Merge pull request #12 from rurimatsuri3/master

an example from Riken database
incf-nidash · Aug 18, 2015 · 0081217 · 0081217
2 parents 0fe6c1d + ea4193d
commit 0081217
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diff --git a/use-cases/abide/abide_terms.ttl b/use-cases/abide/abide_terms.ttl
@@ -9,7 +9,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 abide:ABIDE_FSIQ a prov:Entity ;
-    abide:form "WASI" ;
+    abide:form "WASImorii" ;
     abide:term "ABIDE_FIQ" ;
     prov:definition "FIQ Standard Score" ;
     prov:label "ABIDE vocabulary term" .

diff --git a/use-cases/yoko/.ipynb_checkpoints/play_with_allen-checkpoint.ipynb b/use-cases/yoko/.ipynb_checkpoints/play_with_allen-checkpoint.ipynb
@@ -0,0 +1,157 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import rdflib"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "g=rdflib.Graph()\n",
+    "g.parse('rikenbrc_mouse-6-Gene_Turtle.ttl',format='turtle')\n",
+    "query=\"\"\"\n",
+    "PREFIX riken: <http://metadb.riken.jp/db>\n",
+    "SELECT DISTINCT *\n",
+    "WHERE \n",
+    "{ ?s ?p ?o .\n",
+    "}\n",
+    "\"\"\"\n",
+    "\n",
+    "# print every triplet\n",
+    "#for e in g.query(query):\n",
+    "#    print e"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### this is a simple query"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false,
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(rdflib.term.Literal(u'http://www.informatics.jax.org/marker/MGI:97371', datatype=rdflib.term.URIRef(u'http://www.w3.org/2001/XMLSchema#anyURI')),)\n"
+     ]
+    }
+   ],
+   "source": [
+    "query=\"\"\"\n",
+    "PREFIX riken: <http://metadb.riken.jp/db>\n",
+    "SELECT DISTINCT ?url\n",
+    "WHERE \n",
+    "{ ?s a <http://metadb.riken.jp/db/rikenbrc_mouse/animal_0000006> .\n",
+    "  ?s <http://www.w3.org/2004/02/skos/core#altLabel> \"Npr1\"^^<http://www.w3.org/2001/XMLSchema#string> .\n",
+    "  ?s <http://metadb.riken.jp/db/brc_beta/brc_0000037> ?url .\n",
+    "}\n",
+    "\"\"\"\n",
+    "for e in g.query(query):\n",
+    "    print e"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "def get_url(gene_name):\n",
+    "    \"\"\"\n",
+    "    constr8uct query with name of gene \n",
+    "    \n",
+    "    parameter: \n",
+    "    ----------\n",
+    "    gene_name: String, \n",
+    "        the name of the gene\n",
+    "    \"\"\"\n",
+    "    \n",
+    "    prefix = \"PREFIX riken: <http://metadb.riken.jp/db>\"\n",
+    "    \n",
+    "    query=\"\"\"\n",
+    "SELECT DISTINCT ?url\n",
+    "WHERE \n",
+    "{ ?s a <http://metadb.riken.jp/db/rikenbrc_mouse/animal_0000006> .\n",
+    "  ?s <http://www.w3.org/2004/02/skos/core#altLabel> \"%s\"^^<http://www.w3.org/2001/XMLSchema#string> .\n",
+    "  ?s <http://metadb.riken.jp/db/brc_beta/brc_0000037> ?url .\n",
+    "}\n",
+    "\"\"\"%gene_name\n",
+    "    \n",
+    "    # print prefix + query\n",
+    "    return g.query(prefix + query)\n",
+    "        \n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "e is : (rdflib.term.Literal(u'http://www.informatics.jax.org/marker/MGI:1922151', datatype=rdflib.term.URIRef(u'http://www.w3.org/2001/XMLSchema#anyURI')),)\n",
+      "<class 'rdflib.term.Literal'> <class 'rdflib.query.ResultRow'>\n",
+      "dir e[0] is : ['__abs__', '__add__', '__class__', '__contains__', '__delattr__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__', '__getslice__', '__getstate__', '__gt__', '__hash__', '__init__', '__invert__', '__le__', '__len__', '__lt__', '__mod__', '__module__', '__mul__', '__ne__', '__neg__', '__new__', '__nonzero__', '__pos__', '__reduce__', '__reduce_ex__', '__repr__', '__rmod__', '__rmul__', '__setattr__', '__setstate__', '__sizeof__', '__slots__', '__str__', '__subclasshook__', '_comparable_to', '_datatype', '_formatter_field_name_split', '_formatter_parser', '_language', '_literal_n3', '_quote_encode', '_value', 'capitalize', 'center', 'count', 'datatype', 'decode', 'encode', 'endswith', 'eq', 'expandtabs', 'find', 'format', 'index', 'isalnum', 'isalpha', 'isdecimal', 'isdigit', 'islower', 'isnumeric', 'isspace', 'istitle', 'isupper', 'join', 'language', 'ljust', 'lower', 'lstrip', 'md5_term_hash', 'n3', 'neq', 'normalize', 'partition', 'replace', 'rfind', 'rindex', 'rjust', 'rpartition', 'rsplit', 'rstrip', 'split', 'splitlines', 'startswith', 'strip', 'swapcase', 'title', 'toPython', 'translate', 'upper', 'value', 'zfill']\n",
+      "http://www.informatics.jax.org/marker/MGI:1922151\n"
+     ]
+    }
+   ],
+   "source": [
+    "for e in get_url(\"Kbtbd11\"):\n",
+    "    print \"e is :\", e\n",
+    "    print type(e[0]), type(e)\n",
+    "    print \"dir e[0] is :\", dir(e[0])\n",
+    "    print e[0]"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}