DataSource.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from ecell4 import *\n",
    "from ecell4.datasource import description, whereis\n",
    "from ecell4.datasource import uniprot, pdb, psicquic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "MIND = Species(\"MinD\")\n",
    "MIND.set_attribute(\"uniprot\", \"P0AEZ3\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "UniProtKB - P0AEZ3 (MIND_ECOLI)\n",
      "Protein: Septum site-determining protein MinD, Cell division inhibitor MinD\n",
      "Gene: minD\n",
      "Organism: Escherichia coli (strain K12)\n",
      "Function: ATPase required for the correct placement of the division site. Cell division inhibitors MinC and MinD act in concert to form an inhibitor capable of blocking formation of the polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings.\n",
      "URL: http://www.uniprot.org/uniprot/P0AEZ3\n"
     ]
    }
   ],
   "source": [
    "description(MIND)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "UniProtKB - Cell inner membrane (Cellular Component)\n",
      "Definition: The prokaryotic inner cell membrane is the selectively permeable membrane which separates the cytoplasm from the periplasm in prokaryotes with 2 membranes.\n",
      "Synonyms: Inner membrane, Plasma membrane, Cytoplasmic membrane\n",
      "GO: http://purl.obolibrary.org/obo/GO_0005886\n",
      "URL: http://www.uniprot.org/locations/SL-0037\n",
      "\n",
      "UniProtKB - Peripheral membrane protein (Topology)\n",
      "Definition: Protein that has an affinity for a membrane because it binds either another membrane protein or a lipid head group. Peripheral membrane proteins do not integrate into the hydrophobic core layer.\n",
      "URL: http://www.uniprot.org/locations/SL-9903\n"
     ]
    }
   ],
   "source": [
    "whereis(MIND)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['b1175', 'JW1164']\n"
     ]
    }
   ],
   "source": [
    "print(uniprot.UniProtDataSource(MIND).locus_name())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['MARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEEEKKGFLKRLFGG']\n"
     ]
    }
   ],
   "source": [
    "print(uniprot.UniProtDataSource(MIND).simple_sequence())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'type': {'see_also': 'http://www.uniprot.org/manual/dna_bind', 'label': 'Nucleotide Phosphate Binding', 'name': 'http://purl.uniprot.org/core/NP_Binding_Annotation', 'comment': 'Extent of a nucleotide phosphate-binding region.'}, 'end': 18, 'begin': 11, 'comment': 'ATP'}]\n"
     ]
    }
   ],
   "source": [
    "print(uniprot.UniProtDataSource(MIND).region())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'begin': 16, 'comment': 'Loss of activity.', 'citation': [{'pages': '4371-4380', 'title': 'The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site.', 'year': '1991', 'volume': '10', 'link': 'https://www.ncbi.nlm.nih.gov/pubmed/1836760', 'name': 'EMBO J.', 'author': ['Crossley R.E.', 'Hand A.R.', 'Rothfield L.I.', 'de Boer P.A.J.'], 'about': 'http://purl.uniprot.org/citations/1836760'}], 'type': {'see_also': 'http://www.uniprot.org/manual/mutagen', 'label': 'Mutagenesis Site', 'name': 'http://purl.uniprot.org/core/Mutagenesis_Annotation', 'comment': 'Site which has been experimentally altered.'}, 'end': 17, 'substitution': 'QR'}, {'begin': 16, 'comment': 'Loss of activity.', 'citation': [{'pages': '4371-4380', 'title': 'The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site.', 'year': '1991', 'volume': '10', 'link': 'https://www.ncbi.nlm.nih.gov/pubmed/1836760', 'name': 'EMBO J.', 'author': ['Crossley R.E.', 'Hand A.R.', 'Rothfield L.I.', 'de Boer P.A.J.'], 'about': 'http://purl.uniprot.org/citations/1836760'}], 'type': {'see_also': 'http://www.uniprot.org/manual/mutagen', 'label': 'Mutagenesis Site', 'name': 'http://purl.uniprot.org/core/Mutagenesis_Annotation', 'comment': 'Site which has been experimentally altered.'}, 'end': 16, 'substitution': 'Q'}, {'begin': 15, 'comment': 'Less effective then wild-type.', 'citation': [{'pages': '4371-4380', 'title': 'The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site.', 'year': '1991', 'volume': '10', 'link': 'https://www.ncbi.nlm.nih.gov/pubmed/1836760', 'name': 'EMBO J.', 'author': ['Crossley R.E.', 'Hand A.R.', 'Rothfield L.I.', 'de Boer P.A.J.'], 'about': 'http://purl.uniprot.org/citations/1836760'}], 'type': {'see_also': 'http://www.uniprot.org/manual/mutagen', 'label': 'Mutagenesis Site', 'name': 'http://purl.uniprot.org/core/Mutagenesis_Annotation', 'comment': 'Site which has been experimentally altered.'}, 'end': 15, 'substitution': 'S'}]\n"
     ]
    }
   ],
   "source": [
    "print(uniprot.UniProtDataSource(MIND).experimental_information())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['http://rdf.wwpdb.org/pdb/3Q9L', 'http://rdf.wwpdb.org/pdb/3R9J', 'http://rdf.wwpdb.org/pdb/3R9I']\n"
     ]
    }
   ],
   "source": [
    "print(uniprot.UniProtDataSource(MIND).structure_resource())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PDB - 3Q9L\n",
      "Title: The structure of the dimeric E.coli MinD-ATP complex\n",
      "Gene: minD\n",
      "Organism: Escherichia coli K12\n",
      "See Also: http://www.rcsb.org/pdb/explore.do?structureId=3Q9L\n",
      "See Also: http://www.ebi.ac.uk/pdbe/entry/pdb/3Q9L\n",
      "See Also: http://www.pdbj.org/pdb/3Q9L\n",
      "URL: http://rdf.wwpdb.org/pdb/3Q9L\n"
     ]
    }
   ],
   "source": [
    "description('http://rdf.wwpdb.org/pdb/3Q9L')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"400\"\n",
       "            height=\"400\"\n",
       "            src=\"http://gjbekker.github.io/molmil/#molmil.loadPDB('3Q9L');\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7fb8e78c86d8>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "viz.display_pdb('http://rdf.wwpdb.org/pdb/3Q9L')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "('http://www.uniprot.org/uniprot/P45523', 'http://www.uniprot.org/uniprot/P0A734', 'http://www.uniprot.org/uniprot/P18196', 'http://www.uniprot.org/uniprot/P37052', 'http://www.uniprot.org/uniprot/P0A6F9', 'http://www.uniprot.org/uniprot/P77515', 'http://www.uniprot.org/uniprot/P0A964', 'http://www.uniprot.org/uniprot/P0A9X4', 'http://www.uniprot.org/uniprot/P52102', 'http://www.uniprot.org/uniprot/P37003', 'http://www.uniprot.org/uniprot/P10408', 'http://www.uniprot.org/uniprot/P0ABX8')\n"
     ]
    }
   ],
   "source": [
    "print(psicquic.PSICQUICDataSource(MIND, services='IntAct').interactors())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "UniProtKB - P0A734 (MINE_ECOLI)\n",
      "Protein: Cell division topological specificity factor\n",
      "Gene: minE\n",
      "Organism: Escherichia coli (strain K12)\n",
      "Function: Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell.\n",
      "URL: http://www.uniprot.org/uniprot/P0A734\n"
     ]
    }
   ],
   "source": [
    "description('http://www.uniprot.org/uniprot/P0A734')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'methods': [{'description': 'adenylate cyclase complementation', 'xref': 'psi-mi', 'value': 'MI:0014'}], 'service': 'IntAct', 'A': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mind_ecoli'}, {'description': 'gene name synonym', 'xref': 'uniprotkb', 'value': 'Cell division inhibitor MinD'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minD'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minD'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1175'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1164'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0AEZ3'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-554545'}, {'xref': 'uniprotkb', 'value': 'P18197'}]}, 'types': [{'description': 'physical association', 'xref': 'psi-mi', 'value': 'MI:0915'}], 'B': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mine_ecoli'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minE'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minE'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1174'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1163'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0A734'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-1118020'}, {'xref': 'uniprotkb', 'value': 'P18198'}]}, 'publications': ['https://www.ncbi.nlm.nih.gov/pubmed/21816275', 'http://identifiers.org/imex/IM-16555'], 'databases': [{'description': 'IntAct', 'xref': 'psi-mi', 'value': 'MI:0469'}], 'identifiers': [{'xref': 'intact', 'value': 'EBI-4369430'}, {'xref': 'imex', 'value': 'IM-16555-1'}], 'scores': [{'xref': 'intact-miscore', 'value': '0.41'}]}, {'methods': [{'description': 'x-ray crystallography', 'xref': 'psi-mi', 'value': 'MI:0114'}], 'service': 'IntAct', 'A': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mind_ecoli'}, {'description': 'gene name synonym', 'xref': 'uniprotkb', 'value': 'Cell division inhibitor MinD'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minD'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minD'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1175'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1164'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0AEZ3'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-554545'}, {'xref': 'uniprotkb', 'value': 'P18197'}]}, 'types': [{'description': 'direct interaction', 'xref': 'psi-mi', 'value': 'MI:0407'}], 'B': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mine_ecoli'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minE'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minE'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1174'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1163'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0A734'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-1118020'}, {'xref': 'uniprotkb', 'value': 'P18198'}]}, 'publications': ['https://www.ncbi.nlm.nih.gov/pubmed/21816275', 'http://identifiers.org/imex/IM-16555'], 'databases': [{'description': 'IntAct', 'xref': 'psi-mi', 'value': 'MI:0469'}], 'identifiers': [{'xref': 'intact', 'value': 'EBI-4370024'}, {'xref': 'wwpdb', 'value': '3R9J'}, {'xref': 'imex', 'value': 'IM-16555-3'}], 'scores': [{'xref': 'intact-miscore', 'value': '0.41'}]}, {'methods': [{'description': 'x-ray crystallography', 'xref': 'psi-mi', 'value': 'MI:0114'}], 'service': 'IntAct', 'A': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mind_ecoli'}, {'description': 'gene name synonym', 'xref': 'uniprotkb', 'value': 'Cell division inhibitor MinD'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minD'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minD'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1175'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1164'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0AEZ3'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-554545'}, {'xref': 'uniprotkb', 'value': 'P18197'}]}, 'types': [{'description': 'direct interaction', 'xref': 'psi-mi', 'value': 'MI:0407'}], 'B': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mine_ecoli'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minE'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minE'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1174'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1163'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0A734'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-1118020'}, {'xref': 'uniprotkb', 'value': 'P18198'}]}, 'publications': ['https://www.ncbi.nlm.nih.gov/pubmed/21816275', 'http://identifiers.org/imex/IM-16555'], 'databases': [{'description': 'IntAct', 'xref': 'psi-mi', 'value': 'MI:0469'}], 'identifiers': [{'xref': 'intact', 'value': 'EBI-4370042'}, {'xref': 'wwpdb', 'value': '3R9I'}, {'xref': 'imex', 'value': 'IM-16555-2'}], 'scores': [{'xref': 'intact-miscore', 'value': '0.41'}]}, {'methods': [{'description': 'pull down', 'xref': 'psi-mi', 'value': 'MI:0096'}], 'service': 'IntAct', 'A': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mind_ecoli'}, {'description': 'gene name synonym', 'xref': 'uniprotkb', 'value': 'Cell division inhibitor MinD'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minD'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minD'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1175'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1164'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0AEZ3'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-554545'}, {'xref': 'uniprotkb', 'value': 'P18197'}]}, 'types': [{'description': 'direct interaction', 'xref': 'psi-mi', 'value': 'MI:0407'}], 'B': {'aliases': [{'description': 'display_long', 'xref': 'psi-mi', 'value': 'mine_ecoli'}, {'description': 'gene name', 'xref': 'uniprotkb', 'value': 'minE'}, {'description': 'display_short', 'xref': 'psi-mi', 'value': 'minE'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'b1174'}, {'description': 'locus name', 'xref': 'uniprotkb', 'value': 'JW1163'}], 'taxons': [{'description': 'ecoli', 'xref': 'taxid', 'value': '83333'}, {'description': 'Escherichia coli (strain K12)', 'xref': 'taxid', 'value': '83333'}], 'identifiers': [{'xref': 'uniprotkb', 'value': 'P0A734'}], 'alternatives': [{'xref': 'intact', 'value': 'EBI-1118020'}, {'xref': 'uniprotkb', 'value': 'P18198'}]}, 'publications': ['https://www.ncbi.nlm.nih.gov/pubmed/21816275', 'http://identifiers.org/imex/IM-16555'], 'databases': [{'description': 'IntAct', 'xref': 'psi-mi', 'value': 'MI:0469'}], 'identifiers': [{'xref': 'intact', 'value': 'EBI-4370000'}, {'xref': 'imex', 'value': 'IM-16555-8'}], 'scores': [{'xref': 'intact-miscore', 'value': '0.41'}]}]\n"
     ]
    }
   ],
   "source": [
    "interactions = psicquic.PSICQUICDataSource(MIND, services='IntAct').interactions(partner='http://www.uniprot.org/uniprot/P0A734')\n",
    "print(interactions)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PubMed - 21816275\n",
      "Title: The Min oscillator uses MinD-dependent conformational changes in MinE to spatially regulate cytokinesis.\n",
      "Author(s): Park KT, Wu W, Battaile KP, Lovell S, Holyoak T, Lutkenhaus J\n",
      "Source: Cell\n",
      "SO: 2011 Aug 5;146(3):396-407\n",
      "URL: https://www.ncbi.nlm.nih.gov/pubmed/21816275\n"
     ]
    }
   ],
   "source": [
    "description(interactions[0]['publications'])"
   ]
  }
 ],
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