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Updates and grounding for MedicalAction
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@caufieldjh
caufieldjh committed Dec 13, 2024
1 parent edcbe97 commit fd444d9
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Showing 2 changed files with 159 additions and 18 deletions.
126 changes: 122 additions & 4 deletions src/ontogpt/templates/phenopackets.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,10 @@ class NCITDiagnosticMarkerType(str):
pass


class NCITIntentType(str):
pass



class ExtractionResult(ConfiguredBaseModel):
"""
Expand Down Expand Up @@ -1876,9 +1880,11 @@ class MedicalAction(ConfiguredBaseModel):
'domain_of': ['MedicalAction']} })
responseToTreatment: Optional[str] = Field(None, description="""ARGO mapping treatment::response_to_treatment""", json_schema_extra = { "linkml_meta": {'alias': 'responseToTreatment',
'annotations': {'prompt': {'tag': 'prompt',
'value': 'The response to the treatment. If the '
'response is not specified, do not '
'include a value for this field.'}},
'value': 'The response to the treatment, described '
'as the phenotype observed as a result of '
'the treatment. If the response is not '
'specified, do not include a value for '
'this field.'}},
'domain_of': ['MedicalAction'],
'exact_mappings': ['ARGO:treatment.response_to_treatment']} })
therapeuticRegimen: Optional[str] = Field(None, description="""The therapeutic regimen established as part of the medical action.""", json_schema_extra = { "linkml_meta": {'alias': 'therapeuticRegimen',
Expand All @@ -1905,7 +1911,12 @@ class MedicalAction(ConfiguredBaseModel):
'intention is not specified, do not '
'include a value for this field.'},
'prompt.examples': {'tag': 'prompt.examples',
'value': 'Curative; Palliative'}},
'value': 'Curative Therapy; Palliative '
'Therapy; Functional '
'Improvement; Chronic '
'Management; Diagnostic '
'Procedure; Preventative '
'Intervention'}},
'domain_of': ['MedicalAction'],
'exact_mappings': ['ARGO:treatment.treatment_intent']} })
treatmentTarget: Optional[str] = Field(None, description="""The condition or disease that this treatment was intended to address. FHIR mapping Procedure::reasonCode""", json_schema_extra = { "linkml_meta": {'alias': 'treatmentTarget',
Expand Down Expand Up @@ -2928,6 +2939,57 @@ class VariationSet(ConfiguredBaseModel):
pass


class AdverseEventClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', 'value': 'bioportal:OAE'}},
'from_schema': 'http://w3id.org/ontogpt/phenopackets',
'id_prefixes': ['OAE']})

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 AnatomyClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators',
'value': 'sqlite:obo:uberon'}},
Expand Down Expand Up @@ -3191,6 +3253,60 @@ def pattern_original_spans(cls, v):
return v


class IntentClass(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': ['NCITIntentType']}}})

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': ['NCITIntentType']} })
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 PhenotypeClass(OntologyClass):
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', 'value': 'sqlite:obo:hp'}},
'from_schema': 'http://w3id.org/ontogpt/phenopackets',
Expand Down Expand Up @@ -3427,11 +3543,13 @@ def pattern_original_spans(cls, v):
UtilityVariation.model_rebuild()
Variation.model_rebuild()
VariationSet.model_rebuild()
AdverseEventClass.model_rebuild()
AnatomyClass.model_rebuild()
AssayClass.model_rebuild()
DescriptiveClass.model_rebuild()
DiagnosticMarkerClass.model_rebuild()
EvidenceClass.model_rebuild()
IntentClass.model_rebuild()
PhenotypeClass.model_rebuild()
ProcedureClass.model_rebuild()
UnitClass.model_rebuild()
Expand Down
51 changes: 37 additions & 14 deletions src/ontogpt/templates/phenopackets.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1646,10 +1646,8 @@ classes:
description: ARGO mapping treatment::adverse_events
exact_mappings:
- ARGO:treatment.adverse_events
# inlined_as_list: true
multivalued: true
# range: OntologyClass
range: string
range: AdverseEventClass
annotations:
prompt: >-
A semicolon-separated list of adverse events associated with
Expand Down Expand Up @@ -1681,12 +1679,11 @@ classes:
description: ARGO mapping treatment::response_to_treatment
exact_mappings:
- ARGO:treatment.response_to_treatment
# inlined: true
# range: OntologyClass
range: string
range: PhenotypeClass
annotations:
prompt: >-
The response to the treatment. If the response is not specified,
The response to the treatment, described as the phenotype observed
as a result of the treatment. If the response is not specified,
do not include a value for this field.
therapeuticRegimen:
description: >-
Expand Down Expand Up @@ -1714,22 +1711,19 @@ classes:
ARGO mapping treatment::treatment_intent
exact_mappings:
- ARGO:treatment.treatment_intent
# inlined: true
# range: OntologyClass
range: string
range: IntentClass
annotations:
prompt: >-
The intention of the treatment. If the intention is not specified,
do not include a value for this field.
prompt.examples: >-
Curative; Palliative
Curative Therapy; Palliative Therapy; Functional Improvement;
Chronic Management; Diagnostic Procedure; Preventative Intervention
treatmentTarget:
description: >-
The condition or disease that this treatment was intended to address.
FHIR mapping Procedure::reasonCode
# inlined: true
# range: OntologyClass
range: string
range: PhenotypeClass
annotations:
prompt: >-
The condition or disease that this treatment was intended to
Expand Down Expand Up @@ -3002,6 +2996,13 @@ classes:

# OntoGPT-specific class extensions for grounding

AdverseEventClass:
is_a: OntologyClass
id_prefixes:
- OAE
annotations:
annotators: bioportal:OAE

AnatomyClass:
is_a: OntologyClass
id_prefixes:
Expand Down Expand Up @@ -3041,6 +3042,17 @@ classes:
annotations:
annotators: sqlite:obo:eco

IntentClass:
is_a: OntologyClass
id_prefixes:
- NCIT
annotations:
annotators: sqlite:obo:ncit
slot_usage:
id:
values_from:
- NCITIntentType

PhenotypeClass:
is_a: OntologyClass
id_prefixes:
Expand Down Expand Up @@ -3229,3 +3241,14 @@ enums:
source_ontology: obo:ncit
source_nodes:
- NCIT:C25294

NCITIntentType:
reachable_from:
source_ontology: obo:ncit
source_nodes:
- NCIT:C185614
- NCIT:C15292
- NCIT:C192315
- NCIT:C192601
- NCIT:C18020
- NCIT:C15843

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