 000000000..c59a5df31
--- /dev/null
+++ b/tests/test_validate_artifacts.py
@@ -0,0 +1,22 @@
+import json
+import os.path
+import unittest
+from assertpy import assert_that
+
+MODEL_PATH = 'crdch_model'
+
+
+class ValidateArtifacts(unittest.TestCase):
+    """
+    This is a series of tests for validating that artifacts have been generated correctly.
+    """
+
+    def test_validate_json_schema(self):
+        json_schema_file_path = os.path.join(MODEL_PATH, 'json_schema', 'crdch_model.schema.json')
+        assert_that(json_schema_file_path).exists().is_file()
+
+        with open(json_schema_file_path) as f:
+            json_schema = json.load(f)
+            assert_that(json_schema).is_not_empty()
+
+

From e40998650c12919a436da073a836306bc831774b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 16 Sep 2021 17:29:31 -0400
Subject: [PATCH 3/9] Added test for JSON Schema validation.

---
 Pipfile                          | 1 +
 tests/test_validate_artifacts.py | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/Pipfile b/Pipfile
index d551c8212..38d600db3 100644
--- a/Pipfile
+++ b/Pipfile
@@ -29,6 +29,7 @@ python-dotenv = "*"     # For reading .env files.
 mike = "*"
 mkdocs-material = "*"
 assertpy = "*"
+jsonschema = "*"
 
 [pipenv]
 allow_prereleases = true # added by migration to linkml model template
diff --git a/tests/test_validate_artifacts.py b/tests/test_validate_artifacts.py
index c59a5df31..944706532 100644
--- a/tests/test_validate_artifacts.py
+++ b/tests/test_validate_artifacts.py
@@ -1,7 +1,8 @@
 import json
 import os.path
 import unittest
-from assertpy import assert_that
+from assertpy import assert_that, fail
+import jsonschema
 
 MODEL_PATH = 'crdch_model'
 
@@ -19,4 +20,8 @@ def test_validate_json_schema(self):
             json_schema = json.load(f)
             assert_that(json_schema).is_not_empty()
 
+            try:
+                jsonschema.Draft7Validator.check_schema(json_schema)
+            except jsonschema.exceptions.SchemaError as e:
+                fail(f'JSON Schema {json_schema_file_path} is not valid: {e}')
 

From bde8aced72d2cedefd8e346b46b5f938369e6a05 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Tue, 14 Sep 2021 19:30:13 -0400
Subject: [PATCH 4/9] Updated test for a safer version of Draft202012.

---
 tests/test_validate_artifacts.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/tests/test_validate_artifacts.py b/tests/test_validate_artifacts.py
index 944706532..8c2a2dc35 100644
--- a/tests/test_validate_artifacts.py
+++ b/tests/test_validate_artifacts.py
@@ -17,11 +17,19 @@ def test_validate_json_schema(self):
         assert_that(json_schema_file_path).exists().is_file()
 
         with open(json_schema_file_path) as f:
-            json_schema = json.load(f)
+            try:
+                json_schema = json.load(f)
+            except json.JSONDecodeError as e:
+                fail(f'JSON Schema {json_schema_file_path} is not a valid JSON document: {e}')
+
             assert_that(json_schema).is_not_empty()
 
+            # Idea from https://github.com/Julian/jsonschema/issues/348#issuecomment-647418176
+            class SaferDraft202012Validator(jsonschema.Draft202012Validator):
+                META_SCHEMA = {**jsonschema.Draft202012Validator.META_SCHEMA, "additionalProperties": False}
+
             try:
-                jsonschema.Draft7Validator.check_schema(json_schema)
+                SaferDraft202012Validator.check_schema(json_schema)
             except jsonschema.exceptions.SchemaError as e:
-                fail(f'JSON Schema {json_schema_file_path} is not valid: {e}')
+                fail(f'JSON Schema {json_schema_file_path} is not a valid JSON Schema: {e}')
 

From 582ae7f59acf1f2ec3065947fb67f54a54753197 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 16 Sep 2021 17:48:02 -0400
Subject: [PATCH 5/9] Updated packages with `pipenv update`.

---
 Pipfile.lock | 43 ++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 6751c700f..2de04bfd9 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "ba64635dea74c3cb803f2ccfbd306c39bb09607a554054885244a0599b31aef1"
+            "sha256": "3670c05204ea4e2f3ee8c56a80502454ec207a1dfbf714e6d5fec50a95578a3f"
         },
         "pipfile-spec": 6,
         "requires": {},
@@ -856,6 +856,13 @@
             ],
             "version": "==1.4.4"
         },
+        "assertpy": {
+            "hashes": [
+                "sha256:acc64329934ad71a3221de185517a43af33e373bb44dc05b5a9b174394ef4833"
+            ],
+            "index": "pypi",
+            "version": "==1.1"
+        },
         "attrs": {
             "hashes": [
                 "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1",
@@ -1048,6 +1055,13 @@
             "markers": "python_version >= '3.6'",
             "version": "==3.0.1"
         },
+        "jsonschema": {
+            "hashes": [
+                "sha256:25ebdfe8a3c40974e318cdc250f2fbd6c9c86336c5a03710bb8256d019bb3630",
+                "sha256:6016b56a0f26b93162cfe2eb157fff34f46f631395327d7070c5b11162c0fc81"
+            ],
+            "version": "==4.0.0a6"
+        },
         "keyring": {
             "hashes": [
                 "sha256:6334aee6073db2fb1f30892697b1730105b5e9a77ce7e61fca6b435225493efe",
@@ -1319,6 +1333,33 @@
             "index": "pypi",
             "version": "==2.4.7"
         },
+        "pyrsistent": {
+            "hashes": [
+                "sha256:097b96f129dd36a8c9e33594e7ebb151b1515eb52cceb08474c10a5479e799f2",
+                "sha256:2aaf19dc8ce517a8653746d98e962ef480ff34b6bc563fc067be6401ffb457c7",
+                "sha256:404e1f1d254d314d55adb8d87f4f465c8693d6f902f67eb6ef5b4526dc58e6ea",
+                "sha256:48578680353f41dca1ca3dc48629fb77dfc745128b56fc01096b2530c13fd426",
+                "sha256:4916c10896721e472ee12c95cdc2891ce5890898d2f9907b1b4ae0f53588b710",
+                "sha256:527be2bfa8dc80f6f8ddd65242ba476a6c4fb4e3aedbf281dfbac1b1ed4165b1",
+                "sha256:58a70d93fb79dc585b21f9d72487b929a6fe58da0754fa4cb9f279bb92369396",
+                "sha256:5e4395bbf841693eaebaa5bb5c8f5cdbb1d139e07c975c682ec4e4f8126e03d2",
+                "sha256:6b5eed00e597b5b5773b4ca30bd48a5774ef1e96f2a45d105db5b4ebb4bca680",
+                "sha256:73ff61b1411e3fb0ba144b8f08d6749749775fe89688093e1efef9839d2dcc35",
+                "sha256:772e94c2c6864f2cd2ffbe58bb3bdefbe2a32afa0acb1a77e472aac831f83427",
+                "sha256:773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b",
+                "sha256:a0c772d791c38bbc77be659af29bb14c38ced151433592e326361610250c605b",
+                "sha256:b29b869cf58412ca5738d23691e96d8aff535e17390128a1a52717c9a109da4f",
+                "sha256:c1a9ff320fa699337e05edcaae79ef8c2880b52720bc031b219e5b5008ebbdef",
+                "sha256:cd3caef37a415fd0dae6148a1b6957a8c5f275a62cca02e18474608cb263640c",
+                "sha256:d5ec194c9c573aafaceebf05fc400656722793dac57f254cd4741f3c27ae57b4",
+                "sha256:da6e5e818d18459fa46fac0a4a4e543507fe1110e808101277c5a2b5bab0cd2d",
+                "sha256:e79d94ca58fcafef6395f6352383fa1a76922268fa02caa2272fff501c2fdc78",
+                "sha256:f3ef98d7b76da5eb19c37fda834d50262ff9167c65658d1d8f974d2e4d90676b",
+                "sha256:f4c8cabb46ff8e5d61f56a037974228e978f26bfefce4f61a4b1ac0ba7a2ab72"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==0.18.0"
+        },
         "pytest": {
             "hashes": [
                 "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89",

From b0590fb6843c9e21b5ee346e6d0c10eff7af23c0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 16 Sep 2021 17:52:16 -0400
Subject: [PATCH 6/9] Regenerated CRDCH model.

---
 model/schema/crdch_model.yaml | 406 ++++++++++++++--------------------
 1 file changed, 166 insertions(+), 240 deletions(-)

diff --git a/model/schema/crdch_model.yaml b/model/schema/crdch_model.yaml
index e3a6c3de3..d2bf3320c 100644
--- a/model/schema/crdch_model.yaml
+++ b/model/schema/crdch_model.yaml
@@ -2,7 +2,7 @@ name: CRDC-H
 notes:
 - Derived from [CDM_Dictionary_v1 (Active)](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4)
 id: https://example.org/crdch
-version: v0.2-332-gbe05c1e6-dirty
+version: v0.2-382-g582ae7f5
 imports:
 - linkml:types
 license: https://creativecommons.org/publicdomain/zero/1.0/
@@ -76,7 +76,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.category
-    code_set_version: '2021-09-07T21:08:31.431109+00:00'
+    code_set_version: '2021-09-16T21:49:36.489920+00:00'
   enum_CRDCH_AlcoholExposureObservation_observation_type:
     name: enum_CRDCH_AlcoholExposureObservation_observation_type
     description: Types of observations about a Subject's exposure to alcohol.
@@ -105,21 +105,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.method_type
-    code_set_version: '2021-09-07T21:08:32.116226+00:00'
+    code_set_version: '2021-09-16T21:49:37.311998+00:00'
   enum_CRDCH_AlcoholExposureObservation_value_codeable_concept:
     name: enum_CRDCH_AlcoholExposureObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H AlcoholExposureObservation value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:32.219779+00:00'
+    code_set_version: '2021-09-16T21:49:37.417707+00:00'
   enum_CRDCH_BodySite_site:
     name: enum_CRDCH_BodySite_site
     description: Autogenerated Enumeration for CRDC-H BodySite site
     comments:
     - 'Name according to TCCM: "CRDC-H.BodySite.site"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BodySite.site
-    code_set_version: '2021-09-07T21:08:32.335724+00:00'
+    code_set_version: '2021-09-16T21:49:37.530258+00:00'
     permissible_values:
       Eye and adnexa:
         text: Eye and adnexa
@@ -1610,7 +1610,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.BodySite.qualifier"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BodySite.qualifier
-    code_set_version: '2021-09-07T21:08:33.353553+00:00'
+    code_set_version: '2021-09-16T21:49:38.574042+00:00'
     permissible_values:
       Bilateral:
         text: Bilateral
@@ -1631,14 +1631,14 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.BiologicProduct.product_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BiologicProduct.product_type
-    code_set_version: '2021-09-07T21:08:33.482548+00:00'
+    code_set_version: '2021-09-16T21:49:38.696389+00:00'
   enum_CRDCH_CancerGradeObservation_category:
     name: enum_CRDCH_CancerGradeObservation_category
     description: Autogenerated Enumeration for CRDC-H CancerGradeObservation category
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.category
-    code_set_version: '2021-09-07T21:08:33.589612+00:00'
+    code_set_version: '2021-09-16T21:49:38.807272+00:00'
   enum_CRDCH_CancerGradeObservation_observation_type:
     name: enum_CRDCH_CancerGradeObservation_observation_type
     description: ''
@@ -1693,21 +1693,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.method_type
-    code_set_version: '2021-09-07T21:08:33.813864+00:00'
+    code_set_version: '2021-09-16T21:49:39.035241+00:00'
   enum_CRDCH_CancerGradeObservation_value_codeable_concept:
     name: enum_CRDCH_CancerGradeObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H CancerGradeObservation value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:33.923946+00:00'
+    code_set_version: '2021-09-16T21:49:39.145945+00:00'
   enum_CRDCH_CancerGradeObservationSet_category:
     name: enum_CRDCH_CancerGradeObservationSet_category
     description: Autogenerated Enumeration for CRDC-H CancerGradeObservationSet category
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerGradeObservationSet.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservationSet.category
-    code_set_version: '2021-09-07T21:08:34.033726+00:00'
+    code_set_version: '2021-09-16T21:49:39.256624+00:00'
   enum_CRDCH_CancerGradeObservationSet_method_type:
     name: enum_CRDCH_CancerGradeObservationSet_method_type
     description: A morphologic classification system of malignant tumors, usually
@@ -1737,7 +1737,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerStageObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.category
-    code_set_version: '2021-09-07T21:08:34.257170+00:00'
+    code_set_version: '2021-09-16T21:49:39.478741+00:00'
   enum_CRDCH_CancerStageObservation_observation_type:
     name: enum_CRDCH_CancerStageObservation_observation_type
     description: Types of observations or components of a cancer staging assessment.
@@ -1802,21 +1802,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerStageObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.method_type
-    code_set_version: '2021-09-07T21:08:34.478121+00:00'
+    code_set_version: '2021-09-16T21:49:39.700585+00:00'
   enum_CRDCH_CancerStageObservation_value_codeable_concept:
     name: enum_CRDCH_CancerStageObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H CancerStageObservation value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerStageObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:34.590527+00:00'
+    code_set_version: '2021-09-16T21:49:39.816423+00:00'
   enum_CRDCH_CancerStageObservationSet_category:
     name: enum_CRDCH_CancerStageObservationSet_category
     description: Autogenerated Enumeration for CRDC-H CancerStageObservationSet category
     comments:
     - 'Name according to TCCM: "CRDC-H.CancerStageObservationSet.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservationSet.category
-    code_set_version: '2021-09-07T21:08:34.702334+00:00'
+    code_set_version: '2021-09-16T21:49:39.919163+00:00'
   enum_CRDCH_CancerStageObservationSet_method_type:
     name: enum_CRDCH_CancerStageObservationSet_method_type
     description: Classification systems used for defining the point in the natural
@@ -1921,7 +1921,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Diagnosis.condition"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.condition
-    code_set_version: '2021-09-07T21:08:34.924503+00:00'
+    code_set_version: '2021-09-16T21:49:40.144659+00:00'
     permissible_values:
       Von Recklinghausen disease:
         text: Von Recklinghausen disease
@@ -7248,7 +7248,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Diagnosis.morphology"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.morphology
-    code_set_version: '2021-09-07T21:08:37.859828+00:00'
+    code_set_version: '2021-09-16T21:49:43.208427+00:00'
     permissible_values:
       9261/3:
         text: 9261/3
@@ -9552,7 +9552,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Diagnosis.disease_status"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.disease_status
-    code_set_version: '2021-09-07T21:08:39.251148+00:00'
+    code_set_version: '2021-09-16T21:49:44.530513+00:00'
     permissible_values:
       Initial Diagnosis:
         text: Initial Diagnosis
@@ -9572,7 +9572,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Diagnosis.method_of_diagnosis"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.method_of_diagnosis
-    code_set_version: '2021-09-07T21:08:39.373622+00:00'
+    code_set_version: '2021-09-16T21:49:44.657940+00:00'
     permissible_values:
       Surgical Resection:
         text: Surgical Resection
@@ -9660,7 +9660,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.DimensionalObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservation.category
-    code_set_version: '2021-09-07T21:08:39.516352+00:00'
+    code_set_version: '2021-09-16T21:49:44.803090+00:00'
   enum_CRDCH_DimensionalObservation_observation_type:
     name: enum_CRDCH_DimensionalObservation_observation_type
     description: Types of measurements that describe the physical dimensions of an
@@ -9697,21 +9697,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.DimensionalObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservation.method_type
-    code_set_version: '2021-09-07T21:08:39.730507+00:00'
+    code_set_version: '2021-09-16T21:49:45.020572+00:00'
   enum_CRDCH_DimensionalObservationSet_category:
     name: enum_CRDCH_DimensionalObservationSet_category
     description: Autogenerated Enumeration for CRDC-H DimensionalObservationSet category
     comments:
     - 'Name according to TCCM: "CRDC-H.DimensionalObservationSet.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservationSet.category
-    code_set_version: '2021-09-07T21:08:39.834340+00:00'
+    code_set_version: '2021-09-16T21:49:45.133245+00:00'
   enum_CRDCH_DimensionalObservationSet_method_type:
     name: enum_CRDCH_DimensionalObservationSet_method_type
     description: Autogenerated Enumeration for CRDC-H DimensionalObservationSet method_type
     comments:
     - 'Name according to TCCM: "CRDC-H.DimensionalObservationSet.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservationSet.method_type
-    code_set_version: '2021-09-07T21:08:39.940391+00:00'
+    code_set_version: '2021-09-16T21:49:45.244782+00:00'
   enum_CRDCH_Document_document_type:
     name: enum_CRDCH_Document_document_type
     description: The high-level type of the report (e.g. 'pathology report')
@@ -9732,7 +9732,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.category
-    code_set_version: '2021-09-07T21:08:40.164775+00:00'
+    code_set_version: '2021-09-16T21:49:45.462653+00:00'
   enum_CRDCH_EnvironmentalExposureObservation_observation_type:
     name: enum_CRDCH_EnvironmentalExposureObservation_observation_type
     description: Types of observations about a Subject's environmental exposures.
@@ -9769,7 +9769,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.method_type
-    code_set_version: '2021-09-07T21:08:40.378679+00:00'
+    code_set_version: '2021-09-16T21:49:45.687597+00:00'
   enum_CRDCH_EnvironmentalExposureObservation_value_codeable_concept:
     name: enum_CRDCH_EnvironmentalExposureObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation
@@ -9777,7 +9777,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:40.480235+00:00'
+    code_set_version: '2021-09-16T21:49:45.799416+00:00'
   enum_CRDCH_ExecutionConditionObservation_category:
     name: enum_CRDCH_ExecutionConditionObservation_category
     description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation
@@ -9785,7 +9785,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.category
-    code_set_version: '2021-09-07T21:08:40.583103+00:00'
+    code_set_version: '2021-09-16T21:49:45.921056+00:00'
   enum_CRDCH_ExecutionConditionObservation_observation_type:
     name: enum_CRDCH_ExecutionConditionObservation_observation_type
     description: Types of observations about the environmental conditions under which
@@ -9805,7 +9805,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.method_type
-    code_set_version: '2021-09-07T21:08:40.798174+00:00'
+    code_set_version: '2021-09-16T21:49:46.139594+00:00'
   enum_CRDCH_ExecutionConditionObservation_value_codeable_concept:
     name: enum_CRDCH_ExecutionConditionObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation
@@ -9813,14 +9813,14 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:40.903686+00:00'
+    code_set_version: '2021-09-16T21:49:46.250423+00:00'
   enum_CRDCH_ExecutionTimeObservation_category:
     name: enum_CRDCH_ExecutionTimeObservation_category
     description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation category
     comments:
     - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.category
-    code_set_version: '2021-09-07T21:08:41.012389+00:00'
+    code_set_version: '2021-09-16T21:49:46.360696+00:00'
   enum_CRDCH_ExecutionTimeObservation_observation_type:
     name: enum_CRDCH_ExecutionTimeObservation_observation_type
     description: An observation about the duration of specific aspects / parts of
@@ -9846,7 +9846,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.method_type
-    code_set_version: '2021-09-07T21:08:41.223744+00:00'
+    code_set_version: '2021-09-16T21:49:46.587773+00:00'
   enum_CRDCH_HistologicalCompositionObservation_category:
     name: enum_CRDCH_HistologicalCompositionObservation_category
     description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservation
@@ -9854,7 +9854,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservation.category
-    code_set_version: '2021-09-07T21:08:41.326028+00:00'
+    code_set_version: '2021-09-16T21:49:46.697870+00:00'
   enum_CRDCH_HistologicalCompositionObservation_observation_type:
     name: enum_CRDCH_HistologicalCompositionObservation_observation_type
     description: Types of measurements that describe microscopic characteristics of
@@ -9949,7 +9949,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservation.method_type
-    code_set_version: '2021-09-07T21:08:41.548147+00:00'
+    code_set_version: '2021-09-16T21:49:46.920129+00:00'
   enum_CRDCH_HistologicalCompositionObservationSet_category:
     name: enum_CRDCH_HistologicalCompositionObservationSet_category
     description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet
@@ -9957,7 +9957,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservationSet.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservationSet.category
-    code_set_version: '2021-09-07T21:08:41.650910+00:00'
+    code_set_version: '2021-09-16T21:49:47.041756+00:00'
   enum_CRDCH_HistologicalCompositionObservationSet_method_type:
     name: enum_CRDCH_HistologicalCompositionObservationSet_method_type
     description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet
@@ -9965,63 +9965,63 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservationSet.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservationSet.method_type
-    code_set_version: '2021-09-07T21:08:41.751341+00:00'
+    code_set_version: '2021-09-16T21:49:47.154248+00:00'
   enum_CRDCH_Identifier_type:
     name: enum_CRDCH_Identifier_type
     description: Autogenerated Enumeration for CRDC-H Identifier type
     comments:
     - 'Name according to TCCM: "CRDC-H.Identifier.type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Identifier.type
-    code_set_version: '2021-09-07T21:08:41.852956+00:00'
+    code_set_version: '2021-09-16T21:49:47.263791+00:00'
   enum_CRDCH_Observation_category:
     name: enum_CRDCH_Observation_category
     description: Autogenerated Enumeration for CRDC-H Observation category
     comments:
     - 'Name according to TCCM: "CRDC-H.Observation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.category
-    code_set_version: '2021-09-07T21:08:41.965970+00:00'
+    code_set_version: '2021-09-16T21:49:47.364459+00:00'
   enum_CRDCH_Observation_observation_type:
     name: enum_CRDCH_Observation_observation_type
     description: Autogenerated Enumeration for CRDC-H Observation observation_type
     comments:
     - 'Name according to TCCM: "CRDC-H.Observation.observation_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.observation_type
-    code_set_version: '2021-09-07T21:08:42.074790+00:00'
+    code_set_version: '2021-09-16T21:49:47.463096+00:00'
   enum_CRDCH_Observation_method_type:
     name: enum_CRDCH_Observation_method_type
     description: Autogenerated Enumeration for CRDC-H Observation method_type
     comments:
     - 'Name according to TCCM: "CRDC-H.Observation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.method_type
-    code_set_version: '2021-09-07T21:08:42.175220+00:00'
+    code_set_version: '2021-09-16T21:49:47.563058+00:00'
   enum_CRDCH_Observation_value_codeable_concept:
     name: enum_CRDCH_Observation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H Observation value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.Observation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:42.276728+00:00'
+    code_set_version: '2021-09-16T21:49:47.662542+00:00'
   enum_CRDCH_ObservationSet_category:
     name: enum_CRDCH_ObservationSet_category
     description: Autogenerated Enumeration for CRDC-H ObservationSet category
     comments:
     - 'Name according to TCCM: "CRDC-H.ObservationSet.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ObservationSet.category
-    code_set_version: '2021-09-07T21:08:42.379903+00:00'
+    code_set_version: '2021-09-16T21:49:47.760835+00:00'
   enum_CRDCH_ObservationSet_method_type:
     name: enum_CRDCH_ObservationSet_method_type
     description: Autogenerated Enumeration for CRDC-H ObservationSet method_type
     comments:
     - 'Name according to TCCM: "CRDC-H.ObservationSet.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ObservationSet.method_type
-    code_set_version: '2021-09-07T21:08:42.480631+00:00'
+    code_set_version: '2021-09-16T21:49:47.861133+00:00'
   enum_CRDCH_Quantity_value_codeable_concept:
     name: enum_CRDCH_Quantity_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H Quantity value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.Quantity.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Quantity.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:42.587568+00:00'
+    code_set_version: '2021-09-16T21:49:47.958884+00:00'
   enum_CRDCH_Quantity_unit:
     name: enum_CRDCH_Quantity_unit
     description: The unit for a value
@@ -10060,7 +10060,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ResearchSubject.primary_diagnosis_condition"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ResearchSubject.primary_diagnosis_condition
-    code_set_version: '2021-09-07T21:08:42.904084+00:00'
+    code_set_version: '2021-09-16T21:49:48.270054+00:00'
     permissible_values:
       Soft Tissue Tumors and Sarcomas, NOS:
         text: Soft Tissue Tumors and Sarcomas, NOS
@@ -10351,7 +10351,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.ResearchSubject.index_timepoint"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ResearchSubject.index_timepoint
-    code_set_version: '2021-09-07T21:08:43.139943+00:00'
+    code_set_version: '2021-09-16T21:49:48.520690+00:00'
     permissible_values:
       Diagnosis:
         text: Diagnosis
@@ -10378,8 +10378,8 @@ enums:
     notes:
     - Derived from [Specimen.specimen_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368)
     permissible_values:
-      initial sample:
-        text: initial sample
+      Fresh Specimen:
+        text: Fresh Specimen
         description: A specimen representing the material that was directly collected
           from a subject (i.e. not generated through portioning, aliquoting, or analyte
           extraction from an existing specimen).
@@ -10405,7 +10405,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.analyte_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.analyte_type
-    code_set_version: '2021-09-07T21:08:43.371740+00:00'
+    code_set_version: '2021-09-16T21:49:48.753301+00:00'
     permissible_values:
       Repli-G (Qiagen) DNA:
         text: Repli-G (Qiagen) DNA
@@ -10476,7 +10476,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.source_material_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.source_material_type
-    code_set_version: '2021-09-07T21:08:43.526142+00:00'
+    code_set_version: '2021-09-16T21:49:48.890971+00:00'
     permissible_values:
       Recurrent Blood Derived Cancer - Bone Marrow:
         text: Recurrent Blood Derived Cancer - Bone Marrow
@@ -10657,7 +10657,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.tumor_status_at_collection"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.tumor_status_at_collection
-    code_set_version: '2021-09-07T21:08:43.745325+00:00'
+    code_set_version: '2021-09-16T21:49:49.080717+00:00'
     permissible_values:
       recurrence:
         text: recurrence
@@ -10702,7 +10702,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.cellular_composition_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.cellular_composition_type
-    code_set_version: '2021-09-07T21:08:43.878758+00:00'
+    code_set_version: '2021-09-16T21:49:49.213118+00:00'
     permissible_values:
       Lymphocytes:
         text: Lymphocytes
@@ -10793,169 +10793,48 @@ enums:
         description: Serum
       Not Allowed To Collect:
         text: Not Allowed To Collect
-  enum_CRDCH_Specimen_general_tissue_morphology:
-    name: enum_CRDCH_Specimen_general_tissue_morphology
-    description: Autogenerated Enumeration for CRDC-H Specimen general_tissue_morphology
+  enum_CRDCH_Specimen_general_tissue_pathology:
+    name: enum_CRDCH_Specimen_general_tissue_pathology
+    description: Autogenerated Enumeration for CRDC-H Specimen general_tissue_pathology
     comments:
-    - 'Name according to TCCM: "CRDC-H.Specimen.general_tissue_morphology"'
-    code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.general_tissue_morphology
-    code_set_version: '2021-09-07T21:08:44.026728+00:00'
-    permissible_values:
-      Peritumoral:
-        text: Peritumoral
-        description: Peritumoral
-      Abnormal:
-        text: Abnormal
-        description: Abnormal
-      Normal:
-        text: Normal
-        description: Normal
-      Not Allowed To Collect:
-        text: Not Allowed To Collect
-      Unknown:
-        text: Unknown
-        description: Unknown
-      Tumor:
-        text: Tumor
-        description: Malignant Neoplasm
-      Not Reported:
-        text: Not Reported
-  enum_CRDCH_Specimen_specific_tissue_morphology:
-    name: enum_CRDCH_Specimen_specific_tissue_morphology
-    description: Autogenerated Enumeration for CRDC-H Specimen specific_tissue_morphology
+    - 'Name according to TCCM: "CRDC-H.Specimen.general_tissue_pathology"'
+    code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.general_tissue_pathology
+    code_set_version: '2021-09-16T21:49:49.380359+00:00'
+  enum_CRDCH_Specimen_specific_tissue_pathology:
+    name: enum_CRDCH_Specimen_specific_tissue_pathology
+    description: Autogenerated Enumeration for CRDC-H Specimen specific_tissue_pathology
     comments:
-    - 'Name according to TCCM: "CRDC-H.Specimen.specific_tissue_morphology"'
-    code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.specific_tissue_morphology
-    code_set_version: '2021-09-07T21:08:44.143833+00:00'
-    permissible_values:
-      '61':
-        text: '61'
-      '70':
-        text: '70'
-      '30':
-        text: '30'
-      '63':
-        text: '63'
-      '71':
-        text: '71'
-      '51':
-        text: '51'
-      '80':
-        text: '80'
-      '02':
-        text: '02'
-      '65':
-        text: '65'
-      '04':
-        text: '04'
-      '60':
-        text: '60'
-      '03':
-        text: '03'
-      '50':
-        text: '50'
-      '52':
-        text: '52'
-      '15':
-        text: '15'
-      '10':
-        text: '10'
-      '00':
-        text: '00'
-      '01':
-        text: '01'
-      '21':
-        text: '21'
-      '20':
-        text: '20'
-      '62':
-        text: '62'
-      '40':
-        text: '40'
-      '64':
-        text: '64'
-      '81':
-        text: '81'
-      '41':
-        text: '41'
-      Rhabdoid tumor (kidney) (RT):
-        text: Rhabdoid tumor (kidney) (RT)
-      Acute myeloid leukemia (AML):
-        text: Acute myeloid leukemia (AML)
-      Anal Cancer (all types):
-        text: Anal Cancer (all types)
-      Non cancerous tissue:
-        text: Non cancerous tissue
-      CNS, low grade glioma (LGG):
-        text: CNS, low grade glioma (LGG)
-      Lung Cancer (all types):
-        text: Lung Cancer (all types)
-      CNS, ependymoma:
-        text: CNS, ependymoma
-      Rhabdomyosarcoma:
-        text: Rhabdomyosarcoma
-      Induction Failure AML (AML-IF):
-        text: Induction Failure AML (AML-IF)
-      Soft tissue sarcoma, non-rhabdomyosarcoma:
-        text: Soft tissue sarcoma, non-rhabdomyosarcoma
-      NHL, Burkitt lymphoma (BL):
-        text: NHL, Burkitt lymphoma (BL)
-      Neuroblastoma (NBL):
-        text: Neuroblastoma (NBL)
-      Diffuse Large B-Cell Lymphoma (DLBCL):
-        text: Diffuse Large B-Cell Lymphoma (DLBCL)
-      Acute lymphoblastic leukemia (ALL):
-        text: Acute lymphoblastic leukemia (ALL)
-      CNS, rhabdoid tumor:
-        text: CNS, rhabdoid tumor
-      CNS, medulloblastoma:
-        text: CNS, medulloblastoma
-      Cervical Cancer (all types):
-        text: Cervical Cancer (all types)
-      NHL, anaplastic large cell lymphoma:
-        text: NHL, anaplastic large cell lymphoma
-      Clear cell sarcoma of the kidney (CCSK):
-        text: Clear cell sarcoma of the kidney (CCSK)
-      CNS, glioblastoma (GBM):
-        text: CNS, glioblastoma (GBM)
-      Acute Leukemia of Ambiguous Lineage (ALAL):
-        text: Acute Leukemia of Ambiguous Lineage (ALAL)
-      CNS, other:
-        text: CNS, other
-      Ewing sarcoma:
-        text: Ewing sarcoma
-      Osteosarcoma (OS):
-        text: Osteosarcoma (OS)
-      Wilms tumor (WT):
-        text: Wilms tumor (WT)
+    - 'Name according to TCCM: "CRDC-H.Specimen.specific_tissue_pathology"'
+    code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.specific_tissue_pathology
+    code_set_version: '2021-09-16T21:49:49.494860+00:00'
   enum_CRDCH_Specimen_preinvasive_tissue_morphology:
     name: enum_CRDCH_Specimen_preinvasive_tissue_morphology
     description: Autogenerated Enumeration for CRDC-H Specimen preinvasive_tissue_morphology
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.preinvasive_tissue_morphology"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.preinvasive_tissue_morphology
-    code_set_version: '2021-09-07T21:08:44.301214+00:00'
+    code_set_version: '2021-09-16T21:49:49.607830+00:00'
   enum_CRDCH_Specimen_morphology_assessor_role:
     name: enum_CRDCH_Specimen_morphology_assessor_role
     description: Autogenerated Enumeration for CRDC-H Specimen morphology_assessor_role
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.morphology_assessor_role"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.morphology_assessor_role
-    code_set_version: '2021-09-07T21:08:44.410467+00:00'
+    code_set_version: '2021-09-16T21:49:49.912759+00:00'
   enum_CRDCH_Specimen_morphology_assessment_method:
     name: enum_CRDCH_Specimen_morphology_assessment_method
     description: Autogenerated Enumeration for CRDC-H Specimen morphology_assessment_method
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.morphology_assessment_method"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.morphology_assessment_method
-    code_set_version: '2021-09-07T21:08:44.524474+00:00'
+    code_set_version: '2021-09-16T21:49:50.236173+00:00'
   enum_CRDCH_Specimen_degree_of_dysplasia:
     name: enum_CRDCH_Specimen_degree_of_dysplasia
     description: Autogenerated Enumeration for CRDC-H Specimen degree_of_dysplasia
     comments:
     - 'Name according to TCCM: "CRDC-H.Specimen.degree_of_dysplasia"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.degree_of_dysplasia
-    code_set_version: '2021-09-07T21:08:44.636509+00:00'
+    code_set_version: '2021-09-16T21:49:50.523131+00:00'
   enum_CRDCH_Specimen_section_location:
     name: enum_CRDCH_Specimen_section_location
     related_mappings:
@@ -10982,7 +10861,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenContainer.container_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenContainer.container_type
-    code_set_version: '2021-09-07T21:08:44.851513+00:00'
+    code_set_version: '2021-09-16T21:49:51.182025+00:00'
   enum_CRDCH_SpecimenCreationActivity_activity_type:
     name: enum_CRDCH_SpecimenCreationActivity_activity_type
     description: The high-level type of activity through which the specimen was generated
@@ -11004,7 +10883,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenCreationActivity.collection_method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenCreationActivity.collection_method_type
-    code_set_version: '2021-09-07T21:08:45.084419+00:00'
+    code_set_version: '2021-09-16T21:49:51.955969+00:00'
     permissible_values:
       'Yes':
         text: 'Yes'
@@ -11222,14 +11101,14 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenCreationActivity.derivation_method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenCreationActivity.derivation_method_type
-    code_set_version: '2021-09-07T21:08:45.317644+00:00'
+    code_set_version: '2021-09-16T21:49:52.358192+00:00'
   enum_CRDCH_SpecimenQualityObservation_category:
     name: enum_CRDCH_SpecimenQualityObservation_category
     description: Autogenerated Enumeration for CRDC-H SpecimenQualityObservation category
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenQualityObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQualityObservation.category
-    code_set_version: '2021-09-07T21:08:45.423104+00:00'
+    code_set_version: '2021-09-16T21:49:52.841235+00:00'
   enum_CRDCH_SpecimenQualityObservation_observation_type:
     name: enum_CRDCH_SpecimenQualityObservation_observation_type
     description: Types of measurements that reflect the quality of a specimen or its
@@ -11269,7 +11148,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenQuantityObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQuantityObservation.category
-    code_set_version: '2021-09-07T21:08:45.741776+00:00'
+    code_set_version: '2021-09-16T21:49:53.684414+00:00'
   enum_CRDCH_SpecimenQuantityObservation_observation_type:
     name: enum_CRDCH_SpecimenQuantityObservation_observation_type
     description: Measures related to the quantity of a specimen or analyte it currently
@@ -11297,7 +11176,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenQuantityObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQuantityObservation.method_type
-    code_set_version: '2021-09-07T21:08:45.958852+00:00'
+    code_set_version: '2021-09-16T21:49:53.900052+00:00'
   enum_CRDCH_SpecimenProcessingActivity_activity_type:
     name: enum_CRDCH_SpecimenProcessingActivity_activity_type
     description: The high-level type of processing activity performed.
@@ -11337,8 +11216,8 @@ enums:
     notes:
     - Derived from [SpecimenProcessingActivity.method_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368)
     permissible_values:
-      '-80':
-        text: '-80'
+      Minues 80 Degrees Celsius Freezer:
+        text: Minues 80 Degrees Celsius Freezer
         description: Freezing at -80 degrees celcius
       '-20':
         text: '-20'
@@ -11355,7 +11234,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.SpecimenStorageActivity.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenStorageActivity.method_type
-    code_set_version: '2021-09-07T21:08:46.367201+00:00'
+    code_set_version: '2021-09-16T21:49:54.228963+00:00'
   enum_CRDCH_Subject_species:
     name: enum_CRDCH_Subject_species
     description: The scientific binomial name for the species of the subject
@@ -11525,7 +11404,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Subject.sex"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.sex
-    code_set_version: '2021-09-07T21:08:46.687007+00:00'
+    code_set_version: '2021-09-16T21:49:54.542209+00:00'
     permissible_values:
       unknown:
         text: unknown
@@ -11543,7 +11422,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Subject.ethnicity"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.ethnicity
-    code_set_version: '2021-09-07T21:08:46.793549+00:00'
+    code_set_version: '2021-09-16T21:49:54.646843+00:00'
     permissible_values:
       not hispanic or latino:
         text: not hispanic or latino
@@ -11564,7 +11443,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Subject.race"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.race
-    code_set_version: '2021-09-07T21:08:46.900411+00:00'
+    code_set_version: '2021-09-16T21:49:54.761435+00:00'
     permissible_values:
       not allowed to collect:
         text: not allowed to collect
@@ -11593,7 +11472,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Subject.vital_status"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.vital_status
-    code_set_version: '2021-09-07T21:08:47.016668+00:00'
+    code_set_version: '2021-09-16T21:49:54.879433+00:00'
     permissible_values:
       Unknown:
         text: Unknown
@@ -11613,7 +11492,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Subject.cause_of_death"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.cause_of_death
-    code_set_version: '2021-09-07T21:08:47.200658+00:00'
+    code_set_version: '2021-09-16T21:49:54.989771+00:00'
     permissible_values:
       Infection:
         text: Infection
@@ -11652,7 +11531,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Substance.substance_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Substance.substance_type
-    code_set_version: '2021-09-07T21:08:47.325429+00:00'
+    code_set_version: '2021-09-16T21:49:55.109323+00:00'
     permissible_values:
       Anti-PTK7/Auristatin-0101 Antibody-drug Conjugate PF-06647020:
         text: Anti-PTK7/Auristatin-0101 Antibody-drug Conjugate PF-06647020
@@ -20656,21 +20535,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Substance.role"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Substance.role
-    code_set_version: '2021-09-07T21:08:51.803327+00:00'
+    code_set_version: '2021-09-16T21:49:59.552481+00:00'
   enum_CRDCH_TimePoint_event_type:
     name: enum_CRDCH_TimePoint_event_type
     description: Autogenerated Enumeration for CRDC-H TimePoint event_type
     comments:
     - 'Name according to TCCM: "CRDC-H.TimePoint.event_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TimePoint.event_type
-    code_set_version: '2021-09-07T21:08:51.912452+00:00'
+    code_set_version: '2021-09-16T21:49:59.664833+00:00'
   enum_CRDCH_TobaccoExposureObservation_category:
     name: enum_CRDCH_TobaccoExposureObservation_category
     description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation category
     comments:
     - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.category"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.category
-    code_set_version: '2021-09-07T21:08:52.028296+00:00'
+    code_set_version: '2021-09-16T21:49:59.773141+00:00'
   enum_CRDCH_TobaccoExposureObservation_observation_type:
     name: enum_CRDCH_TobaccoExposureObservation_observation_type
     description: Types of observations about a Subject's exposure to or use of tobacco.
@@ -20723,21 +20602,21 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.method_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.method_type
-    code_set_version: '2021-09-07T21:08:52.252674+00:00'
+    code_set_version: '2021-09-16T21:49:59.996722+00:00'
   enum_CRDCH_TobaccoExposureObservation_value_codeable_concept:
     name: enum_CRDCH_TobaccoExposureObservation_value_codeable_concept
     description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation value_codeable_concept
     comments:
     - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.value_codeable_concept"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.value_codeable_concept
-    code_set_version: '2021-09-07T21:08:52.366000+00:00'
+    code_set_version: '2021-09-16T21:50:00.103991+00:00'
   enum_CRDCH_Treatment_treatment_type:
     name: enum_CRDCH_Treatment_treatment_type
     description: Autogenerated Enumeration for CRDC-H Treatment treatment_type
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_type"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_type
-    code_set_version: '2021-09-07T21:08:52.474538+00:00'
+    code_set_version: '2021-09-16T21:50:00.213820+00:00'
     permissible_values:
       Radiation, Cyberknife:
         text: Radiation, Cyberknife
@@ -20880,7 +20759,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_end_reason"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_end_reason
-    code_set_version: '2021-09-07T21:08:52.640041+00:00'
+    code_set_version: '2021-09-16T21:50:00.381055+00:00'
     permissible_values:
       Other:
         text: Other
@@ -20900,14 +20779,14 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.regimen"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.regimen
-    code_set_version: '2021-09-07T21:08:52.744041+00:00'
+    code_set_version: '2021-09-16T21:50:00.497916+00:00'
   enum_CRDCH_Treatment_treatment_frequency:
     name: enum_CRDCH_Treatment_treatment_frequency
     description: Autogenerated Enumeration for CRDC-H Treatment treatment_frequency
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_frequency"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_frequency
-    code_set_version: '2021-09-07T21:08:52.844226+00:00'
+    code_set_version: '2021-09-16T21:50:00.605331+00:00'
     permissible_values:
       Every Other Day:
         text: Every Other Day
@@ -20937,7 +20816,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_intent"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_intent
-    code_set_version: '2021-09-07T21:08:52.952346+00:00'
+    code_set_version: '2021-09-16T21:50:00.725168+00:00'
     permissible_values:
       Neoadjuvant:
         text: Neoadjuvant
@@ -20970,7 +20849,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_effect"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_effect
-    code_set_version: '2021-09-07T21:08:53.061098+00:00'
+    code_set_version: '2021-09-16T21:50:00.852181+00:00'
     permissible_values:
       'Yes':
         text: 'Yes'
@@ -20996,7 +20875,7 @@ enums:
     comments:
     - 'Name according to TCCM: "CRDC-H.Treatment.treatment_outcome"'
     code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_outcome
-    code_set_version: '2021-09-07T21:08:53.170913+00:00'
+    code_set_version: '2021-09-16T21:50:00.974004+00:00'
     permissible_values:
       Treatment Ongoing:
         text: Treatment Ongoing
@@ -22175,9 +22054,20 @@ classes:
         range: crdch_string
         multivalued: false
         required: true
+      label:
+        name: label
+        description: A human-readable name for the code, as defined by the code system.
+        notes:
+        - 'Cardinality: 0..1'
+        examples:
+        - value: ''
+        domain: Coding
+        range: crdch_string
+        multivalued: false
+        required: false
       system:
         name: system
-        description: The code system where the code is defined.
+        description: The URL of the code system where the code is defined.
         notes:
         - 'Cardinality: 1..1'
         examples:
@@ -22186,9 +22076,9 @@ classes:
         range: crdch_string
         multivalued: false
         required: true
-      systemURL:
-        name: systemURL
-        description: A URL where the code system can be found.
+      system_version:
+        name: system_version
+        description: The version of the code system.
         notes:
         - 'Cardinality: 0..1'
         examples:
@@ -22197,9 +22087,10 @@ classes:
         range: crdch_string
         multivalued: false
         required: false
-      systemVersion:
-        name: systemVersion
-        description: The version of the code system.
+      value_set:
+        name: value_set
+        description: The identifier of the enumeration / value set that the code is
+          a part of in the context of this element
         notes:
         - 'Cardinality: 0..1'
         examples:
@@ -22208,9 +22099,10 @@ classes:
         range: crdch_string
         multivalued: false
         required: false
-      label:
-        name: label
-        description: A human-readable name for the code, as defined by the code system.
+      value_set_version:
+        name: value_set_version
+        description: The version of the enuemration / value set the code is pulled
+          from
         notes:
         - 'Cardinality: 0..1'
         examples:
@@ -22219,6 +22111,18 @@ classes:
         range: crdch_string
         multivalued: false
         required: false
+      tag:
+        name: tag
+        description: original value  |  harmonized value  |
+        notes:
+        - 'Cardinality: 0..m'
+        examples:
+        - value: ''
+        domain: Coding
+        range: crdch_string
+        multivalued: true
+        required: false
+        inlined_as_list: true
   Diagnosis:
     name: Diagnosis
     description: A collection of characteristics that describe an abnormal condition
@@ -22317,20 +22221,28 @@ classes:
         range: Quantity
         multivalued: false
         required: false
-      year_at_diagnosis:
-        name: year_at_diagnosis
-        exact_mappings:
+      diagnosis_date:
+        name: diagnosis_date
+        close_mappings:
         - GDC:Diagnosis.year_of_diagnosis
+        - GDC:Diagnosis.days_to_diagnosis
         - PDC:Diagnosis.year_of_diagnosis
+        - PDC:Diagnosis.days_to_diagnosis
         - HTAN:Diagnosis.YearofDiagnosis
         - ICDC:Diagnosis.date_of_diagnosis
-        description: Numeric value to represent the year of an individual's diagnosis.
+        description: When the diagnosis was made.
         notes:
         - 'Cardinality: 0..1'
+        comments:
+        - 'A TimePoint object supports three ways to specify a point in time, each
+          of which might be used in the context of capturing a diagnosis date - as
+          source node data can report this date as an explicit year or date (e.g.
+          2021-05-05), or an offset from an indexed point in time. See description
+          of the TimePoint entity for more information here. '
         examples:
         - value: ''
         domain: Diagnosis
-        range: crdch_integer
+        range: TimePoint
         multivalued: false
         required: false
       condition:
@@ -24606,6 +24518,8 @@ classes:
         - GDC:Diagnosis.age_at_diagnosis
         - PDC:Diagnosis.age_at_diagnosis
         - HTAN:Diagnosis.AgeatDiagnosis
+        - GDC:Diagnosis.days_to_diagnosis
+        - PDC:Diagnosis.days_to_diagnosis
         description: An amount, in the given units (if specified)
         notes:
         - 'Cardinality: 0..1'
@@ -25289,7 +25203,7 @@ classes:
           values are meant to be mutually exclusive, such that only one can be applied
           to a given specimen.
         examples:
-        - value: Initial Sample
+        - value: Fresh Specimen
         - value: Portion
         - value: Aliquot
         - value: Analyte
@@ -25781,8 +25695,8 @@ classes:
         multivalued: true
         required: false
         inlined_as_list: true
-      general_tissue_morphology:
-        name: general_tissue_morphology
+      general_tissue_pathology:
+        name: general_tissue_pathology
         exact_mappings:
         - GDC:Sample.tissue_type
         - PDC:Sample.tissue_type
@@ -25799,11 +25713,11 @@ classes:
         - value: Peritumoral
         - value: not applicable
         domain: Specimen
-        range: enum_CRDCH_Specimen_general_tissue_morphology
+        range: enum_CRDCH_Specimen_general_tissue_pathology
         multivalued: false
         required: false
-      specific_tissue_morphology:
-        name: specific_tissue_morphology
+      specific_tissue_pathology:
+        name: specific_tissue_pathology
         exact_mappings:
         - GDC:Sample.tumor_code
         - GDC:Sample.tumor_code_id
@@ -25826,7 +25740,7 @@ classes:
         - value: Atypical melanocytic proliferation
         - value: Melanoma in situ, superficial spreading
         domain: Specimen
-        range: enum_CRDCH_Specimen_specific_tissue_morphology
+        range: enum_CRDCH_Specimen_specific_tissue_pathology
         multivalued: false
         required: false
       preinvasive_tissue_morphology:
@@ -27365,10 +27279,18 @@ classes:
   TimePoint:
     name: TimePoint
     description: A structured representation of a single point in time that allows
-      direct/explicit declaration as a dateTime, or specification in terms of offset
-      from a defined index.
+      direct/explicit declaration as a dateTime, specification in terms of offset
+      from a defined index, or description of an event type as a proxy for the time
+      point when it occurred.
     notes:
     - Derived from [TimePoint in sheet TimePoint](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=300932847)
+    comments:
+    - 'The TimePoint object supports three ways to specify a point in time. The date_time
+      field is the most direct - capturing an explicit date (e.g. 2021-05-05). The
+      paired fields index_time_point and  offset_from_index allows specification of
+      a point in time as an offset from a related fixed time point.  Finally, the
+      event_type field uses type of event as a proxy for the time point when the event
+      occurred. '
     is_a: Entity
     attributes:
       id:
@@ -27409,6 +27331,8 @@ classes:
         - PDC:Portion.creation_datetime
         - ICDC:Sample.date_of_sample_collection
         - ICDC:Study.date_of_iacuc_approval
+        - GDC:Diagnosis.year_of_diagnosis
+        - PDC:Diagnosis.year_of_diagnosis
         description: An explicitly specified timepoint described in terms of a date
           and optionally a time on that date.
         notes:
@@ -27443,6 +27367,8 @@ classes:
         - PDC:Treatment.days_to_treatment_end
         - GDC:Treatment.days_to_treatment_start
         - PDC:Treatment.days_to_treatment_start
+        - GDC:Diagnosis.days_to_diagnosis
+        - PDC:Diagnosis.days_to_diagnosis
         description: A quantity of time that, together with the index date or event,
           can be used to derive a specific timepoint.
         notes:
@@ -28000,4 +27926,4 @@ classes:
         range: enum_CRDCH_Treatment_treatment_outcome
         multivalued: false
         required: false
-generation_date: '2021-09-07T21:06:29.719236+00:00'
+generation_date: '2021-09-16T21:49:07.099651+00:00'

From c65e2e7ac69264fc95119bcfd41826c16616c1e5 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 16 Sep 2021 17:55:05 -0400
Subject: [PATCH 7/9] Regenerated artifacts.

---
 crdch_model/crdch_model.py                    |  353 ++---
 crdch_model/csv/crdch_model.csv               |    2 +-
 crdch_model/graphql/crdch_model.graphql       |    8 +-
 .../json_schema/crdch_model.schema.json       |  646 ++++-----
 crdch_model/owl/crdch_model.owl.ttl           | 1207 +++++++++--------
 crdch_model/shex/crdch_model.shex             |   10 +-
 crdch_model/shex/crdch_model.shexj            |   26 +-
 7 files changed, 1069 insertions(+), 1183 deletions(-)

diff --git a/crdch_model/crdch_model.py b/crdch_model/crdch_model.py
index 9910a64f5..71f892f0c 100644
--- a/crdch_model/crdch_model.py
+++ b/crdch_model/crdch_model.py
@@ -1,5 +1,5 @@
 # Auto generated from crdch_model.yaml by pythongen.py version: 0.9.0
-# Generation date: 2021-09-07 17:13
+# Generation date: 2021-09-16 17:54
 # Schema: CRDC-H
 #
 # id: https://example.org/crdch
@@ -485,9 +485,11 @@ class Coding(Entity):
 
     code: Union[str, CrdchString] = None
     system: Union[str, CrdchString] = None
-    systemURL: Optional[Union[str, CrdchString]] = None
-    systemVersion: Optional[Union[str, CrdchString]] = None
     label: Optional[Union[str, CrdchString]] = None
+    system_version: Optional[Union[str, CrdchString]] = None
+    value_set: Optional[Union[str, CrdchString]] = None
+    value_set_version: Optional[Union[str, CrdchString]] = None
+    tag: Optional[Union[Union[str, CrdchString], List[Union[str, CrdchString]]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.code):
@@ -500,15 +502,22 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if not isinstance(self.system, CrdchString):
             self.system = CrdchString(self.system)
 
-        if self.systemURL is not None and not isinstance(self.systemURL, CrdchString):
-            self.systemURL = CrdchString(self.systemURL)
-
-        if self.systemVersion is not None and not isinstance(self.systemVersion, CrdchString):
-            self.systemVersion = CrdchString(self.systemVersion)
-
         if self.label is not None and not isinstance(self.label, CrdchString):
             self.label = CrdchString(self.label)
 
+        if self.system_version is not None and not isinstance(self.system_version, CrdchString):
+            self.system_version = CrdchString(self.system_version)
+
+        if self.value_set is not None and not isinstance(self.value_set, CrdchString):
+            self.value_set = CrdchString(self.value_set)
+
+        if self.value_set_version is not None and not isinstance(self.value_set_version, CrdchString):
+            self.value_set_version = CrdchString(self.value_set_version)
+
+        if not isinstance(self.tag, list):
+            self.tag = [self.tag] if self.tag is not None else []
+        self.tag = [v if isinstance(v, CrdchString) else CrdchString(v) for v in self.tag]
+
         super().__post_init__(**kwargs)
 
 
@@ -529,7 +538,7 @@ class Diagnosis(Entity):
     identifier: Optional[Union[Union[dict, "Identifier"], List[Union[dict, "Identifier"]]]] = empty_list()
     subject: Optional[Union[dict, "Subject"]] = None
     age_at_diagnosis: Optional[Union[dict, "Quantity"]] = None
-    year_at_diagnosis: Optional[Union[int, CrdchInteger]] = None
+    diagnosis_date: Optional[Union[dict, "TimePoint"]] = None
     condition: Optional[Union[str, "EnumCRDCHDiagnosisCondition"]] = None
     primary_site: Optional[Union[Union[dict, BodySite], List[Union[dict, BodySite]]]] = empty_list()
     metastatic_site: Optional[Union[Union[dict, BodySite], List[Union[dict, BodySite]]]] = empty_list()
@@ -555,8 +564,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.age_at_diagnosis is not None and not isinstance(self.age_at_diagnosis, Quantity):
             self.age_at_diagnosis = Quantity(**as_dict(self.age_at_diagnosis))
 
-        if self.year_at_diagnosis is not None and not isinstance(self.year_at_diagnosis, CrdchInteger):
-            self.year_at_diagnosis = CrdchInteger(self.year_at_diagnosis)
+        if self.diagnosis_date is not None and not isinstance(self.diagnosis_date, TimePoint):
+            self.diagnosis_date = TimePoint(**as_dict(self.diagnosis_date))
 
         if self.condition is not None and not isinstance(self.condition, EnumCRDCHDiagnosisCondition):
             self.condition = EnumCRDCHDiagnosisCondition(self.condition)
@@ -1477,8 +1486,8 @@ class Specimen(Entity):
     quality_measure: Optional[Union[Union[dict, "SpecimenQualityObservation"], List[Union[dict, "SpecimenQualityObservation"]]]] = empty_list()
     cellular_composition_type: Optional[Union[str, "EnumCRDCHSpecimenCellularCompositionType"]] = None
     histological_composition_measures: Optional[Union[Union[dict, HistologicalCompositionObservationSet], List[Union[dict, HistologicalCompositionObservationSet]]]] = empty_list()
-    general_tissue_morphology: Optional[Union[str, "EnumCRDCHSpecimenGeneralTissueMorphology"]] = None
-    specific_tissue_morphology: Optional[Union[str, "EnumCRDCHSpecimenSpecificTissueMorphology"]] = None
+    general_tissue_pathology: Optional[Union[str, "EnumCRDCHSpecimenGeneralTissuePathology"]] = None
+    specific_tissue_pathology: Optional[Union[str, "EnumCRDCHSpecimenSpecificTissuePathology"]] = None
     preinvasive_tissue_morphology: Optional[Union[str, "EnumCRDCHSpecimenPreinvasiveTissueMorphology"]] = None
     morphology_pathologically_confirmed: Optional[Union[bool, CrdchBoolean]] = None
     morphology_assessor_role: Optional[Union[str, "EnumCRDCHSpecimenMorphologyAssessorRole"]] = None
@@ -1554,11 +1563,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
         self._normalize_inlined_as_list(slot_name="histological_composition_measures", slot_type=HistologicalCompositionObservationSet, key_name="id", keyed=False)
 
-        if self.general_tissue_morphology is not None and not isinstance(self.general_tissue_morphology, EnumCRDCHSpecimenGeneralTissueMorphology):
-            self.general_tissue_morphology = EnumCRDCHSpecimenGeneralTissueMorphology(self.general_tissue_morphology)
+        if self.general_tissue_pathology is not None and not isinstance(self.general_tissue_pathology, EnumCRDCHSpecimenGeneralTissuePathology):
+            self.general_tissue_pathology = EnumCRDCHSpecimenGeneralTissuePathology(self.general_tissue_pathology)
 
-        if self.specific_tissue_morphology is not None and not isinstance(self.specific_tissue_morphology, EnumCRDCHSpecimenSpecificTissueMorphology):
-            self.specific_tissue_morphology = EnumCRDCHSpecimenSpecificTissueMorphology(self.specific_tissue_morphology)
+        if self.specific_tissue_pathology is not None and not isinstance(self.specific_tissue_pathology, EnumCRDCHSpecimenSpecificTissuePathology):
+            self.specific_tissue_pathology = EnumCRDCHSpecimenSpecificTissuePathology(self.specific_tissue_pathology)
 
         if self.preinvasive_tissue_morphology is not None and not isinstance(self.preinvasive_tissue_morphology, EnumCRDCHSpecimenPreinvasiveTissueMorphology):
             self.preinvasive_tissue_morphology = EnumCRDCHSpecimenPreinvasiveTissueMorphology(self.preinvasive_tissue_morphology)
@@ -2060,8 +2069,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 @dataclass
 class TimePoint(Entity):
     """
-    A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, or
-    specification in terms of offset from a defined index.
+    A structured representation of a single point in time that allows direct/explicit declaration as a dateTime,
+    specification in terms of offset from a defined index, or description of an event type as a proxy for the time
+    point when it occurred.
     """
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -2273,7 +2283,7 @@ class EnumCRDCHAlcoholExposureObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHAlcoholExposureObservationCategory",
         description="Autogenerated Enumeration for CRDC-H AlcoholExposureObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:31.431109+00:00",
+        code_set_version="2021-09-16T21:49:36.489920+00:00",
     )
 
 class EnumCRDCHAlcoholExposureObservationObservationType(EnumDefinitionImpl):
@@ -2302,7 +2312,7 @@ class EnumCRDCHAlcoholExposureObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHAlcoholExposureObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H AlcoholExposureObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:32.116226+00:00",
+        code_set_version="2021-09-16T21:49:37.311998+00:00",
     )
 
 class EnumCRDCHAlcoholExposureObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -2313,7 +2323,7 @@ class EnumCRDCHAlcoholExposureObservationValueCodeableConcept(EnumDefinitionImpl
         name="EnumCRDCHAlcoholExposureObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H AlcoholExposureObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:32.219779+00:00",
+        code_set_version="2021-09-16T21:49:37.417707+00:00",
     )
 
 class EnumCRDCHBodySiteSite(EnumDefinitionImpl):
@@ -2633,7 +2643,7 @@ class EnumCRDCHBodySiteSite(EnumDefinitionImpl):
         name="EnumCRDCHBodySiteSite",
         description="Autogenerated Enumeration for CRDC-H BodySite site",
         code_set=None,
-        code_set_version="2021-09-07T21:08:32.335724+00:00",
+        code_set_version="2021-09-16T21:49:37.530258+00:00",
     )
 
     @classmethod
@@ -3657,7 +3667,7 @@ class EnumCRDCHBodySiteQualifier(EnumDefinitionImpl):
         name="EnumCRDCHBodySiteQualifier",
         description="Autogenerated Enumeration for CRDC-H BodySite qualifier",
         code_set=None,
-        code_set_version="2021-09-07T21:08:33.353553+00:00",
+        code_set_version="2021-09-16T21:49:38.574042+00:00",
     )
 
     @classmethod
@@ -3673,7 +3683,7 @@ class EnumCRDCHBiologicProductProductType(EnumDefinitionImpl):
         name="EnumCRDCHBiologicProductProductType",
         description="Autogenerated Enumeration for CRDC-H BiologicProduct product_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:33.482548+00:00",
+        code_set_version="2021-09-16T21:49:38.696389+00:00",
     )
 
 class EnumCRDCHCancerGradeObservationCategory(EnumDefinitionImpl):
@@ -3684,7 +3694,7 @@ class EnumCRDCHCancerGradeObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHCancerGradeObservationCategory",
         description="Autogenerated Enumeration for CRDC-H CancerGradeObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:33.589612+00:00",
+        code_set_version="2021-09-16T21:49:38.807272+00:00",
     )
 
 class EnumCRDCHCancerGradeObservationObservationType(EnumDefinitionImpl):
@@ -3716,7 +3726,7 @@ class EnumCRDCHCancerGradeObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHCancerGradeObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H CancerGradeObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:33.813864+00:00",
+        code_set_version="2021-09-16T21:49:39.035241+00:00",
     )
 
 class EnumCRDCHCancerGradeObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -3727,7 +3737,7 @@ class EnumCRDCHCancerGradeObservationValueCodeableConcept(EnumDefinitionImpl):
         name="EnumCRDCHCancerGradeObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H CancerGradeObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:33.923946+00:00",
+        code_set_version="2021-09-16T21:49:39.145945+00:00",
     )
 
 class EnumCRDCHCancerGradeObservationSetCategory(EnumDefinitionImpl):
@@ -3738,7 +3748,7 @@ class EnumCRDCHCancerGradeObservationSetCategory(EnumDefinitionImpl):
         name="EnumCRDCHCancerGradeObservationSetCategory",
         description="Autogenerated Enumeration for CRDC-H CancerGradeObservationSet category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.033726+00:00",
+        code_set_version="2021-09-16T21:49:39.256624+00:00",
     )
 
 class EnumCRDCHCancerGradeObservationSetMethodType(EnumDefinitionImpl):
@@ -3770,7 +3780,7 @@ class EnumCRDCHCancerStageObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHCancerStageObservationCategory",
         description="Autogenerated Enumeration for CRDC-H CancerStageObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.257170+00:00",
+        code_set_version="2021-09-16T21:49:39.478741+00:00",
     )
 
 class EnumCRDCHCancerStageObservationObservationType(EnumDefinitionImpl):
@@ -3832,7 +3842,7 @@ class EnumCRDCHCancerStageObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHCancerStageObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H CancerStageObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.478121+00:00",
+        code_set_version="2021-09-16T21:49:39.700585+00:00",
     )
 
 class EnumCRDCHCancerStageObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -3843,7 +3853,7 @@ class EnumCRDCHCancerStageObservationValueCodeableConcept(EnumDefinitionImpl):
         name="EnumCRDCHCancerStageObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H CancerStageObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.590527+00:00",
+        code_set_version="2021-09-16T21:49:39.816423+00:00",
     )
 
 class EnumCRDCHCancerStageObservationSetCategory(EnumDefinitionImpl):
@@ -3854,7 +3864,7 @@ class EnumCRDCHCancerStageObservationSetCategory(EnumDefinitionImpl):
         name="EnumCRDCHCancerStageObservationSetCategory",
         description="Autogenerated Enumeration for CRDC-H CancerStageObservationSet category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.702334+00:00",
+        code_set_version="2021-09-16T21:49:39.919163+00:00",
     )
 
 class EnumCRDCHCancerStageObservationSetMethodType(EnumDefinitionImpl):
@@ -4116,7 +4126,7 @@ class EnumCRDCHDiagnosisCondition(EnumDefinitionImpl):
         name="EnumCRDCHDiagnosisCondition",
         description="Autogenerated Enumeration for CRDC-H Diagnosis condition",
         code_set=None,
-        code_set_version="2021-09-07T21:08:34.924503+00:00",
+        code_set_version="2021-09-16T21:49:40.144659+00:00",
     )
 
     @classmethod
@@ -9077,7 +9087,7 @@ class EnumCRDCHDiagnosisMorphology(EnumDefinitionImpl):
         name="EnumCRDCHDiagnosisMorphology",
         description="Autogenerated Enumeration for CRDC-H Diagnosis morphology",
         code_set=None,
-        code_set_version="2021-09-07T21:08:37.859828+00:00",
+        code_set_version="2021-09-16T21:49:43.208427+00:00",
     )
 
     @classmethod
@@ -11387,7 +11397,7 @@ class EnumCRDCHDiagnosisDiseaseStatus(EnumDefinitionImpl):
         name="EnumCRDCHDiagnosisDiseaseStatus",
         description="Autogenerated Enumeration for CRDC-H Diagnosis disease_status",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.251148+00:00",
+        code_set_version="2021-09-16T21:49:44.530513+00:00",
     )
 
     @classmethod
@@ -11436,7 +11446,7 @@ class EnumCRDCHDiagnosisMethodOfDiagnosis(EnumDefinitionImpl):
         name="EnumCRDCHDiagnosisMethodOfDiagnosis",
         description="Autogenerated Enumeration for CRDC-H Diagnosis method_of_diagnosis",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.373622+00:00",
+        code_set_version="2021-09-16T21:49:44.657940+00:00",
     )
 
     @classmethod
@@ -11494,7 +11504,7 @@ class EnumCRDCHDimensionalObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHDimensionalObservationCategory",
         description="Autogenerated Enumeration for CRDC-H DimensionalObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.516352+00:00",
+        code_set_version="2021-09-16T21:49:44.803090+00:00",
     )
 
 class EnumCRDCHDimensionalObservationObservationType(EnumDefinitionImpl):
@@ -11527,7 +11537,7 @@ class EnumCRDCHDimensionalObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHDimensionalObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H DimensionalObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.730507+00:00",
+        code_set_version="2021-09-16T21:49:45.020572+00:00",
     )
 
 class EnumCRDCHDimensionalObservationSetCategory(EnumDefinitionImpl):
@@ -11538,7 +11548,7 @@ class EnumCRDCHDimensionalObservationSetCategory(EnumDefinitionImpl):
         name="EnumCRDCHDimensionalObservationSetCategory",
         description="Autogenerated Enumeration for CRDC-H DimensionalObservationSet category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.834340+00:00",
+        code_set_version="2021-09-16T21:49:45.133245+00:00",
     )
 
 class EnumCRDCHDimensionalObservationSetMethodType(EnumDefinitionImpl):
@@ -11549,7 +11559,7 @@ class EnumCRDCHDimensionalObservationSetMethodType(EnumDefinitionImpl):
         name="EnumCRDCHDimensionalObservationSetMethodType",
         description="Autogenerated Enumeration for CRDC-H DimensionalObservationSet method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:39.940391+00:00",
+        code_set_version="2021-09-16T21:49:45.244782+00:00",
     )
 
 class EnumCRDCHDocumentDocumentType(EnumDefinitionImpl):
@@ -11578,7 +11588,7 @@ class EnumCRDCHEnvironmentalExposureObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHEnvironmentalExposureObservationCategory",
         description="Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.164775+00:00",
+        code_set_version="2021-09-16T21:49:45.462653+00:00",
     )
 
 class EnumCRDCHEnvironmentalExposureObservationObservationType(EnumDefinitionImpl):
@@ -11609,7 +11619,7 @@ class EnumCRDCHEnvironmentalExposureObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHEnvironmentalExposureObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.378679+00:00",
+        code_set_version="2021-09-16T21:49:45.687597+00:00",
     )
 
 class EnumCRDCHEnvironmentalExposureObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -11620,7 +11630,7 @@ class EnumCRDCHEnvironmentalExposureObservationValueCodeableConcept(EnumDefiniti
         name="EnumCRDCHEnvironmentalExposureObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.480235+00:00",
+        code_set_version="2021-09-16T21:49:45.799416+00:00",
     )
 
 class EnumCRDCHExecutionConditionObservationCategory(EnumDefinitionImpl):
@@ -11631,7 +11641,7 @@ class EnumCRDCHExecutionConditionObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHExecutionConditionObservationCategory",
         description="Autogenerated Enumeration for CRDC-H ExecutionConditionObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.583103+00:00",
+        code_set_version="2021-09-16T21:49:45.921056+00:00",
     )
 
 class EnumCRDCHExecutionConditionObservationObservationType(EnumDefinitionImpl):
@@ -11655,7 +11665,7 @@ class EnumCRDCHExecutionConditionObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHExecutionConditionObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H ExecutionConditionObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.798174+00:00",
+        code_set_version="2021-09-16T21:49:46.139594+00:00",
     )
 
 class EnumCRDCHExecutionConditionObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -11666,7 +11676,7 @@ class EnumCRDCHExecutionConditionObservationValueCodeableConcept(EnumDefinitionI
         name="EnumCRDCHExecutionConditionObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H ExecutionConditionObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:40.903686+00:00",
+        code_set_version="2021-09-16T21:49:46.250423+00:00",
     )
 
 class EnumCRDCHExecutionTimeObservationCategory(EnumDefinitionImpl):
@@ -11677,7 +11687,7 @@ class EnumCRDCHExecutionTimeObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHExecutionTimeObservationCategory",
         description="Autogenerated Enumeration for CRDC-H ExecutionTimeObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.012389+00:00",
+        code_set_version="2021-09-16T21:49:46.360696+00:00",
     )
 
 class EnumCRDCHExecutionTimeObservationObservationType(EnumDefinitionImpl):
@@ -11704,7 +11714,7 @@ class EnumCRDCHExecutionTimeObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHExecutionTimeObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H ExecutionTimeObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.223744+00:00",
+        code_set_version="2021-09-16T21:49:46.587773+00:00",
     )
 
 class EnumCRDCHHistologicalCompositionObservationCategory(EnumDefinitionImpl):
@@ -11715,7 +11725,7 @@ class EnumCRDCHHistologicalCompositionObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHHistologicalCompositionObservationCategory",
         description="Autogenerated Enumeration for CRDC-H HistologicalCompositionObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.326028+00:00",
+        code_set_version="2021-09-16T21:49:46.697870+00:00",
     )
 
 class EnumCRDCHHistologicalCompositionObservationObservationType(EnumDefinitionImpl):
@@ -11777,7 +11787,7 @@ class EnumCRDCHHistologicalCompositionObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHHistologicalCompositionObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H HistologicalCompositionObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.548147+00:00",
+        code_set_version="2021-09-16T21:49:46.920129+00:00",
     )
 
 class EnumCRDCHHistologicalCompositionObservationSetCategory(EnumDefinitionImpl):
@@ -11788,7 +11798,7 @@ class EnumCRDCHHistologicalCompositionObservationSetCategory(EnumDefinitionImpl)
         name="EnumCRDCHHistologicalCompositionObservationSetCategory",
         description="Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.650910+00:00",
+        code_set_version="2021-09-16T21:49:47.041756+00:00",
     )
 
 class EnumCRDCHHistologicalCompositionObservationSetMethodType(EnumDefinitionImpl):
@@ -11799,7 +11809,7 @@ class EnumCRDCHHistologicalCompositionObservationSetMethodType(EnumDefinitionImp
         name="EnumCRDCHHistologicalCompositionObservationSetMethodType",
         description="Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.751341+00:00",
+        code_set_version="2021-09-16T21:49:47.154248+00:00",
     )
 
 class EnumCRDCHIdentifierType(EnumDefinitionImpl):
@@ -11810,7 +11820,7 @@ class EnumCRDCHIdentifierType(EnumDefinitionImpl):
         name="EnumCRDCHIdentifierType",
         description="Autogenerated Enumeration for CRDC-H Identifier type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.852956+00:00",
+        code_set_version="2021-09-16T21:49:47.263791+00:00",
     )
 
 class EnumCRDCHObservationCategory(EnumDefinitionImpl):
@@ -11821,7 +11831,7 @@ class EnumCRDCHObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHObservationCategory",
         description="Autogenerated Enumeration for CRDC-H Observation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:41.965970+00:00",
+        code_set_version="2021-09-16T21:49:47.364459+00:00",
     )
 
 class EnumCRDCHObservationObservationType(EnumDefinitionImpl):
@@ -11832,7 +11842,7 @@ class EnumCRDCHObservationObservationType(EnumDefinitionImpl):
         name="EnumCRDCHObservationObservationType",
         description="Autogenerated Enumeration for CRDC-H Observation observation_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.074790+00:00",
+        code_set_version="2021-09-16T21:49:47.463096+00:00",
     )
 
 class EnumCRDCHObservationMethodType(EnumDefinitionImpl):
@@ -11843,7 +11853,7 @@ class EnumCRDCHObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H Observation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.175220+00:00",
+        code_set_version="2021-09-16T21:49:47.563058+00:00",
     )
 
 class EnumCRDCHObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -11854,7 +11864,7 @@ class EnumCRDCHObservationValueCodeableConcept(EnumDefinitionImpl):
         name="EnumCRDCHObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H Observation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.276728+00:00",
+        code_set_version="2021-09-16T21:49:47.662542+00:00",
     )
 
 class EnumCRDCHObservationSetCategory(EnumDefinitionImpl):
@@ -11865,7 +11875,7 @@ class EnumCRDCHObservationSetCategory(EnumDefinitionImpl):
         name="EnumCRDCHObservationSetCategory",
         description="Autogenerated Enumeration for CRDC-H ObservationSet category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.379903+00:00",
+        code_set_version="2021-09-16T21:49:47.760835+00:00",
     )
 
 class EnumCRDCHObservationSetMethodType(EnumDefinitionImpl):
@@ -11876,7 +11886,7 @@ class EnumCRDCHObservationSetMethodType(EnumDefinitionImpl):
         name="EnumCRDCHObservationSetMethodType",
         description="Autogenerated Enumeration for CRDC-H ObservationSet method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.480631+00:00",
+        code_set_version="2021-09-16T21:49:47.861133+00:00",
     )
 
 class EnumCRDCHQuantityValueCodeableConcept(EnumDefinitionImpl):
@@ -11887,7 +11897,7 @@ class EnumCRDCHQuantityValueCodeableConcept(EnumDefinitionImpl):
         name="EnumCRDCHQuantityValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H Quantity value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.587568+00:00",
+        code_set_version="2021-09-16T21:49:47.958884+00:00",
     )
 
 class EnumCRDCHQuantityUnit(EnumDefinitionImpl):
@@ -11948,7 +11958,7 @@ class EnumCRDCHResearchSubjectPrimaryDiagnosisCondition(EnumDefinitionImpl):
         name="EnumCRDCHResearchSubjectPrimaryDiagnosisCondition",
         description="Autogenerated Enumeration for CRDC-H ResearchSubject primary_diagnosis_condition",
         code_set=None,
-        code_set_version="2021-09-07T21:08:42.904084+00:00",
+        code_set_version="2021-09-16T21:49:48.270054+00:00",
     )
 
     @classmethod
@@ -12221,7 +12231,7 @@ class EnumCRDCHResearchSubjectIndexTimepoint(EnumDefinitionImpl):
         name="EnumCRDCHResearchSubjectIndexTimepoint",
         description="Autogenerated Enumeration for CRDC-H ResearchSubject index_timepoint",
         code_set=None,
-        code_set_version="2021-09-07T21:08:43.139943+00:00",
+        code_set_version="2021-09-16T21:49:48.520690+00:00",
     )
 
     @classmethod
@@ -12261,8 +12271,8 @@ class EnumCRDCHSpecimenSpecimenType(EnumDefinitionImpl):
 
     @classmethod
     def _addvals(cls):
-        setattr(cls, "initial sample",
-                PermissibleValue(text="initial sample",
+        setattr(cls, "Fresh Specimen",
+                PermissibleValue(text="Fresh Specimen",
                                  description="A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen).") )
 
 class EnumCRDCHSpecimenAnalyteType(EnumDefinitionImpl):
@@ -12298,7 +12308,7 @@ class EnumCRDCHSpecimenAnalyteType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenAnalyteType",
         description="Autogenerated Enumeration for CRDC-H Specimen analyte_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:43.371740+00:00",
+        code_set_version="2021-09-16T21:49:48.753301+00:00",
     )
 
     @classmethod
@@ -12349,7 +12359,7 @@ class EnumCRDCHSpecimenSourceMaterialType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenSourceMaterialType",
         description="Autogenerated Enumeration for CRDC-H Specimen source_material_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:43.526142+00:00",
+        code_set_version="2021-09-16T21:49:48.890971+00:00",
     )
 
     @classmethod
@@ -12535,7 +12545,7 @@ class EnumCRDCHSpecimenTumorStatusAtCollection(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenTumorStatusAtCollection",
         description="Autogenerated Enumeration for CRDC-H Specimen tumor_status_at_collection",
         code_set=None,
-        code_set_version="2021-09-07T21:08:43.745325+00:00",
+        code_set_version="2021-09-16T21:49:49.080717+00:00",
     )
 
     @classmethod
@@ -12573,7 +12583,7 @@ class EnumCRDCHSpecimenCellularCompositionType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenCellularCompositionType",
         description="Autogenerated Enumeration for CRDC-H Specimen cellular_composition_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:43.878758+00:00",
+        code_set_version="2021-09-16T21:49:49.213118+00:00",
     )
 
     @classmethod
@@ -12645,149 +12655,28 @@ def _addvals(cls):
         setattr(cls, "Not Allowed To Collect",
                 PermissibleValue(text="Not Allowed To Collect") )
 
-class EnumCRDCHSpecimenGeneralTissueMorphology(EnumDefinitionImpl):
+class EnumCRDCHSpecimenGeneralTissuePathology(EnumDefinitionImpl):
     """
-    Autogenerated Enumeration for CRDC-H Specimen general_tissue_morphology
+    Autogenerated Enumeration for CRDC-H Specimen general_tissue_pathology
     """
-    Peritumoral = PermissibleValue(text="Peritumoral",
-                                             description="Peritumoral")
-    Abnormal = PermissibleValue(text="Abnormal",
-                                       description="Abnormal")
-    Normal = PermissibleValue(text="Normal",
-                                   description="Normal")
-    Unknown = PermissibleValue(text="Unknown",
-                                     description="Unknown")
-    Tumor = PermissibleValue(text="Tumor",
-                                 description="Malignant Neoplasm")
-
     _defn = EnumDefinition(
-        name="EnumCRDCHSpecimenGeneralTissueMorphology",
-        description="Autogenerated Enumeration for CRDC-H Specimen general_tissue_morphology",
+        name="EnumCRDCHSpecimenGeneralTissuePathology",
+        description="Autogenerated Enumeration for CRDC-H Specimen general_tissue_pathology",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.026728+00:00",
+        code_set_version="2021-09-16T21:49:49.380359+00:00",
     )
 
-    @classmethod
-    def _addvals(cls):
-        setattr(cls, "Not Allowed To Collect",
-                PermissibleValue(text="Not Allowed To Collect") )
-        setattr(cls, "Not Reported",
-                PermissibleValue(text="Not Reported") )
-
-class EnumCRDCHSpecimenSpecificTissueMorphology(EnumDefinitionImpl):
+class EnumCRDCHSpecimenSpecificTissuePathology(EnumDefinitionImpl):
     """
-    Autogenerated Enumeration for CRDC-H Specimen specific_tissue_morphology
+    Autogenerated Enumeration for CRDC-H Specimen specific_tissue_pathology
     """
-    Rhabdomyosarcoma = PermissibleValue(text="Rhabdomyosarcoma")
-
     _defn = EnumDefinition(
-        name="EnumCRDCHSpecimenSpecificTissueMorphology",
-        description="Autogenerated Enumeration for CRDC-H Specimen specific_tissue_morphology",
+        name="EnumCRDCHSpecimenSpecificTissuePathology",
+        description="Autogenerated Enumeration for CRDC-H Specimen specific_tissue_pathology",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.143833+00:00",
+        code_set_version="2021-09-16T21:49:49.494860+00:00",
     )
 
-    @classmethod
-    def _addvals(cls):
-        setattr(cls, "61",
-                PermissibleValue(text="61") )
-        setattr(cls, "70",
-                PermissibleValue(text="70") )
-        setattr(cls, "30",
-                PermissibleValue(text="30") )
-        setattr(cls, "63",
-                PermissibleValue(text="63") )
-        setattr(cls, "71",
-                PermissibleValue(text="71") )
-        setattr(cls, "51",
-                PermissibleValue(text="51") )
-        setattr(cls, "80",
-                PermissibleValue(text="80") )
-        setattr(cls, "02",
-                PermissibleValue(text="02") )
-        setattr(cls, "65",
-                PermissibleValue(text="65") )
-        setattr(cls, "04",
-                PermissibleValue(text="04") )
-        setattr(cls, "60",
-                PermissibleValue(text="60") )
-        setattr(cls, "03",
-                PermissibleValue(text="03") )
-        setattr(cls, "50",
-                PermissibleValue(text="50") )
-        setattr(cls, "52",
-                PermissibleValue(text="52") )
-        setattr(cls, "15",
-                PermissibleValue(text="15") )
-        setattr(cls, "10",
-                PermissibleValue(text="10") )
-        setattr(cls, "00",
-                PermissibleValue(text="00") )
-        setattr(cls, "01",
-                PermissibleValue(text="01") )
-        setattr(cls, "21",
-                PermissibleValue(text="21") )
-        setattr(cls, "20",
-                PermissibleValue(text="20") )
-        setattr(cls, "62",
-                PermissibleValue(text="62") )
-        setattr(cls, "40",
-                PermissibleValue(text="40") )
-        setattr(cls, "64",
-                PermissibleValue(text="64") )
-        setattr(cls, "81",
-                PermissibleValue(text="81") )
-        setattr(cls, "41",
-                PermissibleValue(text="41") )
-        setattr(cls, "Rhabdoid tumor (kidney) (RT)",
-                PermissibleValue(text="Rhabdoid tumor (kidney) (RT)") )
-        setattr(cls, "Acute myeloid leukemia (AML)",
-                PermissibleValue(text="Acute myeloid leukemia (AML)") )
-        setattr(cls, "Anal Cancer (all types)",
-                PermissibleValue(text="Anal Cancer (all types)") )
-        setattr(cls, "Non cancerous tissue",
-                PermissibleValue(text="Non cancerous tissue") )
-        setattr(cls, "CNS, low grade glioma (LGG)",
-                PermissibleValue(text="CNS, low grade glioma (LGG)") )
-        setattr(cls, "Lung Cancer (all types)",
-                PermissibleValue(text="Lung Cancer (all types)") )
-        setattr(cls, "CNS, ependymoma",
-                PermissibleValue(text="CNS, ependymoma") )
-        setattr(cls, "Induction Failure AML (AML-IF)",
-                PermissibleValue(text="Induction Failure AML (AML-IF)") )
-        setattr(cls, "Soft tissue sarcoma, non-rhabdomyosarcoma",
-                PermissibleValue(text="Soft tissue sarcoma, non-rhabdomyosarcoma") )
-        setattr(cls, "NHL, Burkitt lymphoma (BL)",
-                PermissibleValue(text="NHL, Burkitt lymphoma (BL)") )
-        setattr(cls, "Neuroblastoma (NBL)",
-                PermissibleValue(text="Neuroblastoma (NBL)") )
-        setattr(cls, "Diffuse Large B-Cell Lymphoma (DLBCL)",
-                PermissibleValue(text="Diffuse Large B-Cell Lymphoma (DLBCL)") )
-        setattr(cls, "Acute lymphoblastic leukemia (ALL)",
-                PermissibleValue(text="Acute lymphoblastic leukemia (ALL)") )
-        setattr(cls, "CNS, rhabdoid tumor",
-                PermissibleValue(text="CNS, rhabdoid tumor") )
-        setattr(cls, "CNS, medulloblastoma",
-                PermissibleValue(text="CNS, medulloblastoma") )
-        setattr(cls, "Cervical Cancer (all types)",
-                PermissibleValue(text="Cervical Cancer (all types)") )
-        setattr(cls, "NHL, anaplastic large cell lymphoma",
-                PermissibleValue(text="NHL, anaplastic large cell lymphoma") )
-        setattr(cls, "Clear cell sarcoma of the kidney (CCSK)",
-                PermissibleValue(text="Clear cell sarcoma of the kidney (CCSK)") )
-        setattr(cls, "CNS, glioblastoma (GBM)",
-                PermissibleValue(text="CNS, glioblastoma (GBM)") )
-        setattr(cls, "Acute Leukemia of Ambiguous Lineage (ALAL)",
-                PermissibleValue(text="Acute Leukemia of Ambiguous Lineage (ALAL)") )
-        setattr(cls, "CNS, other",
-                PermissibleValue(text="CNS, other") )
-        setattr(cls, "Ewing sarcoma",
-                PermissibleValue(text="Ewing sarcoma") )
-        setattr(cls, "Osteosarcoma (OS)",
-                PermissibleValue(text="Osteosarcoma (OS)") )
-        setattr(cls, "Wilms tumor (WT)",
-                PermissibleValue(text="Wilms tumor (WT)") )
-
 class EnumCRDCHSpecimenPreinvasiveTissueMorphology(EnumDefinitionImpl):
     """
     Autogenerated Enumeration for CRDC-H Specimen preinvasive_tissue_morphology
@@ -12796,7 +12685,7 @@ class EnumCRDCHSpecimenPreinvasiveTissueMorphology(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenPreinvasiveTissueMorphology",
         description="Autogenerated Enumeration for CRDC-H Specimen preinvasive_tissue_morphology",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.301214+00:00",
+        code_set_version="2021-09-16T21:49:49.607830+00:00",
     )
 
 class EnumCRDCHSpecimenMorphologyAssessorRole(EnumDefinitionImpl):
@@ -12807,7 +12696,7 @@ class EnumCRDCHSpecimenMorphologyAssessorRole(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenMorphologyAssessorRole",
         description="Autogenerated Enumeration for CRDC-H Specimen morphology_assessor_role",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.410467+00:00",
+        code_set_version="2021-09-16T21:49:49.912759+00:00",
     )
 
 class EnumCRDCHSpecimenMorphologyAssessmentMethod(EnumDefinitionImpl):
@@ -12818,7 +12707,7 @@ class EnumCRDCHSpecimenMorphologyAssessmentMethod(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenMorphologyAssessmentMethod",
         description="Autogenerated Enumeration for CRDC-H Specimen morphology_assessment_method",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.524474+00:00",
+        code_set_version="2021-09-16T21:49:50.236173+00:00",
     )
 
 class EnumCRDCHSpecimenDegreeOfDysplasia(EnumDefinitionImpl):
@@ -12829,7 +12718,7 @@ class EnumCRDCHSpecimenDegreeOfDysplasia(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenDegreeOfDysplasia",
         description="Autogenerated Enumeration for CRDC-H Specimen degree_of_dysplasia",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.636509+00:00",
+        code_set_version="2021-09-16T21:49:50.523131+00:00",
     )
 
 class EnumCRDCHSpecimenSectionLocation(EnumDefinitionImpl):
@@ -12856,7 +12745,7 @@ class EnumCRDCHSpecimenContainerContainerType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenContainerContainerType",
         description="Autogenerated Enumeration for CRDC-H SpecimenContainer container_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:44.851513+00:00",
+        code_set_version="2021-09-16T21:49:51.182025+00:00",
     )
 
 class EnumCRDCHSpecimenCreationActivityActivityType(EnumDefinitionImpl):
@@ -12916,7 +12805,7 @@ class EnumCRDCHSpecimenCreationActivityCollectionMethodType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenCreationActivityCollectionMethodType",
         description="Autogenerated Enumeration for CRDC-H SpecimenCreationActivity collection_method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:45.084419+00:00",
+        code_set_version="2021-09-16T21:49:51.955969+00:00",
     )
 
     @classmethod
@@ -13082,7 +12971,7 @@ class EnumCRDCHSpecimenCreationActivityDerivationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenCreationActivityDerivationMethodType",
         description="Autogenerated Enumeration for CRDC-H SpecimenCreationActivity derivation_method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:45.317644+00:00",
+        code_set_version="2021-09-16T21:49:52.358192+00:00",
     )
 
 class EnumCRDCHSpecimenQualityObservationCategory(EnumDefinitionImpl):
@@ -13093,7 +12982,7 @@ class EnumCRDCHSpecimenQualityObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenQualityObservationCategory",
         description="Autogenerated Enumeration for CRDC-H SpecimenQualityObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:45.423104+00:00",
+        code_set_version="2021-09-16T21:49:52.841235+00:00",
     )
 
 class EnumCRDCHSpecimenQualityObservationObservationType(EnumDefinitionImpl):
@@ -13140,7 +13029,7 @@ class EnumCRDCHSpecimenQuantityObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenQuantityObservationCategory",
         description="Autogenerated Enumeration for CRDC-H SpecimenQuantityObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:45.741776+00:00",
+        code_set_version="2021-09-16T21:49:53.684414+00:00",
     )
 
 class EnumCRDCHSpecimenQuantityObservationObservationType(EnumDefinitionImpl):
@@ -13168,7 +13057,7 @@ class EnumCRDCHSpecimenQuantityObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenQuantityObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H SpecimenQuantityObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:45.958852+00:00",
+        code_set_version="2021-09-16T21:49:53.900052+00:00",
     )
 
 class EnumCRDCHSpecimenProcessingActivityActivityType(EnumDefinitionImpl):
@@ -13205,8 +13094,8 @@ class EnumCRDCHSpecimenProcessingActivityMethodType(EnumDefinitionImpl):
 
     @classmethod
     def _addvals(cls):
-        setattr(cls, "-80",
-                PermissibleValue(text="-80",
+        setattr(cls, "Minues 80 Degrees Celsius Freezer",
+                PermissibleValue(text="Minues 80 Degrees Celsius Freezer",
                                  description="Freezing at -80 degrees celcius") )
         setattr(cls, "-20",
                 PermissibleValue(text="-20",
@@ -13220,7 +13109,7 @@ class EnumCRDCHSpecimenStorageActivityMethodType(EnumDefinitionImpl):
         name="EnumCRDCHSpecimenStorageActivityMethodType",
         description="Autogenerated Enumeration for CRDC-H SpecimenStorageActivity method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:46.367201+00:00",
+        code_set_version="2021-09-16T21:49:54.228963+00:00",
     )
 
 class EnumCRDCHSubjectSpecies(EnumDefinitionImpl):
@@ -13348,7 +13237,7 @@ class EnumCRDCHSubjectSex(EnumDefinitionImpl):
         name="EnumCRDCHSubjectSex",
         description="Autogenerated Enumeration for CRDC-H Subject sex",
         code_set=None,
-        code_set_version="2021-09-07T21:08:46.687007+00:00",
+        code_set_version="2021-09-16T21:49:54.542209+00:00",
     )
 
     @classmethod
@@ -13368,7 +13257,7 @@ class EnumCRDCHSubjectEthnicity(EnumDefinitionImpl):
         name="EnumCRDCHSubjectEthnicity",
         description="Autogenerated Enumeration for CRDC-H Subject ethnicity",
         code_set=None,
-        code_set_version="2021-09-07T21:08:46.793549+00:00",
+        code_set_version="2021-09-16T21:49:54.646843+00:00",
     )
 
     @classmethod
@@ -13397,7 +13286,7 @@ class EnumCRDCHSubjectRace(EnumDefinitionImpl):
         name="EnumCRDCHSubjectRace",
         description="Autogenerated Enumeration for CRDC-H Subject race",
         code_set=None,
-        code_set_version="2021-09-07T21:08:46.900411+00:00",
+        code_set_version="2021-09-16T21:49:54.761435+00:00",
     )
 
     @classmethod
@@ -13428,7 +13317,7 @@ class EnumCRDCHSubjectVitalStatus(EnumDefinitionImpl):
         name="EnumCRDCHSubjectVitalStatus",
         description="Autogenerated Enumeration for CRDC-H Subject vital_status",
         code_set=None,
-        code_set_version="2021-09-07T21:08:47.016668+00:00",
+        code_set_version="2021-09-16T21:49:54.879433+00:00",
     )
 
     @classmethod
@@ -13452,7 +13341,7 @@ class EnumCRDCHSubjectCauseOfDeath(EnumDefinitionImpl):
         name="EnumCRDCHSubjectCauseOfDeath",
         description="Autogenerated Enumeration for CRDC-H Subject cause_of_death",
         code_set=None,
-        code_set_version="2021-09-07T21:08:47.200658+00:00",
+        code_set_version="2021-09-16T21:49:54.989771+00:00",
     )
 
     @classmethod
@@ -14839,7 +14728,7 @@ class EnumCRDCHSubstanceSubstanceType(EnumDefinitionImpl):
         name="EnumCRDCHSubstanceSubstanceType",
         description="Autogenerated Enumeration for CRDC-H Substance substance_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:47.325429+00:00",
+        code_set_version="2021-09-16T21:49:55.109323+00:00",
     )
 
     @classmethod
@@ -21097,7 +20986,7 @@ class EnumCRDCHSubstanceRole(EnumDefinitionImpl):
         name="EnumCRDCHSubstanceRole",
         description="Autogenerated Enumeration for CRDC-H Substance role",
         code_set=None,
-        code_set_version="2021-09-07T21:08:51.803327+00:00",
+        code_set_version="2021-09-16T21:49:59.552481+00:00",
     )
 
 class EnumCRDCHTimePointEventType(EnumDefinitionImpl):
@@ -21108,7 +20997,7 @@ class EnumCRDCHTimePointEventType(EnumDefinitionImpl):
         name="EnumCRDCHTimePointEventType",
         description="Autogenerated Enumeration for CRDC-H TimePoint event_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:51.912452+00:00",
+        code_set_version="2021-09-16T21:49:59.664833+00:00",
     )
 
 class EnumCRDCHTobaccoExposureObservationCategory(EnumDefinitionImpl):
@@ -21119,7 +21008,7 @@ class EnumCRDCHTobaccoExposureObservationCategory(EnumDefinitionImpl):
         name="EnumCRDCHTobaccoExposureObservationCategory",
         description="Autogenerated Enumeration for CRDC-H TobaccoExposureObservation category",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.028296+00:00",
+        code_set_version="2021-09-16T21:49:59.773141+00:00",
     )
 
 class EnumCRDCHTobaccoExposureObservationObservationType(EnumDefinitionImpl):
@@ -21160,7 +21049,7 @@ class EnumCRDCHTobaccoExposureObservationMethodType(EnumDefinitionImpl):
         name="EnumCRDCHTobaccoExposureObservationMethodType",
         description="Autogenerated Enumeration for CRDC-H TobaccoExposureObservation method_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.252674+00:00",
+        code_set_version="2021-09-16T21:49:59.996722+00:00",
     )
 
 class EnumCRDCHTobaccoExposureObservationValueCodeableConcept(EnumDefinitionImpl):
@@ -21171,7 +21060,7 @@ class EnumCRDCHTobaccoExposureObservationValueCodeableConcept(EnumDefinitionImpl
         name="EnumCRDCHTobaccoExposureObservationValueCodeableConcept",
         description="Autogenerated Enumeration for CRDC-H TobaccoExposureObservation value_codeable_concept",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.366000+00:00",
+        code_set_version="2021-09-16T21:50:00.103991+00:00",
     )
 
 class EnumCRDCHTreatmentTreatmentType(EnumDefinitionImpl):
@@ -21197,7 +21086,7 @@ class EnumCRDCHTreatmentTreatmentType(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentType",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_type",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.474538+00:00",
+        code_set_version="2021-09-16T21:50:00.213820+00:00",
     )
 
     @classmethod
@@ -21325,7 +21214,7 @@ class EnumCRDCHTreatmentTreatmentEndReason(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentEndReason",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_end_reason",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.640041+00:00",
+        code_set_version="2021-09-16T21:50:00.381055+00:00",
     )
 
     @classmethod
@@ -21347,7 +21236,7 @@ class EnumCRDCHTreatmentRegimen(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentRegimen",
         description="Autogenerated Enumeration for CRDC-H Treatment regimen",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.744041+00:00",
+        code_set_version="2021-09-16T21:50:00.497916+00:00",
     )
 
 class EnumCRDCHTreatmentTreatmentFrequency(EnumDefinitionImpl):
@@ -21360,7 +21249,7 @@ class EnumCRDCHTreatmentTreatmentFrequency(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentFrequency",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_frequency",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.844226+00:00",
+        code_set_version="2021-09-16T21:50:00.605331+00:00",
     )
 
     @classmethod
@@ -21406,7 +21295,7 @@ class EnumCRDCHTreatmentTreatmentIntent(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentIntent",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_intent",
         code_set=None,
-        code_set_version="2021-09-07T21:08:52.952346+00:00",
+        code_set_version="2021-09-16T21:50:00.725168+00:00",
     )
 
     @classmethod
@@ -21433,7 +21322,7 @@ class EnumCRDCHTreatmentTreatmentEffect(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentEffect",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_effect",
         code_set=None,
-        code_set_version="2021-09-07T21:08:53.061098+00:00",
+        code_set_version="2021-09-16T21:50:00.852181+00:00",
     )
 
     @classmethod
@@ -21461,7 +21350,7 @@ class EnumCRDCHTreatmentTreatmentOutcome(EnumDefinitionImpl):
         name="EnumCRDCHTreatmentTreatmentOutcome",
         description="Autogenerated Enumeration for CRDC-H Treatment treatment_outcome",
         code_set=None,
-        code_set_version="2021-09-07T21:08:53.170913+00:00",
+        code_set_version="2021-09-16T21:50:00.974004+00:00",
     )
 
     @classmethod
diff --git a/crdch_model/csv/crdch_model.csv b/crdch_model/csv/crdch_model.csv
index 68fcfd5bd..4570462ea 100644
--- a/crdch_model/csv/crdch_model.csv
+++ b/crdch_model/csv/crdch_model.csv
@@ -45,7 +45,7 @@ SpecimenTransportActivity,,An activity through which a specimen is transported b
 Subject,,Demographics and other administrative information about an individual or animal receiving care or other health-related services.
 Substance,,"A type of material substance, or instance thereof,  as used in a particular application. May include information about the role the substance played in a particular application."
 TimePeriod,,A period of time between a start and end time point.
-TimePoint,,"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, or specification in terms of offset from a defined index."
+TimePoint,,"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred."
 TobaccoExposureObservation,,"A structured object that describes a single data item about an individual's exposure to tobacco, as generated through a point-in-time observation, measurement, or interpretation."
 Treatment,,Represent medication administration or other treatment types.
 
diff --git a/crdch_model/graphql/crdch_model.graphql b/crdch_model/graphql/crdch_model.graphql
index 3874584a7..f05410d37 100644
--- a/crdch_model/graphql/crdch_model.graphql
+++ b/crdch_model/graphql/crdch_model.graphql
@@ -84,8 +84,10 @@ type Coding
     code: CrdchString!
     label: CrdchString
     system: CrdchString!
-    systemUrl: CrdchString
     systemVersion: CrdchString
+    valueSet: CrdchString
+    valueSetVersion: CrdchString
+    tag: [CrdchString]
   }
 
 type Diagnosis
@@ -325,8 +327,8 @@ type Specimen
     qualityMeasure: [SpecimenQualityObservation]
     cellularCompositionType: EnumCRDCHSpecimenCellularCompositionType
     histologicalCompositionMeasures: [HistologicalCompositionObservationSet]
-    generalTissueMorphology: EnumCRDCHSpecimenGeneralTissueMorphology
-    specificTissueMorphology: EnumCRDCHSpecimenSpecificTissueMorphology
+    generalTissuePathology: EnumCRDCHSpecimenGeneralTissuePathology
+    specificTissuePathology: EnumCRDCHSpecimenSpecificTissuePathology
     preinvasiveTissueMorphology: EnumCRDCHSpecimenPreinvasiveTissueMorphology
     morphologyPathologicallyConfirmed: CrdchBoolean
     morphologyAssessorRole: EnumCRDCHSpecimenMorphologyAssessorRole
diff --git a/crdch_model/json_schema/crdch_model.schema.json b/crdch_model/json_schema/crdch_model.schema.json
index c01209505..bcfb4d7be 100644
--- a/crdch_model/json_schema/crdch_model.schema.json
+++ b/crdch_model/json_schema/crdch_model.schema.json
@@ -1,18 +1,15 @@
 {
-   "$id": "https://example.org/crdch",
-   "$schema": "http://json-schema.org/draft-07/schema#",
-   "additionalProperties": true,
-   "definitions": {
+   "$defs": {
       "AlcoholExposureObservation": {
          "additionalProperties": false,
          "description": "A structured object that describes a single data item about an individual's exposure to alcohol, as generated through a point-in-time observation, measurement, or interpretation.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHAlcoholExposureObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHAlcoholExposureObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -20,23 +17,23 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHAlcoholExposureObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHAlcoholExposureObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHAlcoholExposureObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHAlcoholExposureObservationObservationType",
                "description": "The specific type of alcohol exposure observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHAlcoholExposureObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHAlcoholExposureObservationValueCodeableConcept",
                "description": "The result of the observation, encoded as a CodeableConcept."
             },
             "value_integer": {
@@ -72,7 +69,7 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
@@ -84,7 +81,7 @@
                "type": "array"
             },
             "product_type": {
-               "$ref": "#/definitions/EnumCRDCHBiologicProductProductType",
+               "$ref": "#/$defs/EnumCRDCHBiologicProductProductType",
                "description": "The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid)"
             }
          },
@@ -99,12 +96,12 @@
             "qualifier": {
                "description": "A qualifier that further refines or specifies the location of the body site (e.g. to indicate laterality, upper v. lower, containment, etc).",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHBodySiteQualifier"
+                  "$ref": "#/$defs/EnumCRDCHBodySiteQualifier"
                },
                "type": "array"
             },
             "site": {
-               "$ref": "#/definitions/EnumCRDCHBodySiteSite",
+               "$ref": "#/$defs/EnumCRDCHBodySiteSite",
                "description": "A term describing any site in the body."
             }
          },
@@ -119,11 +116,11 @@
          "description": "A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer grade observation",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHCancerGradeObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHCancerGradeObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -131,19 +128,19 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHCancerGradeObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHCancerGradeObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHCancerGradeObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHCancerGradeObservationObservationType",
                "description": "The cancer grade classification system being used to classify the cancer (e.g. INPC, Gleason, etc.)"
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHCancerGradeObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHCancerGradeObservationValueCodeableConcept",
                "description": "The value from the grade classification system that classifies the cancer (e.g. Poorly differentiated, differentiated, etc.)"
             }
          },
@@ -159,13 +156,13 @@
          "description": "A structured object to hold related data items about the grade of cancer (e.g. overall, primary gleason, secondary gleason, etc.).",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHCancerGradeObservationSetCategory",
+               "$ref": "#/$defs/EnumCRDCHCancerGradeObservationSetCategory",
                "description": "The general category of observation set described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -176,23 +173,23 @@
             "method_type": {
                "description": "The cancer grade classification system being used to classify the cancer (e.g. INPC, Gleason, etc.)",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHCancerGradeObservationSetMethodType"
+                  "$ref": "#/$defs/EnumCRDCHCancerGradeObservationSetMethodType"
                },
                "type": "array"
             },
             "observations": {
                "description": "A set of one or more more atomic observations about the cancer grade that classifies the cancer (e.g. Poorly differentiated, differentiated, etc.)",
                "items": {
-                  "$ref": "#/definitions/CancerGradeObservation"
+                  "$ref": "#/$defs/CancerGradeObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             }
          },
@@ -205,11 +202,11 @@
          "description": "A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer staging observation, such as the Clinical Metastasis (M) component of a clinical TNM staging.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHCancerStageObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHCancerStageObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -217,27 +214,27 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHCancerStageObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHCancerStageObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHCancerStageObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHCancerStageObservationObservationType",
                "description": "The type of cancer staging component being represented (e.g. 'Clinical Metastasis (M)')"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHCancerStageObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHCancerStageObservationValueCodeableConcept",
                "description": "The value for a cancer staging component being represented (e.g. 'M1'), encoded as a CodeableConcept."
             },
             "value_entity": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The value of an observation"
             }
          },
@@ -253,13 +250,13 @@
          "description": "A structured object to hold related data items about the staging of cancer (e.g. overall, T, N, and M components of a Cancer Staging observation).",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHCancerStageObservationSetCategory",
+               "$ref": "#/$defs/EnumCRDCHCancerStageObservationSetCategory",
                "description": "The general category of observation set described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -270,23 +267,23 @@
             "method_type": {
                "description": "A type of method used in generating each of the Observations bundled in the set, in this case, the particular staging system being used to classify the cancer.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHCancerStageObservationSetMethodType"
+                  "$ref": "#/$defs/EnumCRDCHCancerStageObservationSetMethodType"
                },
                "type": "array"
             },
             "observations": {
                "description": "A set of one or more more atomic observations about the cancer stage",
                "items": {
-                  "$ref": "#/definitions/CancerStageObservation"
+                  "$ref": "#/$defs/CancerStageObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             }
          },
@@ -301,7 +298,7 @@
             "coding": {
                "description": "A reference to a code defined by a terminology system",
                "items": {
-                  "$ref": "#/definitions/Coding"
+                  "$ref": "#/$defs/Coding"
                },
                "type": "array"
             },
@@ -327,15 +324,26 @@
                "type": "string"
             },
             "system": {
-               "description": "The code system where the code is defined.",
+               "description": "The URL of the code system where the code is defined.",
                "type": "string"
             },
-            "systemURL": {
-               "description": "A URL where the code system can be found.",
+            "system_version": {
+               "description": "The version of the code system.",
                "type": "string"
             },
-            "systemVersion": {
-               "description": "The version of the code system.",
+            "tag": {
+               "description": "original value  |  harmonized value  |",
+               "items": {
+                  "type": "string"
+               },
+               "type": "array"
+            },
+            "value_set": {
+               "description": "The identifier of the enumeration / value set that the code is a part of in the context of this element",
+               "type": "string"
+            },
+            "value_set_version": {
+               "description": "The version of the enuemration / value set the code is pulled from",
                "type": "string"
             }
          },
@@ -351,21 +359,25 @@
          "description": "A collection of characteristics that describe an abnormal condition of the body as assessed at a point in time. May be used to capture information about neoplastic and non-neoplastic conditions.",
          "properties": {
             "age_at_diagnosis": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The age in days of the individual at the time of diagnosis"
             },
             "condition": {
-               "$ref": "#/definitions/EnumCRDCHDiagnosisCondition",
+               "$ref": "#/$defs/EnumCRDCHDiagnosisCondition",
                "description": "Code that captures the condition being diagnosed (e.g. ICD-O, ICD-10, SNOMED, etc.)"
             },
+            "diagnosis_date": {
+               "$ref": "#/$defs/TimePoint",
+               "description": "When the diagnosis was made."
+            },
             "disease_status": {
-               "$ref": "#/definitions/EnumCRDCHDiagnosisDiseaseStatus",
+               "$ref": "#/$defs/EnumCRDCHDiagnosisDiseaseStatus",
                "description": "A term that refers to the nature and/or clinical outcome of a disease (e.g., primary disease, metastatic disease, recurrent disease, etc.)"
             },
             "grade": {
                "description": "The degree of abnormality of cancer cells, a measure of differentiation, the extent to which cancer cells are similar in appearance and function to healthy cells of the same tissue type. The degree of differentiation often relates to the clinical behavior of the particular tumor. Based on the microscopic findings, tumor grade is commonly described by one of four degrees of severity. Histopathologic grade of a tumor may be used to plan treatment and estimate the future course, outcome, and overall prognosis of disease. Certain types of cancers, such as soft tissue sarcoma, primary brain tumors, lymphomas, and breast have special grading systems.",
                "items": {
-                  "$ref": "#/definitions/CancerGradeObservationSet"
+                  "$ref": "#/$defs/CancerGradeObservationSet"
                },
                "type": "array"
             },
@@ -376,68 +388,64 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "metastatic_site": {
                "description": "The anatomical location(s) of metastatic disease",
                "items": {
-                  "$ref": "#/definitions/BodySite"
+                  "$ref": "#/$defs/BodySite"
                },
                "type": "array"
             },
             "method_of_diagnosis": {
-               "$ref": "#/definitions/EnumCRDCHDiagnosisMethodOfDiagnosis",
+               "$ref": "#/$defs/EnumCRDCHDiagnosisMethodOfDiagnosis",
                "description": "The method used to confirm the patients malignant diagnosis"
             },
             "morphology": {
-               "$ref": "#/definitions/EnumCRDCHDiagnosisMorphology",
+               "$ref": "#/$defs/EnumCRDCHDiagnosisMorphology",
                "description": "Code that represents the histology of the disease using the third edition of the International Classification of Diseases for Oncology, published in 2000, used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms."
             },
             "primary_site": {
                "description": "The anatomical location of the primary condition",
                "items": {
-                  "$ref": "#/definitions/BodySite"
+                  "$ref": "#/$defs/BodySite"
                },
                "type": "array"
             },
             "primary_tumor_dimensional_measures": {
-               "$ref": "#/definitions/DimensionalObservationSet",
+               "$ref": "#/$defs/DimensionalObservationSet",
                "description": "Observations about the current physical dimensions of the primary tumor."
             },
             "prior_diagnosis": {
-               "$ref": "#/definitions/Diagnosis",
+               "$ref": "#/$defs/Diagnosis",
                "description": "A reference to a prior cancer diagnosis.  In the case of relapse/recurrent disease, this attribute may be populated with a reference to the initial diagnosis."
             },
             "related_specimen": {
                "description": "The specimen from which this diagnosis is made",
                "items": {
-                  "$ref": "#/definitions/Specimen"
+                  "$ref": "#/$defs/Specimen"
                },
                "type": "array"
             },
             "stage": {
                "description": "The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body.",
                "items": {
-                  "$ref": "#/definitions/CancerStageObservationSet"
+                  "$ref": "#/$defs/CancerStageObservationSet"
                },
                "type": "array"
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The subject of this diagnosis."
             },
             "supporting_observation": {
                "description": "One or more observations that capture information relevant to this condition or diagnosis.",
                "items": {
-                  "$ref": "#/definitions/Observation"
+                  "$ref": "#/$defs/Observation"
                },
                "type": "array"
-            },
-            "year_at_diagnosis": {
-               "description": "Numeric value to represent the year of an individual's diagnosis.",
-               "type": "integer"
             }
          },
          "required": [],
@@ -449,13 +457,13 @@
          "description": "A structured object that describes a single data item about the physical dimensions  of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHDimensionalObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHDimensionalObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -466,24 +474,24 @@
             "method_type": {
                "description": "A type of method used in generating the Observation result.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHDimensionalObservationMethodType"
+                  "$ref": "#/$defs/EnumCRDCHDimensionalObservationMethodType"
                },
                "type": "array"
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHDimensionalObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHDimensionalObservationObservationType",
                "description": "The specific type of observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             }
          },
@@ -499,13 +507,13 @@
          "description": "A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area).",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHDimensionalObservationSetCategory",
+               "$ref": "#/$defs/EnumCRDCHDimensionalObservationSetCategory",
                "description": "The general category of observation set described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -516,23 +524,23 @@
             "method_type": {
                "description": "A type of method used in generating each of the Observations bundled in the set.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHDimensionalObservationSetMethodType"
+                  "$ref": "#/$defs/EnumCRDCHDimensionalObservationSetMethodType"
                },
                "type": "array"
             },
             "observations": {
                "description": "A set of one or more more atomic observations that are conceptually or logically related - e.g. two components of some compound measurement (e.g. the systolic and diastolic components of a blood pressure measurement), or a panel of related measurements run and interpreted together on the same subject/specimen (e.g. a blood panel, or separate dimensional measurements of a specimen).",
                "items": {
-                  "$ref": "#/definitions/DimensionalObservation"
+                  "$ref": "#/$defs/DimensionalObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             }
          },
@@ -549,11 +557,11 @@
                "type": "string"
             },
             "document_type": {
-               "$ref": "#/definitions/EnumCRDCHDocumentDocumentType",
+               "$ref": "#/$defs/EnumCRDCHDocumentDocumentType",
                "description": "The high-level type of the document (e.g.  'publication', 'pathology report')"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity that the report is primarily about"
             },
             "id": {
@@ -563,7 +571,7 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
@@ -5817,18 +5825,10 @@
          "title": "EnumCRDCHSpecimenDegreeOfDysplasia",
          "type": "string"
       },
-      "EnumCRDCHSpecimenGeneralTissueMorphology": {
-         "description": "Autogenerated Enumeration for CRDC-H Specimen general_tissue_morphology",
-         "enum": [
-            "Peritumoral",
-            "Abnormal",
-            "Normal",
-            "Not Allowed To Collect",
-            "Unknown",
-            "Tumor",
-            "Not Reported"
-         ],
-         "title": "EnumCRDCHSpecimenGeneralTissueMorphology",
+      "EnumCRDCHSpecimenGeneralTissuePathology": {
+         "description": "Autogenerated Enumeration for CRDC-H Specimen general_tissue_pathology",
+         "enum": [],
+         "title": "EnumCRDCHSpecimenGeneralTissuePathology",
          "type": "string"
       },
       "EnumCRDCHSpecimenMorphologyAssessmentMethod": {
@@ -5863,7 +5863,7 @@
       "EnumCRDCHSpecimenProcessingActivityMethodType": {
          "description": "A type of method used to process a specimen (e.g. freezing, fixing, treating, preserving, labeling, etc.).",
          "enum": [
-            "-80",
+            "Minues 80 Degrees Celsius Freezer",
             "-20",
             "LN2",
             "isopentane"
@@ -6018,67 +6018,16 @@
          "title": "EnumCRDCHSpecimenSourceMaterialType",
          "type": "string"
       },
-      "EnumCRDCHSpecimenSpecificTissueMorphology": {
-         "description": "Autogenerated Enumeration for CRDC-H Specimen specific_tissue_morphology",
-         "enum": [
-            "61",
-            "70",
-            "30",
-            "63",
-            "71",
-            "51",
-            "80",
-            "02",
-            "65",
-            "04",
-            "60",
-            "03",
-            "50",
-            "52",
-            "15",
-            "10",
-            "00",
-            "01",
-            "21",
-            "20",
-            "62",
-            "40",
-            "64",
-            "81",
-            "41",
-            "Rhabdoid tumor (kidney) (RT)",
-            "Acute myeloid leukemia (AML)",
-            "Anal Cancer (all types)",
-            "Non cancerous tissue",
-            "CNS, low grade glioma (LGG)",
-            "Lung Cancer (all types)",
-            "CNS, ependymoma",
-            "Rhabdomyosarcoma",
-            "Induction Failure AML (AML-IF)",
-            "Soft tissue sarcoma, non-rhabdomyosarcoma",
-            "NHL, Burkitt lymphoma (BL)",
-            "Neuroblastoma (NBL)",
-            "Diffuse Large B-Cell Lymphoma (DLBCL)",
-            "Acute lymphoblastic leukemia (ALL)",
-            "CNS, rhabdoid tumor",
-            "CNS, medulloblastoma",
-            "Cervical Cancer (all types)",
-            "NHL, anaplastic large cell lymphoma",
-            "Clear cell sarcoma of the kidney (CCSK)",
-            "CNS, glioblastoma (GBM)",
-            "Acute Leukemia of Ambiguous Lineage (ALAL)",
-            "CNS, other",
-            "Ewing sarcoma",
-            "Osteosarcoma (OS)",
-            "Wilms tumor (WT)"
-         ],
-         "title": "EnumCRDCHSpecimenSpecificTissueMorphology",
+      "EnumCRDCHSpecimenSpecificTissuePathology": {
+         "description": "Autogenerated Enumeration for CRDC-H Specimen specific_tissue_pathology",
+         "enum": [],
+         "title": "EnumCRDCHSpecimenSpecificTissuePathology",
          "type": "string"
       },
       "EnumCRDCHSpecimenSpecimenType": {
          "description": "A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source).",
          "enum": [
-            "initial sample",
+            "Fresh Specimen",
             "portion",
             "aliquot",
             "analyte",
@@ -10945,11 +10894,11 @@
          "description": "A structured object that describes a single data item about an individual's exposure to an environmental factor, as generated through a point-in-time observation, measurement, or interpretation.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHEnvironmentalExposureObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHEnvironmentalExposureObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -10957,23 +10906,23 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHEnvironmentalExposureObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHEnvironmentalExposureObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHEnvironmentalExposureObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHEnvironmentalExposureObservationObservationType",
                "description": "The specific type of environmental exposure observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHEnvironmentalExposureObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHEnvironmentalExposureObservationValueCodeableConcept",
                "description": "The result of the observation, encoded as a CodeableConcept."
             }
          },
@@ -10989,11 +10938,11 @@
          "description": "A structured object that describes how long certain parts on an activity took to complete, as determined through a point-in-time observation or measurement.\n\nInformation describing the environmental conditions in which an activity, or a specific part of an activity, was performed.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHExecutionConditionObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHExecutionConditionObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -11001,23 +10950,23 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHExecutionConditionObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHExecutionConditionObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHExecutionConditionObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHExecutionConditionObservationObservationType",
                "description": "The specific type of environmental exposure observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHExecutionConditionObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHExecutionConditionObservationValueCodeableConcept",
                "description": "The result of the observation, encoded as a CodeableConcept."
             }
          },
@@ -11033,11 +10982,11 @@
          "description": "A structured object that describes how long certain parts on an activity took to complete, as determined through a point-in-time observation or measurement.\n\nInformation describing the environmental conditions in which an activity, or a specific part of an activity, was performed.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHExecutionTimeObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHExecutionTimeObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -11045,23 +10994,23 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHExecutionTimeObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHExecutionTimeObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHExecutionTimeObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHExecutionTimeObservationObservationType",
                "description": "The specific type of environmental exposure observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             }
          },
@@ -11079,14 +11028,14 @@
             "alcohol_exposure": {
                "description": "Observations about an individual's exposure to alcohol.",
                "items": {
-                  "$ref": "#/definitions/AlcoholExposureObservation"
+                  "$ref": "#/$defs/AlcoholExposureObservation"
                },
                "type": "array"
             },
             "environmental_exposure": {
                "description": "Observations about an individual's exposure to environmental substances that may impact clinical outcomes.",
                "items": {
-                  "$ref": "#/definitions/EnvironmentalExposureObservation"
+                  "$ref": "#/$defs/EnvironmentalExposureObservation"
                },
                "type": "array"
             },
@@ -11097,18 +11046,18 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "A reference to the Subject that is the subject of this Exposure"
             },
             "tobacco_exposure": {
                "description": "Observations about an individual's exposure to tobacco.",
                "items": {
-                  "$ref": "#/definitions/TobaccoExposureObservation"
+                  "$ref": "#/$defs/TobaccoExposureObservation"
                },
                "type": "array"
             }
@@ -11124,13 +11073,13 @@
          "description": "An observation about characteristics of a specimen at a microscopic level - typically related to its cellular or tissue composition. (e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype).",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHHistologicalCompositionObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHHistologicalCompositionObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11141,24 +11090,24 @@
             "method_type": {
                "description": "A type of method used in generating the Observation result.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHHistologicalCompositionObservationMethodType"
+                  "$ref": "#/$defs/EnumCRDCHHistologicalCompositionObservationMethodType"
                },
                "type": "array"
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHHistologicalCompositionObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHHistologicalCompositionObservationObservationType",
                "description": "The specific type of observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             }
          },
@@ -11174,13 +11123,13 @@
          "description": "A set of one or more discrete observations that quantify the relative or absolute composition of a specimen at cellular level - e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHHistologicalCompositionObservationSetCategory",
+               "$ref": "#/$defs/EnumCRDCHHistologicalCompositionObservationSetCategory",
                "description": "The general category of observation set described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11191,23 +11140,23 @@
             "method_type": {
                "description": "A type of method used in generating each of the Observations bundled in the set.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHHistologicalCompositionObservationSetMethodType"
+                  "$ref": "#/$defs/EnumCRDCHHistologicalCompositionObservationSetMethodType"
                },
                "type": "array"
             },
             "observations": {
                "description": "A set of one or more more atomic observations that are conceptually or logically related - e.g. two components of some compound measurement (e.g. the systolic and diastolic components of a blood pressure measurement), or a panel of related measurements run and interpreted together on the same subject/specimen (e.g. a blood panel, or separate dimensional measurements of a specimen).",
                "items": {
-                  "$ref": "#/definitions/HistologicalCompositionObservation"
+                  "$ref": "#/$defs/HistologicalCompositionObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             }
          },
@@ -11227,7 +11176,7 @@
                "type": "string"
             },
             "type": {
-               "$ref": "#/definitions/EnumCRDCHIdentifierType",
+               "$ref": "#/$defs/EnumCRDCHIdentifierType",
                "description": "A code that defines the type of the identifier."
             },
             "value": {
@@ -11246,13 +11195,13 @@
          "description": "A structured object that describes a single data item about an entity, as generated through a point-in-time observation, measurement, or interpretation.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11263,20 +11212,20 @@
             "method_type": {
                "description": "A type of method used in generating the Observation result.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHObservationMethodType"
+                  "$ref": "#/$defs/EnumCRDCHObservationMethodType"
                },
                "type": "array"
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHObservationObservationType",
                "description": "The specific type of observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_boolean": {
@@ -11284,7 +11233,7 @@
                "type": "boolean"
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHObservationValueCodeableConcept",
                "description": "The result of the observation, encoded as a CodeableConcept."
             },
             "value_date_time": {
@@ -11297,7 +11246,7 @@
                "type": "number"
             },
             "value_entity": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The value of an observation"
             },
             "value_integer": {
@@ -11305,7 +11254,7 @@
                "type": "number"
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             },
             "value_string": {
@@ -11324,13 +11273,13 @@
          "description": "A structured object to hold related data items about an entity, as generated through a point-in-time observation, measurement, or interpretation.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHObservationSetCategory",
+               "$ref": "#/$defs/EnumCRDCHObservationSetCategory",
                "description": "The general category of observation set described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11341,23 +11290,23 @@
             "method_type": {
                "description": "A type of method used in generating each of the Observations bundled in the set.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHObservationSetMethodType"
+                  "$ref": "#/$defs/EnumCRDCHObservationSetMethodType"
                },
                "type": "array"
             },
             "observations": {
                "description": "A set of one or more more atomic observations that are conceptually or logically related - e.g. two components of some compound measurement (e.g. the systolic and diastolic components of a blood pressure measurement), or a panel of related measurements run and interpreted together on the same subject/specimen (e.g. a blood panel, or separate dimensional measurements of a specimen).",
                "items": {
-                  "$ref": "#/definitions/Observation"
+                  "$ref": "#/$defs/Observation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             }
          },
@@ -11383,7 +11332,7 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
@@ -11407,11 +11356,11 @@
          "description": "A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit.",
          "properties": {
             "unit": {
-               "$ref": "#/definitions/EnumCRDCHQuantityUnit",
+               "$ref": "#/$defs/EnumCRDCHQuantityUnit",
                "description": "A coded or free text (in the .text field) representation of the unit."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHQuantityValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHQuantityValueCodeableConcept",
                "description": "A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\")"
             },
             "value_decimal": {
@@ -11430,16 +11379,16 @@
             "associated_timepoint": {
                "description": "A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.)",
                "items": {
-                  "$ref": "#/definitions/TimePoint"
+                  "$ref": "#/$defs/TimePoint"
                },
                "type": "array"
             },
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the research project ended."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the research project began."
             },
             "description": {
@@ -11457,7 +11406,7 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
@@ -11472,19 +11421,19 @@
             "part_of": {
                "description": "A reference to a parent ResearchProject (e.g. a link to the overarching CPTAC ResearchProject from a substudy of CPTAC)",
                "items": {
-                  "$ref": "#/definitions/ResearchProject"
+                  "$ref": "#/$defs/ResearchProject"
                },
                "type": "array"
             },
             "primary_anatomic_site": {
                "description": "The text term used to describe the general location of the malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).  In the context of ResearchProject, this attribute captures the anatomic sites of research interest.",
                "items": {
-                  "$ref": "#/definitions/BodySite"
+                  "$ref": "#/$defs/BodySite"
                },
                "type": "array"
             },
             "research_project_type": {
-               "$ref": "#/definitions/EnumCRDCHResearchProjectResearchProjectType",
+               "$ref": "#/$defs/EnumCRDCHResearchProjectResearchProjectType",
                "description": "The 'type' of ResearchProject represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study')"
             },
             "sponsor": {
@@ -11513,17 +11462,17 @@
          "description": "A research subject is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, \nor a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy.",
          "properties": {
             "age_at_enrollment": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The age in days when the Subject enrolled on the ResearchProject"
             },
             "associated_subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "A reference to the Subject that is this ResearchSubject"
             },
             "comorbid_diagnosis": {
                "description": "One or more diagnosis instance that are comorbid with the primary_diagnosis that qualified a subject for inclusion on a ResearchProject",
                "items": {
-                  "$ref": "#/definitions/Diagnosis"
+                  "$ref": "#/$defs/Diagnosis"
                },
                "type": "array"
             },
@@ -11538,35 +11487,35 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "index_timepoint": {
-               "$ref": "#/definitions/EnumCRDCHResearchSubjectIndexTimepoint",
+               "$ref": "#/$defs/EnumCRDCHResearchSubjectIndexTimepoint",
                "description": "The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date."
             },
             "member_of_research_project": {
-               "$ref": "#/definitions/ResearchProject",
+               "$ref": "#/$defs/ResearchProject",
                "description": "A reference to the Study(s) of which this ResearchSubject is a member"
             },
             "originating_site": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The Organization at which a subject was enrolled on a ResearchProject."
             },
             "primary_diagnosis": {
                "description": "The diagnosis instance that qualified a subject for inclusion on a ResearchProject",
                "items": {
-                  "$ref": "#/definitions/Diagnosis"
+                  "$ref": "#/$defs/Diagnosis"
                },
                "type": "array"
             },
             "primary_diagnosis_condition": {
-               "$ref": "#/definitions/EnumCRDCHResearchSubjectPrimaryDiagnosisCondition",
+               "$ref": "#/$defs/EnumCRDCHResearchSubjectPrimaryDiagnosisCondition",
                "description": "The text term used to describe the type of malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).   This attribute represents the disease that qualified the subject for inclusion on the ResearchProject"
             },
             "primary_diagnosis_site": {
-               "$ref": "#/definitions/BodySite",
+               "$ref": "#/$defs/BodySite",
                "description": "The text term used to describe the primary site of disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). This categorization groups cases into general categories.  This attribute represents the primary site of disease that qualified the subject for inclusion on the ResearchProject."
             }
          },
@@ -11582,37 +11531,37 @@
          "description": "Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation.",
          "properties": {
             "analyte_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenAnalyteType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenAnalyteType",
                "description": "For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA)"
             },
             "associated_project": {
-               "$ref": "#/definitions/ResearchProject",
+               "$ref": "#/$defs/ResearchProject",
                "description": "The Project associated with the specimen."
             },
             "cellular_composition_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenCellularCompositionType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenCellularCompositionType",
                "description": "A term describing the type of cell or cellular material comprising a specimen."
             },
             "contained_in": {
-               "$ref": "#/definitions/SpecimenContainer",
+               "$ref": "#/$defs/SpecimenContainer",
                "description": "A physical container in which a specimen is presently held or attached -  as storage for future use,  a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate)"
             },
             "creation_activity": {
-               "$ref": "#/definitions/SpecimenCreationActivity",
+               "$ref": "#/$defs/SpecimenCreationActivity",
                "description": "The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen."
             },
             "data_provider": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization (e.g.a laboratory, processing center, or research site) that provided data associated with a specimen."
             },
             "degree_of_dysplasia": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenDegreeOfDysplasia",
+               "$ref": "#/$defs/EnumCRDCHSpecimenDegreeOfDysplasia",
                "description": "A term describing the nature/extent of abnormal cells  that are not cancer, as observed upon microscopic assessment of a specimen. Records the degree of dysplasia for the cyst or lesion under consideration."
             },
             "derived_product": {
                "description": "A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid)",
                "items": {
-                  "$ref": "#/definitions/BiologicProduct"
+                  "$ref": "#/$defs/BiologicProduct"
                },
                "type": "array"
             },
@@ -11621,25 +11570,25 @@
                "type": "string"
             },
             "dimensional_measures": {
-               "$ref": "#/definitions/DimensionalObservationSet",
+               "$ref": "#/$defs/DimensionalObservationSet",
                "description": "Observations about the current physical dimensions of an object (e.g. length, width, area)."
             },
             "distance_from_paired_specimen": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The observed distance in the body of the specimen from a 'paired specimen' at the time of collection. (e.g. the distance between the in vivo location of a tumor tissue specimen and its paired normal specimen)"
             },
             "dysplasia_fraction": {
                "description": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces.",
                "type": "string"
             },
-            "general_tissue_morphology": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenGeneralTissueMorphology",
+            "general_tissue_pathology": {
+               "$ref": "#/$defs/EnumCRDCHSpecimenGeneralTissuePathology",
                "description": "The high-level kind of tissue collected when generating a specimen, based on its disease status or proximity to tumor tissue (e.g. is it normal, abnormal, tumor, tumor-adjacent)."
             },
             "histological_composition_measures": {
                "description": "A set of one or more observations that quantify the relative or absolute composition of a specimen at cellular level - e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype.",
                "items": {
-                  "$ref": "#/definitions/HistologicalCompositionObservationSet"
+                  "$ref": "#/$defs/HistologicalCompositionObservationSet"
                },
                "type": "array"
             },
@@ -11650,16 +11599,16 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "morphology_assessment_method": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenMorphologyAssessmentMethod",
+               "$ref": "#/$defs/EnumCRDCHSpecimenMorphologyAssessmentMethod",
                "description": "The general method used to assess a specimens specific tissue morphology"
             },
             "morphology_assessor_role": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenMorphologyAssessorRole",
+               "$ref": "#/$defs/EnumCRDCHSpecimenMorphologyAssessorRole",
                "description": "A term describing the role of the person who histologically assessed the specific tissue morphology of a specimen"
             },
             "morphology_pathologically_confirmed": {
@@ -11669,78 +11618,78 @@
             "parent_specimen": {
                "description": "An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen).",
                "items": {
-                  "$ref": "#/definitions/Specimen"
+                  "$ref": "#/$defs/Specimen"
                },
                "type": "array"
             },
             "preinvasive_tissue_morphology": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenPreinvasiveTissueMorphology",
+               "$ref": "#/$defs/EnumCRDCHSpecimenPreinvasiveTissueMorphology",
                "description": "A term describing the specific pathology exhibited by pre-invasive tissue comprising a specimen."
             },
             "processing_activity": {
                "description": "An activity that modifies the physical structure, composition, or state of a specimen.",
                "items": {
-                  "$ref": "#/definitions/SpecimenProcessingActivity"
+                  "$ref": "#/$defs/SpecimenProcessingActivity"
                },
                "type": "array"
             },
             "quality_measure": {
                "description": "An observation about characteristics of a specimen that are indicative of its quality or suitability for use.",
                "items": {
-                  "$ref": "#/definitions/SpecimenQualityObservation"
+                  "$ref": "#/$defs/SpecimenQualityObservation"
                },
                "type": "array"
             },
             "quantity_measure": {
                "description": "An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration.",
                "items": {
-                  "$ref": "#/definitions/SpecimenQuantityObservation"
+                  "$ref": "#/$defs/SpecimenQuantityObservation"
                },
                "type": "array"
             },
             "related_document": {
                "description": "A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected)",
                "items": {
-                  "$ref": "#/definitions/Document"
+                  "$ref": "#/$defs/Document"
                },
                "type": "array"
             },
             "section_location": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenSectionLocation",
+               "$ref": "#/$defs/EnumCRDCHSpecimenSectionLocation",
                "description": "The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom)"
             },
             "source_material_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenSourceMaterialType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenSourceMaterialType",
                "description": "The general kind of material from which the specimen was derived."
             },
             "source_subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "A specific Subject from which the specimen was directly or indirectly derived."
             },
-            "specific_tissue_morphology": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenSpecificTissueMorphology",
+            "specific_tissue_pathology": {
+               "$ref": "#/$defs/EnumCRDCHSpecimenSpecificTissuePathology",
                "description": "A term describing the specific pathology exhibited by the tissue comprising a specimen."
             },
             "specimen_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenSpecimenType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenSpecimenType",
                "description": "The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source)."
             },
             "storage_activity": {
                "description": "An activity that results in the storage or maintenance of a specimen in a particular location, container, or state.",
                "items": {
-                  "$ref": "#/definitions/SpecimenStorageActivity"
+                  "$ref": "#/$defs/SpecimenStorageActivity"
                },
                "type": "array"
             },
             "transport_activity": {
                "description": "An activity through which the specimen is transported between locations.",
                "items": {
-                  "$ref": "#/definitions/SpecimenTransportActivity"
+                  "$ref": "#/$defs/SpecimenTransportActivity"
                },
                "type": "array"
             },
             "tumor_status_at_collection": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenTumorStatusAtCollection",
+               "$ref": "#/$defs/EnumCRDCHSpecimenTumorStatusAtCollection",
                "description": "The status of the tumor at the time the specimen was collected (e.g. if it was primary, recurrent, metastatic, etc)."
             }
          },
@@ -11755,7 +11704,7 @@
             "additive": {
                "description": "A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth)",
                "items": {
-                  "$ref": "#/definitions/Substance"
+                  "$ref": "#/$defs/Substance"
                },
                "type": "array"
             },
@@ -11764,7 +11713,7 @@
                "type": "string"
             },
             "container_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenContainerContainerType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenContainerContainerType",
                "description": "The kind of the container."
             },
             "id": {
@@ -11774,12 +11723,12 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "parent_container": {
-               "$ref": "#/definitions/SpecimenContainer",
+               "$ref": "#/$defs/SpecimenContainer",
                "description": "A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part)"
             }
          },
@@ -11792,56 +11741,56 @@
          "description": "The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting).",
          "properties": {
             "activity_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenCreationActivityActivityType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenCreationActivityActivityType",
                "description": "The high-level type of creation activity."
             },
             "additive": {
                "description": "A type of material or reagent used applied as input when creating a specimen.",
                "items": {
-                  "$ref": "#/definitions/Substance"
+                  "$ref": "#/$defs/Substance"
                },
                "type": "array"
             },
             "collection_method_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenCreationActivityCollectionMethodType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenCreationActivityCollectionMethodType",
                "description": "The type of method applied in collecting a sample from its original source."
             },
             "collection_site": {
-               "$ref": "#/definitions/BodySite",
+               "$ref": "#/$defs/BodySite",
                "description": "The anatomic site from which a specimen was collected."
             },
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity ended (in this case, a specimen creation event)."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity began (in this case, a specimen creation event)."
             },
             "derivation_method_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenCreationActivityDerivationMethodType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenCreationActivityDerivationMethodType",
                "description": "The type of method applied to derive a new specimen from an existing one."
             },
             "execution_condition_observation": {
                "description": "Information describing the environmental conditions in which an activity, or a specific part of an activity, was performed.",
                "items": {
-                  "$ref": "#/definitions/ExecutionConditionObservation"
+                  "$ref": "#/$defs/ExecutionConditionObservation"
                },
                "type": "array"
             },
             "execution_time_observation": {
                "description": "Information describing how long certain parts on an activity took to complete.",
                "items": {
-                  "$ref": "#/definitions/ExecutionTimeObservation"
+                  "$ref": "#/$defs/ExecutionTimeObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the activity."
             },
             "quantity_collected": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing)"
             },
             "specimen_order": {
@@ -11858,51 +11807,51 @@
          "description": "An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen.",
          "properties": {
             "activity_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenProcessingActivityActivityType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenProcessingActivityActivityType",
                "description": "The high-level type of processing activity"
             },
             "additive": {
                "description": "A type of material or reagent used as input when processing the specimen",
                "items": {
-                  "$ref": "#/definitions/Substance"
+                  "$ref": "#/$defs/Substance"
                },
                "type": "array"
             },
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity began (in this case, a specimen processing event)."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity began (in this case, a specimen processing event)."
             },
             "duration": {
                "description": "The length of time over which the activity was performed.",
                "items": {
-                  "$ref": "#/definitions/Quantity"
+                  "$ref": "#/$defs/Quantity"
                },
                "type": "array"
             },
             "execution_condition_observation": {
                "description": "Information describing the environmental conditions in which an activity, or a specific part of an activity, was performed.",
                "items": {
-                  "$ref": "#/definitions/ExecutionConditionObservation"
+                  "$ref": "#/$defs/ExecutionConditionObservation"
                },
                "type": "array"
             },
             "execution_time_observation": {
                "description": "Information describing how long certain parts on an activity took to complete.",
                "items": {
-                  "$ref": "#/definitions/ExecutionTimeObservation"
+                  "$ref": "#/$defs/ExecutionTimeObservation"
                },
                "type": "array"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenProcessingActivityMethodType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenProcessingActivityMethodType",
                "description": "A specific type of method or procedure performed to process the specimen"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the activity."
             }
          },
@@ -11915,13 +11864,13 @@
          "description": "A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenQualityObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHSpecimenQualityObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11932,24 +11881,24 @@
             "method_type": {
                "description": "A type of method used in generating the Observation result.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHSpecimenQualityObservationMethodType"
+                  "$ref": "#/$defs/EnumCRDCHSpecimenQualityObservationMethodType"
                },
                "type": "array"
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenQualityObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenQualityObservationObservationType",
                "description": "The specific type of observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             }
          },
@@ -11965,13 +11914,13 @@
          "description": "A structured object that describes a single data item about the quantity of an entity, as generated through a point-in-time observation or measurement.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenQuantityObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHSpecimenQuantityObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
                "description": "The entity or entities directly observed/measured in generating an observation result.",
                "items": {
-                  "$ref": "#/definitions/Entity"
+                  "$ref": "#/$defs/Entity"
                },
                "type": "array"
             },
@@ -11982,24 +11931,24 @@
             "method_type": {
                "description": "A type of method used in generating the Observation result.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHSpecimenQuantityObservationMethodType"
+                  "$ref": "#/$defs/EnumCRDCHSpecimenQuantityObservationMethodType"
                },
                "type": "array"
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenQuantityObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenQuantityObservationObservationType",
                "description": "The specific type of observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The result of the observation, encoded as a free-text Quantity."
             }
          },
@@ -12017,28 +11966,28 @@
             "container": {
                "description": "A container in which the specimen is held or affixed during its storage.",
                "items": {
-                  "$ref": "#/definitions/SpecimenContainer"
+                  "$ref": "#/$defs/SpecimenContainer"
                },
                "type": "array"
             },
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity ended (in this case, a storage event)."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity began (in this case, a storage event)."
             },
             "duration": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The length of time over which the activity was performed."
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHSpecimenStorageActivityMethodType",
+               "$ref": "#/$defs/EnumCRDCHSpecimenStorageActivityMethodType",
                "description": "A specific type of method or procedure performed to store the specimen"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the activity."
             }
          },
@@ -12051,11 +12000,11 @@
          "description": "An activity through which a specimen is transported between locations or organizations.",
          "properties": {
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity ended (in this case, a transport event)."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The date when the activity began (in this case, a transport event)."
             },
             "duration": {
@@ -12068,20 +12017,20 @@
             "execution_condition_observation": {
                "description": "Information describing the environmental conditions in which an activity, or a specific part of an activity, was performed.",
                "items": {
-                  "$ref": "#/definitions/ExecutionConditionObservation"
+                  "$ref": "#/$defs/ExecutionConditionObservation"
                },
                "type": "array"
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the activity."
             },
             "transport_destination": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity."
             },
             "transport_origin": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity."
             }
          },
@@ -12094,19 +12043,19 @@
          "description": "Demographics and other administrative information about an individual or animal receiving care or other health-related services.",
          "properties": {
             "age_at_death": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The age of an individual at the time of death, expressed in days since birth"
             },
             "breed": {
-               "$ref": "#/definitions/EnumCRDCHSubjectBreed",
+               "$ref": "#/$defs/EnumCRDCHSubjectBreed",
                "description": "A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species."
             },
             "cause_of_death": {
-               "$ref": "#/definitions/EnumCRDCHSubjectCauseOfDeath",
+               "$ref": "#/$defs/EnumCRDCHSubjectCauseOfDeath",
                "description": "Coded value indicating the circumstance or condition that results in the death of the subject."
             },
             "ethnicity": {
-               "$ref": "#/definitions/EnumCRDCHSubjectEthnicity",
+               "$ref": "#/$defs/EnumCRDCHSubjectEthnicity",
                "description": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau"
             },
             "id": {
@@ -12116,27 +12065,27 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
             "race": {
                "description": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHSubjectRace"
+                  "$ref": "#/$defs/EnumCRDCHSubjectRace"
                },
                "type": "array"
             },
             "sex": {
-               "$ref": "#/definitions/EnumCRDCHSubjectSex",
+               "$ref": "#/$defs/EnumCRDCHSubjectSex",
                "description": "The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics."
             },
             "species": {
-               "$ref": "#/definitions/EnumCRDCHSubjectSpecies",
+               "$ref": "#/$defs/EnumCRDCHSubjectSpecies",
                "description": "The scientific binomial name for the species of the subject (e.g. Homo sapiens, Mus musculus, etc.)"
             },
             "vital_status": {
-               "$ref": "#/definitions/EnumCRDCHSubjectVitalStatus",
+               "$ref": "#/$defs/EnumCRDCHSubjectVitalStatus",
                "description": "Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown."
             },
             "year_of_birth": {
@@ -12161,16 +12110,16 @@
             "role": {
                "description": "A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing)",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHSubstanceRole"
+                  "$ref": "#/$defs/EnumCRDCHSubstanceRole"
                },
                "type": "array"
             },
             "substance_quantity": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "The quantity of substance this instance stands for."
             },
             "substance_type": {
-               "$ref": "#/definitions/EnumCRDCHSubstanceSubstanceType",
+               "$ref": "#/$defs/EnumCRDCHSubstanceSubstanceType",
                "description": "The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds."
             }
          },
@@ -12183,11 +12132,11 @@
          "description": "A period of time between a start and end time point.",
          "properties": {
             "period_end_end": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "When a period of time ended."
             },
             "period_start_start": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "When a period of time started."
             }
          },
@@ -12197,7 +12146,7 @@
       },
       "TimePoint": {
          "additionalProperties": false,
-         "description": "A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, or specification in terms of offset from a defined index.",
+         "description": "A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred.",
          "properties": {
             "date_time": {
                "description": "An explicitly specified timepoint described in terms of a date and optionally a time on that date.",
@@ -12207,7 +12156,7 @@
             "event_type": {
                "description": "An event that occurred at the point in time specified by this TimePoint.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHTimePointEventType"
+                  "$ref": "#/$defs/EnumCRDCHTimePointEventType"
                },
                "type": "array"
             },
@@ -12216,11 +12165,11 @@
                "type": "string"
             },
             "index_time_point": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "Another TimePoint from which this point is offset."
             },
             "offset_from_index": {
-               "$ref": "#/definitions/Quantity",
+               "$ref": "#/$defs/Quantity",
                "description": "A quantity of time that, together with the index date or event, can be used to derive a specific timepoint."
             }
          },
@@ -12233,11 +12182,11 @@
          "description": "A structured object that describes a single data item about an individual's exposure to tobacco, as generated through a point-in-time observation, measurement, or interpretation.",
          "properties": {
             "category": {
-               "$ref": "#/definitions/EnumCRDCHTobaccoExposureObservationCategory",
+               "$ref": "#/$defs/EnumCRDCHTobaccoExposureObservationCategory",
                "description": "The general category of observation described"
             },
             "focus": {
-               "$ref": "#/definitions/Entity",
+               "$ref": "#/$defs/Entity",
                "description": "The entity or entities directly observed/measured in generating an observation result."
             },
             "id": {
@@ -12245,23 +12194,23 @@
                "type": "string"
             },
             "method_type": {
-               "$ref": "#/definitions/EnumCRDCHTobaccoExposureObservationMethodType",
+               "$ref": "#/$defs/EnumCRDCHTobaccoExposureObservationMethodType",
                "description": "A type of method used in generating the Observation result."
             },
             "observation_type": {
-               "$ref": "#/definitions/EnumCRDCHTobaccoExposureObservationObservationType",
+               "$ref": "#/$defs/EnumCRDCHTobaccoExposureObservationObservationType",
                "description": "The specific type of tobacco exposure observation made - i.e. the feature or characteristic that was observed, measured, estimated, etc.."
             },
             "performed_by": {
-               "$ref": "#/definitions/Organization",
+               "$ref": "#/$defs/Organization",
                "description": "The organization or group that performed the observation activity."
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The patient that the observation is about (if not the direct focus).  e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest."
             },
             "value_codeable_concept": {
-               "$ref": "#/definitions/EnumCRDCHTobaccoExposureObservationValueCodeableConcept",
+               "$ref": "#/$defs/EnumCRDCHTobaccoExposureObservationValueCodeableConcept",
                "description": "The result of the observation, encoded as a CodeableConcept."
             },
             "value_integer": {
@@ -12282,16 +12231,16 @@
             "concurrent_treatment": {
                "description": "Treatment instance(s) that are concurrent with this treatment.",
                "items": {
-                  "$ref": "#/definitions/Treatment"
+                  "$ref": "#/$defs/Treatment"
                },
                "type": "array"
             },
             "date_ended": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The timepoint at which the treatment ended."
             },
             "date_started": {
-               "$ref": "#/definitions/TimePoint",
+               "$ref": "#/$defs/TimePoint",
                "description": "The timepoint at which the treatment started."
             },
             "id": {
@@ -12301,7 +12250,7 @@
             "identifier": {
                "description": "A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin.",
                "items": {
-                  "$ref": "#/definitions/Identifier"
+                  "$ref": "#/$defs/Identifier"
                },
                "type": "array"
             },
@@ -12310,53 +12259,53 @@
                "type": "integer"
             },
             "regimen": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentRegimen",
+               "$ref": "#/$defs/EnumCRDCHTreatmentRegimen",
                "description": "The regimen or line of therapy"
             },
             "subject": {
-               "$ref": "#/definitions/Subject",
+               "$ref": "#/$defs/Subject",
                "description": "The subject (person, animal, model system) to which the treatment was administered."
             },
             "therapeutic_agent": {
-               "$ref": "#/definitions/Substance",
+               "$ref": "#/$defs/Substance",
                "description": "One or more therapeutic agents that are administered as part of this treatment."
             },
             "treatment_anatomic_site": {
-               "$ref": "#/definitions/BodySite",
+               "$ref": "#/$defs/BodySite",
                "description": "The anatomical site that the treatment targets."
             },
             "treatment_effect": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentEffect",
+               "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentEffect",
                "description": "The effect of a treatment on the diagnosis or tumor."
             },
             "treatment_end_reason": {
                "description": "The reason the treatment ended.",
                "items": {
-                  "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentEndReason"
+                  "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentEndReason"
                },
                "type": "array"
             },
             "treatment_for_diagnosis": {
                "description": "The diagnosis for which this treatment is intended.",
                "items": {
-                  "$ref": "#/definitions/Diagnosis"
+                  "$ref": "#/$defs/Diagnosis"
                },
                "type": "array"
             },
             "treatment_frequency": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentFrequency",
+               "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentFrequency",
                "description": "The frequency of using the substance described by this instance."
             },
             "treatment_intent": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentIntent",
+               "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentIntent",
                "description": "The medical intent of the treatment."
             },
             "treatment_outcome": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentOutcome",
+               "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentOutcome",
                "description": "The final outcome of the treatment."
             },
             "treatment_type": {
-               "$ref": "#/definitions/EnumCRDCHTreatmentTreatmentType",
+               "$ref": "#/$defs/EnumCRDCHTreatmentTreatmentType",
                "description": "The type of treatment administered, which may include medication/therapeutics or other procedures."
             }
          },
@@ -12365,6 +12314,9 @@
          "type": "object"
       }
    },
+   "$id": "https://example.org/crdch",
+   "$schema": "http://json-schema.org/draft-07/schema#",
+   "additionalProperties": true,
    "properties": {},
    "title": "CRDC-H",
    "type": "object"
diff --git a/crdch_model/owl/crdch_model.owl.ttl b/crdch_model/owl/crdch_model.owl.ttl
index ae26de6be..cb0fa1554 100644
--- a/crdch_model/owl/crdch_model.owl.ttl
+++ b/crdch_model/owl/crdch_model.owl.ttl
@@ -9,13 +9,13 @@
 <https://example.org/crdch> a owl:Ontology ;
     rdfs:label "CRDC-H" ;
     dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
-    pav:version "v0.2-332-gbe05c1e6-dirty" ;
+    pav:version "v0.2-382-g582ae7f5" ;
     skos:editorialNote "Derived from [CDM_Dictionary_v1 (Active)](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4)" ;
-    linkml:generation_date "2021-09-07 17:12" ;
+    linkml:generation_date "2021-09-16 17:54" ;
     linkml:metamodel_version "1.7.0" ;
     linkml:source_file "crdch_model.yaml" ;
-    linkml:source_file_date "Tue Sep  7 17:08:55 2021" ;
-    linkml:source_file_size 1060548 .
+    linkml:source_file_date "Thu Sep 16 17:51:52 2021" ;
+    linkml:source_file_size 1059435 .
 
 <https://example.org/crdch/CrdchCode> a owl:Class,
         linkml:TypeDefinition ;
@@ -653,25 +653,43 @@ linkml:coding__system a owl:ObjectProperty,
     rdfs:label "coding__system" ;
     rdfs:domain <https://example.org/crdch/Coding> ;
     rdfs:range <https://example.org/crdch/CrdchString> ;
-    skos:definition "The code system where the code is defined." ;
+    skos:definition "The URL of the code system where the code is defined." ;
     skos:editorialNote "Cardinality: 1..1" ;
     linkml:examples "Example(value='', description=None)" .
 
-linkml:coding__systemURL a owl:ObjectProperty,
+linkml:coding__system_version a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "coding__systemURL" ;
+    rdfs:label "coding__system_version" ;
     rdfs:domain <https://example.org/crdch/Coding> ;
     rdfs:range <https://example.org/crdch/CrdchString> ;
-    skos:definition "A URL where the code system can be found." ;
+    skos:definition "The version of the code system." ;
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='', description=None)" .
 
-linkml:coding__systemVersion a owl:ObjectProperty,
+linkml:coding__tag a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "coding__systemVersion" ;
+    rdfs:label "coding__tag" ;
     rdfs:domain <https://example.org/crdch/Coding> ;
     rdfs:range <https://example.org/crdch/CrdchString> ;
-    skos:definition "The version of the code system." ;
+    skos:definition "original value  |  harmonized value  |" ;
+    skos:editorialNote "Cardinality: 0..m" ;
+    linkml:examples "Example(value='', description=None)" .
+
+linkml:coding__value_set a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "coding__value_set" ;
+    rdfs:domain <https://example.org/crdch/Coding> ;
+    rdfs:range <https://example.org/crdch/CrdchString> ;
+    skos:definition "The identifier of the enumeration / value set that the code is a part of in the context of this element" ;
+    skos:editorialNote "Cardinality: 0..1" ;
+    linkml:examples "Example(value='', description=None)" .
+
+linkml:coding__value_set_version a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "coding__value_set_version" ;
+    rdfs:domain <https://example.org/crdch/Coding> ;
+    rdfs:range <https://example.org/crdch/CrdchString> ;
+    skos:definition "The version of the enuemration / value set the code is pulled from" ;
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='', description=None)" .
 
@@ -694,6 +712,16 @@ linkml:diagnosis__condition a owl:ObjectProperty,
     skos:note "This attribute will subsume source attributes that are bound to ICD-O and ICD-10 classification systems." ;
     linkml:examples "Example(value='', description=None)" .
 
+linkml:diagnosis__diagnosis_date a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "diagnosis__diagnosis_date" ;
+    rdfs:domain <https://example.org/crdch/Diagnosis> ;
+    rdfs:range <https://example.org/crdch/TimePoint> ;
+    skos:definition "When the diagnosis was made." ;
+    skos:editorialNote "Cardinality: 0..1" ;
+    skos:note "A TimePoint object supports three ways to specify a point in time, each of which might be used in the context of capturing a diagnosis date - as source node data can report this date as an explicit year or date (e.g. 2021-05-05), or an offset from an indexed point in time. See description of the TimePoint entity for more information here. " ;
+    linkml:examples "Example(value='', description=None)" .
+
 linkml:diagnosis__disease_status a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "diagnosis__disease_status" ;
@@ -836,15 +864,6 @@ linkml:diagnosis__supporting_observation a owl:ObjectProperty,
     skos:editorialNote "Cardinality: 0..m" ;
     linkml:examples "Example(value='', description=None)" .
 
-linkml:diagnosis__year_at_diagnosis a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "diagnosis__year_at_diagnosis" ;
-    rdfs:domain <https://example.org/crdch/Diagnosis> ;
-    rdfs:range <https://example.org/crdch/CrdchInteger> ;
-    skos:definition "Numeric value to represent the year of an individual's diagnosis." ;
-    skos:editorialNote "Cardinality: 0..1" ;
-    linkml:examples "Example(value='', description=None)" .
-
 linkml:dimensionalObservationSet__category a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "dimensionalObservationSet__category" ;
@@ -2755,11 +2774,11 @@ linkml:specimen__dysplasia_fraction a owl:ObjectProperty,
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='', description=None)" .
 
-linkml:specimen__general_tissue_morphology a owl:ObjectProperty,
+linkml:specimen__general_tissue_pathology a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "specimen__general_tissue_morphology" ;
+    rdfs:label "specimen__general_tissue_pathology" ;
     rdfs:domain <https://example.org/crdch/Specimen> ;
-    rdfs:range <http://UNKNOWN.org/enum_CRDCH_Specimen_general_tissue_morphology> ;
+    rdfs:range <http://UNKNOWN.org/enum_CRDCH_Specimen_general_tissue_pathology> ;
     skos:definition "The high-level kind of tissue collected when generating a specimen, based on its disease status or proximity to tumor tissue (e.g. is it normal, abnormal, tumor, tumor-adjacent)." ;
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='Abnormal', description=None)",
@@ -2926,11 +2945,11 @@ linkml:specimen__source_subject a owl:ObjectProperty,
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='', description=None)" .
 
-linkml:specimen__specific_tissue_morphology a owl:ObjectProperty,
+linkml:specimen__specific_tissue_pathology a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "specimen__specific_tissue_morphology" ;
+    rdfs:label "specimen__specific_tissue_pathology" ;
     rdfs:domain <https://example.org/crdch/Specimen> ;
-    rdfs:range <http://UNKNOWN.org/enum_CRDCH_Specimen_specific_tissue_morphology> ;
+    rdfs:range <http://UNKNOWN.org/enum_CRDCH_Specimen_specific_tissue_pathology> ;
     skos:definition "A term describing the specific pathology exhibited by the tissue comprising a specimen." ;
     skos:editorialNote "Cardinality: 0..1" ;
     linkml:examples "Example(value='00', description=None)",
@@ -2953,7 +2972,7 @@ linkml:specimen__specimen_type a owl:ObjectProperty,
     skos:note "Our model defines a single 'Specimen' type to cover speific subtypes of specimens delineated in some CRDC node models (e.g. GDC 'Sample', 'Portion', 'Aliquot', 'Analyte', and 'Slide'). The 'specimen_type' field is used to indicate which subtype a given Specimen instance represents.  The enumerated values are meant to be mutually exclusive, such that only one can be applied to a given specimen." ;
     linkml:examples "Example(value='Aliquot', description=None)",
         "Example(value='Analyte', description=None)",
-        "Example(value='Initial Sample', description=None)",
+        "Example(value='Fresh Specimen', description=None)",
         "Example(value='Portion', description=None)",
         "Example(value='Slide', description=None)" .
 
@@ -3567,11 +3586,11 @@ linkml:Uriorcurie a owl:Class,
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:period_start_start ],
+            owl:onProperty linkml:period_end_end ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:period_end_end ],
+            owl:onProperty linkml:period_start_start ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A period of time between a start and end time point." ;
     skos:editorialNote "Derived from [TimePeriod in sheet TimePeriod](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1590126992)" .
@@ -3610,84 +3629,57 @@ linkml:String a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "Exposure" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/EnvironmentalExposureObservation> ;
-            owl:onProperty linkml:environmental_exposure ],
-        [ a owl:Restriction ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/TobaccoExposureObservation> ;
-            owl:onProperty linkml:tobacco_exposure ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/AlcoholExposureObservation> ;
-            owl:onProperty linkml:alcohol_exposure ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Identifier> ;
             owl:onProperty linkml:identifier ],
-        <https://example.org/crdch/Entity> ;
-    skos:definition "Contact between an agent and a target. A state of contact or close proximity to a medicinal product, chemical, pathogen, radioisotope or other substance." ;
-    skos:editorialNote "Derived from [Exposure in sheet Exposure](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1402410931)" .
-
-<https://example.org/crdch/Coding> a owl:Class,
-        linkml:ClassDefinition ;
-    rdfs:label "Coding" ;
-    rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:systemVersion ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:label ],
+            owl:allValuesFrom <https://example.org/crdch/TobaccoExposureObservation> ;
+            owl:onProperty linkml:tobacco_exposure ],
         [ a owl:Restriction ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:system ;
-            owl:qualifiedCardinality 1 ],
+            owl:allValuesFrom <https://example.org/crdch/EnvironmentalExposureObservation> ;
+            owl:onProperty linkml:environmental_exposure ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:code ;
+            owl:onProperty linkml:id ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:systemURL ],
+            owl:allValuesFrom <https://example.org/crdch/AlcoholExposureObservation> ;
+            owl:onProperty linkml:alcohol_exposure ],
         <https://example.org/crdch/Entity> ;
-    skos:definition "A structured representation of a coded/enumerated data value, that includes additional metadata about the code and code system." ;
-    skos:editorialNote "Derived from [Coding in sheet Coding](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1218588936)" .
+    skos:definition "Contact between an agent and a target. A state of contact or close proximity to a medicinal product, chemical, pathogen, radioisotope or other substance." ;
+    skos:editorialNote "Derived from [Exposure in sheet Exposure](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1402410931)" .
 
 <https://example.org/crdch/ObservationSet> a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ObservationSet" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_ObservationSet_method_type> ;
-            owl:onProperty linkml:method_type ],
+            owl:allValuesFrom <https://example.org/crdch/Observation> ;
+            owl:onProperty linkml:observations ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ;
-            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_ObservationSet_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ObservationSet_category> ;
             owl:onProperty linkml:category ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Observation> ;
-            owl:onProperty linkml:observations ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ;
+            owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object to hold related data items about an entity, as generated through a point-in-time observation, measurement, or interpretation." ;
     skos:editorialNote "Derived from [ObservationSet in sheet ObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1243450201)" ;
@@ -3697,11 +3689,18 @@ linkml:String a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "BiologicProduct" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
+        [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/CrdchInteger> ;
             owl:onProperty linkml:passage_number ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
+            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:growth_rate ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_BiologicProduct_product_type> ;
+            owl:onProperty linkml:product_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
@@ -3710,13 +3709,6 @@ linkml:String a owl:Class,
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:description ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_BiologicProduct_product_type> ;
-            owl:onProperty linkml:product_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:growth_rate ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro." ;
     skos:editorialNote "Derived from [BiologicProduct in sheet BiologicProduct](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1097989080)" .
@@ -3726,8 +3718,8 @@ linkml:String a owl:Class,
     rdfs:label "Document" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:description ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Document_document_type> ;
+            owl:onProperty linkml:document_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
@@ -3736,16 +3728,16 @@ linkml:String a owl:Class,
             owl:allValuesFrom <https://example.org/crdch/Identifier> ;
             owl:onProperty linkml:identifier ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Document_document_type> ;
-            owl:onProperty linkml:document_type ],
+            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:url ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:url ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:description ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A collection of information intented to be understood together as a whole, and codified in human-readable form." ;
     skos:editorialNote "Derived from [Document in sheet Document](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=809861603)" .
@@ -3754,13 +3746,20 @@ linkml:String a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "SpecimenStorageActivity" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/SpecimenContainer> ;
+            owl:onProperty linkml:container ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_ended ],
+            owl:onProperty linkml:date_started ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_started ],
+            owl:onProperty linkml:date_ended ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenStorageActivity_method_type> ;
@@ -3769,13 +3768,6 @@ linkml:String a owl:Class,
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:duration ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/SpecimenContainer> ;
-            owl:onProperty linkml:container ],
         <https://example.org/crdch/Entity> ;
     skos:definition """An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the 
 intrinsic physical nature of a specimen.""" ;
@@ -3786,13 +3778,25 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "CancerGradeObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservation_method_type> ;
             owl:onProperty linkml:method_type ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservation_observation_type> ;
             owl:onProperty linkml:observation_type ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservation_category> ;
@@ -3801,18 +3805,6 @@ intrinsic physical nature of a specimen.""" ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer grade observation" ;
     skos:editorialNote "Derived from [CancerGradeObservation in sheet CancerGradeObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1099484640)" .
@@ -3821,30 +3813,30 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "CancerGradeObservationSet" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservationSet_category> ;
+            owl:onProperty linkml:category ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservationSet_category> ;
-            owl:onProperty linkml:category ],
+            owl:allValuesFrom <https://example.org/crdch/CancerGradeObservation> ;
+            owl:onProperty linkml:observations ],
         [ a owl:Restriction ;
             owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_CancerGradeObservationSet_method_type> ;
             owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CancerGradeObservation> ;
-            owl:onProperty linkml:observations ],
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object to hold related data items about the grade of cancer (e.g. overall, primary gleason, secondary gleason, etc.)." ;
     skos:editorialNote "Derived from [CancerGradeObservationSet in sheet CancerGradeObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1025765903)" .
@@ -3853,74 +3845,111 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "CancerStageObservationSet" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservationSet_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/CancerStageObservation> ;
             owl:onProperty linkml:observations ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_CancerStageObservationSet_method_type> ;
             owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservationSet_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object to hold related data items about the staging of cancer (e.g. overall, T, N, and M components of a Cancer Staging observation)." ;
     skos:editorialNote "Derived from [CancerStageObservationSet in sheet CancerStageObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1668576212)" .
 
-<https://example.org/crdch/HistologicalCompositionObservationSet> a owl:Class,
+<https://example.org/crdch/Coding> a owl:Class,
         linkml:ClassDefinition ;
-    rdfs:label "HistologicalCompositionObservationSet" ;
+    rdfs:label "Coding" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:system ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservationSet_method_type> ;
-            owl:onProperty linkml:method_type ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:label ],
         [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ;
-            owl:qualifiedCardinality 1 ],
+            owl:onProperty linkml:system_version ],
         [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservationSet_category> ;
-            owl:onProperty linkml:category ;
-            owl:qualifiedCardinality 1 ],
+            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:tag ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/HistologicalCompositionObservation> ;
-            owl:onProperty linkml:observations ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:value_set_version ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:value_set ],
+        [ a owl:Restriction ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:code ;
+            owl:qualifiedCardinality 1 ],
         <https://example.org/crdch/Entity> ;
-    skos:definition "A set of one or more discrete observations that quantify the relative or absolute composition of a specimen at cellular level - e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype." ;
-    skos:editorialNote "Derived from [HistologicalCompositionObservationSet in sheet HistologicalCompositionObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=815777747)" ;
-    skos:note "An Observation Set is comprised of one or more logically related Observations made about the same entity. The Observations in a set may be grouped because they were generated on a single occasion using a common methodology (e.g. a blood panel), and/or or because describe aspects of the same underlying feature of an entity and as such are considered together as a logical unit of information (e.g. diastolic and systolic measures that comprise a blood pressure observation, or T, N, and M components of a Cancer Staging observation)." .
+    skos:definition "A structured representation of a coded/enumerated data value, that includes additional metadata about the code and code system." ;
+    skos:editorialNote "Derived from [Coding in sheet Coding](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1218588936)" .
 
-<https://example.org/crdch/SpecimenTransportActivity> a owl:Class,
+<https://example.org/crdch/HistologicalCompositionObservationSet> a owl:Class,
         linkml:ClassDefinition ;
-    rdfs:label "SpecimenTransportActivity" ;
+    rdfs:label "HistologicalCompositionObservationSet" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ;
+            owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:transport_destination ],
+            owl:onProperty linkml:performed_by ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/HistologicalCompositionObservation> ;
+            owl:onProperty linkml:observations ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservationSet_method_type> ;
+            owl:onProperty linkml:method_type ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservationSet_category> ;
+            owl:onProperty linkml:category ;
+            owl:qualifiedCardinality 1 ],
+        <https://example.org/crdch/Entity> ;
+    skos:definition "A set of one or more discrete observations that quantify the relative or absolute composition of a specimen at cellular level - e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype." ;
+    skos:editorialNote "Derived from [HistologicalCompositionObservationSet in sheet HistologicalCompositionObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=815777747)" ;
+    skos:note "An Observation Set is comprised of one or more logically related Observations made about the same entity. The Observations in a set may be grouped because they were generated on a single occasion using a common methodology (e.g. a blood panel), and/or or because describe aspects of the same underlying feature of an entity and as such are considered together as a logical unit of information (e.g. diastolic and systolic measures that comprise a blood pressure observation, or T, N, and M components of a Cancer Staging observation)." .
+
+<https://example.org/crdch/SpecimenTransportActivity> a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "SpecimenTransportActivity" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/ExecutionConditionObservation> ;
+            owl:onProperty linkml:execution_condition_observation ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
@@ -3928,21 +3957,18 @@ intrinsic physical nature of a specimen.""" ;
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:onProperty linkml:transport_destination ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
             owl:onProperty linkml:date_started ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:duration ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:transport_origin ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/ExecutionConditionObservation> ;
-            owl:onProperty linkml:execution_condition_observation ],
+            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:duration ],
         <https://example.org/crdch/Entity> ;
     skos:definition "An activity through which a specimen is transported between locations or organizations." ;
     skos:editorialNote "Derived from [SpecimenTransportActivity in sheet SpecimenTransportActivity](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=359352096)" ;
@@ -3952,16 +3978,21 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "DimensionalObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_DimensionalObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
-        [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:value_quantity ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_DimensionalObservation_category> ;
             owl:onProperty linkml:category ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_DimensionalObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
@@ -3970,17 +4001,12 @@ intrinsic physical nature of a specimen.""" ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_DimensionalObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_DimensionalObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a single data item about the physical dimensions  of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement." ;
     skos:editorialNote "Derived from [DimensionalObservation in sheet DimensionalObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1045447308)" ;
@@ -3991,16 +4017,8 @@ intrinsic physical nature of a specimen.""" ;
     rdfs:label "EnvironmentalExposureObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_category> ;
-            owl:onProperty linkml:category ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:onClass <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
@@ -4009,10 +4027,14 @@ intrinsic physical nature of a specimen.""" ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_method_type> ;
             owl:onProperty linkml:method_type ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_EnvironmentalExposureObservation_observation_type> ;
             owl:onProperty linkml:observation_type ;
@@ -4021,6 +4043,10 @@ intrinsic physical nature of a specimen.""" ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a single data item about an individual's exposure to an environmental factor, as generated through a point-in-time observation, measurement, or interpretation." ;
     skos:editorialNote "Derived from [EnvironmentalExposureObservation in sheet EnvironmentalExposureObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=274611680)" .
@@ -4029,35 +4055,35 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "HistologicalCompositionObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_category> ;
-            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:value_quantity ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_HistologicalCompositionObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "An observation about characteristics of a specimen at a microscopic level - typically related to its cellular or tissue composition. (e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype)." ;
     skos:editorialNote "Derived from [HistologicalCompositionObservation in sheet HistologicalCompositionObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1411171873)" .
@@ -4066,35 +4092,35 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "SpecimenQualityObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQualityObservation_category> ;
-            owl:onProperty linkml:category ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQualityObservation_observation_type> ;
             owl:onProperty linkml:observation_type ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQualityObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_SpecimenQualityObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:value_quantity ;
             owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_SpecimenQualityObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement." ;
     skos:editorialNote "Derived from [SpecimenQualityObservation in sheet SpecimenQualityObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=97281875)" .
@@ -4103,35 +4129,35 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "SpecimenQuantityObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
             owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_SpecimenQuantityObservation_method_type> ;
             owl:onProperty linkml:method_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:value_quantity ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQuantityObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQuantityObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQuantityObservation_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenQuantityObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a single data item about the quantity of an entity, as generated through a point-in-time observation or measurement." ;
     skos:editorialNote "Derived from [SpecimenQuantityObservation in sheet SpecimenQuantityObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=9917708)" ;
@@ -4142,40 +4168,40 @@ intrinsic physical nature of a specimen.""" ;
     rdfs:label "AlcoholExposureObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:value_integer ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchInteger> ;
+            owl:onProperty linkml:value_integer ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_AlcoholExposureObservation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a single data item about an individual's exposure to alcohol, as generated through a point-in-time observation, measurement, or interpretation." ;
     skos:editorialNote "Derived from [AlcoholExposureObservation in sheet AlcoholExposureObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1894439514)" .
@@ -4184,41 +4210,41 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "CancerStageObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:value_entity ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
+            owl:onClass <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_value_codeable_concept> ;
             owl:onProperty linkml:value_codeable_concept ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_CancerStageObservation_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:value_entity ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer staging observation, such as the Clinical Metastasis (M) component of a clinical TNM staging." ;
     skos:editorialNote "Derived from [CancerStageObservation in sheet CancerStageObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1189722404)" .
@@ -4227,30 +4253,30 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "DimensionalObservationSet" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_DimensionalObservationSet_category> ;
+            owl:onProperty linkml:category ],
+        [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/DimensionalObservation> ;
             owl:onProperty linkml:observations ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_DimensionalObservationSet_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_DimensionalObservationSet_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
             owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_DimensionalObservationSet_method_type> ;
-            owl:onProperty linkml:method_type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area)." ;
     skos:editorialNote "Derived from [DimensionalObservationSet in sheet DimensionalObservationSet](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1118507095)" .
@@ -4259,23 +4285,17 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "SpecimenProcessingActivity" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:date_started ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenProcessingActivity_method_type> ;
             owl:onProperty linkml:method_type ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
             owl:onProperty linkml:date_ended ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Substance> ;
-            owl:onProperty linkml:additive ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:duration ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenProcessingActivity_activity_type> ;
@@ -4283,13 +4303,19 @@ intrinsic physical nature of a specimen.""" ;
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/ExecutionConditionObservation> ;
             owl:onProperty linkml:execution_condition_observation ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Substance> ;
+            owl:onProperty linkml:additive ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:duration ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/ExecutionTimeObservation> ;
             owl:onProperty linkml:execution_time_observation ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_started ],
         <https://example.org/crdch/Entity> ;
     skos:definition "An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen." ;
     skos:editorialNote "Derived from [SpecimenProcessingActivity in sheet SpecimenProcessingActivity](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1726416617)" ;
@@ -4301,14 +4327,14 @@ intrinsic physical nature of a specimen.""" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_Substance_role> ;
             owl:onProperty linkml:role ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Substance_substance_type> ;
-            owl:onProperty linkml:substance_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:substance_quantity ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Substance_substance_type> ;
+            owl:onProperty linkml:substance_type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A type of material substance, or instance thereof,  as used in a particular application. May include information about the role the substance played in a particular application." ;
     skos:editorialNote "Derived from [Substance in sheet Substance](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=385534272)" .
@@ -4318,36 +4344,36 @@ intrinsic physical nature of a specimen.""" ;
     rdfs:label "TobaccoExposureObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:value_integer ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_method_type> ;
+            owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_observation_type> ;
             owl:onProperty linkml:observation_type ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_method_type> ;
-            owl:onProperty linkml:method_type ],
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ],
+            owl:onClass <https://example.org/crdch/CrdchInteger> ;
+            owl:onProperty linkml:value_integer ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_TobaccoExposureObservation_category> ;
+            owl:onProperty linkml:category ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
@@ -4360,17 +4386,13 @@ intrinsic physical nature of a specimen.""" ;
         linkml:ClassDefinition ;
     rdfs:label "ExecutionTimeObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionTimeObservation_category> ;
-            owl:onProperty linkml:category ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionTimeObservation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:focus ],
+        [ a owl:Restriction ;
+            owl:onClass <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:value_quantity ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Subject> ;
@@ -4379,18 +4401,22 @@ intrinsic physical nature of a specimen.""" ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
-            owl:onClass <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:value_quantity ;
-            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionTimeObservation_method_type> ;
             owl:onProperty linkml:method_type ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionTimeObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
+        [ a owl:Restriction ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionTimeObservation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         <https://example.org/crdch/Entity> ;
     skos:definition """A structured object that describes how long certain parts on an activity took to complete, as determined through a point-in-time observation or measurement.
 
@@ -4401,50 +4427,50 @@ Information describing the environmental conditions in which an activity, or a s
         linkml:ClassDefinition ;
     rdfs:label "ResearchSubject" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
-            owl:onProperty linkml:primary_diagnosis ],
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:age_at_enrollment ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/BodySite> ;
-            owl:onProperty linkml:primary_diagnosis_site ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:description ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
+            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
+            owl:onProperty linkml:comorbid_diagnosis ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:originating_site ],
+        [ a owl:Restriction ;
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:associated_subject ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
+            owl:onProperty linkml:primary_diagnosis ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/ResearchProject> ;
             owl:onProperty linkml:member_of_research_project ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ResearchSubject_index_timepoint> ;
-            owl:onProperty linkml:index_timepoint ],
-        [ a owl:Restriction ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:associated_subject ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:originating_site ],
+            owl:onClass <https://example.org/crdch/BodySite> ;
+            owl:onProperty linkml:primary_diagnosis_site ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ResearchSubject_primary_diagnosis_condition> ;
             owl:onProperty linkml:primary_diagnosis_condition ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:description ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
-            owl:onProperty linkml:comorbid_diagnosis ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ResearchSubject_index_timepoint> ;
+            owl:onProperty linkml:index_timepoint ],
         <https://example.org/crdch/Entity> ;
     skos:definition """A research subject is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, 
 or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject’s privacy.""" ;
@@ -4454,10 +4480,6 @@ or a tissue sample. Human research subjects are usually not traceable to a parti
         linkml:ClassDefinition ;
     rdfs:label "SpecimenContainer" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/SpecimenContainer> ;
             owl:onProperty linkml:parent_container ],
@@ -4469,6 +4491,10 @@ or a tissue sample. Human research subjects are usually not traceable to a parti
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:container_number ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Substance> ;
             owl:onProperty linkml:additive ],
@@ -4483,47 +4509,54 @@ or a tissue sample. Human research subjects are usually not traceable to a parti
         linkml:ClassDefinition ;
     rdfs:label "BodySite" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_BodySite_qualifier> ;
-            owl:onProperty linkml:qualifier ],
-        [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_BodySite_site> ;
             owl:onProperty linkml:site ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_BodySite_qualifier> ;
+            owl:onProperty linkml:qualifier ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A site in the body of an organism, typically described in terms of an anatomical location and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include 'non-anatomic' sites, such as the location of an implanted medical device." ;
     skos:editorialNote "Derived from [BodySite in sheet BodySite](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1097478901)" .
 
+<https://example.org/crdch/CrdchInteger> a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:label "crdch_integer" ;
+    rdfs:subClassOf linkml:Integer ;
+    skos:definition "An integer number.  This data type is based on the decimal type, but the fractional component is not allowed.  There are no restrictions on the size of the integer." ;
+    skos:editorialNote "Derived from [crdch_integer in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447)" .
+
 <https://example.org/crdch/ExecutionConditionObservation> a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ExecutionConditionObservation" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Organization> ;
             owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ;
-            owl:qualifiedCardinality 1 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_category> ;
-            owl:onProperty linkml:category ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_method_type> ;
             owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_observation_type> ;
             owl:onProperty linkml:observation_type ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_ExecutionConditionObservation_category> ;
+            owl:onProperty linkml:category ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Entity> ;
@@ -4538,50 +4571,50 @@ Information describing the environmental conditions in which an activity, or a s
         linkml:ClassDefinition ;
     rdfs:label "SpecimenCreationActivity" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_activity_type> ;
-            owl:onProperty linkml:activity_type ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_ended ],
+            owl:onProperty linkml:date_started ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Substance> ;
-            owl:onProperty linkml:additive ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:performed_by ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/ExecutionConditionObservation> ;
-            owl:onProperty linkml:execution_condition_observation ],
+            owl:allValuesFrom <https://example.org/crdch/ExecutionTimeObservation> ;
+            owl:onProperty linkml:execution_time_observation ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_started ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_activity_type> ;
+            owl:onProperty linkml:activity_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_derivation_method_type> ;
-            owl:onProperty linkml:derivation_method_type ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_collection_method_type> ;
+            owl:onProperty linkml:collection_method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/BodySite> ;
             owl:onProperty linkml:collection_site ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:date_ended ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:quantity_collected ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_collection_method_type> ;
-            owl:onProperty linkml:collection_method_type ],
+            owl:onClass <https://example.org/crdch/CrdchInteger> ;
+            owl:onProperty linkml:specimen_order ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:performed_by ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_SpecimenCreationActivity_derivation_method_type> ;
+            owl:onProperty linkml:derivation_method_type ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:specimen_order ],
+            owl:allValuesFrom <https://example.org/crdch/Substance> ;
+            owl:onProperty linkml:additive ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/ExecutionTimeObservation> ;
-            owl:onProperty linkml:execution_time_observation ],
+            owl:allValuesFrom <https://example.org/crdch/ExecutionConditionObservation> ;
+            owl:onProperty linkml:execution_condition_observation ],
         <https://example.org/crdch/Entity> ;
     skos:definition "The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting)." ;
     skos:editorialNote "Derived from [SpecimenCreationActivity in sheet SpecimenCreationActivity](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=693792130)" ;
@@ -4590,31 +4623,33 @@ Information describing the environmental conditions in which an activity, or a s
 linkml:topValue a owl:DatatypeProperty ;
     rdfs:label "value" .
 
-<https://example.org/crdch/CrdchInteger> a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "crdch_integer" ;
-    rdfs:subClassOf linkml:Integer ;
-    skos:definition "An integer number.  This data type is based on the decimal type, but the fractional component is not allowed.  There are no restrictions on the size of the integer." ;
-    skos:editorialNote "Derived from [crdch_integer in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447)" .
-
 <https://example.org/crdch/Observation> a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "Observation" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchBoolean> ;
-            owl:onProperty linkml:value_boolean ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:value_string ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Entity> ;
-            owl:onProperty linkml:focus ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Observation_observation_type> ;
+            owl:onProperty linkml:observation_type ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchDateTime> ;
-            owl:onProperty linkml:value_date_time ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchBoolean> ;
+            owl:onProperty linkml:value_boolean ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchDecimal> ;
             owl:onProperty linkml:value_integer ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Observation_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
@@ -4632,32 +4667,23 @@ linkml:topValue a owl:DatatypeProperty ;
             owl:onProperty linkml:method_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchDecimal> ;
-            owl:onProperty linkml:value_decimal ],
+            owl:onClass <https://example.org/crdch/CrdchDateTime> ;
+            owl:onProperty linkml:value_date_time ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:value_string ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:value_quantity ],
-        [ a owl:Restriction ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Observation_observation_type> ;
-            owl:onProperty linkml:observation_type ;
-            owl:qualifiedCardinality 1 ],
+            owl:allValuesFrom <https://example.org/crdch/Entity> ;
+            owl:onProperty linkml:focus ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Entity> ;
             owl:onProperty linkml:value_entity ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:onClass <https://example.org/crdch/CrdchDecimal> ;
+            owl:onProperty linkml:value_decimal ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Observation_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ],
+            owl:onClass <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:value_quantity ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object that describes a single data item about an entity, as generated through a point-in-time observation, measurement, or interpretation." ;
     skos:editorialNote "Derived from [Observation in sheet Observation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=550424063)" ;
@@ -4667,69 +4693,69 @@ linkml:topValue a owl:DatatypeProperty ;
         linkml:ClassDefinition ;
     rdfs:label "Treatment" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
+            owl:onProperty linkml:treatment_for_diagnosis ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_frequency> ;
+            owl:onProperty linkml:treatment_frequency ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/BodySite> ;
-            owl:onProperty linkml:treatment_anatomic_site ],
+            owl:onClass <https://example.org/crdch/CrdchInteger> ;
+            owl:onProperty linkml:number_of_cycles ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_started ],
+            owl:onProperty linkml:date_ended ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_outcome> ;
+            owl:onProperty linkml:treatment_outcome ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_regimen> ;
             owl:onProperty linkml:regimen ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Diagnosis> ;
-            owl:onProperty linkml:treatment_for_diagnosis ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:number_of_cycles ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_intent> ;
+            owl:onProperty linkml:treatment_intent ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_ended ],
+            owl:onProperty linkml:date_started ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Treatment> ;
-            owl:onProperty linkml:concurrent_treatment ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/BodySite> ;
+            owl:onProperty linkml:treatment_anatomic_site ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_outcome> ;
-            owl:onProperty linkml:treatment_outcome ],
+            owl:onClass <https://example.org/crdch/Substance> ;
+            owl:onProperty linkml:therapeutic_agent ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_frequency> ;
-            owl:onProperty linkml:treatment_frequency ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Substance> ;
-            owl:onProperty linkml:therapeutic_agent ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/Identifier> ;
             owl:onProperty linkml:identifier ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_intent> ;
-            owl:onProperty linkml:treatment_intent ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_effect> ;
+            owl:onProperty linkml:treatment_effect ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_type> ;
             owl:onProperty linkml:treatment_type ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_effect> ;
-            owl:onProperty linkml:treatment_effect ],
         [ a owl:Restriction ;
             owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_Treatment_treatment_end_reason> ;
             owl:onProperty linkml:treatment_end_reason ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Treatment> ;
+            owl:onProperty linkml:concurrent_treatment ],
         <https://example.org/crdch/Entity> ;
     skos:definition "Represent medication administration or other treatment types." ;
     skos:editorialNote "Derived from [Treatment in sheet Treatment](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=2111784779)" ;
@@ -4739,40 +4765,27 @@ linkml:topValue a owl:DatatypeProperty ;
         linkml:ClassDefinition ;
     rdfs:label "ResearchProject" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/BodySite> ;
-            owl:onProperty linkml:primary_anatomic_site ],
+            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:sponsor ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:name_shortened ],
+            owl:onProperty linkml:description ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:name ],
+            owl:allValuesFrom <https://example.org/crdch/BodySite> ;
+            owl:onProperty linkml:primary_anatomic_site ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/TimePoint> ;
             owl:onProperty linkml:date_ended ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/ResearchProject> ;
-            owl:onProperty linkml:part_of ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:sponsor ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:associated_timepoint ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:name_shortened ],
         [ a owl:Restriction ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_ResearchProject_research_project_type> ;
             owl:onProperty linkml:research_project_type ;
             owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:description ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
@@ -4782,12 +4795,25 @@ linkml:topValue a owl:DatatypeProperty ;
             owl:onProperty linkml:url ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:date_started ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:associated_timepoint ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:description_shortened ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:date_started ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/ResearchProject> ;
+            owl:onProperty linkml:part_of ],
         <https://example.org/crdch/Entity> ;
     skos:definition """A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. 
 This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional 
@@ -4802,66 +4828,66 @@ linkml:TypeDefinition a owl:Class ;
         linkml:ClassDefinition ;
     rdfs:label "Diagnosis" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/BodySite> ;
-            owl:onProperty linkml:primary_site ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CancerGradeObservationSet> ;
-            owl:onProperty linkml:grade ],
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:age_at_diagnosis ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_disease_status> ;
+            owl:onProperty linkml:disease_status ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:subject ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Observation> ;
-            owl:onProperty linkml:supporting_observation ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_morphology> ;
+            owl:onProperty linkml:morphology ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_condition> ;
             owl:onProperty linkml:condition ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:year_at_diagnosis ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:subject ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/BodySite> ;
+            owl:onProperty linkml:metastatic_site ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Specimen> ;
+            owl:onProperty linkml:related_specimen ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/CancerStageObservationSet> ;
+            owl:onProperty linkml:stage ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/CancerGradeObservationSet> ;
+            owl:onProperty linkml:grade ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Diagnosis> ;
             owl:onProperty linkml:prior_diagnosis ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_morphology> ;
-            owl:onProperty linkml:morphology ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Specimen> ;
-            owl:onProperty linkml:related_specimen ],
+            owl:onClass <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:age_at_diagnosis ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/BodySite> ;
-            owl:onProperty linkml:metastatic_site ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
+            owl:onProperty linkml:primary_site ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/CancerStageObservationSet> ;
-            owl:onProperty linkml:stage ],
+            owl:onClass <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:diagnosis_date ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_method_of_diagnosis> ;
             owl:onProperty linkml:method_of_diagnosis ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/DimensionalObservationSet> ;
-            owl:onProperty linkml:primary_tumor_dimensional_measures ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Observation> ;
+            owl:onProperty linkml:supporting_observation ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Diagnosis_disease_status> ;
-            owl:onProperty linkml:disease_status ],
+            owl:onClass <https://example.org/crdch/DimensionalObservationSet> ;
+            owl:onProperty linkml:primary_tumor_dimensional_measures ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A collection of characteristics that describe an abnormal condition of the body as assessed at a point in time. May be used to capture information about neoplastic and non-neoplastic conditions." ;
     skos:editorialNote "Derived from [Diagnosis in sheet Diagnosis](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1015759209)" .
@@ -4870,6 +4896,10 @@ linkml:TypeDefinition a owl:Class ;
         linkml:ClassDefinition ;
     rdfs:label "Identifier" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Identifier_type> ;
+            owl:onProperty linkml:type ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:system ],
@@ -4877,10 +4907,6 @@ linkml:TypeDefinition a owl:Class ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:value ;
             owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Identifier_type> ;
-            owl:onProperty linkml:type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "An Identifier is associated with a unique object or entity within a given system." ;
     skos:editorialNote "Derived from [Identifier in sheet Identifier](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1307792462)" ;
@@ -4891,16 +4917,16 @@ linkml:TypeDefinition a owl:Class ;
     rdfs:label "Quantity" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchDecimal> ;
-            owl:onProperty linkml:value_decimal ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Quantity_value_codeable_concept> ;
+            owl:onProperty linkml:value_codeable_concept ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Quantity_unit> ;
             owl:onProperty linkml:unit ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Quantity_value_codeable_concept> ;
-            owl:onProperty linkml:value_codeable_concept ],
+            owl:onClass <https://example.org/crdch/CrdchDecimal> ;
+            owl:onProperty linkml:value_decimal ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit." ;
     skos:editorialNote "Derived from [Quantity in sheet Quantity](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1941950611)" ;
@@ -4911,53 +4937,68 @@ linkml:TypeDefinition a owl:Class ;
     rdfs:label "Specimen" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Organization> ;
-            owl:onProperty linkml:data_provider ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_section_location> ;
+            owl:onProperty linkml:section_location ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_general_tissue_morphology> ;
-            owl:onProperty linkml:general_tissue_morphology ],
+            owl:onClass <https://example.org/crdch/Subject> ;
+            owl:onProperty linkml:source_subject ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/SpecimenQuantityObservation> ;
-            owl:onProperty linkml:quantity_measure ],
+            owl:allValuesFrom <https://example.org/crdch/HistologicalCompositionObservationSet> ;
+            owl:onProperty linkml:histological_composition_measures ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/BiologicProduct> ;
+            owl:onProperty linkml:derived_product ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Document> ;
+            owl:onProperty linkml:related_document ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Specimen> ;
+            owl:onProperty linkml:parent_specimen ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/ResearchProject> ;
-            owl:onProperty linkml:associated_project ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_specimen_type> ;
+            owl:onProperty linkml:specimen_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_preinvasive_tissue_morphology> ;
-            owl:onProperty linkml:preinvasive_tissue_morphology ],
+            owl:onClass <https://example.org/crdch/SpecimenCreationActivity> ;
+            owl:onProperty linkml:creation_activity ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchBoolean> ;
-            owl:onProperty linkml:morphology_pathologically_confirmed ],
+            owl:onClass <https://example.org/crdch/ResearchProject> ;
+            owl:onProperty linkml:associated_project ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_specific_tissue_morphology> ;
-            owl:onProperty linkml:specific_tissue_morphology ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:id ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:distance_from_paired_specimen ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_degree_of_dysplasia> ;
             owl:onProperty linkml:degree_of_dysplasia ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:dysplasia_fraction ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_cellular_composition_type> ;
+            owl:onProperty linkml:cellular_composition_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/SpecimenStorageActivity> ;
+            owl:onProperty linkml:storage_activity ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Subject> ;
-            owl:onProperty linkml:source_subject ],
+            owl:onClass <https://example.org/crdch/SpecimenContainer> ;
+            owl:onProperty linkml:contained_in ],
         [ a owl:Restriction ;
             owl:allValuesFrom <https://example.org/crdch/SpecimenProcessingActivity> ;
             owl:onProperty linkml:processing_activity ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_morphology_assessor_role> ;
-            owl:onProperty linkml:morphology_assessor_role ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/SpecimenStorageActivity> ;
-            owl:onProperty linkml:storage_activity ],
+            owl:allValuesFrom <https://example.org/crdch/SpecimenTransportActivity> ;
+            owl:onProperty linkml:transport_activity ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_morphology_assessment_method> ;
@@ -4967,70 +5008,55 @@ linkml:TypeDefinition a owl:Class ;
             owl:onProperty linkml:quality_measure ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_specimen_type> ;
-            owl:onProperty linkml:specimen_type ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_source_material_type> ;
+            owl:onProperty linkml:source_material_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/SpecimenQuantityObservation> ;
+            owl:onProperty linkml:quantity_measure ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/DimensionalObservationSet> ;
             owl:onProperty linkml:dimensional_measures ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_tumor_status_at_collection> ;
-            owl:onProperty linkml:tumor_status_at_collection ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/BiologicProduct> ;
-            owl:onProperty linkml:derived_product ],
+            owl:onClass <https://example.org/crdch/Organization> ;
+            owl:onProperty linkml:data_provider ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_section_location> ;
-            owl:onProperty linkml:section_location ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_general_tissue_pathology> ;
+            owl:onProperty linkml:general_tissue_pathology ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
+            owl:onClass <https://example.org/crdch/CrdchBoolean> ;
+            owl:onProperty linkml:morphology_pathologically_confirmed ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_source_material_type> ;
-            owl:onProperty linkml:source_material_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/HistologicalCompositionObservationSet> ;
-            owl:onProperty linkml:histological_composition_measures ],
+            owl:onClass <https://example.org/crdch/CrdchString> ;
+            owl:onProperty linkml:description ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/SpecimenCreationActivity> ;
-            owl:onProperty linkml:creation_activity ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Document> ;
-            owl:onProperty linkml:related_document ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_morphology_assessor_role> ;
+            owl:onProperty linkml:morphology_assessor_role ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_analyte_type> ;
-            owl:onProperty linkml:analyte_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/SpecimenTransportActivity> ;
-            owl:onProperty linkml:transport_activity ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Specimen> ;
-            owl:onProperty linkml:parent_specimen ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_specific_tissue_pathology> ;
+            owl:onProperty linkml:specific_tissue_pathology ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:description ],
+            owl:onProperty linkml:dysplasia_fraction ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_cellular_composition_type> ;
-            owl:onProperty linkml:cellular_composition_type ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_tumor_status_at_collection> ;
+            owl:onProperty linkml:tumor_status_at_collection ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/SpecimenContainer> ;
-            owl:onProperty linkml:contained_in ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_analyte_type> ;
+            owl:onProperty linkml:analyte_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:distance_from_paired_specimen ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Specimen_preinvasive_tissue_morphology> ;
+            owl:onProperty linkml:preinvasive_tissue_morphology ],
         <https://example.org/crdch/Entity> ;
     skos:definition "Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation." ;
     skos:editorialNote "Derived from [Specimen in sheet Specimen](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1439310281)" ;
@@ -5040,6 +5066,10 @@ linkml:TypeDefinition a owl:Class ;
         linkml:ClassDefinition ;
     rdfs:label "TimePoint" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <https://example.org/crdch/TimePoint> ;
+            owl:onProperty linkml:index_time_point ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchDateTime> ;
             owl:onProperty linkml:date_time ],
@@ -5050,17 +5080,14 @@ linkml:TypeDefinition a owl:Class ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/Quantity> ;
             owl:onProperty linkml:offset_from_index ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/TimePoint> ;
-            owl:onProperty linkml:index_time_point ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ],
         <https://example.org/crdch/Entity> ;
-    skos:definition "A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, or specification in terms of offset from a defined index." ;
-    skos:editorialNote "Derived from [TimePoint in sheet TimePoint](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=300932847)" .
+    skos:definition "A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred." ;
+    skos:editorialNote "Derived from [TimePoint in sheet TimePoint](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=300932847)" ;
+    skos:note "The TimePoint object supports three ways to specify a point in time. The date_time field is the most direct - capturing an explicit date (e.g. 2021-05-05). The paired fields index_time_point and  offset_from_index allows specification of a point in time as an offset from a related fixed time point.  Finally, the event_type field uses type of event as a proxy for the time point when the event occurred. " .
 
 linkml:ClassDefinition a owl:Class ;
     rdfs:label "class_definition" ;
@@ -5070,24 +5097,24 @@ linkml:ClassDefinition a owl:Class ;
         linkml:ClassDefinition ;
     rdfs:label "Organization" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:id ;
-            owl:qualifiedCardinality 1 ],
+            owl:onProperty linkml:name ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:alias ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:organization_type ],
+            owl:onProperty linkml:id ;
+            owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
-            owl:onProperty linkml:name ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
+            owl:onProperty linkml:organization_type ],
         <https://example.org/crdch/Entity> ;
     skos:definition "A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university" ;
     skos:editorialNote "Derived from [Organization in sheet Organization](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1477577710)" .
@@ -5097,27 +5124,34 @@ linkml:ClassDefinition a owl:Class ;
     rdfs:label "Subject" ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:year_of_birth ],
+            owl:onClass <https://example.org/crdch/Quantity> ;
+            owl:onProperty linkml:age_at_death ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_vital_status> ;
+            owl:onProperty linkml:vital_status ],
         [ a owl:Restriction ;
             owl:onClass <https://example.org/crdch/CrdchString> ;
             owl:onProperty linkml:id ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_cause_of_death> ;
-            owl:onProperty linkml:cause_of_death ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_sex> ;
+            owl:onProperty linkml:sex ],
         [ a owl:Restriction ;
-            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_Subject_race> ;
-            owl:onProperty linkml:race ],
+            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
+            owl:onProperty linkml:identifier ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <https://example.org/crdch/CrdchInteger> ;
-            owl:onProperty linkml:year_of_death ],
+            owl:onProperty linkml:year_of_birth ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_vital_status> ;
-            owl:onProperty linkml:vital_status ],
+            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_cause_of_death> ;
+            owl:onProperty linkml:cause_of_death ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom <http://UNKNOWN.org/enum_CRDCH_Subject_race> ;
+            owl:onProperty linkml:race ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_species> ;
@@ -5128,19 +5162,12 @@ linkml:ClassDefinition a owl:Class ;
             owl:onProperty linkml:breed ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_sex> ;
-            owl:onProperty linkml:sex ],
+            owl:onClass <https://example.org/crdch/CrdchInteger> ;
+            owl:onProperty linkml:year_of_death ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass <http://UNKNOWN.org/enum_CRDCH_Subject_ethnicity> ;
             owl:onProperty linkml:ethnicity ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass <https://example.org/crdch/Quantity> ;
-            owl:onProperty linkml:age_at_death ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom <https://example.org/crdch/Identifier> ;
-            owl:onProperty linkml:identifier ],
         <https://example.org/crdch/Entity> ;
     skos:definition "Demographics and other administrative information about an individual or animal receiving care or other health-related services." ;
     skos:editorialNote "Derived from [Subject in sheet Subject](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1651956379)" .
diff --git a/crdch_model/shex/crdch_model.shex b/crdch_model/shex/crdch_model.shex
index b96ac27e8..1b0fce186 100644
--- a/crdch_model/shex/crdch_model.shex
+++ b/crdch_model/shex/crdch_model.shex
@@ -165,8 +165,10 @@ linkml:Nodeidentifier NONLITERAL
           <code> @<CrdchString> ;
           <label> @<CrdchString> ? ;
           <system> @<CrdchString> ;
-          <system_url> @<CrdchString> ? ;
-          <system_version> @<CrdchString> ?
+          <system_version> @<CrdchString> ? ;
+          <value_set> @<CrdchString> ? ;
+          <value_set_version> @<CrdchString> ? ;
+          <tag> @<CrdchString> *
        ) ;
        rdf:type [ <Coding> ] ?
     )
@@ -490,8 +492,8 @@ linkml:Nodeidentifier NONLITERAL
           <quality_measure> @<SpecimenQualityObservation> * ;
           <cellular_composition_type> @<EnumCRDCHSpecimenCellularCompositionType> ? ;
           <histological_composition_measures> @<HistologicalCompositionObservationSet> * ;
-          <general_tissue_morphology> @<EnumCRDCHSpecimenGeneralTissueMorphology> ? ;
-          <specific_tissue_morphology> @<EnumCRDCHSpecimenSpecificTissueMorphology> ? ;
+          <general_tissue_pathology> @<EnumCRDCHSpecimenGeneralTissuePathology> ? ;
+          <specific_tissue_pathology> @<EnumCRDCHSpecimenSpecificTissuePathology> ? ;
           <preinvasive_tissue_morphology> @<EnumCRDCHSpecimenPreinvasiveTissueMorphology> ? ;
           <morphology_pathologically_confirmed> @<CrdchBoolean> ? ;
           <morphology_assessor_role> @<EnumCRDCHSpecimenMorphologyAssessorRole> ? ;
diff --git a/crdch_model/shex/crdch_model.shexj b/crdch_model/shex/crdch_model.shexj
index d46f14b17..7bb83f62b 100644
--- a/crdch_model/shex/crdch_model.shexj
+++ b/crdch_model/shex/crdch_model.shexj
@@ -813,17 +813,31 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/system_url",
+                        "predicate": "https://example.org/crdch/system_version",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/system_version",
+                        "predicate": "https://example.org/crdch/value_set",
+                        "valueExpr": "https://example.org/crdch/CrdchString",
+                        "min": 0,
+                        "max": 1
+                     },
+                     {
+                        "type": "TripleConstraint",
+                        "predicate": "https://example.org/crdch/value_set_version",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
+                     },
+                     {
+                        "type": "TripleConstraint",
+                        "predicate": "https://example.org/crdch/tag",
+                        "valueExpr": "https://example.org/crdch/CrdchString",
+                        "min": 0,
+                        "max": -1
                      }
                   ]
                },
@@ -2743,15 +2757,15 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/general_tissue_morphology",
-                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenGeneralTissueMorphology",
+                        "predicate": "https://example.org/crdch/general_tissue_pathology",
+                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenGeneralTissuePathology",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/specific_tissue_morphology",
-                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenSpecificTissueMorphology",
+                        "predicate": "https://example.org/crdch/specific_tissue_pathology",
+                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenSpecificTissuePathology",
                         "min": 0,
                         "max": 1
                      },

From 19dbf8838ac1e3b0ded0723333dbacdc83cac632 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 30 Sep 2021 01:49:45 -0400
Subject: [PATCH 8/9] Removed SaferDraft...Validator.

My reading of https://json-schema.org/understanding-json-schema/structuring.html#ref
makes me think that other keywords in `$ref` should be ignored by the
validator, but this raises an error with the SaferDraft...Validator. So
I'm going to remove it for now.
---
 tests/test_validate_artifacts.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tests/test_validate_artifacts.py b/tests/test_validate_artifacts.py
index 8c2a2dc35..f44376af4 100644
--- a/tests/test_validate_artifacts.py
+++ b/tests/test_validate_artifacts.py
@@ -24,12 +24,8 @@ def test_validate_json_schema(self):
 
             assert_that(json_schema).is_not_empty()
 
-            # Idea from https://github.com/Julian/jsonschema/issues/348#issuecomment-647418176
-            class SaferDraft202012Validator(jsonschema.Draft202012Validator):
-                META_SCHEMA = {**jsonschema.Draft202012Validator.META_SCHEMA, "additionalProperties": False}
-
             try:
-                SaferDraft202012Validator.check_schema(json_schema)
+                jsonschema.Draft202012Validator.check_schema(json_schema)
             except jsonschema.exceptions.SchemaError as e:
                 fail(f'JSON Schema {json_schema_file_path} is not a valid JSON Schema: {e}')
 

From 6d4890b7e8c80014626f8fb653f92d8094202298 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 30 Sep 2021 01:51:41 -0400
Subject: [PATCH 9/9] Updated Pipfile.lock to include assertpy.

---
 Pipfile.lock | 380 ++++++++++++++++++++++++++-------------------------
 1 file changed, 191 insertions(+), 189 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 2de04bfd9..8650d38c8 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -52,11 +52,11 @@
         },
         "cachetools": {
             "hashes": [
-                "sha256:2cc0b89715337ab6dbba85b5b50effe2b0c74e035d83ee8ed637cf52f12ae001",
-                "sha256:61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff"
+                "sha256:0a3d3556c2c3befdbba2f93b78792c199c66201c999e97947ea0b7437758246b",
+                "sha256:6a6fa6802188ab7e77bab2db001d676e854499552b0037d999d5b9f211db5250"
             ],
             "markers": "python_version ~= '3.5'",
-            "version": "==4.2.2"
+            "version": "==4.2.3"
         },
         "certifi": {
             "hashes": [
@@ -73,11 +73,11 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:7098e7e862f6370a2a8d1a6398cd359815c45d12626267652c3f13dec58e2367",
-                "sha256:fa471a601dfea0f492e4f4fca035cd82155e65dc45c9b83bf4322dfab63755dd"
+                "sha256:5d209c0a931f215cee683b6445e2d77677e7e75e159f78def0db09d68fafcaa6",
+                "sha256:5ec46d183433dcbd0ab716f2d7f29d8dee50505b3fdb40c6b985c7c4f5a3591f"
             ],
             "markers": "python_version >= '3'",
-            "version": "==2.0.5"
+            "version": "==2.0.6"
         },
         "click": {
             "hashes": [
@@ -129,59 +129,59 @@
         },
         "greenlet": {
             "hashes": [
-                "sha256:04e1849c88aa56584d4a0a6e36af5ec7cc37993fdc1fda72b56aa1394a92ded3",
-                "sha256:05e72db813c28906cdc59bd0da7c325d9b82aa0b0543014059c34c8c4ad20e16",
-                "sha256:07e6d88242e09b399682b39f8dfa1e7e6eca66b305de1ff74ed9eb1a7d8e539c",
-                "sha256:090126004c8ab9cd0787e2acf63d79e80ab41a18f57d6448225bbfcba475034f",
-                "sha256:1796f2c283faab2b71c67e9b9aefb3f201fdfbee5cb55001f5ffce9125f63a45",
-                "sha256:2f89d74b4f423e756a018832cd7a0a571e0a31b9ca59323b77ce5f15a437629b",
-                "sha256:34e6675167a238bede724ee60fe0550709e95adaff6a36bcc97006c365290384",
-                "sha256:3e594015a2349ec6dcceda9aca29da8dc89e85b56825b7d1f138a3f6bb79dd4c",
-                "sha256:3f8fc59bc5d64fa41f58b0029794f474223693fd00016b29f4e176b3ee2cfd9f",
-                "sha256:3fc6a447735749d651d8919da49aab03c434a300e9f0af1c886d560405840fd1",
-                "sha256:40abb7fec4f6294225d2b5464bb6d9552050ded14a7516588d6f010e7e366dcc",
-                "sha256:44556302c0ab376e37939fd0058e1f0db2e769580d340fb03b01678d1ff25f68",
-                "sha256:476ba9435afaead4382fbab8f1882f75e3fb2285c35c9285abb3dd30237f9142",
-                "sha256:4870b018ca685ff573edd56b93f00a122f279640732bb52ce3a62b73ee5c4a92",
-                "sha256:4adaf53ace289ced90797d92d767d37e7cdc29f13bd3830c3f0a561277a4ae83",
-                "sha256:4eae94de9924bbb4d24960185363e614b1b62ff797c23dc3c8a7c75bbb8d187e",
-                "sha256:5317701c7ce167205c0569c10abc4bd01c7f4cf93f642c39f2ce975fa9b78a3c",
-                "sha256:5c3b735ccf8fc8048664ee415f8af5a3a018cc92010a0d7195395059b4b39b7d",
-                "sha256:5cde7ee190196cbdc078511f4df0be367af85636b84d8be32230f4871b960687",
-                "sha256:655ab836324a473d4cd8cf231a2d6f283ed71ed77037679da554e38e606a7117",
-                "sha256:6ce9d0784c3c79f3e5c5c9c9517bbb6c7e8aa12372a5ea95197b8a99402aa0e6",
-                "sha256:6e0696525500bc8aa12eae654095d2260db4dc95d5c35af2b486eae1bf914ccd",
-                "sha256:75ff270fd05125dce3303e9216ccddc541a9e072d4fc764a9276d44dee87242b",
-                "sha256:8039f5fe8030c43cd1732d9a234fdcbf4916fcc32e21745ca62e75023e4d4649",
-                "sha256:84488516639c3c5e5c0e52f311fff94ebc45b56788c2a3bfe9cf8e75670f4de3",
-                "sha256:84782c80a433d87530ae3f4b9ed58d4a57317d9918dfcc6a59115fa2d8731f2c",
-                "sha256:8ddb38fb6ad96c2ef7468ff73ba5c6876b63b664eebb2c919c224261ae5e8378",
-                "sha256:98b491976ed656be9445b79bc57ed21decf08a01aaaf5fdabf07c98c108111f6",
-                "sha256:990e0f5e64bcbc6bdbd03774ecb72496224d13b664aa03afd1f9b171a3269272",
-                "sha256:9b02e6039eafd75e029d8c58b7b1f3e450ca563ef1fe21c7e3e40b9936c8d03e",
-                "sha256:a11b6199a0b9dc868990456a2667167d0ba096c5224f6258e452bfbe5a9742c5",
-                "sha256:a414f8e14aa7bacfe1578f17c11d977e637d25383b6210587c29210af995ef04",
-                "sha256:a91ee268f059583176c2c8b012a9fce7e49ca6b333a12bbc2dd01fc1a9783885",
-                "sha256:ac991947ca6533ada4ce7095f0e28fe25d5b2f3266ad5b983ed4201e61596acf",
-                "sha256:b050dbb96216db273b56f0e5960959c2b4cb679fe1e58a0c3906fa0a60c00662",
-                "sha256:b97a807437b81f90f85022a9dcfd527deea38368a3979ccb49d93c9198b2c722",
-                "sha256:bad269e442f1b7ffa3fa8820b3c3aa66f02a9f9455b5ba2db5a6f9eea96f56de",
-                "sha256:bf3725d79b1ceb19e83fb1aed44095518c0fcff88fba06a76c0891cfd1f36837",
-                "sha256:c0f22774cd8294078bdf7392ac73cf00bfa1e5e0ed644bd064fdabc5f2a2f481",
-                "sha256:c1862f9f1031b1dee3ff00f1027fcd098ffc82120f43041fe67804b464bbd8a7",
-                "sha256:c8d4ed48eed7414ccb2aaaecbc733ed2a84c299714eae3f0f48db085342d5629",
-                "sha256:cf31e894dabb077a35bbe6963285d4515a387ff657bd25b0530c7168e48f167f",
-                "sha256:d15cb6f8706678dc47fb4e4f8b339937b04eda48a0af1cca95f180db552e7663",
-                "sha256:dfcb5a4056e161307d103bc013478892cfd919f1262c2bb8703220adcb986362",
-                "sha256:e02780da03f84a671bb4205c5968c120f18df081236d7b5462b380fd4f0b497b",
-                "sha256:e2002a59453858c7f3404690ae80f10c924a39f45f6095f18a985a1234c37334",
-                "sha256:e22a82d2b416d9227a500c6860cf13e74060cf10e7daf6695cbf4e6a94e0eee4",
-                "sha256:e41f72f225192d5d4df81dad2974a8943b0f2d664a2a5cfccdf5a01506f5523c",
-                "sha256:f253dad38605486a4590f9368ecbace95865fea0f2b66615d121ac91fd1a1563",
-                "sha256:fddfb31aa2ac550b938d952bca8a87f1db0f8dc930ffa14ce05b5c08d27e7fd1"
+                "sha256:00e44c8afdbe5467e4f7b5851be223be68adb4272f44696ee71fe46b7036a711",
+                "sha256:013d61294b6cd8fe3242932c1c5e36e5d1db2c8afb58606c5a67efce62c1f5fd",
+                "sha256:049fe7579230e44daef03a259faa24511d10ebfa44f69411d99e6a184fe68073",
+                "sha256:14d4f3cd4e8b524ae9b8aa567858beed70c392fdec26dbdb0a8a418392e71708",
+                "sha256:166eac03e48784a6a6e0e5f041cfebb1ab400b394db188c48b3a84737f505b67",
+                "sha256:17ff94e7a83aa8671a25bf5b59326ec26da379ace2ebc4411d690d80a7fbcf23",
+                "sha256:1e12bdc622676ce47ae9abbf455c189e442afdde8818d9da983085df6312e7a1",
+                "sha256:21915eb821a6b3d9d8eefdaf57d6c345b970ad722f856cd71739493ce003ad08",
+                "sha256:288c6a76705dc54fba69fbcb59904ae4ad768b4c768839b8ca5fdadec6dd8cfd",
+                "sha256:32ca72bbc673adbcfecb935bb3fb1b74e663d10a4b241aaa2f5a75fe1d1f90aa",
+                "sha256:356b3576ad078c89a6107caa9c50cc14e98e3a6c4874a37c3e0273e4baf33de8",
+                "sha256:40b951f601af999a8bf2ce8c71e8aaa4e8c6f78ff8afae7b808aae2dc50d4c40",
+                "sha256:572e1787d1460da79590bf44304abbc0a2da944ea64ec549188fa84d89bba7ab",
+                "sha256:58df5c2a0e293bf665a51f8a100d3e9956febfbf1d9aaf8c0677cf70218910c6",
+                "sha256:64e6175c2e53195278d7388c454e0b30997573f3f4bd63697f88d855f7a6a1fc",
+                "sha256:7227b47e73dedaa513cdebb98469705ef0d66eb5a1250144468e9c3097d6b59b",
+                "sha256:7418b6bfc7fe3331541b84bb2141c9baf1ec7132a7ecd9f375912eca810e714e",
+                "sha256:7cbd7574ce8e138bda9df4efc6bf2ab8572c9aff640d8ecfece1b006b68da963",
+                "sha256:7ff61ff178250f9bb3cd89752df0f1dd0e27316a8bd1465351652b1b4a4cdfd3",
+                "sha256:833e1551925ed51e6b44c800e71e77dacd7e49181fdc9ac9a0bf3714d515785d",
+                "sha256:8639cadfda96737427330a094476d4c7a56ac03de7265622fcf4cfe57c8ae18d",
+                "sha256:8c790abda465726cfb8bb08bd4ca9a5d0a7bd77c7ac1ca1b839ad823b948ea28",
+                "sha256:8d2f1fb53a421b410751887eb4ff21386d119ef9cde3797bf5e7ed49fb51a3b3",
+                "sha256:903bbd302a2378f984aef528f76d4c9b1748f318fe1294961c072bdc7f2ffa3e",
+                "sha256:93f81b134a165cc17123626ab8da2e30c0455441d4ab5576eed73a64c025b25c",
+                "sha256:95e69877983ea39b7303570fa6760f81a3eec23d0e3ab2021b7144b94d06202d",
+                "sha256:9633b3034d3d901f0a46b7939f8c4d64427dfba6bbc5a36b1a67364cf148a1b0",
+                "sha256:97e5306482182170ade15c4b0d8386ded995a07d7cc2ca8f27958d34d6736497",
+                "sha256:9f3cba480d3deb69f6ee2c1825060177a22c7826431458c697df88e6aeb3caee",
+                "sha256:aa5b467f15e78b82257319aebc78dd2915e4c1436c3c0d1ad6f53e47ba6e2713",
+                "sha256:abb7a75ed8b968f3061327c433a0fbd17b729947b400747c334a9c29a9af6c58",
+                "sha256:aec52725173bd3a7b56fe91bc56eccb26fbdff1386ef123abb63c84c5b43b63a",
+                "sha256:b11548073a2213d950c3f671aa88e6f83cda6e2fb97a8b6317b1b5b33d850e06",
+                "sha256:b1692f7d6bc45e3200844be0dba153612103db241691088626a33ff1f24a0d88",
+                "sha256:b92e29e58bef6d9cfd340c72b04d74c4b4e9f70c9fa7c78b674d1fec18896dc4",
+                "sha256:be5f425ff1f5f4b3c1e33ad64ab994eed12fc284a6ea71c5243fd564502ecbe5",
+                "sha256:dd0b1e9e891f69e7675ba5c92e28b90eaa045f6ab134ffe70b52e948aa175b3c",
+                "sha256:e30f5ea4ae2346e62cedde8794a56858a67b878dd79f7df76a0767e356b1744a",
+                "sha256:e6a36bb9474218c7a5b27ae476035497a6990e21d04c279884eb10d9b290f1b1",
+                "sha256:e859fcb4cbe93504ea18008d1df98dee4f7766db66c435e4882ab35cf70cac43",
+                "sha256:eb6ea6da4c787111adf40f697b4e58732ee0942b5d3bd8f435277643329ba627",
+                "sha256:ec8c433b3ab0419100bd45b47c9c8551248a5aee30ca5e9d399a0b57ac04651b",
+                "sha256:eff9d20417ff9dcb0d25e2defc2574d10b491bf2e693b4e491914738b7908168",
+                "sha256:f0214eb2a23b85528310dad848ad2ac58e735612929c8072f6093f3585fd342d",
+                "sha256:f276df9830dba7a333544bd41070e8175762a7ac20350786b322b714b0e654f5",
+                "sha256:f3acda1924472472ddd60c29e5b9db0cec629fbe3c5c5accb74d6d6d14773478",
+                "sha256:f70a9e237bb792c7cc7e44c531fd48f5897961701cdaa06cf22fc14965c496cf",
+                "sha256:f9d29ca8a77117315101425ec7ec2a47a22ccf59f5593378fc4077ac5b754fce",
+                "sha256:fa877ca7f6b48054f847b61d6fa7bed5cebb663ebc55e018fda12db09dcc664c",
+                "sha256:fdcec0b8399108577ec290f55551d926d9a1fa6cad45882093a7a07ac5ec147b"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==1.1.1"
+            "version": "==1.1.2"
         },
         "hbreader": {
             "hashes": [
@@ -248,20 +248,20 @@
         },
         "jsonschema": {
             "hashes": [
-                "sha256:25ebdfe8a3c40974e318cdc250f2fbd6c9c86336c5a03710bb8256d019bb3630",
-                "sha256:6016b56a0f26b93162cfe2eb157fff34f46f631395327d7070c5b11162c0fc81"
+                "sha256:bc51325b929171791c42ebc1c70b9713eb134d3bb8ebd5474c8b659b15be6d86",
+                "sha256:c773028c649441ab980015b5b622f4cd5134cf563daaf0235ca4b73cc3734f20"
             ],
-            "version": "==4.0.0a6"
+            "version": "==4.0.0"
         },
         "linkml": {
             "editable": true,
             "git": "https://github.com/cancerDHC/linkml.git",
-            "ref": "1cb6033a50963c4a2f3eece892ae6747e1ed7f06"
+            "ref": "b923b1bd30bfa04cf2182a773d3c1557238d9ec7"
         },
         "linkml-runtime": {
             "editable": true,
             "git": "https://github.com/linkml/linkml-runtime.git",
-            "ref": "77ddfa1daff043de85fd45c92808bdb8a93bda64"
+            "ref": "c22d56de668d46869ab71abd268df92fc3b3859e"
         },
         "lxml": {
             "hashes": [
@@ -403,11 +403,11 @@
         },
         "openpyxl": {
             "hashes": [
-                "sha256:4f2770348c029ce9433316ced8f91ed37d2a605e654f8bfdc93a3524561a8ce2",
-                "sha256:52150a09b660fe444af7abe2592b156c14e324526b1968a57705525547317a7f"
+                "sha256:40f568b9829bf9e446acfffce30250ac1fa39035124d55fc024025c41481c90f",
+                "sha256:8f3b11bd896a95468a4ab162fc4fcd260d46157155d1f8bfaabb99d88cfcf79f"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==3.0.8"
+            "version": "==3.0.9"
         },
         "packaging": {
             "hashes": [
@@ -718,54 +718,54 @@
         },
         "sqlalchemy": {
             "hashes": [
-                "sha256:059c5f41e8630f51741a234e6ba2a034228c11b3b54a15478e61d8b55fa8bd9d",
-                "sha256:07b9099a95dd2b2620498544300eda590741ac54915c6b20809b6de7e3c58090",
-                "sha256:0aa312f9906ecebe133d7f44168c3cae4c76f27a25192fa7682f3fad505543c9",
-                "sha256:0aa746d1173587743960ff17b89b540e313aacfe6c1e9c81aa48393182c36d4f",
-                "sha256:1c15191f2430a30082f540ec6f331214746fc974cfdf136d7a1471d1c61d68ff",
-                "sha256:25e9b2e5ca088879ce3740d9ccd4d58cb9061d49566a0b5e12166f403d6f4da0",
-                "sha256:2bca9a6e30ee425cc321d988a152a5fe1be519648e7541ac45c36cd4f569421f",
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-            "version": "==1.4.23"
+            "version": "==1.4.25"
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-            "version": "==1.26.6"
+            "version": "==1.26.7"
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@@ -897,11 +897,11 @@
         },
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-            "version": "==4.2.2"
+            "version": "==4.2.3"
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@@ -920,11 +920,11 @@
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-                "sha256:fa471a601dfea0f492e4f4fca035cd82155e65dc45c9b83bf4322dfab63755dd"
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-            "version": "==2.0.5"
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         "click": {
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@@ -944,10 +944,10 @@
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-            "version": "==0.3.2"
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@@ -959,16 +959,18 @@
         },
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+            "version": "==3.2.0"
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@@ -980,19 +982,19 @@
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@@ -1057,10 +1059,10 @@
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@@ -1164,11 +1166,11 @@
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@@ -1217,11 +1219,11 @@
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@@ -1319,11 +1321,11 @@
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@@ -1436,49 +1438,49 @@
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         "requests": {
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@@ -1552,11 +1554,11 @@
         },
         "tqdm": {
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             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==4.62.2"
+            "version": "==4.62.3"
         },
         "twine": {
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@@ -1585,11 +1587,11 @@
         },
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             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.6"
+            "version": "==1.26.7"
         },
         "verspec": {
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@@ -1600,11 +1602,11 @@
         },
         "virtualenv": {
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-                "sha256:a4b987ec31c3c9996cf1bc865332f967fe4a0512c41b39652d6224f696e69da5"
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             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==20.8.0"
+            "version": "==20.8.1"
         },
         "watchdog": {
             "hashes": [
@@ -1644,11 +1646,11 @@
         },
         "zipp": {
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-                "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4"
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             ],
             "markers": "python_version >= '3.6'",
-            "version": "==3.5.0"
+            "version": "==3.6.0"
         }
     }
 }