Add metabolights notebook

notebooks/metabolights.ipynb

@@ -0,0 +1,94 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys, os, io, json\n",
+    "from neo4j import GraphDatabase\n",
+    "from py2neo import Graph\n",
+    "from pathlib import Path\n",
+    "from pandas import DataFrame\n",
+    "import pandas as pd\n",
+    "import networkx as nx\n",
+    "\n",
+    "graph = Graph(\"bolt://sarevok:7687\")\n",
+    "driver = GraphDatabase.driver('bolt://sarevok:7687', auth=None)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Which Metabolights studies are associated with chemicals under `\torganofluorine compound` in CHEBI?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "|    | study_id   | study_name                                                                                                                                                                                                                   | chemical_id   | chemical_name             |\n",
+      "|---:|:-----------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------|:--------------------------|\n",
+      "|  0 | MTBLS1693  | Known Metabolite Annotation in Different Biological Samples using Ion Mobility Collision Cross-Section Atlas (AllCCS)                                                                                                        | chebi:36811   | 4-(trifluoromethyl)phenol |\n",
+      "|  1 | MTBLS2406  | Multi-Omics Analysis Reveals Disturbance of Nanosecond Pulsed Electric Field in the Serum Metabolic Spectrum and Gut Microbiota                                                                                              | chebi:36811   | 4-(trifluoromethyl)phenol |\n",
+      "|  2 | MTBLS9451  | Fecal microbiota transplantation treatment maintains post antibiotics gut function by change the gut microbiome and fecal metabolome to reduce gut inflammation and oxidative stress in nile tilapia (Oreochromis niloticus) | chebi:83488   | fipronil-sulfide          |\n",
+      "|  3 | MTBLS3977  | Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs                                                                                                                                                    | chebi:83487   | fipronil sulfone          |\n",
+      "|  4 | MTBLS2145  | Metabolic Dynamics of In Vitro CD8+ T Cell Activation                                                                                                                                                                        | chebi:68540   | teriflunomide             |\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "# chebi:37143 is \"organofluorine compound\"\n",
+    "\n",
+    "df = DataFrame(graph.run(\"\"\"\n",
+    "MATCH (study:`metabolights:Study`)\n",
+    "        -[:`metabolights:ref`]->(metabolights_ref)\n",
+    "        -[:`metabolights:chemical`]->(chemical)\n",
+    "        -[:`biolink:broad_match`*1..]->(chem2)\n",
+    "        -[:sourceId]->(:Id { id: \"chebi:37143\" })\n",
+    "RETURN\n",
+    "    [id in study.id WHERE id =~ \"MTBL.*\" | id][0] AS study_id,\n",
+    "    study.`grebi:name`[0] as study_name,\n",
+    "    [id in chemical.id WHERE id =~ \"chebi:.*\" | id][0] AS chemical_id,\n",
+    "    chemical.`grebi:name`[0] as chemical_name\n",
+    "\"\"\").data())\n",
+    "\n",
+    "print(df.head(5).to_markdown())\n",
+    "\n",
+    "df.to_csv(\"metabolights_organofluorine.csv\", index=False)\n",
+    "\n",
+    "\n",
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "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": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}