From 84366d4e2278dd3e23ece190d1ef4f5be9e9f7ad Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Tue, 27 Aug 2024 19:11:06 -0700
Subject: [PATCH] first pass at adding medical action and medical action to
 phenotype & disease

---
 src/biolink_model/schema/biolink_model.yaml | 80 ++++++++++++++++++++-
 1 file changed, 78 insertions(+), 2 deletions(-)

diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml
index e3a16e45c..20170a92e 100644
--- a/src/biolink_model/schema/biolink_model.yaml
+++ b/src/biolink_model/schema/biolink_model.yaml
@@ -9156,10 +9156,16 @@ classes:
     mixins:
       - gene grouping mixin
 
-  treatment:
+  medical action:
     aliases: ['medical action', 'medical intervention']
-     # 'named thing' seems too generic here but not sure what applies better here
     is_a: named thing
+    description: >-
+      A clinically prescribed procedure, therapy, intervention, or recommendation.
+    exact_mappings:
+      - MAXO:0000001
+
+  treatment:
+    is_a: medical action
     mixins:
       - exposure event
       - chemical or drug or treatment
@@ -9347,6 +9353,22 @@ classes:
       - retrieval source ids
       - p value
       - adjusted p value
+      - subject aspect qualifier
+      - subject direction qualifier
+      - subject form or variant qualifier
+      - subject part qualifier
+      - subject derivative qualifier
+      - subject context qualifier
+      - qualified predicate
+      - object aspect qualifier
+      - object direction qualifier
+      - object form or variant qualifier
+      - object part qualifier
+      - object derivative qualifier
+      - object context qualifier
+      - causal mechanism qualifier
+      - anatomical context qualifier
+      - species context qualifier
     slot_usage:
       type:
         description: rdf:type of biolink:Association should be fixed at rdf:Statement
@@ -9786,6 +9808,46 @@ classes:
         range: disease or phenotypic feature
         description: "the disease or phenotype that is affected by the chemical"
 
+  medical action to disease or phenotypic feature association:
+    is_a: association
+    description: >-
+      This association defines a relationship between a medical action and a disease or phenotypic feature 
+    defining_slots:
+      - subject
+      - predicate
+      - object
+    mixins:
+        - medical action to entity association mixin
+        - entity to disease or phenotypic feature association mixin
+    slot_usage:
+      predicate:
+        subproperty_of:
+
+    medical action to disease association:
+      is_a: medical action to disease or phenotypic feature association
+      description: >-
+        This association defines a relationship between a medical action and a disease
+      defining_slots:
+        - subject
+        - predicate
+        - object
+      mixins:
+        - medical action to entity association mixin
+        - entity to disease association mixin
+
+    medical action to phenotypic feature association:
+      is_a: medical action to disease or phenotypic feature association
+      description: >-
+        This association defines a relationship between a medical action and a phenotypic feature
+      defining_slots:
+        - subject
+        - predicate
+        - object
+      mixins:
+        - medical action to entity association mixin
+        - entity to phenotypic feature association mixin
+
+
   chemical or drug or treatment to disease or phenotypic feature association:
     description: >-
       This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature
@@ -10246,6 +10308,20 @@ classes:
       - object direction qualifier
       - qualified predicate
 
+  medical action to entity association mixin:
+    description: >-
+      An association between a medical action and another entity
+    mixin: true
+    slots:
+      - subject
+      - predicate
+      - object
+    defining_slots:
+      - subject
+    slot_usage:
+      subject:
+        range: medical action
+
   entity to phenotypic feature association mixin:
     mixin: true
     is_a: entity to feature or disease qualifiers mixin