From eb8c6f50583d2bbff98775bdc12cdde44c1f4317 Mon Sep 17 00:00:00 2001 From: ontobot <52354757+ontobot@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:47:29 -0500 Subject: [PATCH] [create-pull-request] automated change (#29413) Co-authored-by: balhoff --- docs/patterns/index.md | 5 +- ...iated_transport_differentiated_by_cargo.md | 6 +-- ...ed_by_cargo_and_start_and_end_locations.md | 49 +++++++++++++++++++ ...fferentiated_by_start_and_end_locations.md | 8 +-- ...d_by_cargo_and_start_and_end_locations.tsv | 1 + .../imports/go-pattern-conformance.ttl | 18 +++---- 6 files changed, 69 insertions(+), 18 deletions(-) create mode 100644 docs/patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md create mode 100644 src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv diff --git a/docs/patterns/index.md b/docs/patterns/index.md index 3f3216feb8..156fe270c2 100644 --- 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 index 606285521a..8411b5115b 100644 --- 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/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md b/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.md new file mode 100644 index 0000000000..7270749a58 --- /dev/null +++ b/docs/patterns/vesicle_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/docs/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.md b/docs/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.md index 9157ce527e..ce3ece69ad 100644 --- a/docs/patterns/vesicle_mediated_transport_differentiated_by_start_and_end_locations.md +++ b/docs/patterns/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/src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv b/src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo_and_start_and_end_locations.tsv new file mode 100644 index 0000000000..b2249a35d3 --- /dev/null +++ b/src/design_patterns/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 index a17262efe9..cc3b0dd4d5 100644 --- a/src/ontology/imports/go-pattern-conformance.ttl +++ b/src/ontology/imports/go-pattern-conformance.ttl @@ -5279,7 +5279,7 @@ . - . + . . @@ -5856,7 +5856,7 @@ . - . + . . @@ -15390,7 +15390,7 @@ . - . + . , @@ -22283,7 +22283,7 @@ . - . + . . @@ -25425,7 +25425,7 @@ . - . + . . @@ -33450,7 +33450,7 @@ . - . + . . @@ -36776,7 +36776,7 @@ . - . + . . @@ -36842,10 +36842,10 @@ . - . + . - . + . .