update invalid study file for database root class

src/data/invalid/Study-include-abstract.yaml

@@ -1,68 +1,27 @@
-id: nmdc:sty-11-ab
-name: see also description, title, objective, various alternatives
-abstract: This study is about a thing.
-description: see also name, title, objective, various alternatives
-alternative_identifiers:
-  - generic:abc1
-related_identifiers: any string R1
-#emsl_proposal_identifier:
-#  - generic:abc1
-#emsl_proposal_doi: any string
-gold_study_identifiers:
-  - GOLD:Gs12345
-  - GOLD:Gs90909
-mgnify_project_identifiers:
-  - mgnify.proj:ABC123
-ecosystem: unconstrained text. should be validated against the controlled vocabulary,
-  by the sample's environmental package. would also be nice to align the CV with MIxS
-  environmental triads
-ecosystem_category: unconstrained text
-ecosystem_type: unconstrained text
-ecosystem_subtype: unconstrained text
-specific_ecosystem: unconstrained text
-principal_investigator:
-  has_raw_value: Craig Venter
-  was_generated_by: nmdc:any_string_1
-  orcid: ORCID:0000-0002-7086-765X
-  profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg
-  email: [email protected]
-  name: J. Craig Venter
-  websites:
-    - https://www.jcvi.org/
-    - https://www.jcvi.org/about/j-craig-venter
-title: Sample Exhaustive Biosample instance. Although all of these values should pass
-  validation, that does not mean that any Biosample of any type would necessarily
-  have this particular combination of values.
-alternative_titles:
-  - any string 1
-  - any string 2
-alternative_descriptions:
-  - any string 1
-  - any string 2
-alternative_names:
-  - any string 1
-  - any string 2
-objective: This record, an instance of class Study from the nmdc-schema was had authored,
-  so that the NMDC team would have at least one instance, using all slots, with a
-  mixture of reasonable values and minimally compliant values.
-websites:
-  - https://w3id.org/nmdc
-  - https://w3id.org/linkml
-publications:
-  - any string 1
-  - any string 2
-ess_dive_datasets:
-  - any string 1
-  - any string 2
-type: any string
-relevant_protocols:
-  - any string 1
-  - any string 2
-funding_sources:
-  - any string 1
-  - any string 2
-has_credit_associations:
-  - applies_to_person:
+study_set:
+  - id: nmdc:sty-11-ab
+    name: see also description, title, objective, various alternatives
+    abstract: This study is about a thing.
+    description: see also name, title, objective, various alternatives
+    alternative_identifiers:
+      - generic:abc1
+    related_identifiers: any string R1
+    #emsl_proposal_identifier:
+    #  - generic:abc1
+    #emsl_proposal_doi: any string
+    gold_study_identifiers:
+      - GOLD:Gs12345
+      - GOLD:Gs90909
+    mgnify_project_identifiers:
+      - mgnify.proj:ABC123
+    ecosystem: unconstrained text. should be validated against the controlled vocabulary,
+      by the sample's environmental package. would also be nice to align the CV with MIxS
+      environmental triads
+    ecosystem_category: unconstrained text
+    ecosystem_type: unconstrained text
+    ecosystem_subtype: unconstrained text
+    specific_ecosystem: unconstrained text
+    principal_investigator:
       has_raw_value: Craig Venter
       was_generated_by: nmdc:any_string_1
       orcid: ORCID:0000-0002-7086-765X
@@ -72,13 +31,55 @@ has_credit_associations:
       websites:
         - https://www.jcvi.org/
         - https://www.jcvi.org/about/j-craig-venter
-    applied_roles:
-      - Supervision
-      - Conceptualization
-    applied_role: Funding acquisition
+    title: Sample Exhaustive Biosample instance. Although all of these values should pass
+      validation, that does not mean that any Biosample of any type would necessarily
+      have this particular combination of values.
+    alternative_titles:
+      - any string 1
+      - any string 2
+    alternative_descriptions:
+      - any string 1
+      - any string 2
+    alternative_names:
+      - any string 1
+      - any string 2
+    objective: This record, an instance of class Study from the nmdc-schema was had authored,
+      so that the NMDC team would have at least one instance, using all slots, with a
+      mixture of reasonable values and minimally compliant values.
+    websites:
+      - https://w3id.org/nmdc
+      - https://w3id.org/linkml
+    publications:
+      - any string 1
+      - any string 2
+    ess_dive_datasets:
+      - any string 1
+      - any string 2
     type: any string
-  - applies_to_person:
-      name: Tanja Davidsen
-    applied_roles:
-      - Investigation
-      - Supervision
+    relevant_protocols:
+      - any string 1
+      - any string 2
+    funding_sources:
+      - any string 1
+      - any string 2
+    has_credit_associations:
+      - applies_to_person:
+          has_raw_value: Craig Venter
+          was_generated_by: nmdc:any_string_1
+          orcid: ORCID:0000-0002-7086-765X
+          profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg
+          email: [email protected]
+          name: J. Craig Venter
+          websites:
+            - https://www.jcvi.org/
+            - https://www.jcvi.org/about/j-craig-venter
+        applied_roles:
+          - Supervision
+          - Conceptualization
+        applied_role: Funding acquisition
+        type: any string
+      - applies_to_person:
+          name: Tanja Davidsen
+        applied_roles:
+          - Investigation
+          - Supervision