cmungall
commented
1 year ago I agree it’s not the best example!
On Wed, May 25, 2022 at 11:07 PM Nico Matentzoglu @.***> wrote:
@.**** commented on this pull request.
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882341847:
+
+#==================================
+# Slots #
+#==================================
+
+slots:
name:
range: string
disease:
range: HumanDisease
vital_status:
enum_range:
permissible_values:
LIVING:
DEAD:
UNDEAD:
😂
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882342173:
- DEAD:
UNDEAD:
+#==================================
+# Enums
+#==================================
+
+enums:
Disease:
reachable_from:
source_ontology: bioregistry:mondo
source_nodes:
- MONDO:0000001 ## disease or disorder
is_direct: false
relationship_types:
- rdfs:subClassOf
Amazing amazing amazing!
Thank you for doing this!
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882342944:
- range: HumanDisease
vital_status:
enum_range:
permissible_values:
LIVING:
DEAD:
UNDEAD:
+#==================================
+# Enums
+#==================================
+
+enums:
Disease:
reachable_from:
source_ontology: bioregistry:mondo
You are using br for denoting sources now? Why not obo:Mondo.owl? just out of curiosity
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882343361:
- reachable_from:
source_ontology: bioregistry:loinc
source_nodes:
- loinc:LP43571-6
is_direct: true
minus:
concepts:
- LOINC:5932-9
HCAExample:
see_also:
include:
- reachable_from:
source_ontology: bioregistry:go
source_nodes: ["GO:0007049", "GO:0022403"]
Different permissible syntax for lists?
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882344786:
- relationship_types:
- rdfs:subClassOf
minus:
permissible_values:
root_node:
meaning: MONDO:0000001 ## disease or disorder
HumanDisease:
description: Extends the Disease value set, including NCIT neoplasms, excluding non-human diseases
inherits:
- Disease
include:
- reachable_from:
source_ontology: bioregistry:ncit
source_nodes:
- NCIT:C3262
minus:
Shouldn't minus be directly under include, or does minus have a meaning beyond removing terms included by include?
In examples/dynamic-enums-example.yaml https://github.com/linkml/linkml-model/pull/106#discussion_r882345553:
- inherits:
- Disease
include:
- reachable_from:
source_ontology: bioregistry:ncit
source_nodes:
- NCIT:C3262
minus:
- reachable_from:
source_ontology: bioregistry:mondo
source_nodes:
- MONDO:0005583 ## non-human animal disease
relationship_types:
- rdfs:subClassOf
- permissible_values:
NOT_THIS_ONE:
Seems a bit odd to need an enum to exclude a single term while you can (above) easily exclude an entire branch?
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See https://github.com/linkml/linkml/issues/274