Merge pull request #246 from alliance-genome/association_slot_refacto…

…r_mk2

Refactor association slots using domain prefix

model/schema/allele.yaml

@@ -178,19 +178,28 @@ classes:
       mod_entity_id:
         required: true
 
-  SequenceTargetingReagentToGeneAssociation:
+  SequenceTargetingReagentAssociation:
+    is_a: EvidenceAssociation
+    abstract: true
+    description: Base class for STR associations
+    attributes:
+      sequence_targeting_reagent_association_subject:
+        range: SequenceTargetingReagent
+        required: true
+
+  SequenceTargetingReagentGeneAssociation:
     description: >-
       the relationship between a Sequence Targeting Reagent and its targeted
       genes. The relation should be a VocabularyTerm with one of the following
       values - targets
-    is_a: EvidenceAssociation
+    is_a: SequenceTargetingReagentAssociation
+    attributes:
+      sequence_targeting_reagent_gene_association_object:
+        range: Gene
+        required: true
     slot_usage:
       relation:
         range: VocabularyTerm
-      subject:
-        range: SequenceTargetingReagent
-      object:
-        range: Gene
 
   # TO DO: create SequenceTargetingReagentToGeneAssociationDTO class? [CG]
 
@@ -384,15 +393,26 @@ classes:
   ## ALLELE ASSOCIATION CLASSES
   ## ------------
 
+  AlleleAssociation:
+    is_a: EvidenceAssociation
+    abstract: true
+    description: Base class for all Allele Associations
+    attributes:
+      allele_association_subject:
+        range: Allele
+        required: true
+
   AlleleAlleleAssociation:
     is_a: AlleleGenomicEntityAssociation
     description: >-
       Association between an allele and another allele
+    attributes:
+      allele_allele_association_object:
+        range: Allele
+        required: true
     slot_usage:
       relation:
         notes: CV 'Allele Allele Association Relation'
-      object:
-        range: Allele
 
   AlleleAlleleAssociationDTO:
     is_a: AlleleGenomicEntityAssociationDTO
@@ -403,18 +423,18 @@ classes:
 
   # do mutant/parent/embryonic cell line associations need to be split out?
   AlleleCellLineAssociation:
-    is_a: EvidenceAssociation
+    is_a: AlleleAssociation
     description: >-
       The relationship between an allele and a cell line.  Includes mutant/
       embryonic stem cell lines known to carry the allele, and parental cell
       line of alleles made in embryonic stem cells.
+    attributes:
+      allele_cell_line_association_object:
+        range: CellLine
+        required: true
     slot_usage:
-      subject:
-        range: Allele
       relation:
         range: VocabularyTerm
-      object:
-        range: CellLine
 
   AlleleCellLineAssociationDTO:
       is_a: EvidenceAssociationDTO
@@ -432,16 +452,16 @@ classes:
     description: >-
       The relationship between an allele and constructs contained in
       that allele.
+    attributes:
+      allele_construct_association_object:
+        range: Construct
+        required: true
     slot_usage:
-      subject:
-        range: Allele
       relation:
         range: VocabularyTerm
         notes: >-
           CV 'Allele Construct Association Relation' including - contains, contains_coinjection_marker,
           contains_phenotypic_sequence_feature, and contains_innocuous_sequence_feature
-      object:
-        range: Construct
 
   AlleleConstructAssociationDTO:
     is_a: AlleleGenomicEntityAssociationDTO
@@ -460,9 +480,10 @@ classes:
     is_a: AlleleGenomicEntityAssociation
     description: >-
       Association between an allele and a gene
-    slot_usage:
-      object:
+    attributes:
+      allele_gene_association_object:
         range: Gene
+        required: true
 
   AlleleGeneAssociationDTO:
     description: >-
@@ -472,18 +493,18 @@ classes:
       - gene_identifier
 
   AlleleGenerationMethodAssociation:
-    is_a: EvidenceAssociation
+    is_a: AlleleAssociation
     slots:
       - mutation_target_strain
+    attributes:
+      allele_generation_method_association_object:
+        range: GenerationMethod
+        required: true
     slot_usage:
-      subject:
-        range: Allele
       relation:
         any_of:
           equals_string: has_generation_method
         notes: CV 'Allele Generation Method Association Relation'
-      object:
-        range: GenerationMethod
 
   AlleleGenerationMethodAssociationDTO:
     is_a: EvidenceAssociationDTO
@@ -499,20 +520,16 @@ classes:
           equals_string: has_generation_method
 
   AlleleGenomicEntityAssociation:
-    is_a: EvidenceAssociation
+    is_a: AlleleAssociation
     abstract: true
     description: >-
       Association between an allele and a genomic entity
     slots:
       - evidence_code
       - related_note
     slot_usage:
-      subject:
-        range: Allele
       relation:
         range: VocabularyTerm # If we can adequately represent all needed relations in RO, this could be ROTerm
-      object:
-        range: GenomicEntity
       evidence:
         required: false # This needs to be not required, at least in the base class
 
@@ -526,18 +543,18 @@ classes:
       - note_dto
 
   AlleleImageAssociation:
-    is_a: EvidenceAssociation
+    is_a: AlleleAssociation
     description: >-
       The relationship between an allele and an image.
     slots:
       - primary_image
+    attributes:
+      allele_image_association_object:
+        range: Image
+        required: true
     slot_usage:
-      subject:
-        range: Allele
       relation:
         range: VocabularyTerm
-      object:
-        range: Image
       primary_image:
         description: >-
           Can be null; if false, maybe you would show all the images.
@@ -559,14 +576,13 @@ classes:
           We need to revisit this issue.
 
   AlleleOriginAssociation:
-    is_a: EvidenceAssociation
+    is_a: AlleleAssociation
     description: >-
       The relationship between an allele and the origin of the allele.
-    slot_usage:
-      subject:
-        range: Allele
-      object:
+    attributes:
+      allele_origin_association_object:
         range: AffectedGenomicModel
+        required: true
 
   AlleleOriginAssociationDTO:
     is_a: EvidenceAssociationDTO
@@ -581,9 +597,11 @@ classes:
     is_a: AlleleGenomicEntityAssociation
     description: >-
       Association between an allele and a protein
-    slot_usage:
-      object:
+    attributes:
+      allele_protein_association_object:
         range: Protein
+        required: true
+
 
   AlleleProteinAssociationDTO:
     is_a: AlleleGenomicEntityAssociationDTO
@@ -596,9 +614,11 @@ classes:
     is_a: AlleleGenomicEntityAssociation
     description: >-
       Association between an allele and a transcript
-    slot_usage:
-      object:
+    attributes:
+      allele_transcript_association_object:
         range: Transcript
+        required: true
+
 
   AlleleTranscriptAssociationDTO:
     is_a: AlleleGenomicEntityAssociationDTO
@@ -613,12 +633,11 @@ classes:
       The relationship between an allele and a variant is many to many. An
       Allele may have many variants and a variant can be present in many
       alleles.
-    slot_usage:
-      subject:
-        range: Allele
-      object:
+    attributes:
+      allele_variant_association_object:
         range: Variant
-
+        required: true
+
   AlleleVariantAssociationDTO:
     is_a: AlleleGenomicEntityAssociationDTO
     description: >-

model/schema/biologicalEntitySet.yaml

@@ -131,15 +131,17 @@ classes:
       - proteins
 
 
-  GeneToPathwayAssociation:
+  GenePathwayAssociation:
     is_a: EvidenceAssociation
+    slots:
+      - gene_association_subject
+    attributes:
+      gene_pathway_association_object:
+        range: Pathway
+        required: true
     slot_usage:
       relation:
         subproperty_of: has_participant
-      subject:
-        range: Gene
-      object:
-        range: Pathway
 
 
 ## ------------

model/schema/core.yaml

@@ -325,22 +325,18 @@ classes:
       of the association, and likewise the object is the curie (or identifier of the class that is the object. The
       relationship between subject and object is defined by the relation slot (which can also be constrained
       using the range of the relation).
-    exact_mappings:
-      - biolink:association
     notes:
       Keeping this more generic than biolink:association by foregoing the
       qualifiers and negated slots.
+      Association child classes must also have subject and object slots defined, but (due to implementation issues)
+      these must have distinct names if the range of the slot inherits from a different base table in the database.
+      Therefore these are defined in the appropriate classes with a prefix indicating the class(es) using the slot, 
+      e.g. disease_annotation_subject, allele_association_subject, allele_construct_association_object.
     slots:
-      - subject
       - relation
-      - object
     slot_usage:
-        subject:
-            required: true
         relation:
             required: true
-        object:
-            required: true
 
   SingleReferenceAssociation:
     abstract: true
@@ -1200,25 +1196,6 @@ slots:
 ## ASSOCIATION SLOTS
 ## --------------------
 
-  subject:
-    is_a: association_slot
-    description: >-
-      connects an association to the subject of the association.
-      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
-    required: true
-    exact_mappings:
-      - owl:annotatedSource
-      - biolink:subject
-
-  object:
-    is_a: association_slot
-    description: >-
-      connects an association to the object of the association.
-      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
-    required: true
-    exact_mappings:
-      - biolink:object
-
   relation:
     is_a: association_slot
     description: >-

model/schema/expression.yaml

@@ -131,17 +131,25 @@ classes:
       - cellular_component
       - spatial_qualifiers
 
-  ExpressionAnnotationImagePane:
+  ExpressionAnnotationAssociation:
+    is_a: EvidenceAssociation
+    abstract: true
+    description: Base class for all ExpressionAnnotation associations
+    attributes:
+      expression_annotation_subject:
+        required: true
+        domain: ExpressionAnnotation
+
+  ExpressionAnnotationImagePaneAssociation:
     is_a: EvidenceAssociation
     notes: >-
       This aims to provide the same functionality as MGI imagepane.
       Some MODs (like ZFIN) point to the whole image. In these cases,
       the pane would encompass the whole image.
-    slot_usage:
-      subject:
-        range: ExpressionAnnotation
-      object:
+    attributes:
+      expression_annotation_image_pane_association_object:
         range: ImagePane
+        required: true
 
   # GeneExpressionStatement:
   #   is_a: EntityStatement     # Update to use Note class instead?