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Expand the Treatment class
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@caufieldjh
caufieldjh committed Dec 13, 2024
1 parent d92b14e commit c39a29e
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Showing 2 changed files with 203 additions and 15 deletions.
149 changes: 145 additions & 4 deletions src/ontogpt/templates/phenopackets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,6 +231,10 @@ class NCITIntentType(str):
pass


class NCITROAType(str):
pass



class ExtractionResult(ConfiguredBaseModel):
"""
Expand Down Expand Up @@ -1981,13 +1985,42 @@ class Treatment(ConfiguredBaseModel):
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets'})

agent: Optional[OntologyClass] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'agent', 'domain_of': ['Treatment']} })
agent: Optional[str] = Field(None, description="""Treatment agent""", json_schema_extra = { "linkml_meta": {'alias': 'agent',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The treatment agent, such as a drug or '
'other therapeutic material. If the agent '
'is not specified, do not include a value '
'for this field.'}},
'domain_of': ['Treatment']} })
cumulativeDose: Optional[Quantity] = Field(None, description="""ARGO mapping chemotherapy::cumulative_drug_dosage""", json_schema_extra = { "linkml_meta": {'alias': 'cumulativeDose',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The cumulative dose of the treatment '
'agent, with value and units. If the '
'cumulative dose is not specified, do not '
'include a value for this field.'}},
'domain_of': ['Treatment'],
'exact_mappings': ['ARGO:chemotherapy.cumulative_drug_dosage']} })
doseIntervals: Optional[List[DoseInterval]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'doseIntervals', 'domain_of': ['Treatment']} })
drugType: Optional[DrugType] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'drugType', 'domain_of': ['Treatment']} })
routeOfAdministration: Optional[OntologyClass] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'routeOfAdministration', 'domain_of': ['Treatment']} })
doseIntervals: Optional[List[str]] = Field(None, description="""Intervals at which the treatment agent is administered.""", json_schema_extra = { "linkml_meta": {'alias': 'doseIntervals', 'domain_of': ['Treatment']} })
drugType: Optional[DrugType] = Field(None, description="""Type of drug used in the treatment.""", json_schema_extra = { "linkml_meta": {'alias': 'drugType',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The type of drug used in the treatment. '
'Must be one of: '
'ADMINISTRATION_RELATED_TO_PROCEDURE, '
'EHR_MEDICATION_LIST, PRESCRIPTION, or '
'UNKNOWN_DRUG_TYPE. If the drug type is '
'not specified, do not include a value '
'for this field.'}},
'domain_of': ['Treatment']} })
routeOfAdministration: Optional[str] = Field(None, description="""Route of administration of the treatment agent.""", json_schema_extra = { "linkml_meta": {'alias': 'routeOfAdministration',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The route of administration of the '
'treatment agent. If the route of '
'administration is not specified, do not '
'include a value for this field.'},
'prompt.examples': {'tag': 'prompt.examples',
'value': 'Intravenous; Oral; '
'Subcutaneous; Intramuscular'}},
'domain_of': ['Treatment']} })


class MetaData(ConfiguredBaseModel):
Expand Down Expand Up @@ -3094,6 +3127,58 @@ def pattern_original_spans(cls, v):
return v


class ChemicalClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators',
'value': 'sqlite:obo:chebi'}},
'from_schema': 'http://w3id.org/ontogpt/phenopackets',
'id_prefixes': ['CHEBI']})

id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
'comments': ['this is populated during the grounding and normalization step'],
'domain_of': ['NamedEntity',
'Publication',
'Phenopacket',
'Family',
'Cohort',
'ExternalReference',
'Biosample',
'Interpretation',
'Individual',
'Resource',
'VariationDescriptor',
'VcfRecord',
'Allele',
'ChromosomeLocation',
'CopyNumber',
'Member',
'SequenceLocation',
'Text']} })
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
'aliases': ['name'],
'annotations': {'owl': {'tag': 'owl',
'value': 'AnnotationProperty, AnnotationAssertion'}},
'domain_of': ['NamedEntity', 'VariationDescriptor'],
'slot_uri': 'rdfs:label'} })
original_spans: Optional[List[str]] = Field(None, description="""The coordinates of the original text span from which the named entity was extracted, inclusive. For example, \"10:25\" means the span starting from the 10th character and ending with the 25th character. The first character in the text has index 0. Newlines are treated as single characters. Multivalued as there may be multiple spans for a single text.""", json_schema_extra = { "linkml_meta": {'alias': 'original_spans',
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
'comments': ['This is determined during grounding and normalization',
'But is based on the full input text'],
'domain_of': ['NamedEntity']} })

@field_validator('original_spans')
def pattern_original_spans(cls, v):
pattern=re.compile(r"^\d+:\d+$")
if isinstance(v,list):
for element in v:
if isinstance(v, str) and not pattern.match(element):
raise ValueError(f"Invalid original_spans format: {element}")
elif isinstance(v,str):
if not pattern.match(v):
raise ValueError(f"Invalid original_spans format: {v}")
return v


class DescriptiveClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators',
'value': 'sqlite:obo:pato'}},
Expand Down Expand Up @@ -3410,6 +3495,60 @@ def pattern_original_spans(cls, v):
return v


class RouteOfAdministrationClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators',
'value': 'sqlite:obo:ncit'}},
'from_schema': 'http://w3id.org/ontogpt/phenopackets',
'id_prefixes': ['NCIT'],
'slot_usage': {'id': {'name': 'id', 'values_from': ['NCITROAType']}}})

id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
'comments': ['this is populated during the grounding and normalization step'],
'domain_of': ['NamedEntity',
'Publication',
'Phenopacket',
'Family',
'Cohort',
'ExternalReference',
'Biosample',
'Interpretation',
'Individual',
'Resource',
'VariationDescriptor',
'VcfRecord',
'Allele',
'ChromosomeLocation',
'CopyNumber',
'Member',
'SequenceLocation',
'Text'],
'values_from': ['NCITROAType']} })
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
'aliases': ['name'],
'annotations': {'owl': {'tag': 'owl',
'value': 'AnnotationProperty, AnnotationAssertion'}},
'domain_of': ['NamedEntity', 'VariationDescriptor'],
'slot_uri': 'rdfs:label'} })
original_spans: Optional[List[str]] = Field(None, description="""The coordinates of the original text span from which the named entity was extracted, inclusive. For example, \"10:25\" means the span starting from the 10th character and ending with the 25th character. The first character in the text has index 0. Newlines are treated as single characters. Multivalued as there may be multiple spans for a single text.""", json_schema_extra = { "linkml_meta": {'alias': 'original_spans',
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
'comments': ['This is determined during grounding and normalization',
'But is based on the full input text'],
'domain_of': ['NamedEntity']} })

@field_validator('original_spans')
def pattern_original_spans(cls, v):
pattern=re.compile(r"^\d+:\d+$")
if isinstance(v,list):
for element in v:
if isinstance(v, str) and not pattern.match(element):
raise ValueError(f"Invalid original_spans format: {element}")
elif isinstance(v,str):
if not pattern.match(v):
raise ValueError(f"Invalid original_spans format: {v}")
return v


class UnitClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', 'value': 'sqlite:obo:uo'}},
'from_schema': 'http://w3id.org/ontogpt/phenopackets',
Expand Down Expand Up @@ -3546,11 +3685,13 @@ def pattern_original_spans(cls, v):
AdverseEventClass.model_rebuild()
AnatomyClass.model_rebuild()
AssayClass.model_rebuild()
ChemicalClass.model_rebuild()
DescriptiveClass.model_rebuild()
DiagnosticMarkerClass.model_rebuild()
EvidenceClass.model_rebuild()
IntentClass.model_rebuild()
PhenotypeClass.model_rebuild()
ProcedureClass.model_rebuild()
RouteOfAdministrationClass.model_rebuild()
UnitClass.model_rebuild()

69 changes: 58 additions & 11 deletions src/ontogpt/templates/phenopackets.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1836,26 +1836,49 @@ classes:
agent, such as a drug
attributes:
agent:
description: ""
inlined: true
range: OntologyClass
description: Treatment agent
range: ChemicalClass
annotations:
prompt: >-
The treatment agent, such as a drug or other therapeutic material.
If the agent is not specified, do not include a value for this
field.
cumulativeDose:
description: ARGO mapping chemotherapy::cumulative_drug_dosage
exact_mappings:
- ARGO:chemotherapy.cumulative_drug_dosage
range: Quantity
annotations:
prompt: >-
The cumulative dose of the treatment agent, with value and units.
If the cumulative dose is not specified, do not include a value for
this field.
doseIntervals:
description: ""
inlined_as_list: true
description: Intervals at which the treatment agent is administered.
# inlined_as_list: true
multivalued: true
range: DoseInterval
# range: DoseInterval
range: string
drugType:
description: ""
description: Type of drug used in the treatment.
range: DrugType
annotations:
prompt: >-
The type of drug used in the treatment. Must be one of:
ADMINISTRATION_RELATED_TO_PROCEDURE, EHR_MEDICATION_LIST,
PRESCRIPTION, or UNKNOWN_DRUG_TYPE.
If the drug type is not specified, do not include a value for this
field.
routeOfAdministration:
description: ""
inlined: true
range: OntologyClass
description: Route of administration of the treatment agent.
range: RouteOfAdministrationClass
annotations:
prompt: >-
The route of administration of the treatment agent.
If the route of administration is not specified, do not include
a value for this field.
prompt.examples: >-
Intravenous; Oral; Subcutaneous; Intramuscular
# core/meta_data

Expand Down Expand Up @@ -3019,6 +3042,13 @@ classes:
annotations:
annotators: sqlite:obo:cmo

ChemicalClass:
is_a: OntologyClass
id_prefixes:
- CHEBI
annotations:
annotators: sqlite:obo:chebi

DescriptiveClass:
is_a: OntologyClass
id_prefixes:
Expand Down Expand Up @@ -3069,6 +3099,17 @@ classes:
annotations:
annotators: sqlite:obo:maxo

RouteOfAdministrationClass:
is_a: OntologyClass
id_prefixes:
- NCIT
annotations:
annotators: sqlite:obo:ncit
slot_usage:
id:
values_from:
- NCITROAType

UnitClass:
is_a: OntologyClass
id_prefixes:
Expand Down Expand Up @@ -3253,4 +3294,10 @@ enums:
- NCIT:C192315
- NCIT:C192601
- NCIT:C18020
- NCIT:C15843
- NCIT:C15843

NCITROAType:
reachable_from:
source_ontology: obo:ncit
source_nodes:
- NCIT:C38114

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