Reconcile rules for predicate_id

sssom/cli.py

@@ -168,7 +168,7 @@ def convert(input: str, output: TextIO, output_format: str):
 )
 @click.option(
     "-E",
-    "--embedded-mode",
+    "--embedded-mode / --non-embedded-mode",
     default=True,
     is_flag=True,
     help="If False, the resultant SSSOM file will be saved\
@@ -484,7 +484,7 @@ def correlations(input: str, output: TextIO, transpose: bool, fields: Tuple):
     help="Boolean indicating the need for reconciliation of the SSSOM tsv file.",
 )
 @output_option
-def merge(inputs: str, output: TextIO, reconcile: bool = True):
+def merge(inputs: str, output: TextIO, reconcile: bool = False):
     """Merge multiple MappingSetDataFrames into one .
 
     if reconcile=True, then dedupe(remove redundant lower confidence mappings) and

sssom/cliques.py

@@ -11,6 +11,17 @@
 # from .sssom_datamodel import Mapping
 from sssom_schema import Mapping
 
+from sssom.constants import (
+    OWL_DIFFERENT_FROM,
+    OWL_EQUIVALENT_CLASS,
+    RDFS_SUBCLASS_OF,
+    SKOS_BROAD_MATCH,
+    SKOS_CLOSE_MATCH,
+    SKOS_EXACT_MATCH,
+    SKOS_NARROW_MATCH,
+    SSSOM_SUPERCLASS_OF,
+)
+
 from .parsers import to_mapping_set_document
 from .sssom_document import MappingSetDocument
 from .util import MappingSetDataFrame
@@ -31,24 +42,22 @@ def to_digraph(msdf: MappingSetDataFrame) -> nx.DiGraph:
 
             pi = None
 
-            if p == "owl:equivalentClass":
+            if p == OWL_EQUIVALENT_CLASS:
                 pi = 2
-            elif p == "skos:exactMatch":
+            elif p == SKOS_EXACT_MATCH:
                 pi = 2
-            elif p == "skos:closeMatch":
+            elif p == SKOS_CLOSE_MATCH:
                 # TODO: consider distributing
                 pi = 2
-            elif p == "owl:subClassOf":
+            elif p == RDFS_SUBCLASS_OF:
                 pi = 0
-            elif p == "skos:broadMatch":
+            elif p == SKOS_BROAD_MATCH:
                 pi = 0
-            elif p == "inverseOf(owl:subClassOf)":
+            elif p == SSSOM_SUPERCLASS_OF:
                 pi = 1
-            elif p == "skos:narrowMatch":
+            elif p == SKOS_NARROW_MATCH:
                 pi = 1
-            elif p == "owl:differentFrom":
-                pi = 3
-            elif p == "dbpedia-owl:different":
+            elif p == OWL_DIFFERENT_FROM:
                 pi = 3
 
             if pi == 0:

sssom/constants.py

@@ -118,6 +118,38 @@
 SUBJECT_SOURCE_ID = "subject_source_id"
 OBJECT_SOURCE_ID = "object_source_id"
 
+# PREDICATES
+OWL_EQUIVALENT_CLASS = "owl:equivalentClass"
+OWL_EQUIVALENT_PROPERTY = "owl:equivalentProperty"
+OWL_DIFFERENT_FROM = "owl:differentFrom"
+RDFS_SUBCLASS_OF = "rdfs:subClassOf"
+RDFS_SUBPROPERTY_OF = "rdfs:subPropertyOf"
+OWL_SAME_AS = "owl:sameAs"
+SKOS_EXACT_MATCH = "skos:exactMatch"
+SKOS_CLOSE_MATCH = "skos:closeMatch"
+SKOS_BROAD_MATCH = "skos:broadMatch"
+SKOS_NARROW_MATCH = "skos:narrowMatch"
+OBO_HAS_DB_XREF = "oboInOwl:hasDbXref"
+SKOS_RELATED_MATCH = "skos:relatedMatch"
+RDF_SEE_ALSO = "rdfs:seeAlso"
+SSSOM_SUPERCLASS_OF = "inverseOf(owl:subClassOf)"
+
+PREDICATE_LIST = [
+    OWL_EQUIVALENT_CLASS,
+    OWL_EQUIVALENT_PROPERTY,
+    RDFS_SUBCLASS_OF,
+    SSSOM_SUPERCLASS_OF,
+    RDFS_SUBPROPERTY_OF,
+    OWL_SAME_AS,
+    SKOS_EXACT_MATCH,
+    SKOS_CLOSE_MATCH,
+    SKOS_BROAD_MATCH,
+    SKOS_NARROW_MATCH,
+    OBO_HAS_DB_XREF,
+    SKOS_RELATED_MATCH,
+    RDF_SEE_ALSO,
+]
+
 
 class SEMAPV(Enum):
     """SEMAPV Enum containing different mapping_justification."""

sssom/util.py

@@ -50,13 +50,24 @@
     OBJECT_ID,
     OBJECT_LABEL,
     OBJECT_SOURCE,
+    OBO_HAS_DB_XREF,
+    OWL_DIFFERENT_FROM,
+    OWL_EQUIVALENT_CLASS,
     PREDICATE_ID,
+    PREDICATE_LIST,
     PREDICATE_MODIFIER,
     PREDICATE_MODIFIER_NOT,
     PREFIX_MAP_MODES,
+    RDFS_SUBCLASS_OF,
     SCHEMA_DICT,
     SCHEMA_YAML,
     SEMAPV,
+    SKOS_BROAD_MATCH,
+    SKOS_CLOSE_MATCH,
+    SKOS_EXACT_MATCH,
+    SKOS_NARROW_MATCH,
+    SKOS_RELATED_MATCH,
+    SSSOM_SUPERCLASS_OF,
     SUBJECT_CATEGORY,
     SUBJECT_ID,
     SUBJECT_LABEL,
@@ -289,13 +300,83 @@ def filter_redundant_rows(
     # will be removed from pandas in a future version.
     # Use pandas.concat instead.
     # return_df = df.append(nan_df).drop_duplicates()
-    return_df = pd.concat([df, nan_df]).drop_duplicates()
+    confidence_reconciled_df = pd.concat([df, nan_df]).drop_duplicates()
+
+    # Reconciling dataframe rows based on the predicates with equal confidence.
+    if PREDICATE_MODIFIER in confidence_reconciled_df.columns:
+        tmp_df = confidence_reconciled_df[
+            [SUBJECT_ID, OBJECT_ID, PREDICATE_ID, CONFIDENCE, PREDICATE_MODIFIER]
+        ]
+        tmp_df = tmp_df[tmp_df[PREDICATE_MODIFIER] != PREDICATE_MODIFIER_NOT].drop(
+            PREDICATE_MODIFIER, axis=1
+        )
+    else:
+        tmp_df = confidence_reconciled_df[
+            [SUBJECT_ID, OBJECT_ID, PREDICATE_ID, CONFIDENCE]
+        ]
+    tmp_df_grp = tmp_df.groupby(
+        [SUBJECT_ID, OBJECT_ID, CONFIDENCE], as_index=False
+    ).count()
+    tmp_df_grp = tmp_df_grp[tmp_df_grp[PREDICATE_ID] > 1].drop(PREDICATE_ID, axis=1)
+    non_predicate_reconciled_df = (
+        confidence_reconciled_df.merge(
+            tmp_df_grp, on=list(tmp_df_grp.columns), how="left", indicator=True
+        )
+        .query('_merge == "left_only"')
+        .drop(columns="_merge")
+    )
+
+    multiple_predicate_df = (
+        confidence_reconciled_df.merge(
+            tmp_df_grp, on=list(tmp_df_grp.columns), how="right", indicator=True
+        )
+        .query('_merge == "both"')
+        .drop(columns="_merge")
+    )
+
+    return_df = non_predicate_reconciled_df
+    for _, row in tmp_df_grp.iterrows():
+        logic_df = multiple_predicate_df[list(tmp_df_grp.columns)] == row
+        concerned_row_index = (
+            logic_df[logic_df[list(tmp_df_grp.columns)]].dropna().index
+        )
+        concerned_df = multiple_predicate_df.iloc[concerned_row_index]
+        # Go down the hierarchical list of PREDICATE_LIST and grab the first match
+        return_df = pd.concat(
+            [get_row_based_on_hierarchy(concerned_df), return_df], axis=0
+        ).drop_duplicates()
 
     if return_df[CONFIDENCE].isnull().all():
         return_df = return_df.drop(columns=[CONFIDENCE], axis=1)
     return return_df
 
 
+def get_row_based_on_hierarchy(df: pd.DataFrame):
+    """Get row based on hierarchy of predicates.
+
+    The hierarchy is as follows:
+    # owl:equivalentClass
+    # owl:equivalentProperty
+    # rdfs:subClassOf
+    # rdfs:subPropertyOf
+    # owl:sameAs
+    # skos:exactMatch
+    # skos:closeMatch
+    # skos:broadMatch
+    # skos:narrowMatch
+    # oboInOwl:hasDbXref
+    # skos:relatedMatch
+    # rdfs:seeAlso
+
+    :param df: Dataframe containing multiple predicates for same subject and object.
+    :return: Dataframe with a single row which ranks higher in the hierarchy.
+    """
+    for pred in PREDICATE_LIST:
+        hierarchical_df = df[df[PREDICATE_ID] == pred]
+        if not hierarchical_df.empty:
+            return hierarchical_df
+
+
 def assign_default_confidence(
     df: pd.DataFrame,
 ) -> Tuple[pd.DataFrame, pd.DataFrame]:
@@ -430,29 +511,27 @@ def dataframe_to_ptable(df: pd.DataFrame, *, inverse_factor: float = None):
         residual_confidence = (1 - (confidence + inverse_confidence)) / 2.0
 
         predicate = row[PREDICATE_ID]
-        if predicate == "owl:equivalentClass":
+        if predicate == OWL_EQUIVALENT_CLASS:
             predicate_type = PREDICATE_EQUIVALENT
-        elif predicate == "skos:exactMatch":
+        elif predicate == SKOS_EXACT_MATCH:
             predicate_type = PREDICATE_EQUIVALENT
-        elif predicate == "skos:closeMatch":
+        elif predicate == SKOS_CLOSE_MATCH:
             # TODO: consider distributing
             predicate_type = PREDICATE_EQUIVALENT
-        elif predicate == "owl:subClassOf":
+        elif predicate == RDFS_SUBCLASS_OF:
             predicate_type = PREDICATE_SUBCLASS
-        elif predicate == "skos:broadMatch":
+        elif predicate == SKOS_BROAD_MATCH:
             predicate_type = PREDICATE_SUBCLASS
-        elif predicate == "inverseOf(owl:subClassOf)":
+        elif predicate == SSSOM_SUPERCLASS_OF:
             predicate_type = PREDICATE_SUPERCLASS
-        elif predicate == "skos:narrowMatch":
+        elif predicate == SKOS_NARROW_MATCH:
             predicate_type = PREDICATE_SUPERCLASS
-        elif predicate == "owl:differentFrom":
-            predicate_type = PREDICATE_SIBLING
-        elif predicate == "dbpedia-owl:different":
+        elif predicate == OWL_DIFFERENT_FROM:
             predicate_type = PREDICATE_SIBLING
         # * Added by H2 ############################
-        elif predicate == "oboInOwl:hasDbXref":
+        elif predicate == OBO_HAS_DB_XREF:
             predicate_type = PREDICATE_HAS_DBXREF
-        elif predicate == "skos:relatedMatch":
+        elif predicate == SKOS_RELATED_MATCH:
             predicate_type = PREDICATE_RELATED_MATCH
         # * ########################################
         else:
@@ -538,7 +617,7 @@ def sha256sum(path: str) -> str:
 
 def merge_msdf(
     *msdfs: MappingSetDataFrame,
-    reconcile: bool = True,
+    reconcile: bool = False,
 ) -> MappingSetDataFrame:
     """Merge multiple MappingSetDataFrames into one.
 
@@ -573,7 +652,10 @@ def merge_msdf(
     merged_msdf.df = df_merged
     if reconcile:
         merged_msdf.df = filter_redundant_rows(merged_msdf.df)
-        if PREDICATE_MODIFIER in merged_msdf.df.columns:
+        if (
+            PREDICATE_MODIFIER in merged_msdf.df.columns
+            and PREDICATE_MODIFIER_NOT in merged_msdf.df[PREDICATE_MODIFIER]
+        ):
             merged_msdf.df = deal_with_negation(merged_msdf.df)  # deals with negation
 
     # TODO: Add default values for license and mapping_set_id.

tests/data/basic.tsv

@@ -154,7 +154,7 @@ z:region	REGION	owl:equivalentClass		y:region	regions	semapv:ManualMappingCurati
 z:tissue	TISSUE	owl:equivalentClass		x:tissue	tissue	semapv:ManualMappingCuration	z:example	x:example	rdf_matcher	0.840714406	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	tissu	.
 z:tissue	TISSUE	owl:equivalentClass		x:tissue	tissue	semapv:LexicalMatching	z:example	x:example	rdf_matcher	0.881856236	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	tissue	.
 z:tissue	TISSUE	owl:equivalentClass		y:tissue	tissues	semapv:ManualMappingCuration	z:example	y:example	rdf_matcher	0.840714406	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	tissu	.
-a:something	XXXXX	owl:subClassOf		b:something	xxxxxx	semapv:LexicalMatching	a:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	XXXXX	rdfs:subClassOf		b:something	xxxxxx	semapv:LexicalMatching	a:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
 c:something	YYYYY	owl:equivalentClass		d:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.81	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
 d:something	YYYYY	owl:equivalentClass	Not	a:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.82	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
 a:something	XYXYX	owl:equivalentClass		c:something	xyxyxy	semapv:LexicalMatching	a:example	c:example	rdf_matcher	0.83	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data

tests/data/basic7.tsv

@@ -0,0 +1,50 @@
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#mapping_set_id: https://w3id.org/sssom/mapping/tests/data/basic3.tsv
+#mapping_tool: "https://github.com/cmungall/rdf_matcher"
+#creator_id:
+#    - "orcid:1234"
+#mapping_date: "2020-05-30"
+#curie_map:
+#  a: "http://example.org/a/"
+#  b: "http://example.org/b/"
+#  c: "http://example.org/c/"
+#  d: "http://example.org/d/"
+#  rdfs: "http://www.w3.org/2000/01/rdf-schema#"
+#  owl: "http://www.w3.org/2002/07/owl#"
+#  orcid: "https://orcid.org/my-orcid?orcid="
+#  semapv: "https://w3id.org/semapv/"
+#  skos: "http://www.w3.org/2004/02/skos/core#"
+subject_id	subject_label	predicate_id	predicate_modifier	object_id	object_label	mapping_justification	subject_source	object_source	mapping_tool	confidence	subject_match_field	object_match_field	subject_category	object_category	match_string	comment
+a:something	YYYYY	owl:equivalentClass		b:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	YYYYY	owl:equivalentProperty		b:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	owl:equivalentProperty		c:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	rdfs:subClassOf		c:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	rdfs:subClassOf		d:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	rdfs:subPropertyOf		d:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	rdfs:subPropertyOf		c:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	owl:sameAs		c:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	owl:sameAs		b:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	skos:exactMatch		b:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	skos:exactMatch		a:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	skos:closeMatch		a:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	YYYYY	skos:closeMatch		c:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	YYYYY	skos:broadMatch		c:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	skos:broadMatch		d:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	skos:narrowMatch		d:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	skos:narrowMatch		a:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	oboInOwl:hasDbXref		a:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	oboInOwl:hasDbXref		b:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	skos:relatedMatch		b:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	YYYYY	skos:relatedMatch		d:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	YYYYY	rdfs:seeAlso		d:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	rdfs:seeAlso		a:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.82	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	owl:equivalentClass	Not	a:something	yyyyyy	semapv:LexicalMatching	d:example	a:example	rdf_matcher	0.82	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	XYXYX	owl:equivalentClass		c:something	xyxyxy	semapv:LexicalMatching	a:example	c:example	rdf_matcher	0.83	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	owl:equivalentClass		b:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.845	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+b:something	XXXXX	owl:equivalentClass		a:something	xxxxxx	semapv:LexicalMatching	b:example	a:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YYYYY	owl:equivalentClass		d:something	yyyyyy	semapv:LexicalMatching	c:example	d:example	rdf_matcher	0.81	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+c:something	YXYXY	owl:equivalentClass	Not	b:something	yxyxyx	semapv:ManualMappingCuration	c:example	b:example	rdf_matcher	0.845	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	XYXYX	owl:equivalentClass		b:something	xyxyxy	semapv:LexicalMatching	d:example	b:example	rdf_matcher	0.83	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	XXXXX	owl:subClassOf		b:something	xxxxxx	semapv:LexicalMatching	a:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+d:something	YYYYY	owl:equivalentClass		a:something	yyyyyy	semapv:ManualMappingCuration	d:example	a:example	rdf_matcher	0.82	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data
+a:something	XXXXX	owl:subClassOf	Not	b:something	xxxxxx	semapv:LexicalMatching	a:example	b:example	rdf_matcher	0.8	rdfs:label	rdfs:label	biolink:AnatomicalEntity	biolink:AnatomicalEntity	xxxxx	mock data

tests/test_merge.py

@@ -21,8 +21,8 @@ def setUp(self) -> None:
     def test_merge_multiple_inputs(self):
         """Test merging of multiple msdfs."""
         merged_msdf = merge_msdf(*self.msdfs)
-        self.assertEqual(123, len(merged_msdf.df))
+        self.assertEqual(275, len(merged_msdf.df))
 
     def test_merge_single_input(self):
         """Test merging when a single msdf is provided."""
-        self.assertEqual(93, len(merge_msdf(self.msdf).df))
+        self.assertEqual(141, len(merge_msdf(self.msdf).df))