notebooks/Map2Slim_GO.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ontobio import OntologyFactory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ont = OntologyFactory().create('go')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "relations=['subClassOf', 'BFO:0000050']\n",
    "m = ont.create_slim_mapping(subset='goslim_generic', relations=relations)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['GO:0051276', 'GO:0006464']"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m['GO:0016577']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0052060 evasion or tolerance by symbiont of host-produced nitric oxide\n",
      "  --> GO:0044403 symbiosis, encompassing mutualism through parasitism\n",
      "GO:0061698 protein deglutarylation\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "GO:0061092 positive regulation of phospholipid translocation\n",
      "  --> GO:0061024 membrane organization\n",
      "GO:0048027 mRNA 5'-UTR binding\n",
      "  --> GO:0003729 mRNA binding\n",
      "GO:0048325 negative regulation of axial mesodermal cell fate determination\n",
      "  --> GO:0008150 biological_process\n",
      "GO:0061444 endocardial cushion cell development\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  --> GO:0030154 cell differentiation\n",
      "GO:0000332 template for synthesis of G-rich strand of telomere DNA activity\n",
      "  --> GO:0009058 biosynthetic process\n",
      "  --> GO:0006259 DNA metabolic process\n",
      "  --> GO:0003677 DNA binding\n",
      "  --> GO:0016779 nucleotidyltransferase activity\n",
      "GO:0034367 macromolecular complex remodeling\n",
      "  --> GO:0008150 biological_process\n",
      "GO:2001238 positive regulation of extrinsic apoptotic signaling pathway\n",
      "  --> GO:0008150 biological_process\n",
      "GO:0003154 BMP signaling pathway involved in determination of left/right symmetry\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  --> GO:0007165 signal transduction\n",
      "GO:0098839 postsynaptic density membrane\n",
      "  --> GO:0043226 organelle\n",
      "  --> GO:0005886 plasma membrane\n",
      "GO:2001116 methanopterin-containing compound biosynthetic process\n",
      "  --> GO:0009058 biosynthetic process\n",
      "  --> GO:0034641 cellular nitrogen compound metabolic process\n"
     ]
    }
   ],
   "source": [
    "# show the first 20 GO terms plus their mappings\n",
    "for n in ont.nodes()[0:20]:\n",
    "    if n.startswith('GO:'):\n",
    "        print('{} {}'.format(n, ont.label(n)))\n",
    "        for x in m[n]:\n",
    "              print('  --> {} {}'.format(x, ont.label(x)))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ontobio.assoc_factory import AssociationSetFactory\n",
    "\n",
    "MOUSE = 'NCBITaxon:10090'\n",
    "\n",
    "# Create association set\n",
    "# Transparently uses remote Monarch service.\n",
    "# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do\n",
    "# not re-execute cell)\n",
    "afactory = AssociationSetFactory()\n",
    "aset = afactory.create(ontology=ont,\n",
    "                       subject_category='gene',\n",
    "                       object_category='function',   # this is ALL GO, not just MF\n",
    "                       taxon=MOUSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['MGI:1349388',\n",
       " 'MGI:3645524',\n",
       " 'MGI:1916411',\n",
       " 'MGI:2444552',\n",
       " 'MGI:2444277',\n",
       " 'MGI:106321',\n",
       " 'MGI:2444891',\n",
       " 'MGI:1933174',\n",
       " 'MGI:2676815',\n",
       " 'MGI:2152450',\n",
       " 'MGI:1349400',\n",
       " 'MGI:88460',\n",
       " 'MGI:2142075',\n",
       " 'MGI:2654437',\n",
       " 'MGI:1342248',\n",
       " 'MGI:2179723',\n",
       " 'MGI:2686534',\n",
       " 'MGI:1918361',\n",
       " 'MGI:2449771',\n",
       " 'MGI:1202388']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample = aset.subjects[0:20]\n",
    "sample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MGI:1349388 Cops7b\n",
      "  GO:0000338 protein deneddylation\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "  GO:0008180 COP9 signalosome\n",
      "  --> GO:0043234 protein complex\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0005634 nucleus\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005654 nucleoplasm\n",
      "  --> GO:0005654 nucleoplasm\n",
      "MGI:3645524 Vmn1r224\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0007606 sensory perception of chemical stimulus\n",
      "  --> GO:0050877 neurological system process\n",
      "  GO:0005575 cellular_component\n",
      "  --> GO:0005575 cellular_component\n",
      "MGI:1916411 Manbal\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0016021 integral component of membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0005575 cellular_component\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0008150 biological_process\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:2444552 Actbl2\n",
      "  GO:0070062 extracellular exosome\n",
      "  --> GO:0043226 organelle\n",
      "  --> GO:0005615 extracellular space\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005856 cytoskeleton\n",
      "  --> GO:0005856 cytoskeleton\n",
      "  GO:0005615 extracellular space\n",
      "  --> GO:0005615 extracellular space\n",
      "  GO:0000166 nucleotide binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005524 ATP binding\n",
      "  --> GO:0043167 ion binding\n",
      "  GO:0008150 biological_process\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:2444277 Islr2\n",
      "  GO:0005515 protein binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0016021 integral component of membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0005886 plasma membrane\n",
      "  --> GO:0005886 plasma membrane\n",
      "  GO:0045773 positive regulation of axon extension\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  --> GO:0030154 cell differentiation\n",
      "  GO:0007275 multicellular organism development\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0007399 nervous system development\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  GO:0009986 cell surface\n",
      "  --> GO:0005623 cell\n",
      "MGI:106321 Dock9\n",
      "  GO:0045296 cadherin binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005085 guanyl-nucleotide exchange factor activity\n",
      "  --> GO:0003674 molecular_function\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0017048 Rho GTPase binding\n",
      "  --> GO:0019899 enzyme binding\n",
      "  GO:0005089 Rho guanyl-nucleotide exchange factor activity\n",
      "  --> GO:0003674 molecular_function\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0007264 small GTPase mediated signal transduction\n",
      "  --> GO:0007165 signal transduction\n",
      "  GO:0043547 positive regulation of GTPase activity\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "MGI:2444891 Abra\n",
      "  GO:0015031 protein transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0030016 myofibril\n",
      "  --> GO:0043226 organelle\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0015629 actin cytoskeleton\n",
      "  --> GO:0005856 cytoskeleton\n",
      "  GO:0035025 positive regulation of Rho protein signal transduction\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0006810 transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0003779 actin binding\n",
      "  --> GO:0008092 cytoskeletal protein binding\n",
      "  GO:0000060 protein import into nucleus, translocation\n",
      "  --> GO:0006913 nucleocytoplasmic transport\n",
      "  GO:0030017 sarcomere\n",
      "  --> GO:0043226 organelle\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0005856 cytoskeleton\n",
      "  --> GO:0005856 cytoskeleton\n",
      "  GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0006355 regulation of transcription, DNA-templated\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0005886 plasma membrane\n",
      "  --> GO:0005886 plasma membrane\n",
      "  GO:0006351 transcription, DNA-templated\n",
      "  --> GO:0009058 biosynthetic process\n",
      "  --> GO:0034641 cellular nitrogen compound metabolic process\n",
      "  GO:0045944 positive regulation of transcription from RNA polymerase II promoter\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0045893 positive regulation of transcription, DNA-templated\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:1933174 Bri3\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0016021 integral component of membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0042802 identical protein binding\n",
      "  --> GO:0003674 molecular_function\n",
      "MGI:2676815 Mir129-1\n",
      "  GO:0045202 synapse\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0060291 long-term synaptic potentiation\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0035195 gene silencing by miRNA\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:2152450 Usp3\n",
      "  GO:0006508 proteolysis\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0016578 histone deubiquitination\n",
      "  --> GO:0051276 chromosome organization\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "  GO:0006511 ubiquitin-dependent protein catabolic process\n",
      "  --> GO:0009056 catabolic process\n",
      "  GO:0000278 mitotic cell cycle\n",
      "  --> GO:0000278 mitotic cell cycle\n",
      "  GO:0007049 cell cycle\n",
      "  --> GO:0007049 cell cycle\n",
      "  GO:0031647 regulation of protein stability\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0008234 cysteine-type peptidase activity\n",
      "  --> GO:0008233 peptidase activity\n",
      "  GO:0008270 zinc ion binding\n",
      "  --> GO:0043167 ion binding\n",
      "  GO:0042393 histone binding\n",
      "  --> GO:0042393 histone binding\n",
      "  GO:0005634 nucleus\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0006281 DNA repair\n",
      "  --> GO:0006259 DNA metabolic process\n",
      "  --> GO:0006950 response to stress\n",
      "  GO:0070938 contractile ring\n",
      "  --> GO:0005623 cell\n",
      "  GO:0016787 hydrolase activity\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0016569 covalent chromatin modification\n",
      "  --> GO:0051276 chromosome organization\n",
      "  GO:0008233 peptidase activity\n",
      "  --> GO:0008233 peptidase activity\n",
      "  GO:0004843 thiol-dependent ubiquitin-specific protease activity\n",
      "  --> GO:0008233 peptidase activity\n",
      "  GO:0000790 nuclear chromatin\n",
      "  --> GO:0000228 nuclear chromosome\n",
      "  GO:0016579 protein deubiquitination\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "  GO:0006974 cellular response to DNA damage stimulus\n",
      "  --> GO:0006950 response to stress\n",
      "  GO:0000122 negative regulation of transcription from RNA polymerase II promoter\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0001046 core promoter sequence-specific DNA binding\n",
      "  --> GO:0003677 DNA binding\n",
      "  GO:0006355 regulation of transcription, DNA-templated\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0005654 nucleoplasm\n",
      "  --> GO:0005654 nucleoplasm\n",
      "  GO:0046872 metal ion binding\n",
      "  --> GO:0043167 ion binding\n",
      "  GO:0003682 chromatin binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0036459 thiol-dependent ubiquitinyl hydrolase activity\n",
      "  --> GO:0008233 peptidase activity\n",
      "MGI:1349400 Cops7a\n",
      "  GO:0000338 protein deneddylation\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "  GO:0008180 COP9 signalosome\n",
      "  --> GO:0043234 protein complex\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0005829 cytosol\n",
      "  --> GO:0005829 cytosol\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0005634 nucleus\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005654 nucleoplasm\n",
      "  --> GO:0005654 nucleoplasm\n",
      "MGI:88460 Col6a2\n",
      "  GO:0031012 extracellular matrix\n",
      "  --> GO:0005576 extracellular region\n",
      "MGI:2142075 Nars2\n",
      "  GO:0004812 aminoacyl-tRNA ligase activity\n",
      "  --> GO:0016874 ligase activity\n",
      "  GO:0016874 ligase activity\n",
      "  --> GO:0016874 ligase activity\n",
      "  GO:0006418 tRNA aminoacylation for protein translation\n",
      "  --> GO:0006412 translation\n",
      "  --> GO:0006520 cellular amino acid metabolic process\n",
      "  --> GO:0006399 tRNA metabolic process\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0005829 cytosol\n",
      "  --> GO:0005829 cytosol\n",
      "  GO:0006421 asparaginyl-tRNA aminoacylation\n",
      "  --> GO:0006412 translation\n",
      "  --> GO:0006520 cellular amino acid metabolic process\n",
      "  --> GO:0006399 tRNA metabolic process\n",
      "  GO:0006412 translation\n",
      "  --> GO:0006412 translation\n",
      "  GO:0000166 nucleotide binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005654 nucleoplasm\n",
      "  --> GO:0005654 nucleoplasm\n",
      "  GO:0004816 asparagine-tRNA ligase activity\n",
      "  --> GO:0016874 ligase activity\n",
      "  GO:0005524 ATP binding\n",
      "  --> GO:0043167 ion binding\n",
      "  GO:0003676 nucleic acid binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005739 mitochondrion\n",
      "  --> GO:0005739 mitochondrion\n",
      "MGI:2654437 Asb16\n",
      "  GO:0000151 ubiquitin ligase complex\n",
      "  --> GO:0005622 intracellular\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0005634 nucleus\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0004842 ubiquitin-protein transferase activity\n",
      "  --> GO:0003674 molecular_function\n",
      "  --> GO:0006464 cellular protein modification process\n",
      "  GO:0031625 ubiquitin protein ligase binding\n",
      "  --> GO:0019899 enzyme binding\n",
      "  GO:0035556 intracellular signal transduction\n",
      "  --> GO:0007165 signal transduction\n",
      "  GO:0008150 biological_process\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:1342248 Slc25a17\n",
      "  GO:0015908 fatty acid transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0055085 transmembrane transport\n",
      "  --> GO:0055085 transmembrane transport\n",
      "  GO:0015230 FAD transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0005779 integral component of peroxisomal membrane\n",
      "  --> GO:0005777 peroxisome\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0006810 transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0006635 fatty acid beta-oxidation\n",
      "  --> GO:0044281 small molecule metabolic process\n",
      "  --> GO:0006629 lipid metabolic process\n",
      "  --> GO:0009056 catabolic process\n",
      "  GO:0098655 cation transmembrane transport\n",
      "  --> GO:0055085 transmembrane transport\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0016021 integral component of membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0080121 AMP transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0005743 mitochondrial inner membrane\n",
      "  --> GO:0005739 mitochondrion\n",
      "  GO:0005739 mitochondrion\n",
      "  --> GO:0005739 mitochondrion\n",
      "  GO:0080122 AMP transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0015867 ATP transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0098656 anion transmembrane transport\n",
      "  --> GO:0055085 transmembrane transport\n",
      "  GO:0051087 chaperone binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0015858 nucleoside transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0015228 coenzyme A transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0005778 peroxisomal membrane\n",
      "  --> GO:0005777 peroxisome\n",
      "  GO:0051724 NAD transporter activity\n",
      "  --> GO:0003674 molecular_function\n",
      "  --> GO:0006810 transport\n",
      "  GO:0006839 mitochondrial transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0005347 ATP transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0015217 ADP transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0044610 FMN transmembrane transporter activity\n",
      "  --> GO:0022857 transmembrane transporter activity\n",
      "  GO:0005777 peroxisome\n",
      "  --> GO:0005777 peroxisome\n",
      "  GO:1901679 nucleotide transmembrane transport\n",
      "  --> GO:0055085 transmembrane transport\n",
      "MGI:2179723 Casc3\n",
      "  GO:0051028 mRNA transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0031965 nuclear membrane\n",
      "  --> GO:0005635 nuclear envelope\n",
      "  GO:0030529 intracellular ribonucleoprotein complex\n",
      "  --> GO:0005622 intracellular\n",
      "  GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay\n",
      "  --> GO:0034655 nucleobase-containing compound catabolic process\n",
      "  GO:0031625 ubiquitin protein ligase binding\n",
      "  --> GO:0019899 enzyme binding\n",
      "  GO:0006810 transport\n",
      "  --> GO:0006810 transport\n",
      "  GO:0019899 enzyme binding\n",
      "  --> GO:0019899 enzyme binding\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0008298 intracellular mRNA localization\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0005634 nucleus\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0006417 regulation of translation\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0006397 mRNA processing\n",
      "  --> GO:0006397 mRNA processing\n",
      "  GO:0042802 identical protein binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0035145 exon-exon junction complex\n",
      "  --> GO:0043234 protein complex\n",
      "  --> GO:0005634 nucleus\n",
      "  GO:0003723 RNA binding\n",
      "  --> GO:0003723 RNA binding\n",
      "  GO:0008380 RNA splicing\n",
      "  --> GO:0034641 cellular nitrogen compound metabolic process\n",
      "  GO:0005515 protein binding\n",
      "  --> GO:0003674 molecular_function\n",
      "MGI:2686534 A630073D07Rik\n",
      "  GO:0003674 molecular_function\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0005575 cellular_component\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0008150 biological_process\n",
      "  --> GO:0008150 biological_process\n",
      "MGI:1918361 Gpr39\n",
      "  GO:0030641 regulation of cellular pH\n",
      "  --> GO:0042592 homeostatic process\n",
      "  GO:0008343 adult feeding behavior\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0042632 cholesterol homeostasis\n",
      "  --> GO:0042592 homeostatic process\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0000187 activation of MAPK activity\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0051281 positive regulation of release of sequestered calcium ion into cytosol\n",
      "  --> GO:0042592 homeostatic process\n",
      "  GO:0005575 cellular_component\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0007186 G-protein coupled receptor signaling pathway\n",
      "  --> GO:0007165 signal transduction\n",
      "  GO:0042391 regulation of membrane potential\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0016021 integral component of membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0019216 regulation of lipid metabolic process\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0004871 signal transducer activity\n",
      "  --> GO:0004871 signal transducer activity\n",
      "  GO:0007165 signal transduction\n",
      "  --> GO:0007165 signal transduction\n",
      "  GO:0004930 G-protein coupled receptor activity\n",
      "  --> GO:0004871 signal transducer activity\n",
      "  GO:0060455 negative regulation of gastric acid secretion\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0071294 cellular response to zinc ion\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0035483 gastric emptying\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0042593 glucose homeostasis\n",
      "  --> GO:0042592 homeostatic process\n",
      "  GO:0005886 plasma membrane\n",
      "  --> GO:0005886 plasma membrane\n",
      "  GO:0032024 positive regulation of insulin secretion\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0002024 diet induced thermogenesis\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0046872 metal ion binding\n",
      "  --> GO:0043167 ion binding\n",
      "MGI:2449771 Cyp2r1\n",
      "  GO:0004497 monooxygenase activity\n",
      "  --> GO:0016491 oxidoreductase activity\n",
      "  GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen\n",
      "  --> GO:0016491 oxidoreductase activity\n",
      "  GO:0016491 oxidoreductase activity\n",
      "  --> GO:0016491 oxidoreductase activity\n",
      "  GO:0020037 heme binding\n",
      "  --> GO:0003674 molecular_function\n",
      "  GO:0043231 intracellular membrane-bounded organelle\n",
      "  --> GO:0043226 organelle\n",
      "  --> GO:0005622 intracellular\n",
      "  GO:0005506 iron ion binding\n",
      "  --> GO:0043167 ion binding\n",
      "  GO:0030343 vitamin D3 25-hydroxylase activity\n",
      "  --> GO:0044281 small molecule metabolic process\n",
      "  --> GO:0009058 biosynthetic process\n",
      "  --> GO:0016491 oxidoreductase activity\n",
      "  --> GO:0006629 lipid metabolic process\n",
      "  GO:0042359 vitamin D metabolic process\n",
      "  --> GO:0044281 small molecule metabolic process\n",
      "  --> GO:0006629 lipid metabolic process\n",
      "  GO:0008395 steroid hydroxylase activity\n",
      "  --> GO:0016491 oxidoreductase activity\n",
      "  GO:0005783 endoplasmic reticulum\n",
      "  --> GO:0005783 endoplasmic reticulum\n",
      "  GO:0055114 oxidation-reduction process\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0016020 membrane\n",
      "  --> GO:0005575 cellular_component\n",
      "  GO:0046872 metal ion binding\n",
      "  --> GO:0043167 ion binding\n",
      "MGI:1202388 Gas7\n",
      "  GO:0030182 neuron differentiation\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  --> GO:0030154 cell differentiation\n",
      "  GO:0008360 regulation of cell shape\n",
      "  --> GO:0008150 biological_process\n",
      "  GO:0030154 cell differentiation\n",
      "  --> GO:0030154 cell differentiation\n",
      "  GO:0005737 cytoplasm\n",
      "  --> GO:0005737 cytoplasm\n",
      "  GO:0051017 actin filament bundle assembly\n",
      "  --> GO:0022607 cellular component assembly\n",
      "  --> GO:0007010 cytoskeleton organization\n",
      "  GO:0048812 neuron projection morphogenesis\n",
      "  --> GO:0030154 cell differentiation\n",
      "  --> GO:0000902 cell morphogenesis\n",
      "  GO:0001726 ruffle\n",
      "  --> GO:0005623 cell\n",
      "  GO:0007275 multicellular organism development\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  GO:0030041 actin filament polymerization\n",
      "  --> GO:0006461 protein complex assembly\n",
      "  --> GO:0007010 cytoskeleton organization\n",
      "  GO:0005884 actin filament\n",
      "  --> GO:0005856 cytoskeleton\n",
      "  GO:0007399 nervous system development\n",
      "  --> GO:0048856 anatomical structure development\n",
      "  GO:0051015 actin filament binding\n",
      "  --> GO:0008092 cytoskeletal protein binding\n"
     ]
    }
   ],
   "source": [
    "for g in sample:\n",
    "    print('{} {}'.format(g,aset.label(g)))\n",
    "    for a in aset.annotations(g):\n",
    "        print('  {} {}'.format(a,ont.label(a)))\n",
    "        for mn in m[a]:\n",
    "            print('  --> {} {}'.format(mn,ont.label(mn)))\n",
    "            \n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['GO:0006629', 'GO:0034641']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "t='GO:0006681'\n",
    "m[t]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "subont=ont.subontology(relations=relations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'GO:0006807', 'GO:0008150', 'GO:0008152', 'GO:0009987', 'GO:0044237'}"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subont.ancestors('GO:0034641')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'GO:0006629', 'GO:0034641'}"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subont.filter_redundant(m[t])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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