{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Ay 119 - Some RDF exercises\n",
    "\n",
    "Here we'll go through some examples of using Python to read RDF documents from NeuroLex.org and make simple queries. NeuroLex.org is a freely editable semantic wiki for community-based curation of the terms used in Neuroscience."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### A simple example\n",
    "\n",
    "Firstly, we'll get an RDF document and count how many statements it contains."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Graph has 483 statements\n"
     ]
    }
   ],
   "source": [
    "import rdflib\n",
    "\n",
    "# Get a Graph object\n",
    "g = rdflib.Graph()\n",
    "\n",
    "# Retrieve an RDF document from NeuroLex and parse it\n",
    "result = g.parse(\"http://neurolex.org/wiki/Special:ExportRDF/birnlex_1489\", format=\"application/rdf+xml\")\n",
    "\n",
    "print \"Graph has %s statements\" % len(g)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can also iterate over all the statements in the graph:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "http://neurolex.org/wiki/Category-3AResource-3AFunctional_Anatomy_of_the_Cerebro-2DCerebellar_System_(FACCS) http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Property-3AAuthors http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:Authors\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASpatially_unbiased_atlas_template_of_the_cerebellum_and_brainstem http://www.w3.org/2000/01/rdf-schema#label Resource:Spatially unbiased atlas template of the cerebellum and brainstem\n",
      "http://neurolex.org/wiki/Property-3AAbout http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:About\n",
      "http://neurolex.org/wiki/Category-3AInfracerebellar_nucleus http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3ARexed_lamina_VII http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/TermImport-3A108300 http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/TermImport:108300\n",
      "http://neurolex.org/wiki/Property-3APublicationDate http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#ObjectProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3AOregon_Brain_Bank http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Oregon_Brain_Bank\n",
      "http://neurolex.org/wiki/Property-3AAbout http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:About\n",
      "http://neurolex.org/wiki/Property-3ASynonym http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:Synonym\n",
      "http://neurolex.org/wiki/Category-3AResource-3AInternet_Brain_Segmentation_Repository http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3ACentral_cervical_nucleus http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3AConfocal_Microscopy_Image_Gallery_-2D_Rat_Brain_Tissue_Sections http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3ARed_nucleus http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Property-3AModifiedDate http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3AStanley_Medical_Research_Institute_Online_Genomics_Database http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Stanley_Medical_Research_Institute_Online_Genomics_Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUCL_Motor_Control_Group http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:UCL_Motor_Control_Group\n",
      "http://neurolex.org/wiki/Property-3AAfferentProjections http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#ObjectProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Development_Transcriptome_Database http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Cerebellar_Development_Transcriptome_Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUCL_Motor_Control_Group http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Property-3AIs_part_of http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#ObjectProperty\n",
      "http://neurolex.org/wiki/Category-3AHindbrain_of_CIVM_postnatal_rat_brain_atlas http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Hindbrain_of_CIVM_postnatal_rat_brain_atlas\n",
      "http://neurolex.org/wiki/Category-3APrimary_fissure http://www.w3.org/2000/01/rdf-schema#label Primary fissure\n",
      "http://neurolex.org/wiki/Category-3AHindbrain_of_WHS11 http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Hindbrain_of_WHS11\n",
      "http://neurolex.org/wiki/Property-3AAbout http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#ObjectProperty\n",
      "http://neurolex.org/wiki/Category-3ACerebrospinal_axis http://www.w3.org/2000/01/rdf-schema#label Cerebrospinal axis\n",
      "http://neurolex.org/wiki/Category-3ACerebellar_Serotonergic_Afferents http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Cerebellar_Serotonergic_Afferents\n",
      "http://neurolex.org/wiki/Category-3AResource-3AStanley_Medical_Research_Institute_Online_Genomics_Database http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AInfracerebellar_nucleus http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Infracerebellar_nucleus\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_E15_Atlas http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:GenePaint_E15_Atlas\n",
      "http://neurolex.org/wiki/Category-3AResource-3ABrain_Atlas_of_the_Mozambique_Tilapia_Oreochromis_mossambicus http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Brain_Atlas_of_the_Mozambique_Tilapia_Oreochromis_mossambicus\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_P7_Atlas http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:GenePaint_P7_Atlas\n",
      "http://neurolex.org/wiki/Property-3APublicationDate http://www.w3.org/2000/01/rdf-schema#label PublicationDate\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Gene_Regulation_in_Time_and_Space_Database http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3AMBL_-2D_The_Mouse_Brain_Library http://www.w3.org/2000/01/rdf-schema#label Resource:MBL - The Mouse Brain Library\n",
      "http://neurolex.org/wiki/Category-3ACerebellar_Corticopontine_Projection http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Cerebellar_Corticopontine_Projection\n",
      "http://neurolex.org/wiki/Category-3APosterior_lobe_of_the_cerebellum http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3ABrain_Gene_Expression_Database http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Property-3AAuthors http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Birnlex_1489 http://neurolex.org/wiki/Property-3ATitle Development of the cerebellar system: in relation to its evolution\n",
      "http://neurolex.org/wiki/Category-3ACerebellum_candelabrum_cell http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Cerebellum_candelabrum_cell\n",
      "http://neurolex.org/wiki/Category-3ACaudal_cerebellum http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUW-2DMadison_Neuroscience_Resources http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Property-3APartiallyOverlapsWith http://www.w3.org/2000/01/rdf-schema#label PartiallyOverlapsWith\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASummary_of_recordings_of_spike_trains_available_for_analysis_and_guide_to_their_context_and_means_for_their_analysis http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Summary_of_recordings_of_spike_trains_available_for_analysis_and_guide_to_their_context_and_means_for_their_analysis\n",
      "http://neurolex.org/wiki/Birnlex_1489 http://neurolex.org/wiki/Property-3ACurationStatus uncurated\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASCAN http://www.w3.org/2000/01/rdf-schema#label Resource:SCAN\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASummary_of_recordings_of_spike_trains_available_for_analysis_and_guide_to_their_context_and_means_for_their_analysis http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3AManually_Labeled_MRI_Brain_Scan_Database http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Manually_Labeled_MRI_Brain_Scan_Database\n",
      "http://neurolex.org/wiki/Property-3ASpecies http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:Species\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Development_Transcriptome_Database http://www.w3.org/2000/01/rdf-schema#label Resource:Cerebellar Development Transcriptome Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3AHistology_World-3A_Nervous_System_Histology http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Histology_World:_Nervous_System_Histology\n",
      "http://neurolex.org/wiki/Property-3AModifiedDate http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:ModifiedDate\n",
      "http://neurolex.org/wiki/Category-3APosterior_lobe_of_the_cerebellum http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Posterior_lobe_of_the_cerebellum\n",
      "http://neurolex.org/wiki/Property-3AIs_part_of http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:Is_part_of\n",
      "http://neurolex.org/wiki/Property-3AISBN http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Property-3ATitle http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Category-3ANucleus_centrobasalis http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Nucleus_centrobasalis\n",
      "http://neurolex.org/wiki/Category-3AResource-3AManually_Labeled_MRI_Brain_Scan_Database http://www.w3.org/2000/01/rdf-schema#label Resource:Manually Labeled MRI Brain Scan Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUCL_Motor_Control_Group http://www.w3.org/2000/01/rdf-schema#label Resource:UCL Motor Control Group\n",
      "http://neurolex.org/wiki/Property-3ACurationStatus http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:CurationStatus\n",
      "http://neurolex.org/wiki/Category-3AResource-3ANeuronDB http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Birnlex_1489 http://neurolex.org/wiki/Property-3ACreated 2006-07-15T00:00:00\n",
      "http://neurolex.org/wiki/Property-3ALabel http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Property-3ADefinition http://www.w3.org/2000/01/rdf-schema#label Definition\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASCAN http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:SCAN\n",
      "http://neurolex.org/wiki/Category-3AHindbrain_of_WHS11 http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Hindbrain_of_WHS11\n",
      "http://neurolex.org/wiki/Category-3AResource-3ABrain_Atlas_Database_of_Japanese_Monkey_for_WWW http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASummary_of_recordings_of_spike_trains_available_for_analysis_and_guide_to_their_context_and_means_for_their_analysis http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Property-3ADefiningCriteria http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3ASCAN http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Property-3AId http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Category-3ACerebellum_of_WHS11 http://www.w3.org/2000/01/rdf-schema#label Cerebellum of WHS11\n",
      "http://neurolex.org/wiki/Property-3APublicationDate http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:PublicationDate\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_E15_Atlas http://www.w3.org/2000/01/rdf-schema#label Resource:GenePaint E15 Atlas\n",
      "http://neurolex.org/wiki/Category-3ARegional_part_of_brain http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Regional_part_of_brain\n",
      "http://neurolex.org/wiki/Property-3ALocated_in http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Property:Located_in\n",
      "http://neurolex.org/wiki/Birnlex_1489 http://neurolex.org/wiki/Property-3ADefinition Part of the rhombencephalon that lies in the posterior cranial fossa behind the brain stem, consisting of the cerebellar cortex, deep cerebellar nuclei and cerebellar white matter.\n",
      "A portion of the brain that helps regulate posture, balance, and coordination. (NIDA Media Guide Glossary)\n",
      "\n",
      "The dorsal topographic division of the hindbrain, connected to the ventral  division-the pons-by a white matter tract, the middle cerebellar peduncle. The cerebellum was discovered and named by Aristotle (De Partibus Animalium) based on macrodissection of a variety of animals not including humans; see translation by Thompson (1910, 494b 30). Older synonyms include parencephalon (Aristotle), hindbrain (Galen, c192).\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Gene_Regulation_in_Time_and_Space_Database http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Cerebellar_Gene_Regulation_in_Time_and_Space_Database\n",
      "http://neurolex.org/wiki/Category-3AInfracerebellar_nucleus http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Infracerebellar_nucleus\n",
      "http://neurolex.org/wiki/Category-3ACerebellum_of_ABA_2009 http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Cerebellum_of_ABA_2009\n",
      "http://neurolex.org/wiki/Category-3AResource-3ADIAN_-2D_Dominantly_Inherited_Alzheimer_Network http://www.w3.org/2000/01/rdf-schema#label Resource:DIAN - Dominantly Inherited Alzheimer Network\n",
      "http://neurolex.org/wiki/Property-3ASuperCategory http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:SuperCategory\n",
      "http://neurolex.org/wiki/Category-3AResource-3ABrain_Atlas_of_the_Mozambique_Tilapia_Oreochromis_mossambicus http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Brain_Atlas_of_the_Mozambique_Tilapia_Oreochromis_mossambicus\n",
      "http://neurolex.org/wiki/Category-3AResource-3ANeuro_Systems_and_Graphics_Computing_Laboratory http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Neuro_Systems_and_Graphics_Computing_Laboratory\n",
      "http://neurolex.org/wiki/Category-3AResource-3AProbabilistic_atlas_of_the_human_cerebellum http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3ANeuronDB http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3ABrain_Gene_Expression_Database http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Brain_Gene_Expression_Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3AInternational_Consortium_for_Brain_Mapping http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:International_Consortium_for_Brain_Mapping\n",
      "http://neurolex.org/wiki/Category-3ACerebellum_nucleus_reciprocal_projections_neuron http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3ACentral_cervical_nucleus http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Central_cervical_nucleus\n",
      "http://neurolex.org/wiki/Category-3ADeep_cerebellar_nuclear_complex http://www.w3.org/2000/01/rdf-schema#label Deep cerebellar nuclear complex\n",
      "http://neurolex.org/wiki/Property-3AKeywords http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:Keywords\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Gene_Regulation_in_Time_and_Space_Database http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Resource:Cerebellar_Gene_Regulation_in_Time_and_Space_Database\n",
      "http://neurolex.org/wiki/Category-3ARexed_lamina_VII http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://neurolex.org/wiki/Special:ExportRDF/Category:Rexed_lamina_VII\n",
      "http://neurolex.org/wiki/Property-3AKeywords http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#ObjectProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3AMichigan_State_University_Brain_Biodiversity_Bank http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3AHuman_Nervous_System_Neuroanatomy http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3ANerve_Tissue http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3ARexed_lamina_V http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Rexed_lamina_V\n",
      "http://neurolex.org/wiki/Category-3AResource-3AHuman_Nervous_System_Neuroanatomy http://www.w3.org/2000/01/rdf-schema#label Resource:Human Nervous System Neuroanatomy\n",
      "http://neurolex.org/wiki/Category-3APosterior_superior_fIssure http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Posterior_superior_fIssure\n",
      "http://neurolex.org/wiki/Category-3APontine_nuclear_complex http://www.w3.org/2000/01/rdf-schema#label Pontine nuclear complex\n",
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      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Gene_Regulation_in_Time_and_Space_Database http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3ACerebellum_of_WHS11 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/FMC http://www.w3.org/2000/01/rdf-schema#label FMC\n",
      "http://neurolex.org/wiki/Category-3AResource-3AWashington_University_School_of_Medicine_Neuroscience_Tutorial http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_E15_Atlas http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:GenePaint_E15_Atlas\n",
      "http://neurolex.org/wiki/Category-3APontine_nuclear_complex http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AFlocculonodular_lobe http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Birnlex_1489 http://neurolex.org/wiki/Property-3ATitle structure\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUCL_Motor_Control_Group http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3ACerebellar_cortex http://www.w3.org/2000/01/rdf-schema#label Cerebellar cortex\n",
      "http://neurolex.org/wiki/Category-3AResource-3AUW-2DMadison_Neuroscience_Resources http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3ACerebellar_Pontocerebellar_Projection http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3APontine_nuclear_complex http://neurolex.org/wiki/Property-3AEfferentProjections http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_P7_Atlas http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Property-3ATitle http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Property:Title\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACell_Properties_Database http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:Cell_Properties_Database\n",
      "http://neurolex.org/wiki/Category-3AResource-3ANeuro_Systems_and_Graphics_Computing_Laboratory http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3AResource-3AGenePaint_P56_Mouse_Atlas http://neurolex.org/wiki/Property-3AKeywords http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Property-3ASuperCategory http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#DatatypeProperty\n",
      "http://neurolex.org/wiki/Category-3AResource-3AAllen_Reference_Atlas http://www.w3.org/2000/01/rdf-schema#label Resource:Allen Reference Atlas\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Platform http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3AHigh_Resolution_Mouse_Brain_Atlas http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Resource:High_Resolution_Mouse_Brain_Atlas\n",
      "http://neurolex.org/wiki/Category-3AHindbrain_of_CIVM_postnatal_rat_brain_atlas http://www.w3.org/2000/01/rdf-schema#label Hindbrain of CIVM postnatal rat brain atlas\n",
      "http://neurolex.org/wiki/Property-3AAfferentProjections http://www.w3.org/2000/01/rdf-schema#label AfferentProjections\n",
      "http://neurolex.org/wiki/Category-3ANucleus_centrobasalis http://semantic-mediawiki.org/swivt/1.0#page http://neurolex.org/wiki/Category:Nucleus_centrobasalis\n",
      "http://neurolex.org/wiki/Category-3AHindbrain_of_CIVM_postnatal_rat_brain_atlas http://neurolex.org/wiki/Property-3APartiallyOverlapsWith http://neurolex.org/wiki/Birnlex_1489\n",
      "http://neurolex.org/wiki/Category-3ACerebellar_Corticopontine_Projection http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n",
      "http://neurolex.org/wiki/Category-3AResource-3ACerebellar_Development_Transcriptome_Database http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2002/07/owl#Class\n"
     ]
    }
   ],
   "source": [
    "for s, p, o in g:\n",
    "    print s, p, o"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Querying the graph\n",
    "\n",
    "When working with big documents (RDF stores), we really want to be querying rather than iterating. So we'll use SPARQL to find a specific statement, the definition, and print it. The SPARQL query is:\n",
    "\n",
    "    SELECT DISTINCT ?b\n",
    "        WHERE {\n",
    "            ?a property:Definition ?b .\n",
    "        }\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Definition: Part of the rhombencephalon that lies in the posterior cranial fossa behind the brain stem, consisting of the cerebellar cortex, deep cerebellar nuclei and cerebellar white matter.\n",
      "A portion of the brain that helps regulate posture, balance, and coordination. (NIDA Media Guide Glossary)\n",
      "\n",
      "The dorsal topographic division of the hindbrain, connected to the ventral  division-the pons-by a white matter tract, the middle cerebellar peduncle. The cerebellum was discovered and named by Aristotle (De Partibus Animalium) based on macrodissection of a variety of animals not including humans; see translation by Thompson (1910, 494b 30). Older synonyms include parencephalon (Aristotle), hindbrain (Galen, c192).\n"
     ]
    }
   ],
   "source": [
    "import rdflib\n",
    "\n",
    "# Get the graph\n",
    "g = rdflib.Graph()\n",
    "result = g.parse(\"http://neurolex.org/wiki/Special:ExportRDF/birnlex_1489\", format=\"application/rdf+xml\")\n",
    "\n",
    "# Query the graph\n",
    "qres = g.query(\"\"\"SELECT DISTINCT ?b WHERE {?a property:Definition ?b .}\"\"\",\n",
    "               initNs = dict(\n",
    "    property=rdflib.Namespace(\"http://neurolex.org/wiki/Property-3A\"),\n",
    "        wiki=rdflib.Namespace(\"http://neurolex.org/wiki/\")))\n",
    "\n",
    "print \"Definition: %s\" % qres.bindings[0]['b']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "Now let's add a second term to the query:\n",
    "\n",
    "    SELECT DISTINCT ?label ?def\n",
    "        WHERE {\n",
    "            ?a property:Label ?label .\n",
    "            ?a property:Definition ?def .\n",
    "        }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Label: Cerebellum\n",
      "Definition: Part of the rhombencephalon that lies in the posterior cranial fossa behind the brain stem, consisting of the cerebellar cortex, deep cerebellar nuclei and cerebellar white matter.\n",
      "A portion of the brain that helps regulate posture, balance, and coordination. (NIDA Media Guide Glossary)\n",
      "\n",
      "The dorsal topographic division of the hindbrain, connected to the ventral  division-the pons-by a white matter tract, the middle cerebellar peduncle. The cerebellum was discovered and named by Aristotle (De Partibus Animalium) based on macrodissection of a variety of animals not including humans; see translation by Thompson (1910, 494b 30). Older synonyms include parencephalon (Aristotle), hindbrain (Galen, c192).\n"
     ]
    }
   ],
   "source": [
    "import rdflib\n",
    "\n",
    "# Get the graph\n",
    "g = rdflib.Graph()\n",
    "result = g.parse(\"http://neurolex.org/wiki/Special:ExportRDF/birnlex_1489\", format=\"application/rdf+xml\")\n",
    "\n",
    "# Query the graph\n",
    "qres = g.query(\"\"\"SELECT DISTINCT ?label ?def WHERE {?a property:Label ?label . ?a\n",
    "property:Definition ?def .}\"\"\",\n",
    "               initNs = dict(\n",
    "    property=rdflib.Namespace(\"http://neurolex.org/wiki/Property-3A\"),\n",
    "        wiki=rdflib.Namespace(\"http://neurolex.org/wiki/\")))\n",
    "\n",
    "print \"Label: %s\" % qres.bindings[0]['label'].value\n",
    "print \"Definition: %s\" % qres.bindings[0]['def'].value"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Looping look-up\n",
    "\n",
    "Now let's take a list of NeuroLex ids and encode them:\n",
    "\n",
    "sao185580330\n",
    "PATO_0001463\n",
    "nlx_15593\n",
    "nlx_147643\n",
    "sao1394521419\n",
    "birnlex_826\n",
    "birnlex_1565\n",
    "birnlex_1197\n",
    "birnlex_1373\n",
    "sao1211023249\n",
    "birnlex_147\n",
    "birnlex_1508\n",
    "nlx_inv_090914\n",
    "sao1744435799\n",
    "nlx_414\n",
    "birnlex_12500\n",
    "CHEBI:15765\n",
    "birnlex_7004\n",
    "GO:0040011\n",
    "PATO_0000051\n",
    "sao1417703748\n",
    "birnlex_727\n",
    "birnlex_2339\n",
    "birnlex_2098\n",
    "nlx_subcell_20090508\n",
    "nlx_subcell_20090511\n",
    "birnlex_1298\n",
    "birnlex_1672\n",
    "sao914572699\n",
    "sao1071221672\n",
    "birnlex_2337\n",
    "birnlex_954\n",
    "sao221389602"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Label: Acetylcholine\n",
      "Definition: A neurotransmitter. Acetylcholine in vertebrates is the major transmitter at neuromuscular junctions, autonomic ganglia, parasympathetic effector junctions, a subset of sympathetic effector junctions, and at many sites in the central nervous system. It is generally not used as an administered drug because it is broken down very rapidly by cholinesterases, but it is useful in some ophthalmological applications (MSH).\n",
      "\n",
      "Label: Action potential\n",
      "Definition: A large, brief, all-or-nothing, regenerative electrical potential, that propagates along the axon, muscle fiber, or some dendrites.  Action potentials are usually generated at the axon hillock and propagate uni-directionally down the axon.  Adapted from Nicholls, Martin and Wallace 3rd edition.\n",
      "\n",
      "Label: Afferent\n",
      "Definition: An axon that is incoming into a brain region.  Could also refer to the neuron that gives rise to the axon.\n",
      "\n",
      "(A connection, or a pathway to a node. A node can be an individual neuron, a neuron class, a gray matter region, or a site. Afferent and its complementary term efferent were used for the first time by Unzer, 1771, to indicate toward or away from the central nervous system or other non-neural tissues. Adapted from Swanson, 2014).\n",
      "\n",
      "Label: Antennal lobe\n",
      "Definition: Synaptic neuropil domain of the deuterocerebrum that is the main target for innervation from the antennal nerve.\n",
      "\n",
      "Label: Astrocyte\n",
      "Definition: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from \"star\" cells) are irregularly shaped with many long processes, including those with \"end feet\" which form the glial (limiting) membrane.  The cell body of an astrocyte spans 10-20 microns and its processes radiate out for another 20-30 microns. Astrocytes stain for the intermediate filament GFAP.  Astrocytes are recognized in the transmission electron microscope by their irregular shape, numerous glycogen granules, a relatively clear cytoplasm and bundles of intermediate filaments (adapted from MSH and Synapse Web)., A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from \"star\" cells) are irregularly shaped with many long processes, including those with \"end feet\" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and \"reactive astrocytes\" (along with microglia) respond to injury (MSH).\n",
      "\n",
      "Label: Basal ganglia\n",
      "Definition: Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system.  The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus.  Some also include the nucleus accumbens and ventral pallidum.\n",
      "\n",
      "Label: Brainstem\n",
      "Definition: The lower portion of the brain through which the forebrain sends information to, and receives information from, the spinal cord and peripheral nerves. Major functions located in the brainstem include those necessary for survival, e.g., breathing, heart rate, blood pressure, and arousal. (NIDA Media Guide Glossary).  Note that the definition of brainstem varies in different nomenclatures, for example, some definitions include the diencephalon.\n",
      "\n",
      "Label: CA1\n",
      "Definition: Part of hippocampus proper bounded by CA2 and the subiculum, characterized by pyramidal neurons that receive projections from pyramidal neurons of CA3 via the Schaffer collaterals.\n",
      "\n",
      "Label: Caudate nucleus\n",
      "Definition: Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle.  It is divided into a head, body and tail in some species.\n",
      "\n",
      "Label: Dendrite\n",
      "Definition: A branching protoplasmic process of a neuron that receive and integrate signals coming from axons of other neurons, and convey the resulting signal to the body of the cell (Gene Ontology)., One of several similar processes that issue from the perikaryon of a neuron, generally specialized for receiving synaptic input from other neurons or transduction of signals from the environment.\n",
      "\n",
      "Label: Drosophila\n",
      "Definition: a genus of small flies, belonging to the family Drosophilidae, whose members are often called \"fruit flies\"\n",
      "\n",
      "Label: Entorhinal cortex\n",
      "Definition: Component of the temporal lobe on the mesial surface.  The rostral and caudal boundaries of the entorhinal cortex are the rostral end of the collateral sulcus and the caudal end of the amygdala respectively.  The medial boundary is the medial aspect of the temporal lobe and the lateral boundary is the collateral sulcus. (DK)\n",
      "\n",
      "nlx_inv_090914\n",
      "\n",
      "Label: Glutamate\n",
      "Definition: The carboxylate anion of glutamic acid; and the major excitatory neurotransmitter in the central nervous system of vertebrates, the peripheral nervous system of invertebrates.\n",
      "\n",
      "Label: Granule\n",
      "Definition: Small, generally round or drop-like shape that is densely packed together with many other cells\n",
      "\n",
      "Label: Huntingtons disease\n",
      "Definition: A familial disorder inherited as an autosomal dominant trait and characterized by the onset of progressive CHOREA and DEMENTIA in the fourth or fifth decade of life. Common initial manifestations include paranoia; poor impulse control; DEPRESSION; HALLUCINATIONS; and DELUSIONS. Eventually intellectual impairment; loss of fine motor control; ATHETOSIS; and diffuse chorea involving axial and limb musculature develops, leading to a vegetative state within 10-15 years of disease onset. The juvenile variant has a more fulminant course including SEIZURES; ATAXIA; dementia; and chorea.\n",
      "\n",
      "Label: Levodopa\n",
      "Definition: An amino acid precursor of dopamine with antiparkinsonian properties. L-DOPA is a prodrug that is converted to dopamine by DOPA decarboxylase and can cross the blood-brain barrier. When in the brain, L-DOPA is decarboxylated to dopamine and stimulates the dopaminergic receptors. (Adapted from NCI Thesaurus) \n",
      "\n",
      "Levodopa is naturally occurring form of dihydroxyphenylalanine and the immediate precursor of dopamine. Unlike dopamine itself, it can be taken orally and crosses the blood-brain barrier. It is rapidly taken up by dopaminergic neurons and converted to dopamine. It is used for the treatment of parkinsonian disorders and is usually given with agents that inhibit its conversion to dopamine outside of the central nervous system. (PubChem) Pharmacology: Levodopa (L-dopa) is used to replace dopamine lost in Parkinson's disease because dopamine itself cannot cross the blood-brain barrier where its precursor can. However, L-DOPA is converted to dopamine in the periphery as well as in the CNS, so it is administered with a peripheral DDC (dopamine decarboxylase) inhibitor such as carbidopa, without which 90% is metabolised in the gut wall, and with a COMT inhibitor if possible; this prevents about a 5% loss. The form given therapeutically is therefore a prodrug which avoids decarboxylation in the stomach and periphery, can cross the blood-brain barrier, and once in the brain is converted to the neurotransmitter dopamine by the enzyme aromatic-L-amino-acid decarboxylase. Mechanism of action: Striatal dopamine levels in symptomatic Parkinson's disease are decreased by 60 to 80%, striatal dopaminergic neurotransmission may be enhanced by exogenous supplementation of dopamine through administration of dopamine's precursor, levodopa. A small percentage of each levodopa dose crosses the blood-brain barrier and is decarboxylated to dopamine. This newly formed dopamine then is available to stimulate dopaminergic receptors, thus compensating for the depleted supply of endogenous dopamine. Drug type: Approved. Small Molecule. Drug category: Antidyskinetics. Antiparkinson Agents. Dopamine Agents\n",
      "\n",
      "Label: Limulus\n",
      "Definition: any horseshoe crab of the genus Limulus\n",
      "\n",
      "Label: Locomotion\n",
      "Definition: Self-propelled movement of a cell or organism from one location to another.\n",
      "\n",
      "Label: Morphology\n",
      "Definition: A quality inhering in the bearer by virtue of its size, shape, and structure.\n",
      "\n",
      "Cognitive Atlas Definition=(linguistics) the study of the structure and content of word forms; (biology) the study of the form or shape of an organism or part thereof; (materials science), the study of shape, size, texture and phase distribution of physical objects.\n",
      "\n",
      "Label: Neuron\n",
      "Definition: The basic cellular units of nervous tissue. Neurons are polarized cells with defined regions consisting of the cell body, an axon, and dendrites, although some types of neurons lack axons or dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. Neurons can be classified a number of different ways: anatomical, physiological, and developmental.  Anatomical classes are defined first by the location of the neuron in the nervous system.  Neurons are further distinguished from each other by features which include dendritic and axon morphology.  Anatomical features also include synaptic connectivity (inputs and outputs) and molecular phenotype(the particular neurotransmitters, receptors, and ion channels expressed by a neuron).  Neurons can be classified by their physiological properties.  This includes their general function (Sensory, motor, interneuron).  Functions can also include whether the neuron is a relay neuron or a local interneuron or whether it is involved in sensory processing or correction of motor responses.  Physiological actions can also include the firing properties of the neuron (bursting, tonic, quiescent).  Developmental classifications of neurons are based upon the lineage that the cell derives from.  The number of neurons in a particular class can vary over orders of magnitude from individual neurons in some classes to millions of neurons in other classes.\n",
      "\n",
      "Label: Nucleus accumbens\n",
      "Definition: A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen.  (caudoputamen in rodent) and continuous with these structures.  There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum.  Its principle neuron is the medium spiny neuron.  Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum.\n",
      "\n",
      "Label: Ontology\n",
      "Definition: In both computer science and information science, an ontology represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about the objects within that domain.  Ontologies are used in artificial intelligence, the semantic web, software engineering, biomedical informatics and information architecture as a form of knowledge representation about the world or some part of it. Ontologies generally describe:      \n",
      "* Individuals: the basic or \"ground level\" objects     \n",
      "* Classes: sets, collections, or types of objects     \n",
      "* Attributes: properties, features, characteristics, or parameters that objects can have and share     \n",
      "* Relations: ways that objects can be related to one another     \n",
      "* Events: the changing of attributes or relations\n",
      "\n",
      "NITRC definition: Controlled, standardized vocabulary that describes objects and the relations between them.\n",
      "\n",
      "Label: Parkinsons disease\n",
      "Definition: * A disease characterized as a progressive motor disability manifested by tremors, shaking, muscular rigidity, and lack of postural reflexes. (PSY)       * A progressive, degenerative neurologic disease characterized by a TREMOR that is maximal at rest, retropulsion (i.e. a tendency to fall backwards), rigidity, stooped posture, slowness of voluntary movements, and a masklike facial expression. Pathologic features include loss of melanin containing neurons in the substantia nigra and other pigmented nuclei of the brainstem. LEWY BODIES are present in the substantia nigra and locus coeruleus but may also be found in a related condition (LEWY BODY DISEASE, DIFFUSE) characterized by dementia in combination with varying degrees of parkinsonism. (Adams et al., Principles of Neurology, 6th ed, p1059, pp1067-75) (MSH)       * progressive, degenerative disorder of the nervous system characterized by tremors, rigidity, bradykinesia, postural instability, and gait abnormalities; caused by a loss of neurons and a decrease of dopamine in the basal ganglia. (CSP)\n",
      "\n",
      "Label: Perforant path\n",
      "Definition: Projection arising from entorhinal cortex, predominantly from cells in layers 2 and 3, and terminating in all subdivisions of the hippocampal formation  (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 477)\n",
      "\n",
      "Label: Schaffer collateral\n",
      "Definition: Part of axon of the CA3 pyramidal neuron that projects to hippocampal area CA1\n",
      "\n",
      "Label: Stratum radiatum\n",
      "Definition: Layer of the hippocampus lying just superficial to the stratum lucidum in CA3 and the pyramidal cell layer in CA1 and CA2 defined by the the location of CA3 to CA3 associational fibers and the Schaffer collaterals in area CA1.  Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460)\n",
      "\n",
      "Label: Striatum\n",
      "Definition: * Externally Sourced Definition: A region of the brain consisting of the phylogenetically newer part of the Corpus_striatum (Caudate_nucleus and Putamen).\n",
      "\n",
      "Label: Synapse\n",
      "Definition: The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane (Gene Ontology).\n",
      "\n",
      "Label: Synaptic Vesicle\n",
      "Definition: Secretory organelles, some 50 nm in diameter, of pre-synaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the pre-synaptic plasma membrane (Gene Ontology).\n",
      "\n",
      "birnlex_2337\n",
      "\n",
      "Label: Thalamus\n",
      "Definition: Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH).\n",
      "\n",
      "The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87).\n",
      "\n",
      "Label: Vesicle\n",
      "Definition: Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology).\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import rdflib\n",
    "\n",
    "ids = ['sao185580330', 'PATO_0001463', 'nlx_15593', 'nlx_147643', 'sao1394521419', 'birnlex_826', \n",
    "       'birnlex_1565', 'birnlex_1197', 'birnlex_1373', 'sao1211023249', 'birnlex_147', \n",
    "       'birnlex_1508', 'nlx_inv_090914', 'sao1744435799', 'nlx_414', 'birnlex_12500', \n",
    "       'CHEBI:15765', 'birnlex_7004', 'GO:0040011', 'PATO_0000051', 'sao1417703748', \n",
    "       'birnlex_727', 'birnlex_2339', 'birnlex_2098', 'nlx_subcell_20090508', \n",
    "       'nlx_subcell_20090511', 'birnlex_1298', 'birnlex_1672', 'sao914572699', 'sao1071221672', \n",
    "       'birnlex_2337', 'birnlex_954', 'sao221389602']\n",
    "\n",
    "# Loop over the ids\n",
    "for id in ids:\n",
    "    # Get the graph\n",
    "    g = rdflib.Graph()\n",
    "    result = g.parse(\"http://neurolex.org/wiki/Special:ExportRDF/%s\" % id, \n",
    "                     format=\"application/rdf+xml\")\n",
    "\n",
    "    # Query the graph\n",
    "    qres = g.query(\"\"\"SELECT DISTINCT ?label ?def WHERE {?a property:Label ?label . ?a \n",
    "    property:Definition ?def .}\"\"\",\n",
    "                   initNs = dict(\n",
    "        property=rdflib.Namespace(\"http://neurolex.org/wiki/Property-3A\"),\n",
    "            wiki=rdflib.Namespace(\"http://neurolex.org/wiki/\")))\n",
    "\n",
    "    try:\n",
    "        print \"Label: %s\" % qres.bindings[0]['label'].value\n",
    "        print \"Definition: %s\" % qres.bindings[0]['def'].value\n",
    "    except IndexError:\n",
    "        print id\n",
    "        pass\n",
    "    print \n",
    "    "
   ]
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