Adding utilities to score mondo grounding predictions

Fixes #14

src/malco/post_process/mondo_score_utils.py

@@ -0,0 +1,90 @@
+from functools import lru_cache
+from typing import List
+
+from oaklib import get_adapter
+from oaklib.datamodels.vocabulary import IS_A
+from oaklib.interfaces import OboGraphInterface, MappingProviderInterface
+
+FULL_SCORE = 1.0
+PARTIAL_SCORE = 0.5
+
+
+@lru_cache
+def mondo_adapter() -> OboGraphInterface:
+    """
+    Get the adapter for the MONDO ontology.
+
+    Returns:
+        Adapter: The adapter.
+    """
+    return get_adapter("sqlite:obo:mondo")
+
+
+@lru_cache()
+def omim_mappings(term: str) -> List[str]:
+    """
+    Get the OMIM mappings for a term.
+
+    Example:
+
+    >>> omim_mappings("MONDO:0007566")
+    ['OMIM:132800']
+
+    Args:
+        term (str): The term.
+
+    Returns:
+        str: The OMIM mappings.
+    """
+    adapter = mondo_adapter()
+    if not isinstance(adapter, MappingProviderInterface):
+        raise ValueError("Adapter is not an MappingProviderInterface")
+    omims = []
+    for m in adapter.sssom_mappings([term], "OMIM"):
+        if m.predicate_id == "skos:exactMatch":
+            omims.append(m.object_id)
+    return omims
+
+
+def score_grounded_result(prediction: str, ground_truth: str) -> float:
+    """
+    Score the grounded result.
+
+    Exact match:
+
+    >>> score_grounded_result("OMIM:132800", "OMIM:132800")
+    1.0
+
+    The predicted Mondo is equivalent to the ground truth OMIM
+    (via skos:exactMatches in Mondo):
+
+    >>> score_grounded_result("MONDO:0007566", "OMIM:132800")
+    1.0
+
+    The predicted Mondo is a disease entity that groups multiple
+    OMIMs, one of which is the ground truth:
+
+    >>> score_grounded_result("MONDO:0008029", "OMIM:158810")
+    0.5
+
+    Args:
+        prediction (str): The prediction.
+        ground_truth (str): The ground truth.
+
+    Returns:
+        float: The score.
+    """
+    if prediction == ground_truth:
+        # predication is the correct OMIM
+        return FULL_SCORE
+    if ground_truth in omim_mappings(prediction):
+        # prediction is a MONDO that directly maps to a correct OMIM
+        return FULL_SCORE
+    mondo = mondo_adapter()
+    for mondo_descendant in mondo.descendants([prediction], predicates=[IS_A], reflexive=True):
+        if ground_truth in omim_mappings(mondo_descendant):
+            # prediction is a MONDO that maps to a correct OMIM via a descendant
+            return PARTIAL_SCORE
+    return 0.0
+
+