Skip to content

Instantly share code, notes, and snippets.

@detrout

detrout/gist:4396dfae354b131f319d

Created June 10, 2014 21:13
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save detrout/4396dfae354b131f319d to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save detrout/4396dfae354b131f319d to your computer and use it in GitHub Desktop.
Download ZIP
check for starting amounts.
Raw
gistfile1.txt
{
"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/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS791FEH/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS839NNF/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS860IIZ/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS919MHE/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS934CYZ/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS991XFG/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Loading: https://www.encodedcc.org/biosamples/ENCBS998GBF/"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n"
]
}
],
"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": {}
}
]
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment