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Expand Measurement and Procedure classes
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@caufieldjh
caufieldjh committed Dec 11, 2024
1 parent 91a3bad commit 4479238
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Showing 2 changed files with 179 additions and 35 deletions.
113 changes: 97 additions & 16 deletions src/ontogpt/templates/phenopackets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -505,7 +505,7 @@ class Phenopacket(ConfiguredBaseModel):
'to resolve the phenotype (if '
'applicable), and its severity.'}},
'domain_of': ['Phenopacket']} })
measurements: Optional[List[str]] = Field(None, description="""Quantifiable measurements related to the individual""", json_schema_extra = { "linkml_meta": {'alias': 'measurements',
measurements: Optional[List[Measurement]] = Field(None, description="""Quantifiable measurements related to the individual""", json_schema_extra = { "linkml_meta": {'alias': 'measurements',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A semicolon-separated list of '
'measurements taken from the individual '
Expand Down Expand Up @@ -805,9 +805,12 @@ class Procedure(ConfiguredBaseModel):
body_site: Optional[str] = Field(None, description="""FHIR mapping: Procedure.bodySite""", json_schema_extra = { "linkml_meta": {'alias': 'body_site',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The code for the body site of the '
'procedure.'}},
'procedure. This may require inference '
'from the procedure, e.g., a colonoscopy '
'is done on the colon, bronchoscopy is '
'done on the lungs, and so on.'}},
'domain_of': ['Procedure']} })
performed: Optional[TimeElement] = Field(None, description="""When the procedure was performed.""", json_schema_extra = { "linkml_meta": {'alias': 'performed',
performed: Optional[str] = Field(None, description="""When the procedure was performed.""", json_schema_extra = { "linkml_meta": {'alias': 'performed',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The date and time the procedure was '
'performed.'}},
Expand Down Expand Up @@ -1284,7 +1287,14 @@ class ComplexValue(ConfiguredBaseModel):
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets'})

typedQuantities: Optional[List[TypedQuantity]] = Field(None, description="""The quantities required to fully describe the complex value. For example the systolic and diastolic blood pressure quantities""", json_schema_extra = { "linkml_meta": {'alias': 'typedQuantities', 'domain_of': ['ComplexValue']} })
typedQuantities: Optional[List[TypedQuantity]] = Field(None, description="""The quantities required to fully describe the complex value. For example the systolic and diastolic blood pressure quantities""", json_schema_extra = { "linkml_meta": {'alias': 'typedQuantities',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A semicolon-delimited list of the '
'quantities required to fully describe '
'the complex value. For example, the '
'systolic and diastolic blood pressure '
'quantities.'}},
'domain_of': ['ComplexValue']} })


class Measurement(ConfiguredBaseModel):
Expand All @@ -1297,17 +1307,36 @@ class Measurement(ConfiguredBaseModel):
{'slot_conditions': {'complexValue': {'name': 'complexValue',
'required': True}}}]}}]})

assay: Optional[str] = Field(None, description="""An ontology class which describes the assay used to produce the measurement. For example \"body temperature\" (CMO:0000015) or \"Platelets [#/volume] in Blood\" (LOINC:26515-7) FHIR mapping: Observation.code'""", json_schema_extra = { "linkml_meta": {'alias': 'assay', 'domain_of': ['Measurement']} })
complexValue: Optional[ComplexValue] = Field(None, description="""The measurement result, expressed as multiple values.""", json_schema_extra = { "linkml_meta": {'alias': 'complexValue', 'domain_of': ['Measurement']} })
assay: Optional[str] = Field(None, description="""An ontology class which describes the assay used to produce the measurement. For example \"body temperature\" (CMO:0000015) or \"Platelets [#/volume] in Blood\" (LOINC:26515-7) FHIR mapping: Observation.code'""", json_schema_extra = { "linkml_meta": {'alias': 'assay',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The assay used to produce the '
'measurement. Do not include acronyms or '
'abbreviations; if the assay is referred '
'to with an acronym then expand to its '
'full name.'},
'prompt.examples': {'tag': 'prompt.examples',
'value': 'body temperature; platelets in '
'blood'}},
'domain_of': ['Measurement']} })
complexValue: Optional[ComplexValue] = Field(None, description="""The measurement result, expressed as multiple values.""", json_schema_extra = { "linkml_meta": {'alias': 'complexValue',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The measurement result, expressed as '
'multiple values.'}},
'domain_of': ['Measurement']} })
description: Optional[str] = Field(None, description="""Free-text description of the feature. Note this is not a acceptable place to document/describe the phenotype - the type and onset etc... fields should be used for this purpose.""", json_schema_extra = { "linkml_meta": {'alias': 'description',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'Free-text description of the feature. '
'Describe only the observed feature, not '
'the phenotype. Do not include type or '
'onset.'}},
'domain_of': ['Cohort',
'ExternalReference',
'Biosample',
'Measurement',
'PhenotypicFeature',
'GeneDescriptor',
'VariationDescriptor']} })
procedure: Optional[str] = Field(None, description="""Clinical procedure performed on the subject in order to produce the measurement.""", json_schema_extra = { "linkml_meta": {'alias': 'procedure',
procedure: Optional[Procedure] = Field(None, description="""Clinical procedure performed on the subject in order to produce the measurement.""", json_schema_extra = { "linkml_meta": {'alias': 'procedure',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The clinical procedure performed on the '
'subject in order to produce the '
Expand All @@ -1316,8 +1345,18 @@ class Measurement(ConfiguredBaseModel):
'body site, and the time the procedure '
'was performed, if known.'}},
'domain_of': ['Biosample', 'Measurement', 'MedicalAction']} })
timeObserved: Optional[TimeElement] = Field(None, description="""The time at which the measurement was made""", json_schema_extra = { "linkml_meta": {'alias': 'timeObserved', 'domain_of': ['Measurement']} })
value: Optional[str] = Field(None, description="""The result of the measurement.""", json_schema_extra = { "linkml_meta": {'alias': 'value',
timeObserved: Optional[str] = Field(None, description="""The time at which the measurement was made""", json_schema_extra = { "linkml_meta": {'alias': 'timeObserved',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The time at which the measurement was '
'made. This should be an ISO 8601 '
'timestamp.'}},
'domain_of': ['Measurement']} })
value: Optional[Value] = Field(None, description="""The result of the measurement.""", json_schema_extra = { "linkml_meta": {'alias': 'value',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The result of the measurement. This '
'should be a single value. If the '
'measurement is complex, use the '
'complexValue field.'}},
'domain_of': ['Measurement',
'Quantity',
'Expression',
Expand All @@ -1327,11 +1366,30 @@ class Measurement(ConfiguredBaseModel):


class Quantity(ConfiguredBaseModel):
"""
A single quantifiable value, along with its units and reference range, if known.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets'})

referenceRange: Optional[ReferenceRange] = Field(None, description="""Reference range for the quantity e.g. The normal range of platelets is 150,000 to 450,000 platelets/uL.""", json_schema_extra = { "linkml_meta": {'alias': 'referenceRange', 'domain_of': ['Quantity']} })
unit: Optional[OntologyClass] = Field(None, description="""For instance, NCIT subhierarchy, Unit of Measure (Code C25709), https://www.ebi.ac.uk/ols/ontologies/uo""", json_schema_extra = { "linkml_meta": {'alias': 'unit', 'domain_of': ['Quantity', 'ReferenceRange']} })
value: Optional[float] = Field(None, description="""the value of the quantity in the units e.g. 2.0 mg""", json_schema_extra = { "linkml_meta": {'alias': 'value',
referenceRange: Optional[str] = Field(None, description="""Reference range for the quantity e.g. The normal range of platelets is 150,000 to 450,000 platelets/uL.""", json_schema_extra = { "linkml_meta": {'alias': 'referenceRange',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The reference range for the quantity. If '
'the reference range is not known, this '
'value should be UNKNOWN.'}},
'domain_of': ['Quantity']} })
unit: Optional[str] = Field(None, description="""For instance, NCIT subhierarchy, Unit of Measure (Code C25709), https://www.ebi.ac.uk/ols/ontologies/uo""", json_schema_extra = { "linkml_meta": {'alias': 'unit',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The unit of measure for the quantity. '
'This should be a human-readable string, '
"e.g. 'mg/dL'. If the unit is not known, "
'this value should be UNKNOWN.'}},
'domain_of': ['Quantity', 'ReferenceRange']} })
value: Optional[str] = Field(None, description="""the value of the quantity in the units e.g. 2.0 mg""", json_schema_extra = { "linkml_meta": {'alias': 'value',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The value of the quantity in the units. '
'This should be a single value. Do not '
'include units or any non-numeric '
'value.'}},
'domain_of': ['Measurement',
'Quantity',
'Expression',
Expand All @@ -1354,19 +1412,42 @@ class TypedQuantity(ConfiguredBaseModel):
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets'})

quantity: Optional[Quantity] = Field(None, description="""e.g. mm Hg""", json_schema_extra = { "linkml_meta": {'alias': 'quantity', 'domain_of': ['TypedQuantity', 'Value', 'DoseInterval']} })
type: Optional[OntologyClass] = Field(None, description="""e.g. diastolic, systolic""", json_schema_extra = { "linkml_meta": {'alias': 'type', 'domain_of': ['TypedQuantity', 'PhenotypicFeature']} })
quantity: Optional[Quantity] = Field(None, description="""e.g. mm Hg""", json_schema_extra = { "linkml_meta": {'alias': 'quantity',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A single quantifiable value of the '
'measurement, along with its units and '
'reference range, if known.'}},
'domain_of': ['TypedQuantity', 'Value', 'DoseInterval']} })
type: Optional[str] = Field(None, description="""e.g. diastolic, systolic""", json_schema_extra = { "linkml_meta": {'alias': 'type',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A categorical or descriptive value of '
"the measurement, e.g., 'diastolic' or "
"'systolic'."}},
'domain_of': ['TypedQuantity', 'PhenotypicFeature']} })


class Value(ConfiguredBaseModel):
"""
A single specific value.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets',
'rules': [{'postconditions': {'exactly_one_of': [{'slot_conditions': {'quantity': {'name': 'quantity',
'required': True}}},
{'slot_conditions': {'ontologyClass': {'name': 'ontologyClass',
'required': True}}}]}}]})

ontologyClass: Optional[OntologyClass] = Field(None, description="""for use with things such as categories 'red', 'yellow' or 'absent'/'present'""", json_schema_extra = { "linkml_meta": {'alias': 'ontologyClass', 'domain_of': ['Value', 'TherapeuticRegimen']} })
quantity: Optional[Quantity] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'quantity', 'domain_of': ['TypedQuantity', 'Value', 'DoseInterval']} })
ontologyClass: Optional[str] = Field(None, description="""for use with things such as categories 'red', 'yellow' or 'absent'/'present'""", json_schema_extra = { "linkml_meta": {'alias': 'ontologyClass',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A categorical or descriptive value of '
"the measurement, e.g., 'red', 'yellow', "
"'absent', or 'present'."}},
'domain_of': ['Value', 'TherapeuticRegimen']} })
quantity: Optional[Quantity] = Field(None, description="""A single quantifiable value.""", json_schema_extra = { "linkml_meta": {'alias': 'quantity',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'A single quantifiable value of the '
'measurement, along with its units and '
'reference range, if known.'}},
'domain_of': ['TypedQuantity', 'Value', 'DoseInterval']} })


class DoseInterval(ConfiguredBaseModel):
Expand Down
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