From d69fda71e6ae2b15ae89ebb1d680fd0d37358caf Mon Sep 17 00:00:00 2001 From: Nomi Harris Date: Wed, 4 Sep 2024 21:04:09 -0700 Subject: [PATCH 1/2] update descriptions of ClassCreation and ObjectPropertyCreation Updating ClassCreation description as per @cmungall's suggestion. I guessed at how to update the description for ObjectPropertyCreation; not sure I got it right. Fixed a few minor typos I noticed. BTW, I do not understand these comments (which appeared twice starting at line 928): - if a node obsoletion C, C about N1, and C has direct replacement N2, and there exists an edge with an edge property referencing N1, it is possible to replace with N2 - if a node obsoletion C C about N1, and C has direct replacement N2, then N1 IAO:0100001 N2 (Mostly I don't understand "C about N1". Should "about" be some other word?) --- src/kgcl_schema/schema/kgcl.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/kgcl_schema/schema/kgcl.yaml b/src/kgcl_schema/schema/kgcl.yaml index d397151..453f63e 100644 --- a/src/kgcl_schema/schema/kgcl.yaml +++ b/src/kgcl_schema/schema/kgcl.yaml @@ -675,7 +675,7 @@ classes: - http://wiki.geneontology.org/index.php/Guidelines_for_creating_a_GO_term ClassCreation: is_a: NodeCreation - description: A node creation where the owl type is 'owl:Class' + description: A node creation where the node is a class (as opposed to a relation) slots: - superclass slot_usage: @@ -683,7 +683,7 @@ classes: string_serialization: create class {about_node} ObjectPropertyCreation: is_a: NodeCreation - description: A node creation where the owl type is 'ObjectProperty' + description: A node creation where the node is a property slot_usage: change_description: string_serialization: create object property {about_node} @@ -691,7 +691,7 @@ classes: is_a: NodeChange mixins: - Deletion - description: Deletion of a node from the graph. Note it is recommended nodes are + description: Deletion of a node from the graph. Note: it is recommended nodes are obsoleted and never merged, but this operation exists to represent deletions in ontologies, accidental or otherwise slot_usage: @@ -881,7 +881,7 @@ slots: deprecated: no longer required description: 'The type of a property (URI, CURIE, label) ' change_description: - description: A string serialization of the change. This should be both human-readable, + description: A string serialization of the change. This should be both human-readable and parseable. comments: - Form 1: IRIs are denoted by CURIEs, optionally followed by label in parenthesis @@ -896,7 +896,7 @@ slots: under 'biological process' retaining as 'exact synonym' has_textual_diff: description: A representation of character-level changes on a textual literal - property. For example, if a text definition may change by only a single character + property. For example, if a text definition changes by only a single character such as addition of a period, it is useful to be able to see this visually. comments: - this is NOT for representing the diff of the change as a whole. @@ -928,7 +928,7 @@ slots: - if a node obsoletion C, C about N1, and C has direct replacement N2, and there exists an edge with an edge property referencing N1, it is possible to replace with N2 - - if a node obsoletion C C about N1, and Chas direct replacement N2, then N1 IAO:0100001 + - if a node obsoletion C C about N1, and C has direct replacement N2, then N1 IAO:0100001 N2 has_nondirect_replacement: range: Node From e9f2cc0c790e6ab3f31121341d5df89aa30e0ba0 Mon Sep 17 00:00:00 2001 From: Nomi Harris Date: Wed, 4 Sep 2024 21:08:38 -0700 Subject: [PATCH 2/2] remove colon in description I didn't realize that was a syntax error --- src/kgcl_schema/schema/kgcl.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/kgcl_schema/schema/kgcl.yaml b/src/kgcl_schema/schema/kgcl.yaml index 453f63e..787277b 100644 --- a/src/kgcl_schema/schema/kgcl.yaml +++ b/src/kgcl_schema/schema/kgcl.yaml @@ -629,7 +629,7 @@ classes: is_a: change_set description: 'All changes forced as a result of this obsoletion. For example, starting with `A subClassOf B subClassOf C`, if we obsolete node B, then - we may decide to bundle in a node move change of A from B to C. Note: this + we may decide to bundle in a node move change of A from B to C. Note that this change set is not considered a part of the obsoletion, as obsoletion is considered atomic/simple. Instead this is a reference to a change set that may exist elsewhere'