From c5d073a0df6c354f08127913281861d4b32daa32 Mon Sep 17 00:00:00 2001
From: James McLaughlin <james@mclgh.net>
Date: Wed, 4 Dec 2024 17:54:33 +0000
Subject: [PATCH] add gwas_x_impc notebook

---
 notebooks/gwas_x_impc.ipynb | 75 +++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 notebooks/gwas_x_impc.ipynb

diff --git a/notebooks/gwas_x_impc.ipynb b/notebooks/gwas_x_impc.ipynb
new file mode 100644
index 0000000..b0d5aa4
--- /dev/null
+++ b/notebooks/gwas_x_impc.ipynb
@@ -0,0 +1,75 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "from pathlib import Path\n",
+    "from py2neo import Graph\n",
+    "from pandas import DataFrame\n",
+    "graph = Graph(\"bolt://localhost:7687\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "df = DataFrame(graph.run(\"\"\"\n",
+    "MATCH (snp:`gwas:SNP`)-[:`gwas:associated_with`]->(measurement)\n",
+    "MATCH (measurement)<-[:`upheno:phenotypeToTrait`]-(phenotype)\n",
+    "MATCH (phenotype)<-[:`biolink:broad_match`]-(descendantPhenotype)-[:sourceId]->(descendantSourceId)\n",
+    "WHERE \"OLS.mp\" IN descendantPhenotype.`grebi:datasources`\n",
+    "MATCH (descendantPhenotype)<-[:`impc:phenotype`]-(mouseGene)\n",
+    "WHERE \"IMPC\" IN mouseGene.`grebi:datasources`\n",
+    "RETURN DISTINCT [id in snp.id WHERE id =~ \"rs[0-9]*\" | id][0] AS gwas_variant,\n",
+    "[id in measurement.id WHERE id =~ \"oba:.*\" | id][0] AS measurement_id,\n",
+    "measurement.`grebi:name`[0] as measurement_name,\n",
+    "[id in phenotype.id WHERE id =~ \"upheno:[0-9]*\" | id][0] AS species_neutral_phenotype_id,\n",
+    "phenotype.`grebi:name`[0] AS species_neutral_phenotype_name,\n",
+    "[id in descendantPhenotype.id WHERE id =~ \"mp:[0-9]*\" | id][0] AS mouse_phenotype,\n",
+    "descendantPhenotype.`grebi:name`[0] AS mouse_phenotype_name,\n",
+    "mouseGene.`grebi:name`[0] AS mouse_gene_name,\n",
+    "[id in mouseGene.id WHERE id =~ \"mgi:[0-9]*\" | id][0] AS mouse_gene_id\n",
+    "\"\"\").data())\n",
+    "\n",
+    "#print(df.head(5).to_markdown())\n",
+    "df.to_csv(\"gwas_to_impc.csv\", index=False)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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
+}