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June 10, 2014 21:13
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:6a5b9dfb303e905036e3a15bfa0a3e0b41ad4bf9d5244673e6fdb3ba58c218ea" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ | |
| { | |
| "cell_type": "heading", | |
| "level": 1, | |
| "metadata": {}, | |
| "source": [ | |
| "Introduction" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "I needed to explore how the objects provided by the ENCODE 3 DCC's encoded submission site fit together. This notebook shows some of my initial queries as I tried to work out how to connect aliases attached to encode libraries for a particular dataset." | |
| ] | |
| }, | |
| { | |
| "cell_type": "heading", | |
| "level": 2, | |
| "metadata": {}, | |
| "source": [ | |
| "Setup" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "Setup the python environment." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "from __future__ import print_function" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 1 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "import sys\n", | |
| "import os" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 2 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "def custom():\n", | |
| " htsw = os.path.expanduser('~/proj/solexa/htsworkflow')\n", | |
| " if htsw not in sys.path:\n", | |
| " sys.path.append(htsw)\n", | |
| "custom()" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 3 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "from htsworkflow.submission.encoded import ENCODED\n", | |
| "from htsworkflow.util.rdfhelp import get_model, dump_model\n", | |
| "from htsworkflow.util.rdfjsonld import load_into_model" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 4 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%load_ext rdfmagic" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 5 | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "This is some initialization code for my extension <a href=\"https://github.com/detrout/rdfmagic\">rdfmagic</a>. It provides a short alias name for the long URIs that RDF likes. I can use the prefixes in the sparql query magic, and the extension uses them to abbreviate the display of the query." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "# encoded schemas\n", | |
| "%addns biosample https://www.encodedcc.org/profiles/biosample.json#\n", | |
| "%addns experiment https://www.encodedcc.org/profiles/experiment.json#\n", | |
| "%addns dataset https://www.encodedcc.org/profiles/dataset.json#\n", | |
| "%addns file https://www.encodedcc.org/profiles/file.json#\n", | |
| "%addns library https://www.encodedcc.org/profiles/library.json#\n", | |
| "%addns replicate https://www.encodedcc.org/profiles/replicate.json#\n", | |
| "\n", | |
| "# encoded links to objects\n", | |
| "%addns experiments https://www.encodedcc.org/experiments/\n", | |
| "%addns files https://www.encodedcc.org/files/\n", | |
| "%addns replicates https://www.encodedcc.org/replicates/\n", | |
| "%addns libraries https://www.encodedcc.org/libraries/\n", | |
| " \n", | |
| "# htsw schemas\n", | |
| "%addns htsw http://jumpgate.caltech.edu/wiki/LibraryOntology#" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 6 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "server = ENCODED('www.encodedcc.org')\n", | |
| "server.load_netrc()" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 7 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "model = get_model(use_contexts=False)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 8 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "def load_jsonld(model, url, **kwargs):\n", | |
| " load_into_model(model, server.get_jsonld(url, **kwargs))" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 9 | |
| }, | |
| { | |
| "cell_type": "heading", | |
| "level": 1, | |
| "metadata": {}, | |
| "source": [ | |
| "Load Data" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "experiments = [\n", | |
| " '/barbara-wold:Hs_UMB5408_6_M_CN_Purkinje_30pool',\n", | |
| " '/barbara-wold:Hs_UMB5408_6_M_CN_Purkinje_30pool',\n", | |
| " '/barbara-wold:Hs_UMB5408_6_M_CN_granule',\n", | |
| " '/barbara-wold:Hs_UMB5408_6_M_CN_granule',\n", | |
| " '/barbara-wold:Hs_UMB4727_20_M_CN_Purkinje_30pool',\n", | |
| " '/barbara-wold:Hs_UMB4727_20_M_CN_Purkinje_30pool',\n", | |
| " '/barbara-wold:Hs_UMB4727_20 M_CN_granule',\n", | |
| " '/barbara-wold:Hs_UMB4727_20 M_CN_granule',\n", | |
| " '/barbara-wold:Hs_UMB4727_20_M_CN_midFI_pyramids_30pool',\n", | |
| " '/barbara-wold:Hs_UMB4727_20_M_CN_midFI_pyramids_30pool',\n", | |
| " '/barbara-wold:Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool',\n", | |
| " '/barbara-wold:Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool',\n", | |
| " '/ENCSR000AJD',\n", | |
| " '/ENCSR000AJG',\n", | |
| " '/ENCSR000AIZ'\n", | |
| "]" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 10 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "for exp in experiments:\n", | |
| " print('Loading: {}'.format(exp))\n", | |
| " load_jsonld(model, exp, Embed=False)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "Loading: /barbara-wold:Hs_UMB5408_6_M_CN_Purkinje_30pool\n", | |
| "Loading: /barbara-wold:Hs_UMB5408_6_M_CN_Purkinje_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB5408_6_M_CN_granule" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB5408_6_M_CN_granule" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20_M_CN_Purkinje_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20_M_CN_Purkinje_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20 M_CN_granule" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20 M_CN_granule" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20_M_CN_midFI_pyramids_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB4727_20_M_CN_midFI_pyramids_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /barbara-wold:Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /ENCSR000AJD" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /ENCSR000AJG" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: /ENCSR000AIZ" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 11 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%sparql -m model\n", | |
| "select distinct ?t\n", | |
| "where {\n", | |
| " ?s a ?t .\n", | |
| "}\n", | |
| "order by ?t" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stderr", | |
| "text": [ | |
| "/usr/lib/python2.7/dist-packages/RDF.py:2014: RedlandWarning: Variable s was bound but is unused in the query\n", | |
| " results = Redland.librdf_query_execute(self._query,model._model)\n" | |
| ] | |
| }, | |
| { | |
| "html": [ | |
| "<table><tr><td>t</td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/award.json#award\">https://www.encodedcc.org/profiles/award.json#award</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/award.json#item\">https://www.encodedcc.org/profiles/award.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/biosample.json#biosample\">biosample:biosample</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/biosample.json#item\">biosample:item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/experiment.json#dataset\">experiment:dataset</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/experiment.json#experiment\">experiment:experiment</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/experiment.json#item\">experiment:item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/file.json#file\">file:file</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/file.json#item\">file:item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/human_donor.json#donor\">https://www.encodedcc.org/profiles/human_donor.json#donor</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/human_donor.json#human_donor\">https://www.encodedcc.org/profiles/human_donor.json#human_donor</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/human_donor.json#item\">https://www.encodedcc.org/profiles/human_donor.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/lab.json#item\">https://www.encodedcc.org/profiles/lab.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/lab.json#lab\">https://www.encodedcc.org/profiles/lab.json#lab</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/library.json#item\">library:item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/library.json#library\">library:library</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/organism.json#item\">https://www.encodedcc.org/profiles/organism.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/organism.json#organism\">https://www.encodedcc.org/profiles/organism.json#organism</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/platform.json#item\">https://www.encodedcc.org/profiles/platform.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/platform.json#platform\">https://www.encodedcc.org/profiles/platform.json#platform</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/replicate.json#item\">replicate:item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/replicate.json#replicate\">replicate:replicate</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/source.json#item\">https://www.encodedcc.org/profiles/source.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/source.json#source\">https://www.encodedcc.org/profiles/source.json#source</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/user.json#item\">https://www.encodedcc.org/profiles/user.json#item</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/profiles/user.json#user\">https://www.encodedcc.org/profiles/user.json#user</a></td></tr></table>" | |
| ], | |
| "metadata": {}, | |
| "output_type": "pyout", | |
| "prompt_number": 12, | |
| "text": [ | |
| "<rdfmagic.LibRdfResults at 0x7ffc86292090>" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 12 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%sparql -m model -o biosamples\n", | |
| "select distinct ?s\n", | |
| "where {\n", | |
| " ?s a biosample:biosample .\n", | |
| "}\n", | |
| "order by ?s" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 13 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "biosamples" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "html": [ | |
| "<table><tr><td>s</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS009SRE/\">https://www.encodedcc.org/biosamples/ENCBS009SRE/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS051VQG/\">https://www.encodedcc.org/biosamples/ENCBS051VQG/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS122LNO/\">https://www.encodedcc.org/biosamples/ENCBS122LNO/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS188JNJ/\">https://www.encodedcc.org/biosamples/ENCBS188JNJ/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS236ZAD/\">https://www.encodedcc.org/biosamples/ENCBS236ZAD/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS487GLA/\">https://www.encodedcc.org/biosamples/ENCBS487GLA/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS503XXB/\">https://www.encodedcc.org/biosamples/ENCBS503XXB/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS590LDH/\">https://www.encodedcc.org/biosamples/ENCBS590LDH/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS651ADZ/\">https://www.encodedcc.org/biosamples/ENCBS651ADZ/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS677XMX/\">https://www.encodedcc.org/biosamples/ENCBS677XMX/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS791FEH/\">https://www.encodedcc.org/biosamples/ENCBS791FEH/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS839NNF/\">https://www.encodedcc.org/biosamples/ENCBS839NNF/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS860IIZ/\">https://www.encodedcc.org/biosamples/ENCBS860IIZ/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS919MHE/\">https://www.encodedcc.org/biosamples/ENCBS919MHE/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS934CYZ/\">https://www.encodedcc.org/biosamples/ENCBS934CYZ/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS991XFG/\">https://www.encodedcc.org/biosamples/ENCBS991XFG/</a></td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS998GBF/\">https://www.encodedcc.org/biosamples/ENCBS998GBF/</a></td></tr></table>" | |
| ], | |
| "metadata": {}, | |
| "output_type": "pyout", | |
| "prompt_number": 14, | |
| "text": [ | |
| "<rdfmagic.LibRdfResults at 0x7ffc78fb3f50>" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 14 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "for row in biosamples:\n", | |
| " sample = row['s']\n", | |
| " print('Loading: {}'.format(sample))\n", | |
| " try:\n", | |
| " load_jsonld(model, '{}'.format(sample), Embed=False)\n", | |
| " except Exception as err:\n", | |
| " print ('failed: ', err)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS009SRE/\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS051VQG/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS122LNO/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS188JNJ/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS236ZAD/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS487GLA/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS503XXB/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS590LDH/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS651ADZ/" | |
| ] | |
| }, | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS677XMX/" | |
| ] | |
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| "output_type": "stream", | |
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| "Loading: https://www.encodedcc.org/biosamples/ENCBS839NNF/" | |
| ] | |
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| "Loading: https://www.encodedcc.org/biosamples/ENCBS860IIZ/" | |
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| "stream": "stdout", | |
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| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS919MHE/" | |
| ] | |
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| "stream": "stdout", | |
| "text": [ | |
| "\n", | |
| "Loading: https://www.encodedcc.org/biosamples/ENCBS934CYZ/" | |
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| "stream": "stdout", | |
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| "Loading: https://www.encodedcc.org/biosamples/ENCBS991XFG/" | |
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| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "\n" | |
| ] | |
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| ], | |
| "prompt_number": 19 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%sparql -m model\n", | |
| "select distinct ?s ?desc ?amount ?units\n", | |
| "where {\n", | |
| " ?s a biosample:biosample ;\n", | |
| " rdf:description ?desc .\n", | |
| " OPTIONAL { ?s biosample:starting_amount ?amount . }\n", | |
| " OPTIONAL { ?s biosample:starting_amount_units ?units . }\n", | |
| " \n", | |
| "}\n", | |
| "order by ?s" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "html": [ | |
| "<table><tr><td>s</td><td>desc</td><td>amount</td><td>units</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS009SRE/\">https://www.encodedcc.org/biosamples/ENCBS009SRE/</a></td><td>Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS035OKV/\">https://www.encodedcc.org/biosamples/ENCBS035OKV/</a></td><td>single piece of cerebellum recieved from brain bank 20 year human male</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS051VQG/\">https://www.encodedcc.org/biosamples/ENCBS051VQG/</a></td><td>Hs_UMB5408_6_M_CN_Purkinje_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS122LNO/\">https://www.encodedcc.org/biosamples/ENCBS122LNO/</a></td><td>Hs_UMB4727_20 M_CN_granule</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS188JNJ/\">https://www.encodedcc.org/biosamples/ENCBS188JNJ/</a></td><td>Hs_UMB4727_20 M_CN_granule</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS195IGI/\">https://www.encodedcc.org/biosamples/ENCBS195IGI/</a></td><td>GM12878 growth</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS236ZAD/\">https://www.encodedcc.org/biosamples/ENCBS236ZAD/</a></td><td>GM12878 11 cell pool</td><td>11</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS356HRP/\">https://www.encodedcc.org/biosamples/ENCBS356HRP/</a></td><td>single piece of cerebellum recieved from brain bank 6 year human male</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS446XRJ/\">https://www.encodedcc.org/biosamples/ENCBS446XRJ/</a></td><td>single piece of cerebellum recieved from brain bank 27 year human male</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS487GLA/\">https://www.encodedcc.org/biosamples/ENCBS487GLA/</a></td><td>GM12878 bulk prep 10 ngs</td><td>1.000000000000000E-05</td><td>mg</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS503XXB/\">https://www.encodedcc.org/biosamples/ENCBS503XXB/</a></td><td>Hs_UMB4727_20_M_CN_Purkinje_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS590LDH/\">https://www.encodedcc.org/biosamples/ENCBS590LDH/</a></td><td>Hs_UMB4727_20_M_CN_midFI_pyramids_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS651ADZ/\">https://www.encodedcc.org/biosamples/ENCBS651ADZ/</a></td><td>Hs_UMB4727_20_M_CN_midFI_pyramids_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS677XMX/\">https://www.encodedcc.org/biosamples/ENCBS677XMX/</a></td><td>Hs_UMB5408_6_M_CN_granule</td><td>None</td><td>None</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS791FEH/\">https://www.encodedcc.org/biosamples/ENCBS791FEH/</a></td><td>GM12878 30 cell pool A (analysis group in paper)</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS839NNF/\">https://www.encodedcc.org/biosamples/ENCBS839NNF/</a></td><td>GM12878 30 cell pool B (analysis group in paper)</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS860IIZ/\">https://www.encodedcc.org/biosamples/ENCBS860IIZ/</a></td><td>Hs_UMB4727_20_M_CN_Purkinje_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS919MHE/\">https://www.encodedcc.org/biosamples/ENCBS919MHE/</a></td><td>Hs_UMB602_27_M_CN_FI_slb9_pyramids_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS934CYZ/\">https://www.encodedcc.org/biosamples/ENCBS934CYZ/</a></td><td>GM12878 10 cell pool</td><td>10</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS991XFG/\">https://www.encodedcc.org/biosamples/ENCBS991XFG/</a></td><td>Hs_UMB5408_6_M_CN_Purkinje_30pool</td><td>30</td><td>cells</td></tr><tr><td><a href=\"https://www.encodedcc.org/biosamples/ENCBS998GBF/\">https://www.encodedcc.org/biosamples/ENCBS998GBF/</a></td><td>Hs_UMB5408_6_M_CN_granule</td><td>None</td><td>None</td></tr></table>" | |
| ], | |
| "metadata": {}, | |
| "output_type": "pyout", | |
| "prompt_number": 23, | |
| "text": [ | |
| "<rdfmagic.LibRdfResults at 0x7ffc86292190>" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 23 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "dump_model(model, open('/tmp/encode-datasets.turtle','w'))" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 21 | |
| } | |
| ], | |
| "metadata": {} | |
| } | |
| ] | |
| } |
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