Refine transport patterns. (#29412)

src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo.yaml

@@ -1,18 +1,18 @@
 pattern_name: vesicle-mediated transport differentiated by cargo
 
-pattern_iri: http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport.yaml
+pattern_iri: http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_cargo.yaml
 
-description: TODO
+description: This pattern is for representing vesicle-mediated transport, differentiated by the type of cargo.
 
 classes:
   vesicle-mediated transport: "GO:0016192"
-  cellular component: "GO:0005575"
+  cellular anatomical structure: 'GO:0110165'
 
 relations:
-  has_primary_input: 'RO:0004009'
+  has primary input: 'RO:0004009'
 
 vars:
- target: "'cellular component'"
+  target: "'cellular anatomical structure'"
 
 name:
   text: "%s vesicle-mediated transport"
@@ -25,6 +25,6 @@ def:
      -  target
 
 equivalentTo:
-  text: "'vesicle-mediated transport' and 'has_primary_input' some %s"
+  text: "'vesicle-mediated transport' and ('has primary input' some %s)"
   vars:
     -  target

src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.yaml

@@ -0,0 +1,41 @@
+pattern_name: vesicle-mediated transport differentiated by cargo and start and end locations
+
+pattern_iri: http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.yaml
+
+description: This pattern is for representing transmembrane transport, differentiated by the type of cargo as well as the start and end locations.
+
+classes:
+  vesicle-mediated transport: 'GO:0016192'
+  cellular anatomical structure: 'GO:0110165'
+  chemical entity: 'CHEBI:24431'
+
+relations:
+  has primary input: 'RO:0004009'
+  has target start location: 'RO:0002338'
+  has target end location: 'RO:0002339'
+
+vars:
+  cargo: "'chemical entity'"
+  start location: "'cellular anatomical structure'"
+  end location: "'cellular anatomical structure'"
+
+name:
+  text: "%s vesicle-mediated transport from %s to %s"
+  vars:
+    - 'cargo'
+    - 'start location'
+    - 'end location'
+
+def:
+  text: "The vesicle-mediated and directed movement of %s from %s to %s."
+  vars:
+    - 'cargo'
+    - 'start location'
+    - 'end location'
+
+equivalentTo:
+  text: "'vesicle-mediated transport' and ('has primary input' some %s) and ('has target start location' some %s) and ('has target end location' some %s)"
+  vars:
+    - 'cargo'
+    - 'start location'
+    - 'end location'

src/design_patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml

@@ -1,35 +1,35 @@
 pattern_name: vesicle-mediated transport differentiated by start and end locations
 
-pattern_iri: http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml
+pattern_iri: http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml
 
-description: TODO
+description: This pattern is for representing vesicle-mediated transport, differentiated by the start and end locations.
 
 classes:
-  vesicle-mediated transport: GO:0016192
-  cellular component: GO:0005575
+  vesicle-mediated transport: 'GO:0016192'
+  cellular anatomical structure: 'GO:0110165'
 
 relations: 
-  has_target_start_location: RO:0002338
-  has_target_end_location: RO:0002339
+  has target start location: 'RO:0002338'
+  has target end location: 'RO:0002339'
 
 vars:
- start location: "'cellular component'"
- end location: "'cellular component'"
+  start location: "'cellular anatomical structure'"
+  end location: "'cellular anatomical structure'"
 
 name:
-    text: "%s to %s vesicle-mediated transport"
-    vars:
-    - start location
-    - end location
+  text: "%s to %s vesicle-mediated transport"
+  vars:
+    - 'start location'
+    - 'end location'
 
 def:
-    text: "The vesicle-mediated and directed movement of substances from %s to %s."
-    vars:
-    - start location
-    - end location 
+  text: "The vesicle-mediated and directed movement of substances from %s to %s."
+  vars:
+    - 'start location'
+    - 'end location'
 
 equivalentTo:
-  text: "'vesicle-mediated transport' and 'has_target_start_location' some %s and 'has_target_end_location' some %s"
+  text: "'vesicle-mediated transport' and ('has target start location' some %s) and ('has target end location' some %s)"
   vars:
-    - start location
-    - end location 
+    - 'start location'
+    - 'end location'