For JP. monarch-initiative/operations#91 (comment)

notebooks/Lookup_KEGG_Genes_by_Pathway_Name.ipynb

@@ -0,0 +1,153 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Looking up genes by KEGG\n",
+    "\n",
+    "V quick query for JP, not well documented!\n",
+    "https://github.com/monarch-initiative/operations/issues/91#issuecomment-308893761"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "from ontobio.ontol_factory import OntologyFactory\n",
+    "ofactory= OntologyFactory()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<ontobio.config.Config at 0x108c61a90>"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# For SciGraph we need to use a config file that maps the SciGraph\n",
+    "# handle onto a URL\n",
+    "from ontobio.config import set_config\n",
+    "set_config('../conf/config.yaml')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sgo = ofactory.create('scigraph:data')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['KEGG-path:map00061']"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matches = sgo.search('Fatty acid biosynthesis')\n",
+    "matches"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ontobio.golr.golr_query import GolrAssociationQuery"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "q = GolrAssociationQuery(subject_category='gene', object=matches[0], subject_taxon='NCBITaxon:9606')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assocs = q.exec()['associations']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "NCBIGene:31 ACACA\n",
+      "NCBIGene:27349 MCAT\n",
+      "NCBIGene:2194 FASN\n",
+      "NCBIGene:55301 OLAH\n",
+      "NCBIGene:54995 OXSM\n",
+      "NCBIGene:32 ACACB\n"
+     ]
+    }
+   ],
+   "source": [
+    "for a in assocs:\n",
+    "    gene = a['subject']\n",
+    "    print(\"{} {}\".format(gene['id'], gene['label']))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.5.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}