Add more comments to modeling regnet file and fix minor bug, rerun sc…

…ript to regenerate qual regnet amr
gyorilab · Apr 25, 2024 · 6ebf100 · 6ebf100
1 parent 7ebffad
commit 6ebf100
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Showing 24 changed files with 2,006 additions and 2,004 deletions.
diff --git a/mira/modeling/amr/regnet.py b/mira/modeling/amr/regnet.py
@@ -132,6 +132,7 @@ def __init__(self, model: Model):
             # Possibilities are:
             # - ControlledReplication / GroupedControlledProduction
             # - ControlledDegradation / GroupedControlledDegradation
+            # - ControlledProduction if the control and produced concept are not the same
             else:
                 # If we have multiple controls then the thing that replicates
                 # is both a control and a produced variable.
@@ -146,7 +147,7 @@ def __init__(self, model: Model):
                         # There is one corner case where both controllers are also
                         # the same as the produced variable, in which case.
                         if not indep_ctrl:
-                            indep_ctrl = {transition.consumed[0].key}
+                            indep_ctrl = {transition.produced[0].key}
 
                         for controller in indep_ctrl:
                             self.create_edge(
@@ -163,7 +164,7 @@ def __init__(self, model: Model):
                             transition.consumed[0].key
                         }
                         # There is one corner case where both controllers are also
-                        # the same as the produced variable, in which case.
+                        # the same as the consumed variable, in which case.
                         if not indep_ctrl:
                             indep_ctrl = {transition.consumed[0].key}
 
@@ -177,6 +178,7 @@ def __init__(self, model: Model):
 
                             edge_id += 1
                 else:
+                    # ControlledProduction if produced and controller are not the same
                     # ControlledDegradation
                     target = vmap[
                         transition.consumed[0].key

diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json
@@ -411,13 +411,13 @@
    },
    {
     "id": "t7",
-    "source": "TRADD",
+    "source": "FADD",
     "target": "TRADD/FADD_complex",
     "sign": true
    },
    {
     "id": "t8",
-    "source": "FADD",
+    "source": "TRADD",
     "target": "TRADD/FADD_complex",
     "sign": true
    },
@@ -429,7 +429,7 @@
    },
    {
     "id": "t10",
-    "source": "AKT1",
+    "source": "CASP9_cell",
     "target": "Apoptosome_complex",
     "sign": true
    },
@@ -441,7 +441,7 @@
    },
    {
     "id": "t12",
-    "source": "CASP9_cell",
+    "source": "AKT1",
     "target": "Apoptosome_complex",
     "sign": true
    },
@@ -465,7 +465,7 @@
    },
    {
     "id": "t16",
-    "source": "BID",
+    "source": "BCL2/MCL1/BCL2L1_complex",
     "target": "BAX",
     "sign": true
    },
@@ -477,7 +477,7 @@
    },
    {
     "id": "t18",
-    "source": "BCL2/MCL1/BCL2L1_complex",
+    "source": "BID",
     "target": "BAX",
     "sign": true
    },
@@ -489,13 +489,13 @@
    },
    {
     "id": "t20",
-    "source": "BAX",
+    "source": "MAPK14",
     "target": "CYCS",
     "sign": true
    },
    {
     "id": "t21",
-    "source": "MAPK14",
+    "source": "BAX",
     "target": "CYCS",
     "sign": true
    },
@@ -525,79 +525,79 @@
    },
    {
     "id": "t26",
-    "source": "CASP9_cell_active",
+    "source": "CASP8",
     "target": "CASP3",
     "sign": true
    },
    {
     "id": "t27",
-    "source": "CASP8",
+    "source": "CASP9_cell_active",
     "target": "CASP3",
     "sign": true
    },
    {
     "id": "t28",
-    "source": "TRADD/FADD_complex",
+    "source": "FADD",
     "target": "CASP8",
     "sign": true
    },
    {
     "id": "t29",
-    "source": "Orf3a",
+    "source": "TRADD/FADD_complex",
     "target": "CASP8",
     "sign": true
    },
    {
     "id": "t30",
-    "source": "FADD",
+    "source": "Orf3a",
     "target": "CASP8",
     "sign": true
    },
    {
     "id": "t31",
-    "source": "CASP3",
+    "source": "N",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t32",
-    "source": "N",
+    "source": "S",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t33",
-    "source": "Orf8a",
+    "source": "Orf9b",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t34",
-    "source": "Orf9b",
+    "source": "CASP3",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t35",
-    "source": "Orf3b",
+    "source": "CASP7",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t36",
-    "source": "Orf6",
+    "source": "Orf8a",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t37",
-    "source": "S",
+    "source": "Orf3b",
     "target": "Apoptosis_phenotype",
     "sign": true
    },
    {
     "id": "t38",
-    "source": "CASP7",
+    "source": "Orf6",
     "target": "Apoptosis_phenotype",
     "sign": true
    },

diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json
@@ -423,13 +423,13 @@
    },
    {
     "id": "t29",
-    "source": "egfr",
+    "source": "ph",
     "target": "sos",
     "sign": true
    },
    {
     "id": "t30",
-    "source": "ph",
+    "source": "egfr",
     "target": "sos",
     "sign": true
    }