Merge pull request #164 from BioDataFuse/PCS_usecase_upadets

generator bug fix
BioDataFuse · Aug 30, 2024 · 59353f8 · 59353f8
2 parents b459ca4 + b1db67e
commit 59353f8
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/src/pyBiodatafuse/annotators/opentargets.py b/src/pyBiodatafuse/annotators/opentargets.py
@@ -13,6 +13,7 @@
 from pyBiodatafuse import id_mapper
 from pyBiodatafuse.constants import (
     OPENTARGETS,
+    OPENTARGETS_COMPOUND_DISEASE_RELATION,
     OPENTARGETS_COMPOUND_INPUT_ID,
     OPENTARGETS_COMPOUND_OUTPUT_DICT,
     OPENTARGETS_COMPOUND_QUERY_INPUT_ID,
@@ -1061,7 +1062,7 @@ def get_disease_compound_interactions(
     )
     intermediate_df["compound_cid"] = mapped_df["target"]
 
-    intermediate_df["relation"] = "treats"
+    intermediate_df["relation"] = OPENTARGETS_COMPOUND_DISEASE_RELATION
 
     # Check if all keys in df match the keys in OUTPUT_DICT
     check_columns_against_constants(

diff --git a/src/pyBiodatafuse/constants.py b/src/pyBiodatafuse/constants.py
@@ -177,6 +177,7 @@
 DRUGBANK_ID = "DB"
 RELATION = "inhibits|activates"
 OPENTARGETS_GENE_COMPOUND_COL = f"{OPENTARGETS}_gene_compounds"
+OPENTARGETS_COMPOUND_DISEASE_RELATION = "treats"
 OPENTARGETS_DISEASE_COMPOUND_COL = f"{OPENTARGETS}_disease_compounds"
 
 # MolMeDB - Gene/Protein input
@@ -234,14 +235,14 @@
     "source": BGEE,
     "name": None,
     "id": None,
-    "developmental_stage_name": None,
-    "developmental_stage_id": None,
     "labels": ANATOMICAL_NODE_LABELS,
 }
 BGEE_GENE_ANATOMICAL_EDGE_LABEL = "expressed_by"
 BGEE_EDGE_ATTRS = {
     "source": BGEE,
     "expression_level": None,
+    "developmental_stage_name": None,
+    "developmental_stage_id": None,
     "confidence_level_name": None,
     "confidence_level_id": None,
     "label": BGEE_GENE_ANATOMICAL_EDGE_LABEL,
@@ -364,7 +365,7 @@
     "source_pmid": None,
     "labels": COMPOUND_NODE_LABELS,
 }
-MOLMEDB_PROTEIN_COMPOUND_EDGE_LABEL = "inhibited_by"
+MOLMEDB_PROTEIN_COMPOUND_EDGE_LABEL = "inhibits"
 MOLMEDB_PROTEIN_COMPOUND_EDGE_ATTRS = {
     "source": MOLMEDB,
     "label": MOLMEDB_PROTEIN_COMPOUND_EDGE_LABEL,

diff --git a/src/pyBiodatafuse/graph/generator.py b/src/pyBiodatafuse/graph/generator.py
@@ -569,8 +569,8 @@ def add_molmedb_gene_inhibitor_subgraph(g, gene_node_label, annot_list):
 
             if len(node_exists) == 0:
                 g.add_edge(
-                    gene_node_label,
                     annot_node_label,
+                    gene_node_label,
                     label=MOLMEDB_PROTEIN_COMPOUND_EDGE_LABEL,
                     attr_dict=edge_attrs,
                 )
@@ -615,8 +615,8 @@ def add_pubchem_assay_subgraph(g, gene_node_label, annot_list):
 
             if len(node_exists) == 0:
                 g.add_edge(
-                    gene_node_label,
                     annot_node_label,
+                    gene_node_label,
                     label=annot["outcome"],
                     attr_dict=edge_attrs,
                 )