Merge pull request #82 from chinchien-lin/main

updated tut 3

tutorials/tutorial_3_add_sparc_tools_to_knowledge_graph/tutorial_3_add_sparc_tools_to_knowledge_graph.ipynb

@@ -0,0 +1,232 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "58dcd0c7",
+   "metadata": {},
+   "source": [
+    "# Tutorial 3: Adding tools created from existing SPARC datasets to the knowledge graph\n",
+    "\n",
+    "This tutorial demonstrates how tools and models stored in SDS from Tutorial 1 can be added to the knowledge graph created in Tutorial 2. \n",
+    "\n",
+    "** data is sourced from https://sparc.science/datasets/262?type=dataset"
+   ]
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Prerequisites\n",
+    "Please see Tutorial 1 for how to add tools and models to a SDS dataset; and Tutorial 2 for creating knowledge graphs."
+   ],
+   "id": "b873792b2a2703a5"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "# Requirements\n",
+    "!pip install -U sparc_assemble\n",
+    "# !pip install -U sparc_flow\n",
+    "# !pip install -U sparc_me\n",
+    "from sparc_assemble.core.kg import KG"
+   ],
+   "id": "28a4e66147375179",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Step 1: Initialise knowledge graph"
+   ],
+   "id": "6c3c75e76db405fa"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "We will initialise the knowledge graph, KG, from a default ontology, \"EDAM\"."
+   ],
+   "id": "538d81f6db0d35e4"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-13T03:36:12.450189500Z",
+     "start_time": "2024-08-13T03:36:12.040131200Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "kg = KG()"
+   ],
+   "id": "c535a0124b0aec22",
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Step 2: Add tools from SPARC dataset to knowledge graphs"
+   ],
+   "id": "42742867538d19f8"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Navigate to a tool dataset generated from Tutorial 1, use this as the input for adding tools to knowledge graphs."
+   ],
+   "id": "30e64b90fb4ea46b"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-13T03:37:17.831374500Z",
+     "start_time": "2024-08-13T03:37:17.809377Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "tools_sds = 'resources/tools_dataset'\n",
+    "kg.add_tools(tool_library=tools_sds)"
+   ],
+   "id": "9189e7be765b269d",
+   "outputs": [],
+   "execution_count": 4
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [],
+   "id": "fcfdb6979681ca59"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Step 3: Add models from SPARC dataset to knowledge graphs"
+   ],
+   "id": "5af9176bc0ebb324"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Recall Tutorial 1 where we downloaded a model dataset. Here, we use the simulation.json file from that dataset to add this model to the knowledge graph."
+   ],
+   "id": "5ee56629083aeaaa"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-13T03:37:24.701925200Z",
+     "start_time": "2024-08-13T03:37:24.671927700Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "model_file = 'resources/models/simulation.json'\n",
+    "kg.add_sparc_model(model_path=model_file)"
+   ],
+   "id": "9510b3f174385b3a",
+   "outputs": [],
+   "execution_count": 5
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Step 4: List all tools and models in knowledge graph"
+   ],
+   "id": "79034b2f8426c802"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Show what models and tools does this knowledge graph keep a record of."
+   ],
+   "id": "5b0b590a67707091"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-13T03:37:27.496585600Z",
+     "start_time": "2024-08-13T03:37:27.341588800Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "kg.list()"
+   ],
+   "id": "3bb1118ff16ac87c",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\t 1- vsl.Stimulation level,ssl.Stimulation level,sm.Simulation mode -> HumanSAN_Fabbri_Fantini_Wilders_Severi_2017 -> vm.Membrane/V, time.environment/time\n",
+      "\t 2- example_data -> extract_mode -> sm.Simulation mode\n"
+     ]
+    }
+   ],
+   "execution_count": 6
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Step 5: Save knowledge graph"
+   ],
+   "id": "fc3c96d6f62bfb27"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Now we save the knowledge graph for future use."
+   ],
+   "id": "f7ad7ef936569d38"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-13T03:37:37.413164Z",
+     "start_time": "2024-08-13T03:37:37.242124200Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "kg.save(save_path=\"resources/kg_sparc_model.owl\")"
+   ],
+   "id": "aa02d8b054488071",
+   "outputs": [],
+   "execution_count": 7
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}