Merge branch 'master' of github.com:geneontology/go-ontology into iss…

…ue-29336
geneontology · Dec 10, 2024 · 2cda4b4 · 2cda4b4
2 parents 14efb73 + eb8c6f5
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diff --git a/docs/patterns/index.md b/docs/patterns/index.md
@@ -53,5 +53,6 @@
 | [transmembrane import into cytosol](transmembrane_import_into_cytosol.md) | TODO |
 | [transmembrane transport](transmembrane_transport.md) | This pattern is for representing transmembrane transport, differentiated by the type of cargo. |
 | [transport of a cellular component](cc_transport.md) | Transport of a cellular component, differentiated by the component being transported. |
-| [vesicle-mediated transport differentiated by cargo](vesicle_mediated_transport_differentiated_by_cargo.md) | TODO |
-| [vesicle-mediated transport differentiated by start and end locations](vesicle_mediated_transport_differentiated_by_start_and_end_locations.md) | TODO |
+| [vesicle-mediated transport differentiated by cargo](vesicle_mediated_transport_differentiated_by_cargo.md) | This pattern is for representing vesicle-mediated transport, differentiated by the type of cargo. |
+| [vesicle-mediated transport differentiated by cargo and start and end locations](vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md) | This pattern is for representing transmembrane transport, differentiated by the type of cargo as well as the start and end locations. |
+| [vesicle-mediated transport differentiated by start and end locations](vesicle_mediated_transport_differentiated_by_start_and_end_locations.md) | This pattern is for representing vesicle-mediated transport, differentiated by the start and end locations. |
diff --git a/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo.md b/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo.md
@@ -1,10 +1,10 @@
 # vesicle-mediated transport differentiated by cargo
 
-[http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport.yaml](http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport.yaml)
+[http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_cargo.yaml](http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_cargo.yaml)
 
 ## Description
 
-TODO
+This pattern is for representing vesicle-mediated transport, differentiated by the type of cargo.
 
 
 
@@ -13,7 +13,7 @@ TODO
 
 | Variable name | Allowed type |
 |:--------------|:-------------|
-| `{target}` | [cellular_component](http://purl.obolibrary.org/obo/GO_0005575) |
+| `{target}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
 
 ## Name
 

diff --git a/...sicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md b/...sicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md
@@ -0,0 +1,49 @@
+# vesicle-mediated transport differentiated by cargo and start and end locations
+
+[http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.yaml](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.
+
+
+
+
+## Variables
+
+| Variable name | Allowed type |
+|:--------------|:-------------|
+| `{cargo}` | [chemical entity](http://purl.obolibrary.org/obo/CHEBI_24431) |
+| `{start location}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
+| `{end location}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
+
+## Name
+
+"`{cargo}` vesicle-mediated transport from `{start location}` to `{end location}`"^^[string](http://www.w3.org/2001/XMLSchema#string)
+
+## Annotations
+
+
+
+## Definition
+
+"The vesicle-mediated and directed movement of `{cargo}` from `{start location}` to `{end location}`."^^[string](http://www.w3.org/2001/XMLSchema#string)
+
+## Equivalent to
+
+[vesicle-mediated transport](http://purl.obolibrary.org/obo/GO_0016192)  and ([has target start location](http://purl.obolibrary.org/obo/RO_0002338) some `{start location}`)  and ([has target end location](http://purl.obolibrary.org/obo/RO_0002339) some `{end location}`)  and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some `{cargo}`)
+
+
+
+
+
+
+
+## Data preview
+
+*See full table [here](https://github.com/geneontology/go-ontology/tree/master/src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv)*
+
+|  |
+|
+
+
diff --git a/...atterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.md b/...atterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.md
@@ -1,10 +1,10 @@
 # vesicle-mediated transport differentiated by start and end locations
 
-[http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml](http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml)
+[http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml](http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml)
 
 ## Description
 
-TODO
+This pattern is for representing vesicle-mediated transport, differentiated by the start and end locations.
 
 
 
@@ -13,8 +13,8 @@ TODO
 
 | Variable name | Allowed type |
 |:--------------|:-------------|
-| `{start location}` | [cellular_component](http://purl.obolibrary.org/obo/GO_0005575) |
-| `{end location}` | [cellular_component](http://purl.obolibrary.org/obo/GO_0005575) |
+| `{start location}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
+| `{end location}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
 
 ## Name
 

diff --git a/...tterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv b/...tterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv
@@ -0,0 +1 @@
+defined_class	defined_class_label	cargo	cargo_label	end_location	end_location_label	start_location	start_location_label
diff --git a/src/ontology/imports/go-pattern-conformance.ttl b/src/ontology/imports/go-pattern-conformance.ttl
@@ -5279,7 +5279,7 @@
 <http://purl.obolibrary.org/obo/GO_0006885> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/regulation_of_characteristic.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0006893> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0006893> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0006904> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/involved_in_x_y.yaml> .
@@ -5856,7 +5856,7 @@
 <http://purl.obolibrary.org/obo/GO_0008328> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/protein_complex_by_activity.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0008333> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0008333> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0008348> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/negative_regulation.yaml> .
@@ -15390,7 +15390,7 @@
                                                                                   <http://purl.obolibrary.org/obo/go/patterns/regulation_by.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0032456> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0032456> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0032459> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/regulation.yaml> ,
@@ -22283,7 +22283,7 @@
 <http://purl.obolibrary.org/obo/GO_0045323> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/protein_complex_by_activity.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0045324> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0045324> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0045329> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/biosynthetic_process.yaml> .
@@ -25425,7 +25425,7 @@
 <http://purl.obolibrary.org/obo/GO_0048216> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/negative_regulation.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0048227> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0048227> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0048237> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/part_of_cell_component.yaml> .
@@ -33450,7 +33450,7 @@
 <http://purl.obolibrary.org/obo/GO_0071950> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/binding.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0071955> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0071955> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0071971> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/cc_assembly.yaml> .
@@ -36776,7 +36776,7 @@
 <http://purl.obolibrary.org/obo/GO_0098922> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/part_of_cell_component.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0098927> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0098927> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0098938> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/part_of_cell_component.yaml> .
@@ -36842,10 +36842,10 @@
 <http://purl.obolibrary.org/obo/GO_0099052> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/involved_in_x_y.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0099074> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0099074> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0099076> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_from_to.yaml> .
+<http://purl.obolibrary.org/obo/GO_0099076> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.yaml> .
 
 
 <http://purl.obolibrary.org/obo/GO_0099091> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/part_of_cell_component.yaml> .
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		defined_class defined_class_label cargo cargo_label end_location end_location_label start_location start_location_label