Update: SNOMED Complex Map: Now filters out any mappings that aren't of 'ALWAYS' level of confidence.

Author: joeflack4

sssom/parsers.py

@@ -146,17 +146,21 @@ def read_snomed_complex_map_tsv(
     file_path: str,
     prefix_map: Dict[str, str] = None,
     meta: Dict[str, str] = None,
+    filter_by_confident_mappings=True
 ) -> MappingSetDataFrame:
     """Parse special SNOMED ICD10CM mapping file and translates it into a MappingSetDataFrame.
 
-    :param file_path: The path to the obographs file
+    :param file_path: The path to the source file
     :param prefix_map: an optional prefix map
     :param meta: an optional dictionary of metadata elements
+    :param filter_by_confident_mappings: Will only include mapping rows where the `mapAdvice` field includes an 'ALWAYS
+      <code>' pattern.
     :return: A SSSOM MappingSetDataFrame
     """
     raise_for_bad_path(file_path)
     df = read_pandas(file_path)
-    df2 = from_snomed_complex_map_tsv(df, prefix_map=prefix_map, meta=meta)
+    df2 = from_snomed_complex_map_tsv(
+        df, prefix_map=prefix_map, meta=meta, filter_by_confident_mappings=filter_by_confident_mappings)
     return df2
 
 
@@ -524,12 +528,15 @@ def from_snomed_complex_map_tsv(
     df: pd.DataFrame,
     prefix_map: Optional[PrefixMap] = None,
     meta: Optional[MetadataType] = None,
+    filter_by_confident_mappings=True
 ) -> MappingSetDataFrame:
     """Convert a snomed_icd10cm_map dataframe to a MappingSetDataFrame.
 
     :param df: A mappings dataframe
     :param prefix_map: A prefix map
     :param meta: A metadata dictionary
+    :param filter_by_confident_mappings: Will only include mapping rows where the `mapAdvice` field includes an 'ALWAYS
+      <code>' pattern.
     :return: MappingSetDataFrame
 
     # Field descriptions
@@ -563,11 +570,23 @@ def from_snomed_complex_map_tsv(
     - mapCategoryId,SctId,Identifies the SNOMED CT concept in the metadata hierarchy which is the MapCategory for the
     associated map record. This is a subtype of 447634004 |ICD-10 Map Category value|.,
     """
+    # Local variables
     # https://www.findacode.com/snomed/447561005--snomed-ct-source-code-to-target-map-correlation-not-specified.html
     match_type_snomed_unspecified_id = 447561005
+    # - Note: joeflack4: I used this info as a reference for this pattern.
+    # https://www.medicalbillingandcoding.org/icd-10-cm/#:~:text=ICD%2D10%2DCM%20is%20a,decimal%20point%20and%20the%20subcategory.
+    always_confidence_pattern = 'ALWAYS [A-Z]{1}[0-9]{1,2}\.[0-9A-Z]{1,4}'
+    always_confidence_antipattern = always_confidence_pattern + '\?'
     prefix_map = _ensure_prefix_map(prefix_map)
     ms = _init_mapping_set(meta)
 
+    # Filtering
+    if filter_by_confident_mappings:
+        df = df[
+            (df['mapAdvice'].str.contains(always_confidence_pattern, regex=True, na=False)) &
+            (~df['mapAdvice'].str.contains(always_confidence_antipattern, regex=True, na=False))]
+
+    # Map mappings
     mlist: List[Mapping] = []
     for _, row in df.iterrows():
         mdict = {