Merge pull request #1055 from microbiomedata/issue340-remove-abstract…

…-slot

remove abstract slot globally from schema

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

@@ -0,0 +1,85 @@
+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
+      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:
+          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

src/data/valid/Study-exhaustive.yaml

@@ -43,7 +43,6 @@ alternative_descriptions:
 alternative_names:
   - any string 1
   - any string 2
-abstract: Nothing was studied.
 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.

src/schema/core.yaml

@@ -683,13 +683,6 @@ slots:
     range: string
     description: >-
       MD5 checksum of file (pre-compressed)
-  
-  abstract:
-    range: string
-    description: >-
-      The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.
-    exact_mappings:
-      - dcterms:abstract
 
   keywords:
     range: string

src/schema/nmdc.yaml

@@ -1344,7 +1344,6 @@ classes:
       ## Related IDs
       #- insdc_bioproject_identifiers
       #- insdc_sra_ena_study_identifiers
-      - abstract
       - alternative_descriptions
       - alternative_names
       - alternative_titles