From 5430fa7695679bd71c0738b399dcbd13e9cbd90d Mon Sep 17 00:00:00 2001
From: Tooba Abbassi-Daloii <t.abbassidaloii@maastrichtuniversity.nl>
Date: Tue, 17 Sep 2024 09:28:29 +0200
Subject: [PATCH] add literature

---
 src/pyBiodatafuse/constants.py       | 4 ++++
 src/pyBiodatafuse/graph/generator.py | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/src/pyBiodatafuse/constants.py b/src/pyBiodatafuse/constants.py
index 4a438fab..280c263e 100644
--- a/src/pyBiodatafuse/constants.py
+++ b/src/pyBiodatafuse/constants.py
@@ -97,6 +97,9 @@
 }
 DISGENET_DISEASE_COL = f"{DISGENET}_diseases"
 
+# literature based disease info
+LITERATURE_DISEASE_COL = "literature_based_info"
+
 # Open Targets - Disease
 OPENTARGETS_DISEASE_OUTPUT_DICT = {
     "disease_name": str,
@@ -280,6 +283,7 @@
     "label": GENE_DISEASE_EDGE_LABEL,
 }
 # Literature
+
 LITERATURE_DISEASE_NODE_ATTRS = {
     "source": None,
     "name": None,
diff --git a/src/pyBiodatafuse/graph/generator.py b/src/pyBiodatafuse/graph/generator.py
index 4a8c7968..3ab1af8c 100644
--- a/src/pyBiodatafuse/graph/generator.py
+++ b/src/pyBiodatafuse/graph/generator.py
@@ -33,6 +33,7 @@
     GO_MF_NODE_LABELS,
     GO_NODE_ATTRS,
     GO_NODE_MAIN_LABEL,
+    LITERATURE_DISEASE_COL,
     LITERATURE_DISEASE_EDGE_ATTRS,
     LITERATURE_DISEASE_NODE_ATTRS,
     MINERVA,
@@ -883,6 +884,7 @@ def networkx_graph(combined_df: pd.DataFrame, disease_compound=None):
     func_dict = {
         BGEE_GENE_EXPRESSION_LEVELS_COL: add_gene_bgee_subgraph,
         DISGENET_DISEASE_COL: add_disgenet_gene_disease_subgraph,
+        LITERATURE_DISEASE_COL: add_literature_gene_disease_subgraph,
         MINERVA: add_minerva_gene_pathway_subgraph,
         WIKIPATHWAYS: add_wikipathways_gene_pathway_subgraph,
         OPENTARGETS_REACTOME_COL: add_opentargets_gene_reactome_pathway_subgraph,