feat!: add support for transforming civic diagnostic evidence items

src/metakb/harvesters/moa.py

@@ -151,24 +151,27 @@ def _harvest_assertion(self, assertion: dict, variants_list: list[dict]) -> dict
         assertion_record = {
             "id": assertion["assertion_id"],
             "context": assertion["context"],
+            "deprecated": assertion["deprecated"],
             "description": assertion["description"],
             "disease": {
                 "name": assertion["disease"],
                 "oncotree_code": assertion["oncotree_code"],
                 "oncotree_term": assertion["oncotree_term"],
             },
-            "therapy_name": assertion["therapy_name"],
-            "therapy_type": assertion["therapy_type"],
-            "clinical_significance": self._get_therapy(
-                assertion["therapy_resistance"], assertion["therapy_sensitivity"]
-            ),
+            "therapy": {
+                "name": assertion["therapy_name"],
+                "type": assertion["therapy_type"],
+                "strategy": assertion["therapy_strategy"],
+                "resistance": assertion["therapy_resistance"],
+                "sensitivity": assertion["therapy_sensitivity"],
+            },
             "predictive_implication": assertion["predictive_implication"],
             "favorable_prognosis": assertion["favorable_prognosis"],
             "created_on": assertion["created_on"],
             "last_updated": assertion["last_updated"],
             "submitted_by": assertion["submitted_by"],
             "validated": assertion["validated"],
-            "source_ids": assertion["sources"][0]["source_id"],
+            "source_id": assertion["sources"][0]["source_id"],
         }
 
         for v in variants_list:
@@ -177,19 +180,6 @@ def _harvest_assertion(self, assertion: dict, variants_list: list[dict]) -> dict
 
         return assertion_record
 
-    def _get_therapy(self, resistance: bool, sensitivity: bool) -> str | None:
-        """Get therapy response data.
-
-        :param resistance: `True` if Therapy Resistance. `False` if not Therapy Resistance
-        :param sensitivity: `True` if Therapy Sensitivity. `False` if not Therapy Sensitivity
-        :return: whether the therapy response is resistance or sensitivity
-        """
-        if resistance:
-            return "resistance"
-        if sensitivity:
-            return "sensitivity"
-        return None
-
     def _get_feature(self, v: dict) -> dict:
         """Get feature name from the harvested variants
 

src/metakb/query.py

@@ -15,6 +15,7 @@
 )
 from ga4gh.core.entity_models import Coding, Document, Extension, Method
 from ga4gh.va_spec.profiles.var_study_stmt import (
+    VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
@@ -69,6 +70,14 @@ class TherapeuticProcedureType(str, Enum):
     SUBSTITUTES = "TherapeuticSubstituteGroup"
 
 
+# Statement types to corresponding class mapping
+STMT_TYPE_TO_CLASS = {
+    "VariantDiagnosticStudyStatement": VariantDiagnosticStudyStatement,
+    "VariantPrognosticStudyStatement": VariantPrognosticStudyStatement,
+    "VariantTherapeuticResponseStudyStatement": VariantTherapeuticResponseStudyStatement,
+}
+
+
 def _deserialize_field(node: dict, field_name: str) -> None | dict:
     """Deserialize JSON blob property.
 
@@ -493,8 +502,8 @@ def _get_nested_stmts(self, statement_nodes: list[Node]) -> list[dict]:
 
     def _get_nested_stmt(self, stmt_node: Node) -> dict:
         """Get information related to a statement
-        Only VariantTherapeuticResponseStudyStatement and VariantPrognosticStudyStatement
-        are supported at the moment
+        Only VariantTherapeuticResponseStudyStatement, VariantPrognosticStudyStatement,
+        and VariantDiagnosticStudyStatement are supported at the moment
 
         :param stmt_node: Neo4j graph node for statement
         :return: Nested statement
@@ -503,15 +512,14 @@ def _get_nested_stmt(self, stmt_node: Node) -> dict:
         if study_stmt_type not in {
             "VariantTherapeuticResponseStudyStatement",
             "VariantPrognosticStudyStatement",
+            "VariantDiagnosticStudyStatement",
         }:
             return {}
 
-        if study_stmt_type == "VariantPrognosticStudyStatement":
-            study_stmt_cls = VariantPrognosticStudyStatement
-            condition_key = "objectCondition"
-        else:
-            study_stmt_cls = VariantTherapeuticResponseStudyStatement
+        if study_stmt_type == "VariantTherapeuticResponseStudyStatement":
             condition_key = "conditionQualifier"
+        else:
+            condition_key = "objectCondition"
 
         params = {
             condition_key: None,
@@ -559,7 +567,7 @@ def _get_nested_stmt(self, stmt_node: Node) -> dict:
             else:
                 logger.warning("relation type not supported: %s", rel_type)
 
-        return study_stmt_cls(**params).model_dump()
+        return STMT_TYPE_TO_CLASS[study_stmt_type](**params).model_dump()
 
     @staticmethod
     def _get_vicc_normalizer_extension(node: dict) -> ViccNormalizerDataExtension:
@@ -917,10 +925,6 @@ async def batch_search_statements(
             statement_nodes = [r[0] for r in result]
         response.statement_ids = [n["id"] for n in statement_nodes]
         stmts = self._get_nested_stmts(statement_nodes)
-        response.statements = [
-            VariantTherapeuticResponseStudyStatement(**s)
-            if s["type"] == "VariantTherapeuticResponseStudyStatement"
-            else VariantPrognosticStudyStatement(**s)
-            for s in stmts
-        ]
+
+        response.statements = [STMT_TYPE_TO_CLASS[s["type"]](**s) for s in stmts]
         return response

src/metakb/schemas/api.py

@@ -3,6 +3,7 @@
 from typing import Literal
 
 from ga4gh.va_spec.profiles.var_study_stmt import (
+    VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
@@ -48,7 +49,9 @@ class SearchStatementsService(BaseModel):
     warnings: list[StrictStr] = []
     statement_ids: list[StrictStr] = []
     statements: list[
-        VariantTherapeuticResponseStudyStatement | VariantPrognosticStudyStatement
+        VariantTherapeuticResponseStudyStatement
+        | VariantPrognosticStudyStatement
+        | VariantDiagnosticStudyStatement
     ] = []
     service_meta_: ServiceMeta
 
@@ -73,6 +76,8 @@ class BatchSearchStatementsService(BaseModel):
     warnings: list[StrictStr] = []
     statement_ids: list[StrictStr] = []
     statements: list[
-        VariantTherapeuticResponseStudyStatement | VariantPrognosticStudyStatement
+        VariantTherapeuticResponseStudyStatement
+        | VariantPrognosticStudyStatement
+        | VariantDiagnosticStudyStatement
     ] = []
     service_meta_: ServiceMeta

src/metakb/transformers/base.py

@@ -25,6 +25,7 @@
 )
 from ga4gh.core.entity_models import Coding, Document, Extension, Method
 from ga4gh.va_spec.profiles.var_study_stmt import (
+    VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
@@ -111,7 +112,9 @@ class TransformedData(BaseModel):
     """Define model for transformed data"""
 
     statements: list[
-        VariantTherapeuticResponseStudyStatement | VariantPrognosticStudyStatement
+        VariantTherapeuticResponseStudyStatement
+        | VariantPrognosticStudyStatement
+        | VariantDiagnosticStudyStatement
     ] = []
     categorical_variants: list[CategoricalVariant] = []
     variations: list[Allele] = []

src/metakb/transformers/civic.py

@@ -22,8 +22,10 @@
 )
 from ga4gh.va_spec.profiles.var_study_stmt import (
     AlleleOriginQualifier,
+    DiagnosticPredicate,
     PrognosticPredicate,
     TherapeuticResponsePredicate,
+    VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
@@ -91,6 +93,8 @@
     "RESISTANCE": TherapeuticResponsePredicate.RESISTANCE,
     "POOR_OUTCOME": PrognosticPredicate.WORSE_OUTCOME,
     "BETTER_OUTCOME": PrognosticPredicate.BETTER_OUTCOME,
+    "POSITIVE": DiagnosticPredicate.INCLUSIVE,
+    "NEGATIVE": DiagnosticPredicate.EXCLUSIVE,
 }
 
 
@@ -121,6 +125,7 @@ class _CivicEvidenceType(str, Enum):
 
     PREDICTIVE = "PREDICTIVE"
     PROGNOSTIC = "PROGNOSTIC"
+    DIAGNOSTIC = "DIAGNOSTIC"
 
 
 class _VariationCache(BaseModel):
@@ -359,8 +364,10 @@ def _add_variant_study_stmt(
         if evidence_type == _CivicEvidenceType.PREDICTIVE:
             params["objectTherapeutic"] = civic_therapeutic
             statement = VariantTherapeuticResponseStudyStatement(**params)
-        else:
+        elif evidence_type == _CivicEvidenceType.PROGNOSTIC:
             statement = VariantPrognosticStudyStatement(**params)
+        else:
+            statement = VariantDiagnosticStudyStatement(**params)
 
         self.processed_data.statements.append(statement)