Add grounding and units

gyorilab · Jul 10, 2023 · 0c35df3 · 0c35df3
1 parent 43f01fe
commit 0c35df3
Show file tree

Hide file tree

Showing 2 changed files with 181 additions and 59 deletions.
diff --git a/notebooks/hackathon_2023.07/scenario2.ipynb b/notebooks/hackathon_2023.07/scenario2.ipynb
@@ -28,7 +28,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 30,
+ "execution_count": 3,
  "id": "0991209a",
  "metadata": {},
  "outputs": [],
@@ -41,7 +41,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 31,
+ "execution_count": 4,
  "id": "716217a7",
  "metadata": {},
  "outputs": [],
@@ -51,28 +51,54 @@
  "per_day_units = Unit(expression=1/sympy.Symbol('day'))\n",
  "dimensionless_units = Unit(expression=sympy.Integer('1'))\n",
  "\n",
- "populations = ['S', 'SVR', 'V1', 'V2', 'I', 'IV', 'IR',\n",
- " 'A', 'AR', 'R', 'R2']\n",
+ "populations = {\n",
+ " # Susceptible\n",
+ " 'S': [{'ido': '0000514'}, {'vaccination_status': 'vo:0001377'}],\n",
+ " # Susceptible lost immunity\n",
+ " 'SVR': [{'ido': '0000514'}, {'disease_history': 'ido:0000592'}],\n",
+ " # Vaccinated once\n",
+ " 'V1': [{'ido': '0000514'}, {'vaccination_status': 'askemo:0000018'}],\n",
+ " # Vaccinated twice\n",
+ " 'V2': [{'ido': '0000514'}, {'vaccination_status': 'askemo:0000019'}],\n",
+ " # Infected\n",
+ " 'I': [{'ido': '0000511'}, {}],\n",
+ " # Infected vaccinated\n",
+ " 'IV': [{'ido': '0000511'}, {'vaccination_status': 'vo:0001376'}],\n",
+ " # Infected after recovery\n",
+ " 'IR': [{'ido': '0000511'}, {'disease_history': 'ido:0000592'}],\n",
+ " # Asymptomatic\n",
+ " 'A': [{'ido': '0000511'}, {'disease_severity': 'ncit:C3833'}],\n",
+ " # Asymptomatic after recovery\n",
+ " 'AR': [{'ido': '0000511'}, {'disease_severity': 'ncit:C3833'}],\n",
+ " # Recovered\n",
+ " 'R': [{'ido': '0000514'}, {'disease_severity': 'ido:0000592'}],\n",
+ " # Recovered after second infection\n",
+ " 'R2': [{'ido': '0000592'}, {}],\n",
+ "}\n",
+ "\n",
+ "c = {\n",
+ " pop: Concept(name=pop, units=dimensionless_units,\n",
+ " identifiers=indentifiers, context=context)\n",
+ " for pop, (indentifiers, context) in populations.items()\n",
+ "}\n",
  "\n",
- "c = {pop: Concept(name=pop, units=dimensionless_units)\n",
- " for pop in populations}\n",
  "\n",
  "parameters = [\n",
- " Parameter(name='beta', value=3.3e-9),\n",
- " Parameter(name='beta_v1', value=0.2*3.3e-9),\n",
- " Parameter(name='beta_v2', value=0.05*3.3e-9),\n",
- " Parameter(name='beta_R', value=0.05*3.3e-9),\n",
- " Parameter(name='gamma', value=1/28),\n",
- " Parameter(name='mu', value=109019/(14570000*365)),\n",
- " Parameter(name='mu_I', value=0.001),\n",
- " Parameter(name='mu_IV', value=0.15*0.001),\n",
- " Parameter(name='nu_R', value=1/(4*365)),\n",
- " Parameter(name='nu_v1', value=1/365),\n",
- " Parameter(name='nu_v2', value=1/(4*365)),\n",
- " Parameter(name='ai', value=0.5), # paper uses sigma instead of ai\n",
- " Parameter(name='ai_V', value=0.85),\n",
- " Parameter(name='ai_R', value=0.85),\n",
- " Parameter(name='ai_beta_ratio', value=3.0)\n",
+ " Parameter(name='beta', value=3.3e-9, units=per_day_units),\n",
+ " Parameter(name='beta_v1', value=0.2*3.3e-9, units=per_day_units),\n",
+ " Parameter(name='beta_v2', value=0.05*3.3e-9, units=per_day_units),\n",
+ " Parameter(name='beta_R', value=0.05*3.3e-9, units=per_day_units),\n",
+ " Parameter(name='gamma', value=1/28, units=per_day_units),\n",
+ " Parameter(name='mu', value=109019/(14570000*365), units=per_day_units),\n",
+ " Parameter(name='mu_I', value=0.001, units=per_day_units),\n",
+ " Parameter(name='mu_IV', value=0.15*0.001, units=per_day_units),\n",
+ " Parameter(name='nu_R', value=1/(4*365), units=per_day_units),\n",
+ " Parameter(name='nu_v1', value=1/365, units=per_day_units),\n",
+ " Parameter(name='nu_v2', value=1/(4*365), units=per_day_units),\n",
+ " Parameter(name='ai', value=0.5, units=dimensionless_units), # paper uses sigma instead of ai\n",
+ " Parameter(name='ai_V', value=0.85, units=dimensionless_units),\n",
+ " Parameter(name='ai_R', value=0.85, units=dimensionless_units),\n",
+ " Parameter(name='ai_beta_ratio', value=3.0, units=dimensionless_units),\n",
  "]\n",
  "\n",
  "initials = {\n",
@@ -92,7 +118,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 32,
+ "execution_count": 5,
  "id": "f91e5e06",
  "metadata": {},
  "outputs": [],
@@ -102,7 +128,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 33,
+ "execution_count": 6,
  "id": "45045c21",
  "metadata": {},
  "outputs": [],
@@ -113,7 +139,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 34,
+ "execution_count": 7,
  "id": "563bef26",
  "metadata": {},
  "outputs": [],
@@ -191,7 +217,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 35,
+ "execution_count": 8,
  "id": "25dfad3d",
  "metadata": {},
  "outputs": [],