diff --git a/src/ontogpt/templates/phenopackets.py b/src/ontogpt/templates/phenopackets.py index ba3acd79a..108870dfa 100644 --- a/src/ontogpt/templates/phenopackets.py +++ b/src/ontogpt/templates/phenopackets.py @@ -1336,17 +1336,19 @@ class Interpretation(ConfiguredBaseModel): diagnosis: Optional[Diagnosis] = Field(None, description="""The diagnosis made in this interpretation.""", json_schema_extra = { "linkml_meta": {'alias': 'diagnosis', 'annotations': {'prompt': {'tag': 'prompt', 'value': 'The diagnosis made in this ' - 'interpretation. Include the following, ' - 'as available: the name of the disease or ' - 'condition with all acronyms spelled out, ' - 'the identifier of the individual or ' - 'biosample, and any details regarding ' - 'genetic or genomic interpretation ' - '(including the gene, the status of the ' - 'genetic interpretation, and/or any ' - 'details regarding the specific variant). ' - 'Include this information even if it is ' - 'also present in the summary field.'}}, + 'interpretation. If this is not provided, ' + 'do not include a value for this field. ' + 'Include the following, as available: the ' + 'name of the disease or condition with ' + 'all acronyms spelled out, the identifier ' + 'of the individual or biosample, and any ' + 'details regarding genetic or genomic ' + 'interpretation (including the gene, the ' + 'status of the genetic interpretation, ' + 'and/or any details regarding the ' + 'specific variant). Include this ' + 'information even if it is also present ' + 'in the summary field.'}}, 'domain_of': ['Interpretation']} }) id: Optional[str] = Field(None, description="""id of the interpretation""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'annotations': {'prompt': {'tag': 'prompt', diff --git a/src/ontogpt/templates/phenopackets.yaml b/src/ontogpt/templates/phenopackets.yaml index 9fe63c780..216c660c6 100644 --- a/src/ontogpt/templates/phenopackets.yaml +++ b/src/ontogpt/templates/phenopackets.yaml @@ -1170,10 +1170,12 @@ classes: diagnosis: description: The diagnosis made in this interpretation. range: Diagnosis + inlined: true annotations: prompt: >- The diagnosis made in this interpretation. - Include the following, as available: + If this is not provided, do not include a value for this + field. Include the following, as available: the name of the disease or condition with all acronyms spelled out, the identifier of the individual or biosample, and any details regarding genetic or