Merge pull request #169 from cancervariants/issue-168

feat: Add transformed regulatory_approval field from Therapy Normalizer

metakb/database.py

@@ -203,6 +203,15 @@ def _add_descriptor(tx, descriptor: Dict, added_ids: Set[str]):
                                                       'description', 'xrefs',
                                                       'alternate_labels'))
 
+        if descr_type == 'TherapyDescriptor':
+            # capture regulatory_approval field in therapy descriptor extensions
+            extensions = descriptor.get('extensions', [])
+            for ext in extensions:
+                name = ext['name']
+                if name == 'regulatory_approval':
+                    descriptor[name] = json.dumps(ext['value'])
+                    descr_keys += f", {name}:${name}"
+
         query = f'''
         MERGE (descr:{descr_type} {{ {descr_keys} }})
         MERGE (value:{value_type} {{ id:${value_id} }})

metakb/normalizers.py

@@ -2,10 +2,10 @@
 from typing import Optional, Tuple
 
 from ga4gh.vrsatile.pydantic.vrs_models import VRSTypes
-from ga4gh.vrsatile.pydantic.vrsatile_models import VariationDescriptor
+from ga4gh.vrsatile.pydantic.vrsatile_models import VariationDescriptor, Extension
 from variation.query import QueryHandler as VariationQueryHandler
 from therapy.query import QueryHandler as TherapyQueryHandler
-from therapy.schemas import NormalizationService as NormalizedTherapy
+from therapy.schemas import NormalizationService as NormalizedTherapy, ApprovalRating
 from disease.query import QueryHandler as DiseaseQueryHandler
 from disease.schemas import NormalizationService as NormalizedDisease
 from gene.query import QueryHandler as GeneQueryHandler
@@ -133,3 +133,55 @@ def normalize_therapy(self, queries)\
                     if highest_match == 100:
                         break
         return therapy_norm_resp, normalized_therapy_id
+
+    @staticmethod
+    def get_regulatory_approval_extension(
+        therapy_norm_resp: NormalizedTherapy
+    ) -> Optional[Extension]:
+        """Given therapy normalization service response, extract out the regulatory
+        approval extension
+
+        :param NormalizedTherapy therapy_norm_resp: Response from normalizing therapy
+        :return: Extension containing transformed regulatory approval and indication
+            data if it `regulatory_approval` extensions exists in therapy normalizer
+        """
+        regulatory_approval_extension = None
+        tn_resp_exts = therapy_norm_resp.dict().get("therapy_descriptor", {}).get("extensions") or []  # noqa: E501
+        tn_ext = [v for v in tn_resp_exts if v["name"] == "regulatory_approval"]
+
+        if tn_ext:
+            ext_value = tn_ext[0]["value"]
+            approval_ratings = ext_value.get("approval_ratings", [])
+            matched_ext_value = None
+
+            if any(ar in {ApprovalRating.FDA_PRESCRIPTION, ApprovalRating.FDA_OTC}
+                    for ar in approval_ratings):
+                if ApprovalRating.FDA_DISCONTINUED not in approval_ratings or \
+                    ApprovalRating.CHEMBL_4 in approval_ratings:  # noqa: E125
+                    matched_ext_value = "FDA"
+            elif ApprovalRating.CHEMBL_4 in approval_ratings:
+                matched_ext_value = "chembl_phase_4"
+
+            if matched_ext_value:
+                has_indications = ext_value.get("has_indication", [])
+                matched_indications = list()
+
+                for indication in has_indications:
+                    indication_exts = indication.get("extensions", [])
+                    for indication_ext in indication_exts:
+                        if indication_ext["value"] == matched_ext_value:
+                            matched_indications.append({
+                                "id": indication["id"],
+                                "type": indication["type"],
+                                "label": indication["label"],
+                                "disease_id": indication["disease_id"]
+                            })
+
+                regulatory_approval_extension = Extension(
+                    name="regulatory_approval",
+                    value={
+                        "approval_rating": "FDA" if matched_ext_value == "FDA" else "ChEMBL",  # noqa: E501
+                        "has_indications": matched_indications
+                    })
+
+        return regulatory_approval_extension

metakb/query.py

@@ -836,9 +836,17 @@ def _get_therapy_descriptor(
             "label": therapy_descriptor.get("label"),
             "therapy_id": None,
             "alternate_labels": therapy_descriptor.get("alternate_labels"),
-            "xrefs": therapy_descriptor.get("xrefs")
+            "xrefs": therapy_descriptor.get("xrefs"),
+            "extensions": []
         }
 
+        key = "regulatory_approval"
+        val = therapy_descriptor.get(key)
+        if val:
+            td_params["extensions"].append(Extension(name=key, value=json.loads(val)))
+        else:
+            del td_params["extensions"]
+
         with self.driver.session() as session:
             value_object = session.read_transaction(
                 self._find_descriptor_value_object, td_params["id"]

metakb/transform/civic.py

@@ -679,21 +679,25 @@ def _get_therapy_descriptor(self, drug) \
         ncit_id = f"ncit:{drug['ncit_id']}"
         queries = [ncit_id, label]
 
-        _, normalized_therapy_id = \
+        therapy_norm_resp, normalized_therapy_id = \
             self.vicc_normalizers.normalize_therapy(queries)
 
         if not normalized_therapy_id:
             logger.warning(f"Therapy Normalizer unable to normalize: "
                            f"using queries {ncit_id} and {label}")
             return None
 
+        regulatory_approval_extension = \
+            self.vicc_normalizers.get_regulatory_approval_extension(therapy_norm_resp)
+
         therapy_descriptor = ValueObjectDescriptor(
             id=therapy_id,
             type="TherapyDescriptor",
             label=label,
             therapy_id=normalized_therapy_id,
             alternate_labels=drug['aliases'],
-            xrefs=[ncit_id]
+            xrefs=[ncit_id],
+            extensions=[regulatory_approval_extension] if regulatory_approval_extension else None  # noqa: E501
         ).dict(exclude_none=True)
         return therapy_descriptor
 

metakb/transform/moa.py

@@ -381,12 +381,15 @@ def _get_therapy_descriptors(self, assertion):
             return []
 
         if normalized_therapy_id:
+            regulatory_approval_extension = \
+                self.vicc_normalizers.get_regulatory_approval_extension(therapy_norm_resp)  # noqa: E501
             therapy_descriptor = ValueObjectDescriptor(
                 id=f"{schemas.SourceName.MOA.value}."
                    f"{therapy_norm_resp.therapy_descriptor.id}",
                 type="TherapyDescriptor",
                 label=label,
-                therapy_id=normalized_therapy_id
+                therapy_id=normalized_therapy_id,
+                extensions=[regulatory_approval_extension] if regulatory_approval_extension else None  # noqa: E501
             ).dict(exclude_none=True)
         else:
             return []

metakb/version.py

@@ -1,4 +1,4 @@
 """MetaKB version"""
 # REQ: EACH TIME VERSION IS UPDATED, MUST ALSO UPDATE LAST_UPDATED
-__version__ = "1.1.0-alpha.6"
-LAST_UPDATED = "2022-04-07"
+__version__ = "1.1.0-alpha.7"
+LAST_UPDATED = "2022-05-04"

tests/conftest.py

@@ -173,6 +173,29 @@ def civic_tid146():
         ],
         "xrefs": [
             "ncit:C66940"
+        ],
+        "extensions": [
+            {
+                "type": "Extension",
+                "name": "regulatory_approval",
+                "value": {
+                    "approval_rating": "FDA",
+                    "has_indications": [
+                        {
+                            "id": "hemonc:25316",
+                            "type": "DiseaseDescriptor",
+                            "label": "Non-small cell lung cancer Squamous",
+                            "disease_id": None
+                        },
+                        {
+                            "id": "hemonc:642",
+                            "type": "DiseaseDescriptor",
+                            "label": "Non-small cell lung cancer",
+                            "disease_id": "ncit:C2926"
+                        }
+                    ]
+                }
+            }
         ]
     }
 
@@ -1192,7 +1215,58 @@ def moa_imatinib():
         "id": "moa.normalize.therapy:Imatinib",
         "type": "TherapyDescriptor",
         "label": "Imatinib",
-        "therapy_id": "rxcui:282388"
+        "therapy_id": "rxcui:282388",
+        "extensions": [{
+            "type": "Extension",
+            "name": "regulatory_approval",
+            "value": {
+                "approval_rating": "FDA",
+                "has_indications": [
+                    {
+                        "id": "hemonc:634",
+                        "type": "DiseaseDescriptor",
+                        "label": "Myelodysplastic syndrome",
+                        "disease_id": "ncit:C3247"
+                    },
+                    {
+                        "id": "hemonc:616",
+                        "type": "DiseaseDescriptor",
+                        "label": "Hypereosinophilic syndrome",
+                        "disease_id": "ncit:C27038"
+                    },
+                    {
+                        "id": "hemonc:582",
+                        "type": "DiseaseDescriptor",
+                        "label": "Chronic myelogenous leukemia",
+                        "disease_id": "ncit:C3174"
+                    },
+                    {
+                        "id": "hemonc:669",
+                        "type": "DiseaseDescriptor",
+                        "label": "Systemic mastocytosis",
+                        "disease_id": "ncit:C9235"
+                    },
+                    {
+                        "id": "hemonc:24309",
+                        "type": "DiseaseDescriptor",
+                        "label": "Acute lymphoblastic leukemia",
+                        "disease_id": "ncit:C3167"
+                    },
+                    {
+                        "id": "hemonc:667",
+                        "type": "DiseaseDescriptor",
+                        "label": "Soft tissue sarcoma",
+                        "disease_id": "ncit:C9306"
+                    },
+                    {
+                        "id": "hemonc:602",
+                        "type": "DiseaseDescriptor",
+                        "label": "Gastrointestinal stromal tumor",
+                        "disease_id": "ncit:C3868"
+                    }
+                ]
+            }
+        }]
     }