Add units and groundings fror scenario 1

gyorilab · Jul 8, 2023 · a3ebf01 · a3ebf01
1 parent cac7c2f
commit a3ebf01
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Showing 4 changed files with 147 additions and 45 deletions.
diff --git a/notebooks/hackathon_2023.07/scenario1.ipynb b/notebooks/hackathon_2023.07/scenario1.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
  {
+ "attachments": {},
  "cell_type": "markdown",
  "id": "c947d97c",
  "metadata": {},
@@ -38,13 +39,14 @@
  "day_units = Unit(expression=sympy.Symbol('day'))\n",
  "per_day_units = Unit(expression=1/sympy.Symbol('day'))\n",
  "dimensionless_units = Unit(expression=sympy.Integer('1'))\n",
+ "per_day_per_person_units = Unit(expression=1/(sympy.Symbol('day')*sympy.Symbol('person')))\n",
  "\n",
  "c = {\n",
- " 'S': Concept(name='S', units=person_units),\n",
- " 'E': Concept(name='E', units=person_units),\n",
- " 'I': Concept(name='I', units=person_units),\n",
- " 'R': Concept(name='R', units=person_units),\n",
- " 'D': Concept(name='D', units=person_units)\n",
+ " 'S': Concept(name='S', units=person_units, identifiers={'ido': '0000514'}),\n",
+ " 'E': Concept(name='E', units=person_units, identifiers={'apollosv': '0000154'}),\n",
+ " 'I': Concept(name='I', units=person_units, identifiers={'ido': '0000511'}),\n",
+ " 'R': Concept(name='R', units=person_units, identifiers={'ido': '0000592'}),\n",
+ " 'D': Concept(name='D', units=person_units, identifiers={'ncit': 'C28554'}),\n",
  "}\n",
  "\n",
  "\n",
@@ -54,13 +56,13 @@
  " 'alpha': Parameter(name='alpha', value=0.000064, units=dimensionless_units),\n",
  " 'rho': Parameter(name='rho', value=1/9, units=per_day_units),\n",
  " 'N': Parameter(name='N', value=5_600_000, units=person_units),\n",
- " 'beta_s': Parameter(name='beta_s', value=1),\n",
- " 'beta_c': Parameter(name='beta_c', value=0.4),\n",
- " 't_0': Parameter(name='t_0', value=89, unts=day_units),\n",
+ " 'beta_s': Parameter(name='beta_s', value=1, units=per_day_per_person_units),\n",
+ " 'beta_c': Parameter(name='beta_c', value=0.4, units=per_day_per_person_units),\n",
+ " 't_0': Parameter(name='t_0', value=89, unts=day_units, units=day_units),\n",
  " # D=11, gamma = 1/D, R_0 = 5 and\n",
  " # beta = R_0 * gamma * mask(t) so kappa = 5/11\n",
- " 'kappa': Parameter(name='kappa', value=5/11),\n",
- " 'k': Parameter(name='k', value=5.0)\n",
+ " 'kappa': Parameter(name='kappa', value=5/11, units=per_day_units),\n",
+ " 'k': Parameter(name='k', value=5.0, units=dimensionless_units),\n",
  "}\n",
  "\n",
  "initials = {\n",
@@ -118,6 +120,7 @@
  ]
  },
  {
+ "attachments": {},
  "cell_type": "markdown",
  "id": "48e4ed6a",
  "metadata": {},
@@ -137,8 +140,8 @@
  "outputs": [],
  "source": [
  "k_1, k_2, t_1, beta_nc = sympy.symbols('k_1 k_2 t_1 beta_nc')\n",
- "parameters['k_1'] = Parameter(name='k_1', value=5.0)\n",
- "parameters['k_2'] = Parameter(name='k_2', value=1.0)\n",
+ "parameters['k_1'] = Parameter(name='k_1', value=5.0, units=dimensionless_units)\n",
+ "parameters['k_2'] = Parameter(name='k_2', value=1.0, units=dimensionless_units)\n",
  "parameters['t_1'] = Parameter(name='t_1', value=154, units=day_units)\n",
  "parameters['beta_nc'] = Parameter(name='beta_nc', value=0.5)\n",
  "tm.parameters = parameters\n",
@@ -191,6 +194,7 @@
  ]
  },
  {
+ "attachments": {},
  "cell_type": "markdown",
  "id": "6e3374f9",
  "metadata": {},
@@ -207,7 +211,7 @@
  "outputs": [],
  "source": [
  "epsilon = sympy.Symbol('epsilon')\n",
- "parameters['epsilon'] = Parameter(name='epsilon', value=1/90)\n",
+ "parameters['epsilon'] = Parameter(name='epsilon', value=1/90, units=per_day_units)\n",
  "tm.parameters = parameters\n",
  "tm.annotations = Annotations(name='Scenario 1d')\n",
  "t5 = NaturalConversion(subject=c['R'],\n",

diff --git a/notebooks/hackathon_2023.07/scenario1_a.json b/notebooks/hackathon_2023.07/scenario1_a.json
@@ -11,7 +11,9 @@
  "id": "S",
  "name": "S",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000514"
+ },
  "modifiers": {}
  },
  "units": {
@@ -23,7 +25,9 @@
  "id": "I",
  "name": "I",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000511"
+ },
  "modifiers": {}
  },
  "units": {
@@ -35,7 +39,9 @@
  "id": "E",
  "name": "E",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "apollosv": "0000154"
+ },
  "modifiers": {}
  },
  "units": {
@@ -47,7 +53,9 @@
  "id": "R",
  "name": "R",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000592"
+ },
  "modifiers": {}
  },
  "units": {
@@ -59,7 +67,9 @@
  "id": "D",
  "name": "D",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ncit": "C28554"
+ },
  "modifiers": {}
  },
  "units": {
@@ -183,23 +193,43 @@
  },
  {
  "id": "beta_c",
- "value": 0.4
+ "value": 0.4,
+ "units": {
+ "expression": "1/(day*person)",
+ "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>"
+ }
  },
  {
  "id": "beta_s",
- "value": 1.0
+ "value": 1.0,
+ "units": {
+ "expression": "1/(day*person)",
+ "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>"
+ }
  },
  {
  "id": "k",
- "value": 5.0
+ "value": 5.0,
+ "units": {
+ "expression": "1",
+ "expression_mathml": "<cn>1</cn>"
+ }
  },
  {
  "id": "kappa",
- "value": 0.45454545454545453
+ "value": 0.45454545454545453,
+ "units": {
+ "expression": "1/day",
+ "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+ }
  },
  {
  "id": "t_0",
- "value": 89.0
+ "value": 89.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
  },
  {
  "id": "delta",

diff --git a/notebooks/hackathon_2023.07/scenario1_c.json b/notebooks/hackathon_2023.07/scenario1_c.json
@@ -11,7 +11,9 @@
  "id": "S",
  "name": "S",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000514"
+ },
  "modifiers": {}
  },
  "units": {
@@ -23,7 +25,9 @@
  "id": "I",
  "name": "I",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000511"
+ },
  "modifiers": {}
  },
  "units": {
@@ -35,7 +39,9 @@
  "id": "E",
  "name": "E",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "apollosv": "0000154"
+ },
  "modifiers": {}
  },
  "units": {
@@ -47,7 +53,9 @@
  "id": "R",
  "name": "R",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ido": "0000592"
+ },
  "modifiers": {}
  },
  "units": {
@@ -59,7 +67,9 @@
  "id": "D",
  "name": "D",
  "grounding": {
- "identifiers": {},
+ "identifiers": {
+ "ncit": "C28554"
+ },
  "modifiers": {}
  },
  "units": {
@@ -175,31 +185,55 @@
  "parameters": [
  {
  "id": "beta_c",
- "value": 0.4
+ "value": 0.4,
+ "units": {
+ "expression": "1/(day*person)",
+ "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>"
+ }
  },
  {
  "id": "beta_nc",
  "value": 0.5
  },
  {
  "id": "beta_s",
- "value": 1.0
+ "value": 1.0,
+ "units": {
+ "expression": "1/(day*person)",
+ "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>"
+ }
  },
  {
  "id": "k_1",
- "value": 5.0
+ "value": 5.0,
+ "units": {
+ "expression": "1",
+ "expression_mathml": "<cn>1</cn>"
+ }
  },
  {
  "id": "k_2",
- "value": 1.0
+ "value": 1.0,
+ "units": {
+ "expression": "1",
+ "expression_mathml": "<cn>1</cn>"
+ }
  },
  {
  "id": "kappa",
- "value": 0.45454545454545453
+ "value": 0.45454545454545453,
+ "units": {
+ "expression": "1/day",
+ "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+ }
  },
  {
  "id": "t_0",
- "value": 89.0
+ "value": 89.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
  },
  {
  "id": "t_1",