Merge pull request #133 from ghga-de/fix/model_fixes

Model fixes enabling use with metldata / dskit
ghga-de · Aug 1, 2023 · f17e0ec · f17e0ec
2 parents 16285c8 + 0ebd143
commit f17e0ec
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diff --git a/docs/schema_markdown/AccessionMixin.md b/docs/schema_markdown/AccessionMixin.md
diff --git a/docs/schema_markdown/AccessionMixin_accession.md b/docs/schema_markdown/AccessionMixin_accession.md
diff --git a/docs/schema_markdown/accession.md b/docs/schema_markdown/accession.md
diff --git a/docs/schema_markdown/index.md b/docs/schema_markdown/index.md
@@ -4,7 +4,7 @@
 
 **metamodel version:** 1.7.0
 
-**version:** 1.0.0
+**version:** 1.0.1
 
 
 The submission centric metadata schema for the German Human Genome-Phenome Archive (GHGA).
@@ -38,7 +38,6 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi
 
 ### Mixins
 
- * [AccessionMixin](AccessionMixin.md) - Mixin for entities that can be assigned a GHGA accession.
  * [AliasMixin](AliasMixin.md) - Mixin for entities that can be assigned an alias at the time of metadata submission.
  * [IdentifiedByAliasMixin](IdentifiedByAliasMixin.md)
  * [AttributeMixin](AttributeMixin.md) - Mixin for entities that can have one or more attributes.
@@ -48,8 +47,6 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi
 
  * [abstract](abstract.md) - The study abstract that describes the goals. Can also hold abstract from a publication related to this study
  * [Publication➞abstract](Publication_abstract.md) - The study abstract that describes the goals. Can also hold abstract from a publication related to this study.
- * [accession](accession.md) - A unique GHGA identifier assigned to an entity for the sole purpose of referring to that entity in a global scope.
- * [AccessionMixin➞accession](AccessionMixin_accession.md)
  * [affiliations](affiliations.md) - The Institution(s) associated with an entity.
  * [Study➞affiliations](Study_affiliations.md)
  * [age_at_sampling](age_at_sampling.md) - Age of an individual.

diff --git a/spreadsheets/ghga_submission_full.xlsx b/spreadsheets/ghga_submission_full.xlsx
diff --git a/spreadsheets/ghga_submission_individual.xlsx b/spreadsheets/ghga_submission_individual.xlsx
diff --git a/spreadsheets/ghga_submission_minimal.xlsx b/spreadsheets/ghga_submission_minimal.xlsx
diff --git a/spreadsheets/ghga_submission_sample.xlsx b/spreadsheets/ghga_submission_sample.xlsx
diff --git a/spreadsheets/ghga_submission_seq.xlsx b/spreadsheets/ghga_submission_seq.xlsx
diff --git a/src/schema/submission.yaml b/src/schema/submission.yaml
@@ -2,7 +2,7 @@ id: https://w3id.org/GHGA-Submission-Metadata-Schema
 name: GHGA-Submission-Metadata-Schema
 description: >-
  The submission centric metadata schema for the German Human Genome-Phenome Archive (GHGA).
-version: 1.0.0
+version: 1.0.1
 imports:
  - linkml:types
 
@@ -14,6 +14,8 @@ prefixes:
  SIO: http:https://semanticscience.org/resource/SIO_
  biolink: https://w3id.org/biolink/vocab/
  linkml: https://w3id.org/linkml/
+ GSSO: http:https://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl
+ DUO: http:https://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl
 
 default_prefix: GHGA
 default_range: string
@@ -75,15 +77,6 @@ classes:
  alias:
  identifier: true
 
- AccessionMixin:
- mixin: true
- description: Mixin for entities that can be assigned a GHGA accession.
- slots:
- - accession
- slot_usage:
- accession:
- required: true
-
  AttributeMixin:
  mixin: true
  description: Mixin for entities that can have one or more attributes.
@@ -934,11 +927,6 @@ slots:
  alias:
  description: The alias for an entity at the time of submission.
 
- accession:
- description: >-
- A unique GHGA identifier assigned to an entity for the sole purpose of
- referring to that entity in a global scope.
-
  description:
  description: Description of an entity.
  exact_mappings: