Regenerate artifacts

jsonld-context/allianceModel.context.jsonld

@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from allianceModel.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-07-06T23:42:21\n    Schema: AllianceModel\n    metamodel version: 1.7.0\n    model version: 0.0.1\n    \n    id: https://github.com/alliance-genome/agr_curation_schema/alliance_schema\n    description: \n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from allianceModel.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-07-07T00:34:53\n    Schema: AllianceModel\n    metamodel version: 1.7.0\n    model version: 0.0.1\n    \n    id: https://github.com/alliance-genome/agr_curation_schema/alliance_schema\n    description: \n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "BIOGRID": "http://identifiers.org/biogrid/",
       "DIP": "http://identifiers.org/dip/",

python/affectedGenomicModel.py

@@ -1,5 +1,5 @@
 # Auto generated from affectedGenomicModel.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:12
+# Generation date: 2022-07-07T00:33:40
 # Schema: Alliance-Schema-Prototype-Affected-Genomic-Model
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/affectedGenomicModel

python/agent.py

@@ -1,5 +1,5 @@
 # Auto generated from agent.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:40:50
+# Generation date: 2022-07-07T00:33:17
 # Schema: person
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/person

python/allele.py

@@ -1,5 +1,5 @@
 # Auto generated from allele.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:47
+# Generation date: 2022-07-07T00:34:17
 # Schema: Alliance-Schema-Prototype-Allele
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/allele

python/allianceModel.py

@@ -1,5 +1,5 @@
 # Auto generated from allianceModel.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:34
+# Generation date: 2022-07-07T00:34:03
 # Schema: AllianceModel
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
@@ -1909,6 +1909,7 @@ class ExpressionAnnotation(AuditedObject):
     negated: Optional[Union[bool, Bool]] = None
     uncertain: Optional[Union[bool, Bool]] = None
     associated_with_figure: Optional[Union[Union[str, FigureCurie], List[Union[str, FigureCurie]]]] = empty_list()
+    assay_notes: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.belongs_to_expression_experiment):
@@ -1935,6 +1936,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.associated_with_figure = [self.associated_with_figure] if self.associated_with_figure is not None else []
         self.associated_with_figure = [v if isinstance(v, FigureCurie) else FigureCurie(v) for v in self.associated_with_figure]
 
+        if self.assay_notes is not None and not isinstance(self.assay_notes, str):
+            self.assay_notes = str(self.assay_notes)
+
         super().__post_init__(**kwargs)
 
 
@@ -1956,7 +1960,6 @@ class TemporalContext(AuditedObject):
     developmental_stage_stop: Optional[Union[str, StageTermCurie]] = None
     age: Optional[str] = None
     temporal_qualifiers: Optional[Union[str, "TemporalQualifierSet"]] = None
-    stage_uncertainty: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.developmental_stage_start is not None and not isinstance(self.developmental_stage_start, StageTermCurie):
@@ -1971,9 +1974,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.temporal_qualifiers is not None and not isinstance(self.temporal_qualifiers, TemporalQualifierSet):
             self.temporal_qualifiers = TemporalQualifierSet(self.temporal_qualifiers)
 
-        if self.stage_uncertainty is not None and not isinstance(self.stage_uncertainty, str):
-            self.stage_uncertainty = str(self.stage_uncertainty)
-
         super().__post_init__(**kwargs)
 
 
@@ -2043,7 +2043,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 class GeneExpressionStatement(EntityStatement):
     """
     Free-text describing some aspect(s) of a gene's expression, particularly nuanced information that is not readily
-    captured in annotations. May summarize data from many annotations and/or many publications.
+    captured in annotations. May summarize data from many annotations and/or many experiments.
     """
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -4843,8 +4843,6 @@ def _addvals(cls):
 
 class TemporalQualifierSet(EnumDefinitionImpl):
 
-    progressive = PermissibleValue(text="progressive",
-                                             description="An event that gets more pronounced with time.")
     throughout = PermissibleValue(text="throughout",
                                            description="An event that happens from start to end times included in the annotation")
     sometime_during = PermissibleValue(text="sometime_during",
@@ -4867,8 +4865,6 @@ class ExpressionStatementTypeEnum(EnumDefinitionImpl):
 
     expression_summary = PermissibleValue(text="expression_summary",
                                                            description="Free-text that summarizes expression across many annotations, experiments or publictaions.")
-    when_expressed_note = PermissibleValue(text="when_expressed_note",
-                                                             description="Additional free-text describing the stage/age of expression in an expression annotation.")
     where_expressed_note = PermissibleValue(text="where_expressed_note",
                                                                description="Additional free-text describing the anatomical site of expression in an expression annotation.")
     expression_annotation_note = PermissibleValue(text="expression_annotation_note",
@@ -6237,9 +6233,6 @@ class slots:
 slots.specimen_genomic_model = Slot(uri=ALLIANCE.specimen_genomic_model, name="specimen_genomic_model", curie=ALLIANCE.curie('specimen_genomic_model'),
                    model_uri=ALLIANCE.specimen_genomic_model, domain=ExpressionExperiment, range=Optional[Union[str, AffectedGenomicModelCurie]])
 
-slots.stage_uncertainty = Slot(uri=ALLIANCE.stage_uncertainty, name="stage_uncertainty", curie=ALLIANCE.curie('stage_uncertainty'),
-                   model_uri=ALLIANCE.stage_uncertainty, domain=TemporalContext, range=Optional[str])
-
 slots.temporal_qualifiers = Slot(uri=ALLIANCE.temporal_qualifiers, name="temporal_qualifiers", curie=ALLIANCE.curie('temporal_qualifiers'),
                    model_uri=ALLIANCE.temporal_qualifiers, domain=TemporalContext, range=Optional[Union[str, "TemporalQualifierSet"]])
 
@@ -6249,6 +6242,9 @@ class slots:
 slots.where_expressed = Slot(uri=ALLIANCE.where_expressed, name="where_expressed", curie=ALLIANCE.curie('where_expressed'),
                    model_uri=ALLIANCE.where_expressed, domain=ExpressionAnnotation, range=Optional[Union[dict, "AnatomicalSite"]])
 
+slots.assay_notes = Slot(uri=ALLIANCE.assay_notes, name="assay_notes", curie=ALLIANCE.curie('assay_notes'),
+                   model_uri=ALLIANCE.assay_notes, domain=None, range=Optional[str])
+
 slots.gene_type = Slot(uri=ALLIANCE.gene_type, name="gene_type", curie=ALLIANCE.curie('gene_type'),
                    model_uri=ALLIANCE.gene_type, domain=Gene, range=Optional[Union[str, SOTermCurie]])
 

python/biologicalEntitySet.py

@@ -1,5 +1,5 @@
 # Auto generated from biologicalEntitySet.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:40:57
+# Generation date: 2022-07-07T00:33:25
 # Schema: Alliance-Schema-Prototype-Biological-Entity-Set
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/biologicalEntitySet.yaml

python/bulkload.py

@@ -1,5 +1,5 @@
 # Auto generated from bulkload.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:01
+# Generation date: 2022-07-07T00:33:29
 # Schema: bulkload.yaml
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/bulkload.yaml

python/controlledVocabulary.py

@@ -1,5 +1,5 @@
 # Auto generated from controlledVocabulary.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:42:01
+# Generation date: 2022-07-07T00:34:32
 # Schema: Alliance-Schema-Prototype-Controlled-Vocabulary
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/controlledVocabulary.yaml

python/core.py

@@ -1,5 +1,5 @@
 # Auto generated from core.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:54
+# Generation date: 2022-07-07T00:34:25
 # Schema: core
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/core.yaml

python/curationReport.py

@@ -1,5 +1,5 @@
 # Auto generated from curationReport.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:19
+# Generation date: 2022-07-07T00:33:48
 # Schema: bulkload.yaml
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/bulkload.yaml

python/expression.py

@@ -1,5 +1,5 @@
 # Auto generated from expression.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:23
+# Generation date: 2022-07-07T00:33:52
 # Schema: expression.yaml
 #
 # id: https://github.com/alliance-genome/agr_persistent_schema/src/schema/expression.yaml
@@ -456,6 +456,7 @@ class ExpressionAnnotation(AuditedObject):
     negated: Optional[Union[bool, Bool]] = None
     uncertain: Optional[Union[bool, Bool]] = None
     associated_with_figure: Optional[Union[Union[str, FigureCurie], List[Union[str, FigureCurie]]]] = empty_list()
+    assay_notes: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.belongs_to_expression_experiment):
@@ -482,6 +483,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.associated_with_figure = [self.associated_with_figure] if self.associated_with_figure is not None else []
         self.associated_with_figure = [v if isinstance(v, FigureCurie) else FigureCurie(v) for v in self.associated_with_figure]
 
+        if self.assay_notes is not None and not isinstance(self.assay_notes, str):
+            self.assay_notes = str(self.assay_notes)
+
         super().__post_init__(**kwargs)
 
 
@@ -503,7 +507,6 @@ class TemporalContext(AuditedObject):
     developmental_stage_stop: Optional[Union[str, StageTermCurie]] = None
     age: Optional[str] = None
     temporal_qualifiers: Optional[Union[str, "TemporalQualifierSet"]] = None
-    stage_uncertainty: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.developmental_stage_start is not None and not isinstance(self.developmental_stage_start, StageTermCurie):
@@ -518,9 +521,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.temporal_qualifiers is not None and not isinstance(self.temporal_qualifiers, TemporalQualifierSet):
             self.temporal_qualifiers = TemporalQualifierSet(self.temporal_qualifiers)
 
-        if self.stage_uncertainty is not None and not isinstance(self.stage_uncertainty, str):
-            self.stage_uncertainty = str(self.stage_uncertainty)
-
         super().__post_init__(**kwargs)
 
 
@@ -1277,7 +1277,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 class GeneExpressionStatement(EntityStatement):
     """
     Free-text describing some aspect(s) of a gene's expression, particularly nuanced information that is not readily
-    captured in annotations. May summarize data from many annotations and/or many publications.
+    captured in annotations. May summarize data from many annotations and/or many experiments.
     """
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -4128,8 +4128,6 @@ def _addvals(cls):
 
 class TemporalQualifierSet(EnumDefinitionImpl):
 
-    progressive = PermissibleValue(text="progressive",
-                                             description="An event that gets more pronounced with time.")
     throughout = PermissibleValue(text="throughout",
                                            description="An event that happens from start to end times included in the annotation")
     sometime_during = PermissibleValue(text="sometime_during",
@@ -4152,8 +4150,6 @@ class ExpressionStatementTypeEnum(EnumDefinitionImpl):
 
     expression_summary = PermissibleValue(text="expression_summary",
                                                            description="Free-text that summarizes expression across many annotations, experiments or publictaions.")
-    when_expressed_note = PermissibleValue(text="when_expressed_note",
-                                                             description="Additional free-text describing the stage/age of expression in an expression annotation.")
     where_expressed_note = PermissibleValue(text="where_expressed_note",
                                                                description="Additional free-text describing the anatomical site of expression in an expression annotation.")
     expression_annotation_note = PermissibleValue(text="expression_annotation_note",
@@ -4536,9 +4532,6 @@ class slots:
 slots.specimen_genomic_model = Slot(uri=ALLIANCE.specimen_genomic_model, name="specimen_genomic_model", curie=ALLIANCE.curie('specimen_genomic_model'),
                    model_uri=ALLIANCE.specimen_genomic_model, domain=ExpressionExperiment, range=Optional[Union[str, AffectedGenomicModelCurie]])
 
-slots.stage_uncertainty = Slot(uri=ALLIANCE.stage_uncertainty, name="stage_uncertainty", curie=ALLIANCE.curie('stage_uncertainty'),
-                   model_uri=ALLIANCE.stage_uncertainty, domain=TemporalContext, range=Optional[str])
-
 slots.temporal_qualifiers = Slot(uri=ALLIANCE.temporal_qualifiers, name="temporal_qualifiers", curie=ALLIANCE.curie('temporal_qualifiers'),
                    model_uri=ALLIANCE.temporal_qualifiers, domain=TemporalContext, range=Optional[Union[str, "TemporalQualifierSet"]])
 
@@ -4548,6 +4541,9 @@ class slots:
 slots.where_expressed = Slot(uri=ALLIANCE.where_expressed, name="where_expressed", curie=ALLIANCE.curie('where_expressed'),
                    model_uri=ALLIANCE.where_expressed, domain=ExpressionAnnotation, range=Optional[Union[dict, "AnatomicalSite"]])
 
+slots.assay_notes = Slot(uri=ALLIANCE.assay_notes, name="assay_notes", curie=ALLIANCE.curie('assay_notes'),
+                   model_uri=ALLIANCE.assay_notes, domain=None, range=Optional[str])
+
 slots.subtype = Slot(uri=ALLIANCE.subtype, name="subtype", curie=ALLIANCE.curie('subtype'),
                    model_uri=ALLIANCE.subtype, domain=AffectedGenomicModel, range=Union[str, "SubtypeValues"])
 

python/gene.py

@@ -1,5 +1,5 @@
 # Auto generated from gene.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:27
+# Generation date: 2022-07-07T00:33:56
 # Schema: gene
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/gene.yaml

python/geneInteraction.py

@@ -1,5 +1,5 @@
 # Auto generated from geneInteraction.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:31
+# Generation date: 2022-07-07T00:34:00
 # Schema: Alliance-Gene-Interaction-Schema-Prototype
 #
 # id: https://github.com/alliance-genome/agr_persistent_schema/geneInteraction.yaml

python/image.py

@@ -1,5 +1,5 @@
 # Auto generated from image.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:50
+# Generation date: 2022-07-07T00:34:21
 # Schema: image.yaml
 #
 # id: https://github.com/alliance-genome/agr_persistent_schema/src/schema/image.yaml

python/ingest.py

@@ -1,5 +1,5 @@
 # Auto generated from ingest.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:43
+# Generation date: 2022-07-07T00:34:13
 # Schema: Alliance-Schema-Ingest
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/model/schema/ingest

python/mod.py

@@ -1,5 +1,5 @@
 # Auto generated from mod.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:39
+# Generation date: 2022-07-07T00:34:09
 # Schema: mod
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/mod

python/modCorpusAssociation.py

@@ -1,5 +1,5 @@
 # Auto generated from modCorpusAssociation.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:42:11
+# Generation date: 2022-07-07T00:34:44
 # Schema: modCorpusAssociation
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/modCorpusAssociation

python/ontologyTerm.py

@@ -1,5 +1,5 @@
 # Auto generated from ontologyTerm.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:40:46
+# Generation date: 2022-07-07T00:33:12
 # Schema: Alliance-Schema-Prototype-Ontology-Term
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/ontologyTerm.yaml

python/orthology.py

@@ -1,5 +1,5 @@
 # Auto generated from orthology.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:42:04
+# Generation date: 2022-07-07T00:34:36
 # Schema: Alliance-Schema-Orthology-Term
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/ontologyTerm

python/phenotypeAndDiseaseAnnotation.py

@@ -1,5 +1,5 @@
 # Auto generated from phenotypeAndDiseaseAnnotation.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:40:54
+# Generation date: 2022-07-07T00:33:21
 # Schema: Alliance-Schema-Prototype-Phenotype-and-Disease-Annotation
 #
 # id: https://github.com/alliance-genome/agr_persistent_schema/phenotypeAndDiseaseAnnotation.yaml

python/reagent.py

@@ -1,5 +1,5 @@
 # Auto generated from reagent.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:15
+# Generation date: 2022-07-07T00:33:44
 # Schema: reagent.yaml
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/reagent.yaml

python/reference.py

@@ -1,5 +1,5 @@
 # Auto generated from reference.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:57
+# Generation date: 2022-07-07T00:34:28
 # Schema: reference
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/reference

python/resource.py

@@ -1,5 +1,5 @@
 # Auto generated from resource.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:08
+# Generation date: 2022-07-07T00:33:37
 # Schema: resource
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/resource

python/variantConsequence.py

@@ -1,5 +1,5 @@
 # Auto generated from variantConsequence.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:42:08
+# Generation date: 2022-07-07T00:34:40
 # Schema: variantConsequence
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence

python/variation.py

@@ -1,5 +1,5 @@
 # Auto generated from variation.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-07-06T23:41:05
+# Generation date: 2022-07-07T00:33:33
 # Schema: Alliance-Schema-Prototype-Variation
 #
 # id: https://github.com/alliance-genome/agr_curation_schema/src/schema/variation

shex/allianceModel.shex

@@ -578,7 +578,8 @@ linkml:Nodeidentifier NONLITERAL
           <expression_qualifiers> @<ExpressionQualifierSet> ? ;
           <negated> @linkml:Boolean ? ;
           <uncertain> @linkml:Boolean ? ;
-          <associated_with_figure> @<Figure> *
+          <associated_with_figure> @<Figure> * ;
+          <assay_notes> @linkml:String ?
        ) ;
        rdf:type [ <ExpressionAnnotation> ] ?
     )
@@ -1237,8 +1238,7 @@ linkml:Nodeidentifier NONLITERAL
           <developmental_stage_start> @<StageTerm> ? ;
           <developmental_stage_stop> @<StageTerm> ? ;
           <age> @linkml:String ? ;
-          <temporal_qualifiers> @<TemporalQualifierSet> ? ;
-          <stage_uncertainty> @linkml:String ?
+          <temporal_qualifiers> @<TemporalQualifierSet> ?
        ) ;
        rdf:type [ <TemporalContext> ] ?
     )

shex/expression.shex

@@ -576,7 +576,8 @@ linkml:Nodeidentifier NONLITERAL
           <expression_qualifiers> @<ExpressionQualifierSet> ? ;
           <negated> @linkml:Boolean ? ;
           <uncertain> @linkml:Boolean ? ;
-          <associated_with_figure> @<Figure> *
+          <associated_with_figure> @<Figure> * ;
+          <assay_notes> @linkml:String ?
        ) ;
        rdf:type [ <ExpressionAnnotation> ] ?
     )
@@ -1107,8 +1108,7 @@ linkml:Nodeidentifier NONLITERAL
           <developmental_stage_start> @<StageTerm> ? ;
           <developmental_stage_stop> @<StageTerm> ? ;
           <age> @linkml:String ? ;
-          <temporal_qualifiers> @<TemporalQualifierSet> ? ;
-          <stage_uncertainty> @linkml:String ?
+          <temporal_qualifiers> @<TemporalQualifierSet> ?
        ) ;
        rdf:type [ <TemporalContext> ] ?
     )