Merge pull request #258 from alliance-genome/HTP-expression-data-mode…

…ling-first-pass

HTP expression data modeling first pass

model/schema/affectedGenomicModel.yaml

@@ -64,7 +64,7 @@ classes:
       - sequence_targeting_reagent_identifiers
       - component_dtos
     slot_usage:
-      mod_entity_id:
+      primary_external_id:
         required: true
 
   AgmSecondaryIdSlotAnnotation:
@@ -177,7 +177,7 @@ slots:
     range: string
     multivalued: true
     description: >-
-      Identifiers (curie/mod_entity_id/mod_internal_id) of the STRs
+      Identifiers (curie/primary_external_id/mod_internal_id) of the STRs
 
   parental_populations:
     singular_name: parental_population

model/schema/agent.yaml

@@ -79,7 +79,7 @@ classes:
       - orcid
       - emails
       - old_emails
-      - mod_entity_id
+      - primary_external_id
       - unique_id
       - affiliated_alliance_member
     exact_mappings:

model/schema/allele.yaml

@@ -123,7 +123,7 @@ classes:
     slot_usage:
       note_dtos:
         notes: note_type CV 'Allele Note Type'
-      mod_entity_id:
+      primary_external_id:
         required: true
 
   # Some classes roughly grouped with the Allele class because they have relationships to Allele and were
@@ -139,7 +139,7 @@ classes:
     description: >-
       Dummy cell line DTO class
     slot_usage:
-      mod_entity_id:
+      primary_external_id:
         required: true
 
   GenerationMethod:
@@ -182,7 +182,7 @@ classes:
       - synonyms
       - secondary_identifiers
     slot_usage:
-      mod_entity_id:
+      primary_external_id:
         required: true
 
   SequenceTargetingReagentAssociation:
@@ -708,7 +708,7 @@ slots:
 
   allele_identifier:
     description: >-
-      Identifier (curie/mod_entity_id/mod_internal_id) of the allele
+      Identifier (curie/primary_external_id/mod_internal_id) of the allele
     range: string
     required: true
 
@@ -892,7 +892,7 @@ slots:
 
   cell_line_identifier:
     description: >-
-      Identifier (curie/mod_entity_id/mod_internal_id) of the cell line
+      Identifier (curie/primary_external_id/mod_internal_id) of the cell line
     range: string
     required: true
 
@@ -1081,8 +1081,8 @@ slots:
 
   mutation_target_strain_identifier:
     description: >-
-      Identifier (curie/mod_entity_id/mod_internal_id) of the particular strain that is targeted by the generation method
-      for a particular allele (MGI only)
+      Identifier (curie/primary_external_id/mod_internal_id) of the particular strain
+      that is targeted by the generation method for a particular allele (MGI only)
     domain: AlleleGenerationMethodAssociationDTO
     range: string
 
@@ -1117,7 +1117,7 @@ slots:
 
   object_allele_identifier:
     description: >-
-      The identifier (curie/mod_entity_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation
+      The identifier (curie/primary_external_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation
     domain: AlleleAlleleAssociationDTO
     range: string
 
@@ -1149,7 +1149,7 @@ slots:
     multivalued: false
     domain: SequenceTargetingReagentAssociationDTO
     description: >-
-      Identifier (curie/mod_entity_id/mod_internal_id) of the STR
+      Identifier (curie/primary_external_id/mod_internal_id) of the STR
 
   sequence_targeting_reagent_gene_associations:
     domain: SequenceTargetingReagent

model/schema/allianceModel.yaml

@@ -40,12 +40,13 @@ imports:
   - expression
   - gene
   - geneInteraction
+  - highThroughputExpression
+  - homology
   - image
   - ingest
-  - modCorpusAssociation
   - linkml:types
+  - modCorpusAssociation
   - ontologyTerm
-  - homology
   - phenotypeAndDiseaseAnnotation
   - reagent
   - reference

model/schema/core.yaml

@@ -96,14 +96,14 @@ classes:
       Parent class for LinkML classes of submitted entities
       that may have a public or internal MOD ID/curie
     slots:
-      - mod_entity_id
+      - primary_external_id
       - mod_internal_id
       - data_provider
 
   SubmittedObjectDTO:
     is_a: AuditedObjectDTO
     slots:
-      - mod_entity_id
+      - primary_external_id
       - mod_internal_id
       - data_provider_dto
 
@@ -1243,11 +1243,11 @@ slots:
     multivalued: false
     range: string
 
-  mod_entity_id:
+  primary_external_id:
     description: >-
-      The model organism database (MOD) identifier/curie for the object. Note
-      that this may be an external identifier for an object, like a UniProt ID
-      for a protein, but acts as the MOD's primary key for the entity.
+      The primary external (non-Alliance) database identifier/curie for the object. Note
+      that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID
+      for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
     range: string
 
   mod_internal_id: