Add taxon & taxon label fields for subject & object (#228)

Adds subject_taxon, subject_taxon_label, object_taxon, object_taxon_label fields
monarch-initiative · Jul 18, 2023 · 8b38a7a · 8b38a7a
1 parent 73303b5
commit 8b38a7a
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Showing 19 changed files with 10,466 additions and 3,553 deletions.
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "monarch-py"
-version = "0.13.4"
+version = "0.13.5"
 description = "Python package for interacting with Monarch Initiative knowledge graph"
 authors = [
     "glass-ships <[email protected]>",

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
@@ -60,6 +60,8 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
     )
+    subject_taxon: Optional[str] = Field(None)
+    subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
@@ -74,6 +76,8 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
     )
+    object_taxon: Optional[str] = Field(None)
+    object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     category: Optional[str] = Field(None)
@@ -204,6 +208,8 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
     )
+    subject_taxon: Optional[str] = Field(None)
+    subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
@@ -218,6 +224,8 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
     )
+    object_taxon: Optional[str] = Field(None)
+    object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     category: Optional[str] = Field(None)

diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
@@ -34,6 +34,8 @@ classes:
     - subject_closure
     - subject_label
     - subject_closure_label
+    - subject_taxon
+    - subject_taxon_label
     - predicate
     - object
     - original_object
@@ -42,6 +44,8 @@ classes:
     - object_closure
     - object_label
     - object_closure_label
+    - object_taxon
+    - object_taxon_label
     - primary_knowledge_source
     - aggregator_knowledge_source
     - category
@@ -401,6 +405,10 @@ slots:
   subject_closure_label:
     multivalued: true
     description: Field containing subject name and the names of all of it's ancestors
+  subject_taxon:
+    is_a: in_taxon
+  subject_taxon_label:
+    is_a: in_taxon_label
   object_label:
     is_a: name
     description: The name of the object entity
@@ -416,6 +424,10 @@ slots:
   object_closure_label:
     multivalued: true
     description: Field containing object name and the names of all of it's ancestors
+  object_taxon:
+    is_a: in_taxon
+  object_taxon_label:
+    is_a: in_taxon_label
   frequency_qualifier_label:
     is_a: name
     description: The name of the frequency_qualifier entity

diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py
@@ -7,17 +7,17 @@ def association_counts():
         "items": [
             {
                 "label": "Phenotypes",
-                "count": 4011,
+                "count": 4312,
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
             },
             {
                 "label": "Causal Genes",
-                "count": 121,
+                "count": 123,
                 "category": "biolink:CausalGeneToDiseaseAssociation",
             },
             {
                 "label": "Correlated Genes",
-                "count": 147,
+                "count": 149,
                 "category": "biolink:CorrelatedGeneToDiseaseAssociation",
             },
         ]