From 52ed92ba5d7d80ec84f80b53f2c28e7b5b29cfb2 Mon Sep 17 00:00:00 2001
From: Inga Ulusoy <inga.ulusoy@uni-heidelberg.de>
Date: Mon, 13 Jul 2026 16:40:19 +0200
Subject: [PATCH] add second adapter

---
 config/schema_config.yaml | 18 +++++++++-
 create_knowledge_graph.py | 71 ++++++++++++++++++---------------------
 2 files changed, 49 insertions(+), 40 deletions(-)

diff --git a/config/schema_config.yaml b/config/schema_config.yaml
index 635dfac..40bdb99 100644
--- a/config/schema_config.yaml
+++ b/config/schema_config.yaml
@@ -7,6 +7,11 @@ protein:
     namespace: uniprot
     input_label: uniprot_protein
 
+pathway:
+    represented_as: node
+    namespace: reactome
+    input_label: reactome_pathway
+
 #-------------------------------------------------------------------
 #------------------      RELATIONSHIPS (EDGES)     -----------------
 #-------------------------------------------------------------------
@@ -52,4 +57,15 @@ ubiquitination:
     is_a: protein protein interaction
     inherit_properties: true
     represented_as: edge
-    input_label: ubiquitination
\ No newline at end of file
+    input_label: ubiquitination
+
+participates_in:
+    is_a: association
+    represented_as: edge
+    source: protein
+    target: pathway
+    input_label: participates_in
+    properties:
+        evidence_code: str
+        source_database: str
+        is_synthetic: bool
\ No newline at end of file
diff --git a/create_knowledge_graph.py b/create_knowledge_graph.py
index 2f888f9..d478395 100644
--- a/create_knowledge_graph.py
+++ b/create_knowledge_graph.py
@@ -1,50 +1,43 @@
 from biocypher import BioCypher
-from src.adapters.adapter_synthetic_proteins import (
-    AdapterNodeType,
-    AdapterProteinField,
-    AdapterEdgeType,
-    Adapter,
-    TSV_FILE_PATH_SYNTHETIC_PROTEINS
-)
+from src.adapters import adapter_synthetic_pathways, adapter_synthetic_proteins
 
 # Create an instance of BioCypher
 bc = BioCypher()
 
-# Choose the node type you want appear in the Knowledge Graph
-node_types = [AdapterNodeType.PROTEIN]
-
-# Choose protein adapter fields to include in the knowledge graph.
-node_fields = [
-    AdapterProteinField.ID,
-    AdapterProteinField.PREFERRED_ID,
-    AdapterProteinField.GENE_SYMBOL,
-    AdapterProteinField.NCBI_TAX_ID,
-]
-
-# Choose the node type you want appear in the Knowledge Graph
-edge_types = [
-    AdapterEdgeType.PROTEIN_PROTEIN_INTERACTION,
-    AdapterEdgeType.BINDING,
-    AdapterEdgeType.ACTIVATION,
-    AdapterEdgeType.PHOSPHORYLATION,
-    AdapterEdgeType.UBIQUITINATION,
-    AdapterEdgeType.INHIBITION,
-]
-
-# (there is not code here!) Choose interaction adapter fields to include in the knowledge graph.
-# By default, in case of not specifying this, BioCypher will bring all the fields defined in the adapter
+# Configure the protein interaction adapter.
+protein_adapter = adapter_synthetic_proteins.Adapter(
+    tsv_path=adapter_synthetic_proteins.TSV_FILE_PATH_SYNTHETIC_PROTEINS,
+    node_types=[adapter_synthetic_proteins.AdapterNodeType.PROTEIN],
+    node_fields=[
+        adapter_synthetic_proteins.AdapterProteinField.ID,
+        adapter_synthetic_proteins.AdapterProteinField.PREFERRED_ID,
+        adapter_synthetic_proteins.AdapterProteinField.GENE_SYMBOL,
+        adapter_synthetic_proteins.AdapterProteinField.NCBI_TAX_ID,
+    ],
+    edge_types=[
+        adapter_synthetic_proteins.AdapterEdgeType.PROTEIN_PROTEIN_INTERACTION,
+        adapter_synthetic_proteins.AdapterEdgeType.BINDING,
+        adapter_synthetic_proteins.AdapterEdgeType.ACTIVATION,
+        adapter_synthetic_proteins.AdapterEdgeType.PHOSPHORYLATION,
+        adapter_synthetic_proteins.AdapterEdgeType.UBIQUITINATION,
+        adapter_synthetic_proteins.AdapterEdgeType.INHIBITION,
+    ],
+)
 
-# Create an adapter instance
-adapter = Adapter(
-    tsv_path=TSV_FILE_PATH_SYNTHETIC_PROTEINS,
-    node_types=node_types,
-    node_fields=node_fields,
-    edge_types=edge_types,
+# Configure the pathway participation adapter.
+pathway_adapter = adapter_synthetic_pathways.Adapter(
+    tsv_path=adapter_synthetic_pathways.TSV_FILE_PATH_SYNTHETIC_PATHWAYS,
+    node_types=[
+        adapter_synthetic_pathways.AdapterNodeType.PROTEIN,
+        adapter_synthetic_pathways.AdapterNodeType.PATHWAY,
+    ],
+    edge_types=[adapter_synthetic_pathways.AdapterEdgeType.PARTICIPATES_IN],
 )
 
-# Create a knowledge graph from the adapter
-bc.write_nodes(adapter.get_nodes())
-bc.write_edges(adapter.get_edges())
+# Create a knowledge graph from both adapters.
+for adapter in (protein_adapter, pathway_adapter):
+    bc.write_nodes(adapter.get_nodes())
+    bc.write_edges(adapter.get_edges())
 
 # Generate assets for Neo4j exportation
 bc.write_import_call()