From 7ebffadafeecf16287a6a3e1d1774c099e2391f8 Mon Sep 17 00:00:00 2001
From: nanglo123 <tnanglo1998@gmail.com>
Date: Wed, 24 Apr 2024 16:57:46 -0400
Subject: [PATCH] Update script to save BIOMD0000000562 to sbml qual examples

---
 .../process_covid19_diseasemaps_sbml.py       |  9 +++
 .../regnet_amr_sbml/BIOMD0000000562.json      | 68 +++++++++++++------
 2 files changed, 55 insertions(+), 22 deletions(-)

diff --git a/scripts/covid19_diseasemaps/process_covid19_diseasemaps_sbml.py b/scripts/covid19_diseasemaps/process_covid19_diseasemaps_sbml.py
index 28edbf52..3e4a4d97 100644
--- a/scripts/covid19_diseasemaps/process_covid19_diseasemaps_sbml.py
+++ b/scripts/covid19_diseasemaps/process_covid19_diseasemaps_sbml.py
@@ -4,6 +4,8 @@
 
 from mira.sources.sbml import template_model_from_sbml_qual_string
 from mira.modeling.amr.regnet import template_model_to_regnet_json
+from mira.sources.biomodels import get_sbml_model
+
 
 
 models = [
@@ -46,3 +48,10 @@
         regnet = template_model_to_regnet_json(tm)
         with open(f"regnet_amr_sbml/{model}.json", "w") as fh:
             json.dump(regnet, fh, indent=1)
+
+    model_id = "BIOMD0000000562"
+    model_text = get_sbml_model(model_id)
+    tm = template_model_from_sbml_qual_string(model_text)
+    regnet = template_model_to_regnet_json(tm)
+    with open(f"regnet_amr_sbml/{model_id}.json", "w") as fh:
+        json.dump(regnet, fh, indent=1)
diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json
index f3f8939e..758c9803 100644
--- a/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json
+++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json
@@ -274,140 +274,164 @@
    {
     "id": "t4",
     "source": "map3k1",
-    "target": "mkk4",
+    "target": "mkk7",
     "sign": true
    },
    {
     "id": "t5",
     "source": "map3k7",
-    "target": "nik",
+    "target": "mkk4",
     "sign": true
    },
    {
     "id": "t6",
+    "source": "map3k1",
+    "target": "mkk4",
+    "sign": true
+   },
+   {
+    "id": "t7",
+    "source": "map3k7",
+    "target": "nik",
+    "sign": true
+   },
+   {
+    "id": "t8",
     "source": "mkk7",
     "target": "jnk",
     "sign": true
    },
    {
-    "id": "t7",
+    "id": "t9",
     "source": "tnfr",
     "target": "traf2",
     "sign": true
    },
    {
-    "id": "t8",
+    "id": "t10",
     "source": "egfr",
     "target": "pi3k",
     "sign": true
    },
    {
-    "id": "t9",
+    "id": "t11",
+    "source": "ikk",
+    "target": "ikb",
+    "sign": true
+   },
+   {
+    "id": "t12",
     "source": "ex",
     "target": "ikb",
     "sign": true
    },
    {
-    "id": "t10",
+    "id": "t13",
     "source": "mek",
     "target": "erk",
     "sign": true
    },
    {
-    "id": "t11",
+    "id": "t14",
     "source": "ras",
     "target": "map3k1",
     "sign": true
    },
    {
-    "id": "t12",
+    "id": "t15",
     "source": "ras",
     "target": "raf1",
     "sign": true
    },
    {
-    "id": "t13",
+    "id": "t16",
     "source": "tnfa",
     "target": "tnfr",
     "sign": true
    },
    {
-    "id": "t14",
+    "id": "t17",
     "source": "traf2",
     "target": "map3k7",
     "sign": true
    },
    {
-    "id": "t15",
+    "id": "t18",
     "source": "traf2",
     "target": "ask1",
     "sign": true
    },
    {
-    "id": "t16",
+    "id": "t19",
     "source": "akt",
     "target": "akt",
     "sign": false
    },
    {
-    "id": "t17",
+    "id": "t20",
     "source": "pi3k",
     "target": "akt",
     "sign": true
    },
    {
-    "id": "t18",
+    "id": "t21",
     "source": "egf",
     "target": "egfr",
     "sign": true
    },
    {
-    "id": "t19",
+    "id": "t22",
     "source": "ikb",
     "target": "ikb",
     "sign": false
    },
    {
-    "id": "t20",
+    "id": "t23",
     "source": "nfkb",
     "target": "ex",
     "sign": true
    },
    {
-    "id": "t21",
+    "id": "t24",
     "source": "cjun",
     "target": "ap1",
     "sign": true
    },
    {
-    "id": "t22",
+    "id": "t25",
     "source": "jnk",
     "target": "cjun",
     "sign": true
    },
    {
-    "id": "t23",
+    "id": "t26",
     "source": "erk",
     "target": "ph",
     "sign": true
    },
    {
-    "id": "t24",
+    "id": "t27",
     "source": "raf1",
     "target": "mek",
     "sign": true
    },
    {
-    "id": "t25",
+    "id": "t28",
     "source": "sos",
     "target": "ras",
     "sign": true
    },
    {
-    "id": "t26",
+    "id": "t29",
     "source": "egfr",
     "target": "sos",
     "sign": true
+   },
+   {
+    "id": "t30",
+    "source": "ph",
+    "target": "sos",
+    "sign": true
    }
   ],
   "parameters": []