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Predicate inverses & tests #1532

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merged 4 commits into from
Oct 28, 2024
Merged

Predicate inverses & tests #1532

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5e62b15
remove inverse on 'affects response to' and replace it by an inverse …
sierra-moxon Oct 28, 2024
2a86455
add test to validate that a predicate may have a canonical annotation…
sierra-moxon Oct 28, 2024
6cbb67d
fix makefile target to run pytests
sierra-moxon Oct 28, 2024
53862e6
fix makefile target to run pytests
sierra-moxon Oct 28, 2024
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,7 @@ test-schema: gen-project

test-python:
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(RUN) python -m unittest discover -p 'test_*.py'
$(RUN) pytest

lint:
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
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9 changes: 1 addition & 8 deletions biolink-model.yaml
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Expand Up @@ -2703,7 +2703,6 @@ slots:
- translator_minimal
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
inverse: response affected by
annotations:
canonical_predicate: true
exact_mappings:
Expand All @@ -2719,6 +2718,7 @@ slots:
- translator_minimal
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
inverse: affects response to

increases response to:
description: >-
Expand Down Expand Up @@ -2842,7 +2842,6 @@ slots:
range: gene
annotations:
canonical_predicate: true
inverse: has gene product
in_subset:
- translator_minimal

Expand Down Expand Up @@ -2883,7 +2882,6 @@ slots:
range: gene
annotations:
canonical_predicate: true
inverse: transcribed to
description: >-
x is transcribed from y if and only if x is synthesized from template y
exact_mappings:
Expand All @@ -2896,7 +2894,6 @@ slots:
range: protein
annotations:
canonical_predicate: true
inverse: translation of
description: >-
x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome
reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)
Expand Down Expand Up @@ -4525,7 +4522,6 @@ slots:
canonical_predicate: true
in_subset:
- translator_minimal
inverse: enabled by
exact_mappings:
- RO:0002327

Expand Down Expand Up @@ -4572,7 +4568,6 @@ slots:
in_subset:
- translator_minimal
- samples
inverse: derives into
exact_mappings:
- RO:0001000
- FMA:derives_from
Expand Down Expand Up @@ -4684,7 +4679,6 @@ slots:
opposite_of: is excipient of
in_subset:
- translator_minimal
inverse: is active ingredient of
mappings:
- RO:0002248

Expand Down Expand Up @@ -4838,7 +4832,6 @@ slots:
range: occurrent
annotations:
canonical_predicate: true
inverse: preceded by
in_subset:
- translator_minimal
close_mappings:
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17 changes: 16 additions & 1 deletion poetry.lock
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2 changes: 1 addition & 1 deletion project/jsonld/biolink_model.context.jsonld
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2024-10-14T23:06:39",
"generation_date": "2024-10-28T13:35:21",
"source": "biolink_model.yaml"
},
"@context": {
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6 changes: 3 additions & 3 deletions project/jsonld/biolink_model.jsonld
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Expand Up @@ -35761,9 +35761,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "biolink_model.yaml",
"source_file_date": "2024-10-14T23:06:36",
"source_file_size": 401471,
"generation_date": "2024-10-14T23:06:41",
"source_file_date": "2024-10-28T13:35:17",
"source_file_size": 401272,
"generation_date": "2024-10-28T13:35:23",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/biolink_model.context.jsonld",
Expand Down
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