Absence #719

src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntity.yaml

@@ -8,11 +8,13 @@ contributors:
   - https://orcid.org/0000-0001-5208-3432
   - https://orcid.org/0000-0001-7941-2961
   - https://orcid.org/0000-0003-4148-4606
+  - https://orcid.org/0000-0002-7073-9172
 
 classes:
   absent: PATO:0000462
   abnormal: PATO:0000460
   anatomical entity: UBERON:0001062
+  'multicellular organism': UBERON:0000468
 
 relations: 
   inheres_in: RO:0000052
@@ -42,6 +44,7 @@ def:
     - anatomical_entity
 
 equivalentTo:
-  text: "'has_part' some ('absent' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
+  text: "'has part' some ('lacks all parts of type' and ('inheres in' some 'organism') and ('towards' value %s) and ('has modifier' some 'abnormal'))"
+     vars:
   vars:
     - anatomical_entity

src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml

@@ -4,6 +4,7 @@ description: "Absence of an anatomical entity in a location, such as absent aort
 
 contributors:
   - https://orcid.org/0000-0001-5208-3432
+  - https://orcid.org/0000-0002-7073-9172
 
 classes:
   absent: PATO:0000462
@@ -45,7 +46,8 @@ def:
     - location
 
 equivalentTo:
-  text: "'has_part' some ('absent' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
+  text: "'has part' some ('lacks all parts of type' and ('inheres in' some %s) and ('towards' value %s) and ('has modifier' some 'abnormal'))"
   vars:
-    - anatomical_entity
     - location
+    - anatomical_entity
+

src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml

@@ -38,7 +38,14 @@ def:
   vars:
     - anatomical_entity
 
-equivalentTo:
-  text: "'has_part' some ('decreased amount' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
-  vars:
-    - anatomical_entity
+logical_axioms: 
+   -  
+      axiom_type: EquivalentTo
+      text: has_part some ('has fewer parts of type' and (inheres_in some 'multicellular organism') and ('towards' value %s)
+      vars:
+        - anatomical_entity
+  -  
+      axiom_type: EquivalentTo
+      text: has_part some 'has fewer parts of type' and (inheres_in some multicellular organism') and ('towards' some %s)
+      vars:
+        - anatomical_entity

src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntityInLocation.yaml

@@ -6,6 +6,7 @@ contributors:
 - https://orcid.org/0000-0002-7356-1779
 - https://orcid.org/0000-0001-5208-3432
 - https://orcid.org/0000-0002-3528-5267
+
 classes:
   decreased amount: PATO:0001997
   abnormal: PATO:0000460
@@ -45,8 +46,16 @@ def:
   - anatomical_entity
   - location
 
-equivalentTo:
-  text: "'has_part' some ('decreased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
-  vars:
-  - anatomical_entity
-  - location
+logical_axioms: 
+   -  
+      axiom_type: EquivalentTo
+      text: has_part some ('has fewer parts of type' and ('inheres in' some '%s) and ('towards' value %s) and ('has modifier' some 'abnormal'))
+      vars:
+        - location
+        - anatomical_entity
+  -  
+      axiom_type: EquivalentTo
+      text: has_part some 'has fewer parts of type' and ('inheres in' some %s') and ('towards' some %s) and ('has modifier' some 'abnormal'))
+      vars:
+        - location
+        - anatomical_entity