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ialarmedalien merged 3 commits into from
Oct 8, 2025
Merged

DateTimeValue and some attr/value reorganisation #78

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6338268
adding in a new type of attribute/value: the datetime value
ialarmedalien Sep 16, 2025
7477054
Removed unused NamedQuantityValue from the schema and some surplus wo…
ialarmedalien Sep 16, 2025
d583b5f
artefacts
ialarmedalien Sep 16, 2025
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92 changes: 47 additions & 45 deletions src/schema/datamodel/bertron_schema_pydantic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,9 @@ class AttributeValue(ConfiguredBaseModel):
'from_schema': 'https://w3id.org/ber-data/bertron_types'})

attribute: Attribute = Field(default=..., description="""The attribute being represented.""", json_schema_extra = { "linkml_meta": {'alias': 'attribute', 'domain_of': ['AttributeValue']} })
raw_value: Optional[str] = Field(default=None, description="""The raw value.""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value', 'domain_of': ['AttributeValue', 'NamedQuantityValue']} })
raw_value: Optional[str] = Field(default=None, description="""The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value',
'domain_of': ['AttributeValue'],
'mappings': ['nmdc:raw_value']} })


class Attribute(ConfiguredBaseModel):
Expand All @@ -173,63 +175,35 @@ class Attribute(ConfiguredBaseModel):

class QuantityValue(AttributeValue):
"""
A simple quantity, e.g. 2cm
A simple quantity, e.g. 2cm.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'nmdc:QuantityValue',
'from_schema': 'https://w3id.org/ber-data/bertron_types',
'mappings': ['schema:QuantityValue'],
'slot_usage': {'numeric_value': {'description': 'The number part of the '
'quantity',
'name': 'numeric_value'},
'raw_value': {'description': 'Unnormalized atomic string '
'slot_usage': {'raw_value': {'description': 'Unnormalized atomic string '
'representation, suggested syntax '
'{number} {unit}',
'name': 'raw_value'},
'unit': {'description': 'The unit of the quantity',
'name': 'unit'}}})
'name': 'raw_value'}}})

maximum_numeric_value: Optional[float] = Field(default=None, description="""The maximum value part, expressed as number, of the quantity value when the value covers a range.""", json_schema_extra = { "linkml_meta": {'alias': 'maximum_numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'domain_of': ['QuantityValue'],
'is_a': 'numeric_value',
'mappings': ['nmdc:maximum_numeric_value']} })
minimum_numeric_value: Optional[float] = Field(default=None, description="""The minimum value part, expressed as number, of the quantity value when the value covers a range.""", json_schema_extra = { "linkml_meta": {'alias': 'minimum_numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'domain_of': ['QuantityValue'],
'is_a': 'numeric_value',
'mappings': ['nmdc:minimum_numeric_value']} })
numeric_value: Optional[float] = Field(default=None, description="""The number part of the quantity""", json_schema_extra = { "linkml_meta": {'alias': 'numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'mappings': ['nmdc:numeric_value', 'qud:quantityValue', 'schema:value']} })
unit: Optional[str] = Field(default=None, description="""The unit of the quantity""", json_schema_extra = { "linkml_meta": {'alias': 'unit',
'aliases': ['scale'],
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'mappings': ['nmdc:unit', 'qud:unit', 'schema:unitCode']} })
attribute: Attribute = Field(default=..., description="""The attribute being represented.""", json_schema_extra = { "linkml_meta": {'alias': 'attribute', 'domain_of': ['AttributeValue']} })
raw_value: Optional[str] = Field(default=None, description="""Unnormalized atomic string representation, suggested syntax {number} {unit}""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value', 'domain_of': ['AttributeValue', 'NamedQuantityValue']} })


class NamedQuantityValue(ConfiguredBaseModel):
"""
A quantity value where the attribute is already specified.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/ber-data/bertron_types'})

maximum_numeric_value: Optional[float] = Field(default=None, description="""The maximum value part, expressed as number, of the quantity value when the value covers a range.""", json_schema_extra = { "linkml_meta": {'alias': 'maximum_numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'is_a': 'numeric_value',
'mappings': ['nmdc:maximum_numeric_value']} })
minimum_numeric_value: Optional[float] = Field(default=None, description="""The minimum value part, expressed as number, of the quantity value when the value covers a range.""", json_schema_extra = { "linkml_meta": {'alias': 'minimum_numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'is_a': 'numeric_value',
'mappings': ['nmdc:minimum_numeric_value']} })
numeric_value: Optional[float] = Field(default=None, description="""Links a quantity value to a number""", json_schema_extra = { "linkml_meta": {'alias': 'numeric_value',
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
numeric_value: Optional[float] = Field(default=None, description="""The numerical part of a quantity value.""", json_schema_extra = { "linkml_meta": {'alias': 'numeric_value',
'domain_of': ['QuantityValue'],
'mappings': ['nmdc:numeric_value', 'qud:quantityValue', 'schema:value']} })
unit: Optional[str] = Field(default=None, description="""Links a QuantityValue to a unit. Units should be taken from the UCUM unit collection or the Unit Ontology.""", json_schema_extra = { "linkml_meta": {'alias': 'unit',
'aliases': ['scale'],
'domain_of': ['QuantityValue', 'NamedQuantityValue'],
'mappings': ['nmdc:unit', 'qud:unit', 'schema:unitCode']} })
raw_value: Optional[str] = Field(default=None, description="""The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value',
'domain_of': ['AttributeValue', 'NamedQuantityValue'],
'domain_of': ['QuantityValue'],
'mappings': ['nmdc:unit', 'qud:unit', 'schema:unitCode', 'UO:0000000']} })
unit_cv_id: Optional[str] = Field(default=None, description="""The unit of the quantity, expressed as a CURIE from the Unit Ontology.""", json_schema_extra = { "linkml_meta": {'alias': 'unit_cv_id', 'domain_of': ['QuantityValue']} })
attribute: Attribute = Field(default=..., description="""The attribute being represented.""", json_schema_extra = { "linkml_meta": {'alias': 'attribute', 'domain_of': ['AttributeValue']} })
raw_value: Optional[str] = Field(default=None, description="""Unnormalized atomic string representation, suggested syntax {number} {unit}""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value',
'domain_of': ['AttributeValue'],
'mappings': ['nmdc:raw_value']} })


Expand All @@ -240,10 +214,38 @@ class TextValue(AttributeValue):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'nmdc:TextValue',
'from_schema': 'https://w3id.org/ber-data/bertron_types'})

value: Optional[str] = Field(default=None, description="""The value, as a text string.""", json_schema_extra = { "linkml_meta": {'alias': 'value', 'domain_of': ['TextValue']} })
value: Optional[str] = Field(default=None, description="""The value, as a text string.""", json_schema_extra = { "linkml_meta": {'alias': 'value', 'domain_of': ['TextValue', 'DateTimeValue']} })
value_cv_id: Optional[str] = Field(default=None, description="""For values that are in a controlled vocabulary (CV), this attribute should capture the controlled vocabulary ID for the value.""", json_schema_extra = { "linkml_meta": {'alias': 'value_cv_id', 'domain_of': ['TextValue']} })
attribute: Attribute = Field(default=..., description="""The attribute being represented.""", json_schema_extra = { "linkml_meta": {'alias': 'attribute', 'domain_of': ['AttributeValue']} })
raw_value: Optional[str] = Field(default=None, description="""The raw value.""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value', 'domain_of': ['AttributeValue', 'NamedQuantityValue']} })
raw_value: Optional[str] = Field(default=None, description="""The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value',
'domain_of': ['AttributeValue'],
'mappings': ['nmdc:raw_value']} })


class DateTimeValue(AttributeValue):
"""
A date or date and time value.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'nmdc:DateTimeValue',
'from_schema': 'https://w3id.org/ber-data/bertron_types',
'slot_usage': {'value': {'description': 'The date or date/time value, '
'expressed in ISO 8601-compatible '
'form. Dates should be expressed as '
'YYYY-MM-DD; times should be '
'expressed as HH:MM:SS with optional '
'milliseconds and an indication of '
'the timezone.',
'examples': [{'value': '2025-11-09'},
{'value': '2025-09-16T22:48:54Z'}],
'name': 'value'}}})

value: Optional[str] = Field(default=None, description="""The date or date/time value, expressed in ISO 8601-compatible form. Dates should be expressed as YYYY-MM-DD; times should be expressed as HH:MM:SS with optional milliseconds and an indication of the timezone.""", json_schema_extra = { "linkml_meta": {'alias': 'value',
'domain_of': ['TextValue', 'DateTimeValue'],
'examples': [{'value': '2025-11-09'}, {'value': '2025-09-16T22:48:54Z'}]} })
attribute: Attribute = Field(default=..., description="""The attribute being represented.""", json_schema_extra = { "linkml_meta": {'alias': 'attribute', 'domain_of': ['AttributeValue']} })
raw_value: Optional[str] = Field(default=None, description="""The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"""", json_schema_extra = { "linkml_meta": {'alias': 'raw_value',
'domain_of': ['AttributeValue'],
'mappings': ['nmdc:raw_value']} })


class Entity(ConfiguredBaseModel):
Expand Down Expand Up @@ -393,8 +395,8 @@ class DataCollection(ConfiguredBaseModel):
AttributeValue.model_rebuild()
Attribute.model_rebuild()
QuantityValue.model_rebuild()
NamedQuantityValue.model_rebuild()
TextValue.model_rebuild()
DateTimeValue.model_rebuild()
Entity.model_rebuild()
Coordinates.model_rebuild()
Name.model_rebuild()
Expand Down
87 changes: 40 additions & 47 deletions src/schema/jsonschema/bertron_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,35 @@
"title": "DataCollection",
"type": "object"
},
"DateTimeValue": {
"additionalProperties": false,
"description": "A date or date and time value.",
"properties": {
"attribute": {
"$ref": "#/$defs/Attribute",
"description": "The attribute being represented."
},
"raw_value": {
"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"",
"type": [
"string",
"null"
]
},
"value": {
"description": "The date or date/time value, expressed in ISO 8601-compatible form. Dates should be expressed as YYYY-MM-DD; times should be expressed as HH:MM:SS with optional milliseconds and an indication of the timezone.",
"type": [
"string",
"null"
]
}
},
"required": [
"attribute"
],
"title": "DateTimeValue",
"type": "object"
},
"Entity": {
"additionalProperties": false,
"description": "An object retrieved by BERtron from a BER data API.",
Expand Down Expand Up @@ -277,52 +306,9 @@
"title": "NameType",
"type": "string"
},
"NamedQuantityValue": {
"additionalProperties": false,
"description": "A quantity value where the attribute is already specified.",
"properties": {
"maximum_numeric_value": {
"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.",
"type": [
"number",
"null"
]
},
"minimum_numeric_value": {
"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.",
"type": [
"number",
"null"
]
},
"numeric_value": {
"description": "Links a quantity value to a number",
"type": [
"number",
"null"
]
},
"raw_value": {
"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"",
"type": [
"string",
"null"
]
},
"unit": {
"description": "Links a QuantityValue to a unit. Units should be taken from the UCUM unit collection or the Unit Ontology.",
"type": [
"string",
"null"
]
}
},
"title": "NamedQuantityValue",
"type": "object"
},
"QuantityValue": {
"additionalProperties": false,
"description": "A simple quantity, e.g. 2cm",
"description": "A simple quantity, e.g. 2cm.",
"properties": {
"attribute": {
"$ref": "#/$defs/Attribute",
Expand All @@ -343,7 +329,7 @@
]
},
"numeric_value": {
"description": "The number part of the quantity",
"description": "The numerical part of a quantity value.",
"type": [
"number",
"null"
Expand All @@ -357,7 +343,14 @@
]
},
"unit": {
"description": "The unit of the quantity",
"description": "Links a QuantityValue to a unit. Units should be taken from the UCUM unit collection or the Unit Ontology.",
"type": [
"string",
"null"
]
},
"unit_cv_id": {
"description": "The unit of the quantity, expressed as a CURIE from the Unit Ontology.",
"type": [
"string",
"null"
Expand All @@ -379,7 +372,7 @@
"description": "The attribute being represented."
},
"raw_value": {
"description": "The raw value.",
"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"",
"type": [
"string",
"null"
Expand Down
77 changes: 42 additions & 35 deletions src/schema/linkml/bertron_types.yaml
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Expand Up @@ -15,8 +15,13 @@ default_range: string

slots:

attribute:
description: The attribute being represented.
range: Attribute
required: true

numeric_value:
description: Links a quantity value to a number
description: The numerical part of a quantity value.
range: float
mappings:
- nmdc:numeric_value
Expand Down Expand Up @@ -45,11 +50,24 @@ slots:
description: Links a QuantityValue to a unit. Units should be taken from the UCUM unit collection or the Unit Ontology.
aliases:
- scale
range: unit
range: string
mappings:
- nmdc:unit
- qud:unit
- schema:unitCode
- UO:0000000

unit_cv_id:
description: The unit of the quantity, expressed as a CURIE from the Unit Ontology.
range: curie

value:
description: The value, as a text string.
range: string

value_cv_id:
description: For values that are in a controlled vocabulary (CV), this attribute should capture the controlled vocabulary ID for the value.
range: curie

classes:

Expand All @@ -61,14 +79,9 @@ classes:
class_uri: nmdc:AttributeValue
description: >-
The value for any value of attribute for an entity. This object can hold both the un-normalized atomic value and the structured value.
attributes:
attribute:
description: The attribute being represented.
range: Attribute
required: true
raw_value:
range: string
description: The raw value.
slots:
- attribute
- raw_value

Attribute:
description: A domain, measurement, attribute, property, or any descriptor for additional properties to be added to an entity. Where available, please use OBO Foundry ontologies or other controlled vocabularies for attributes; the label should be the term name from the ontology and the id should be the fully-qualified CURIE.
Expand All @@ -86,40 +99,41 @@ classes:
QuantityValue:
class_uri: nmdc:QuantityValue
is_a: AttributeValue
description: A simple quantity, e.g. 2cm
description: A simple quantity, e.g. 2cm.
slots:
- maximum_numeric_value
- minimum_numeric_value
- numeric_value
- unit
- unit_cv_id
slot_usage:
raw_value:
description: Unnormalized atomic string representation, suggested syntax {number} {unit}
unit:
description: The unit of the quantity
numeric_value:
description: The number part of the quantity
mappings:
- schema:QuantityValue

NamedQuantityValue:
description: A quantity value where the attribute is already specified.
slots:
- maximum_numeric_value
- minimum_numeric_value
- numeric_value
- unit
- raw_value

TextValue:
class_uri: nmdc:TextValue
is_a: AttributeValue
description: A quality, described using a text string.
attributes:
slots:
- value
- value_cv_id

DateTimeValue:
class_uri: nmdc:DateTimeValue
is_a: AttributeValue
description: A date or date and time value.
slots:
- value
slot_usage:
value:
description: The value, as a text string.
value_cv_id:
description: For values that are in a controlled vocabulary (CV), this attribute should capture the controlled vocabulary ID for the value.
description: The date or date/time value, expressed in ISO 8601-compatible form. Dates should be expressed as YYYY-MM-DD; times should be expressed as HH:MM:SS with optional milliseconds and an indication of the timezone.
# TODO: add pattern for ISO 8601 timestamps
examples:
- value: "2025-11-09"
- value: "2025-09-16T22:48:54Z"


types:
decimal degree:
Expand All @@ -128,10 +142,3 @@ types:
base: float
see_also:
- https://en.wikipedia.org/wiki/Decimal_degrees

unit:
base: str
uri: xsd:string
mappings:
- qud:Unit
- UO:0000000