{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Explore Mappings (xrefs) from Uberon\n",
"\n",
"Draft notebook showing the xref graph functionality of OntoBio"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"## First fetch ontology\n",
"from ontobio.ontol_factory import OntologyFactory\n",
"\n",
"ofactory = OntologyFactory()\n",
"ont = ofactory.create(\"uberon\") ## Connect remotely to Uberon over SPARQL\n",
"##\n",
"## Note: Jupyter may show '*' to indicate kernel busy while this is being\n",
"## fetched - should only take a few seconds. Wait before proceeding"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'UBERON:0006956'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## select a class\n",
"[cls] = ont.search(\"buccal mucosa\")\n",
"cls"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['FMA:59785',\n",
" 'http://linkedlifedata.com/resource/umls/id/C1578559',\n",
" 'UMLS:C1578559',\n",
" 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12505',\n",
" 'CALOHA:TS-2349',\n",
" 'http://www.snomedbrowser.com/Codes/Details/16811007',\n",
" 'BTO:0003833']"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## Get xrefs for a class\n",
"ont.xrefs(cls)"
]
},
{
"cell_type": "code",
"execution_count": 64,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"100535"
]
},
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## Get a networkx graph object\n",
"xg = ont.xref_graph\n",
"len(xg.edges())"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['FMA:59785',\n",
" 'UMLS:C1578559',\n",
" 'UMLS:C1578559',\n",
" 'NCIT:C12505',\n",
" 'CALOHA:TS-2349',\n",
" 'SCTID:16811007',\n",
" 'BTO:0003833']"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## Hacky convenience function to deal with URL xrefs\n",
"## TODO: use prefixcommons\n",
"\n",
"def contract_xref(x):\n",
" x = x.replace('http://linkedlifedata.com/resource/umls/id/','UMLS:')\n",
" x = x.replace('http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#', 'NCIT:')\n",
" x = x.replace('http://www.snomedbrowser.com/Codes/Details/', 'SCTID:')\n",
" return x\n",
"\n",
"[contract_xref(x) for x in ont.xrefs(cls)]"
]
},
{
"cell_type": "code",
"execution_count": 54,
"metadata": {},
"outputs": [],
"source": [
"## Prepare to make a DataFrame\n",
"## Each item is a class\n",
"## Each column is a database\n",
"import pandas as pd\n",
"items = []\n",
"for c in ont.nodes():\n",
" label = ont.label(c)\n",
" d = dict(id=c, label=label)\n",
" items.append(d)\n",
" for x in ont.xrefs(c):\n",
" toks = contract_xref(x).split(\":\")\n",
" if len(toks) == 2:\n",
" d[toks[0]] = toks[1]\n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": 55,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style>\n",
" .dataframe thead tr:only-child th {\n",
" text-align: right;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: left;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th></th>\n",
" <th>AAO</th>\n",
" <th>ABA</th>\n",
" <th>AEO</th>\n",
" <th>AEO_RETIRED</th>\n",
" <th>ANISEED</th>\n",
" <th>BAMS</th>\n",
" <th>BILA</th>\n",
" <th>BILS</th>\n",
" <th>BM</th>\n",
" <th>BSA</th>\n",
" <th>...</th>\n",
" <th>XtroDO</th>\n",
" <th>ZFA</th>\n",
" <th>ZFA_RETIRED</th>\n",
" <th>ZFS</th>\n",
" <th>galen</th>\n",
" <th>http</th>\n",
" <th>https</th>\n",
" <th>ncithesaurus</th>\n",
" <th>nodeID</th>\n",
" <th>span</th>\n",
" </tr>\n",
" <tr>\n",
" <th>id</th>\n",
" <th>label</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>UBERON:3010014</th>\n",
" <th>inguinal glands</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:2000723</th>\n",
" <th>obsolete slow muscle cell somite 5</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td>0000723</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0000113</th>\n",
" <th>post-juvenile adult stage</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>0000113</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>0000044</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0006590</th>\n",
" <th>remnant of embryonic structure</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0024559</th>\n",
" <th>obsolete predominantly gray regional part of habenula</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:2001409</th>\n",
" <th>infraorbital 4</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td>0001409</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0005587</th>\n",
" <th>rhombomere 7 roof plate</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td>0000951</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:4300088</th>\n",
" <th>metapterygium bone</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0023317</th>\n",
" <th>obsolete regional part of ventral cochlear nucleus</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0002929</th>\n",
" <th>dentate gyrus pyramidal layer</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0000011</th>\n",
" <th>parasympathetic nervous system</th>\n",
" <td>0010488</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td>0001575</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>//en.wikipedia.org/wiki/Parasympathetic_nervou...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0000325</th>\n",
" <th>gastric gland</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0010884</th>\n",
" <th>forelimb bone pre-cartilage condensation</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0002693</th>\n",
" <th>occipitotemporal sulcus</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>ots</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>Tel-Cx-OTS</td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>//braininfo.rprc.washington.edu/centraldirecto...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0001536</th>\n",
" <th>left common carotid artery plus branches</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>//en.wikipedia.org/wiki/Left_common_carotid_ar...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0004773</th>\n",
" <th>superior eyelid tarsus</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>//en.wikipedia.org/wiki/Tarsus_%28eyelids%29</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0009138</th>\n",
" <th>right common cardinal vein</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0001440</th>\n",
" <th>forelimb skeleton</th>\n",
" <td>0000202</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0006813</th>\n",
" <th>nasal skeleton</th>\n",
" <td>0000320</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBERON:0005373</th>\n",
" <th>spinal cord dorsal column</th>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>dc</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>//braininfo.rprc.washington.edu/centraldirecto...</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>20 rows × 98 columns</p>\n",
"</div>"
],
"text/plain": [
" AAO \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system 0010488 \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton 0000202 \n",
"UBERON:0006813 nasal skeleton 0000320 \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ABA AEO \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" AEO_RETIRED \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ANISEED \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" BAMS BILA \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus ots \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column dc \n",
"\n",
" BILS \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage 0000113 \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" BM \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus Tel-Cx-OTS \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" BSA ... \\\n",
"id label ... \n",
"UBERON:3010014 inguinal glands ... \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 ... \n",
"UBERON:0000113 post-juvenile adult stage ... \n",
"UBERON:0006590 remnant of embryonic structure ... \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... ... \n",
"UBERON:2001409 infraorbital 4 ... \n",
"UBERON:0005587 rhombomere 7 roof plate ... \n",
"UBERON:4300088 metapterygium bone ... \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus ... \n",
"UBERON:0002929 dentate gyrus pyramidal layer ... \n",
"UBERON:0000011 parasympathetic nervous system ... \n",
"UBERON:0000325 gastric gland ... \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation ... \n",
"UBERON:0002693 occipitotemporal sulcus ... \n",
"UBERON:0001536 left common carotid artery plus branches ... \n",
"UBERON:0004773 superior eyelid tarsus ... \n",
"UBERON:0009138 right common cardinal vein ... \n",
"UBERON:0001440 forelimb skeleton ... \n",
"UBERON:0006813 nasal skeleton ... \n",
"UBERON:0005373 spinal cord dorsal column ... \n",
"\n",
" XtroDO \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ZFA \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 0000723 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 0001409 \n",
"UBERON:0005587 rhombomere 7 roof plate 0000951 \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system 0001575 \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ZFA_RETIRED \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ZFS \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage 0000044 \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" galen \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" http \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system //en.wikipedia.org/wiki/Parasympathetic_nervou... \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus //braininfo.rprc.washington.edu/centraldirecto... \n",
"UBERON:0001536 left common carotid artery plus branches //en.wikipedia.org/wiki/Left_common_carotid_ar... \n",
"UBERON:0004773 superior eyelid tarsus //en.wikipedia.org/wiki/Tarsus_%28eyelids%29 \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column //braininfo.rprc.washington.edu/centraldirecto... \n",
"\n",
" https \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" ncithesaurus \\\n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
" nodeID span \n",
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of ha... \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system \n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches \n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column \n",
"\n",
"[20 rows x 98 columns]"
]
},
"execution_count": 55,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## Make dataframe\n",
"df = pd.DataFrame.from_records(items, index=['id','label'])\n",
"df=df.fillna('')\n",
"df[0:20]"
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"id label \n",
"UBERON:3010014 inguinal glands \n",
"UBERON:2000723 obsolete slow muscle cell somite 5 \n",
"UBERON:0000113 post-juvenile adult stage \n",
"UBERON:0006590 remnant of embryonic structure \n",
"UBERON:0024559 obsolete predominantly gray regional part of habenula \n",
"UBERON:2001409 infraorbital 4 \n",
"UBERON:0005587 rhombomere 7 roof plate \n",
"UBERON:4300088 metapterygium bone \n",
"UBERON:0023317 obsolete regional part of ventral cochlear nucleus \n",
"UBERON:0002929 dentate gyrus pyramidal layer \n",
"UBERON:0000011 parasympathetic nervous system C12764\n",
"UBERON:0000325 gastric gland \n",
"UBERON:0010884 forelimb bone pre-cartilage condensation \n",
"UBERON:0002693 occipitotemporal sulcus \n",
"UBERON:0001536 left common carotid artery plus branches C32956\n",
"UBERON:0004773 superior eyelid tarsus \n",
"UBERON:0009138 right common cardinal vein \n",
"UBERON:0001440 forelimb skeleton \n",
"UBERON:0006813 nasal skeleton \n",
"UBERON:0005373 spinal cord dorsal column C33355\n",
"Name: NCIT, dtype: object"
]
},
"execution_count": 60,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"## Fetch sample of NCIT mappings\n",
"df['NCIT'][0:20]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"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
}