SPARQL_Ontology_ESIP_mmisw_endpoints.ipynb

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   "source": [
    "# ESIP and MMISW SPARQL Enpoint Testing for data retrieval and processing\n",
    "# T. Wellman BCB, U.S. Geological Survey 6-14-2018\n",
    "\n",
    "from SPARQLWrapper import SPARQLWrapper, JSON\n",
    "import pprint\n",
    "import pandas as pd\n",
    "import rdflib\n",
    "pd.set_option('max_colwidth', 1000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 198,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'head': {'vars': ['obj', 'pred', 'sub']},\n",
      " 'results': {'bindings': [{'obj': {'type': 'bnode', 'value': 'b1D80F6C3x14172'},\n",
      "                           'pred': {'type': 'uri',\n",
      "                                    'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf'},\n",
      "                           'sub': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront'}},\n",
      "                          {'obj': {'type': 'uri',\n",
      "                                   'value': 'http://www.w3.org/2002/07/owl#Class'},\n",
      "                           'pred': {'type': 'uri',\n",
      "                                    'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'},\n",
      "                           'sub': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront'}},\n",
      "                          {'obj': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena'},\n",
      "                           'pred': {'type': 'uri',\n",
      "                                    'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf'},\n",
      "                           'sub': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint'}},\n",
      "                          {'obj': {'type': 'uri',\n",
      "                                   'value': 'http://www.w3.org/2002/07/owl#Class'},\n",
      "                           'pred': {'type': 'uri',\n",
      "                                    'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'},\n",
      "                           'sub': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint'}},\n",
      "                          {'obj': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena'},\n",
      "                           'pred': {'type': 'uri',\n",
      "                                    'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf'},\n",
      "                           'sub': {'type': 'uri',\n",
      "                                   'value': 'http://sweetontology.net/phenAtmoFront/FrontRegion'}}]}}\n"
     ]
    },
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>obj</th>\n",
       "      <th>pred</th>\n",
       "      <th>sub</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>{'value': 'b1D80F6C3x14172', 'type': 'bnode'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>{'value': 'http://www.w3.org/2002/07/owl#Class', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>{'value': 'http://www.w3.org/2002/07/owl#Class', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://sweetontology.net/phenAtmoFront/FrontRegion', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      "text/plain": [
       "                                                                                     obj  \\\n",
       "0                                          {'value': 'b1D80F6C3x14172', 'type': 'bnode'}   \n",
       "1                        {'value': 'http://www.w3.org/2002/07/owl#Class', 'type': 'uri'}   \n",
       "2  {'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena', 'type': 'uri'}   \n",
       "3                        {'value': 'http://www.w3.org/2002/07/owl#Class', 'type': 'uri'}   \n",
       "4  {'value': 'http://sweetontology.net/phenAtmo/MeteorologicalPhenomena', 'type': 'uri'}   \n",
       "\n",
       "                                                                          pred  \\\n",
       "0  {'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}   \n",
       "1  {'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}   \n",
       "2  {'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}   \n",
       "3  {'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}   \n",
       "4  {'value': 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'type': 'uri'}   \n",
       "\n",
       "                                                                                 sub  \n",
       "0  {'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront', 'type': 'uri'}  \n",
       "1  {'value': 'http://sweetontology.net/phenAtmoFront/SeaBreezeFront', 'type': 'uri'}  \n",
       "2     {'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint', 'type': 'uri'}  \n",
       "3     {'value': 'http://sweetontology.net/phenAtmoFront/TriplePoint', 'type': 'uri'}  \n",
       "4     {'value': 'http://sweetontology.net/phenAtmoFront/FrontRegion', 'type': 'uri'}  "
      ]
     },
     "execution_count": 198,
     "metadata": {},
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    }
   ],
   "source": [
    "# Run ESIP (Earth Science Information Partners) test - data retrieval\n",
    "# Retrieve ESIP data via the SPARQL endpoint, \n",
    "# display as dictionary and dataframe\n",
    "\n",
    "query_tag = \"\"\"\n",
    "SELECT * WHERE {\n",
    "  ?sub ?pred ?obj .\n",
    "} \n",
    "LIMIT 5\n",
    "    \"\"\"\n",
    "\n",
    "sparql = SPARQLWrapper(\"http://cor.esipfed.org/sparql\")\n",
    "sparql.setQuery(query_tag)\n",
    "sparql.setReturnFormat(JSON)\n",
    "\n",
    "try :\n",
    "    results = sparql.query()\n",
    "    results = results.convert()\n",
    "except:\n",
    "    print('exception occurred - reconfigure query')\n",
    "\n",
    "# print results as dictionary\n",
    "pprint.pprint(results)\n",
    "\n",
    "# print results as dataframe\n",
    "pd.DataFrame(results['results']['bindings'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 199,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>obj</th>\n",
       "      <th>pred</th>\n",
       "      <th>sub</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/Standard_Name', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>{'value': '\"Northward\" indicates a vector component which is positive when directed northward (negative southward). The specification of a physical process by the phrase due_to_process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Parameterized eddy advection in an ocean model means the part due to a scheme representing parameterized eddy-induced advective effects not included in the resolved model velocity field. Parameterized eddy advection can be represented on various spatial scales and there are standard names for parameterized_mesoscale_eddy_advection and parameterized_submesoscale_eddy_advection which both contribute to the total parameterized eddy advection.', 'type': 'literal'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/2004/02/skos/core#definition', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>{'value': 'kg s-1', 'type': 'literal'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/canonical_units', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/Standard_Name', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/downwelling_longwave_radiance_in_air', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>{'value': '\"longwave\" means longwave radiation. Downwelling radiation is radiation from above. It does not mean \"net downward\". Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction from which it is coming must be specified, for instance with a coordinate of zenith_angle. If the radiation does not depend on direction, a standard name of isotropic radiance should be chosen instead.', 'type': 'literal'}</td>\n",
       "      <td>{'value': 'http://www.w3.org/2004/02/skos/core#definition', 'type': 'uri'}</td>\n",
       "      <td>{'value': 'http://mmisw.org/ont/cf/parameter/downwelling_longwave_radiance_in_air', 'type': 'uri'}</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
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      "text/plain": [
       "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    obj  \\\n",
       "0                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           {'value': 'http://mmisw.org/ont/cf/parameter/Standard_Name', 'type': 'uri'}   \n",
       "1  {'value': '\"Northward\" indicates a vector component which is positive when directed northward (negative southward). The specification of a physical process by the phrase due_to_process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Parameterized eddy advection in an ocean model means the part due to a scheme representing parameterized eddy-induced advective effects not included in the resolved model velocity field. Parameterized eddy advection can be represented on various spatial scales and there are standard names for parameterized_mesoscale_eddy_advection and parameterized_submesoscale_eddy_advection which both contribute to the total parameterized eddy advection.', 'type': 'literal'}   \n",
       "2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                {'value': 'kg s-1', 'type': 'literal'}   \n",
       "3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           {'value': 'http://mmisw.org/ont/cf/parameter/Standard_Name', 'type': 'uri'}   \n",
       "4                                                                                                                                                                                                                                                                                                                                                       {'value': '\"longwave\" means longwave radiation. Downwelling radiation is radiation from above. It does not mean \"net downward\". Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction from which it is coming must be specified, for instance with a coordinate of zenith_angle. If the radiation does not depend on direction, a standard name of isotropic radiance should be chosen instead.', 'type': 'literal'}   \n",
       "\n",
       "                                                                            pred  \\\n",
       "0    {'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}   \n",
       "1     {'value': 'http://www.w3.org/2004/02/skos/core#definition', 'type': 'uri'}   \n",
       "2  {'value': 'http://mmisw.org/ont/cf/parameter/canonical_units', 'type': 'uri'}   \n",
       "3    {'value': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'type': 'uri'}   \n",
       "4     {'value': 'http://www.w3.org/2004/02/skos/core#definition', 'type': 'uri'}   \n",
       "\n",
       "                                                                                                                                sub  \n",
       "0  {'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}  \n",
       "1  {'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}  \n",
       "2  {'value': 'http://mmisw.org/ont/cf/parameter/northward_ocean_salt_transport_due_to_parameterized_eddy_advection', 'type': 'uri'}  \n",
       "3                                {'value': 'http://mmisw.org/ont/cf/parameter/downwelling_longwave_radiance_in_air', 'type': 'uri'}  \n",
       "4                                {'value': 'http://mmisw.org/ont/cf/parameter/downwelling_longwave_radiance_in_air', 'type': 'uri'}  "
      ]
     },
     "execution_count": 199,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Run MMI ORR data retrieval (Marine Metadata Interoperability Ontology Registry and Repository, http://mmisw.org/) \n",
    "# Retrieve MMI data via the SPARQL endpoint, display as  dataframe\n",
    "\n",
    "query_tag = \"\"\"\n",
    "SELECT * WHERE {\n",
    "\n",
    "  ?sub ?pred ?obj .\n",
    "} \n",
    "LIMIT 5\n",
    "    \"\"\"\n",
    "\n",
    "sparql = SPARQLWrapper(\"https://mmisw.org/sparql\")\n",
    "sparql.setQuery(query_tag)\n",
    "sparql.setReturnFormat(JSON)\n",
    "\n",
    "try :\n",
    "    results = sparql.query()\n",
    "    results = results.convert()\n",
    "except:\n",
    "    print('exception occurred - reconfigure query')\n",
    "\n",
    "# print results as dataframe\n",
    "pd.DataFrame(results['results']['bindings'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 196,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>def</th>\n",
       "      <th>ref</th>\n",
       "      <th>subject</th>\n",
       "      <th>term</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Brief name of the type of binoculars used (e.g. BE = Big Eye) corresponding to the number of reticles recorded in the term reticles, or Naked Eye if sighting distance was estimated without binoculars. If codes for type of binoculars are used, they must be used consistently within a dataset and they must be explained in metadata. Metadata should also include additional information about the specific binoculars used, such as power (magnification X objective diameter in mm)</td>\n",
       "      <td>http://rs.gbif.org/sandbox/extension/mbg-vlts.xml</td>\n",
       "      <td>http://mmisw.org/ont/ioos/marine_biogeography/distanceEstimationMethod</td>\n",
       "      <td>distanceEstimationMethod</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>This is a one-character string with enumerated values indicating what type of quantification this record represents. \"P\" for presence (and no quantification), \"Q\" for quantified or \"A\" for absence.</td>\n",
       "      <td>http://rs.gbif.org/sandbox/extension/mbg-common-terms.xml</td>\n",
       "      <td>http://mmisw.org/ont/ioos/marine_biogeography/quantificationStatus</td>\n",
       "      <td>quantificationStatus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>The number of reticles below the horizon using a specified type of binoculars. Reticle 0 indicates the sighting is at the horizon. The type of binoculars must be specified in the term distanceEstimationMethod. If distanceEstimationMethod did not include binoculars with reticles then no values will be required for this field.</td>\n",
       "      <td>http://rs.gbif.org/sandbox/extension/mbg-vlts.xml</td>\n",
       "      <td>http://mmisw.org/ont/ioos/marine_biogeography/reticles</td>\n",
       "      <td>reticles</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>For boat-based surveys: Radial distance in meters between the animal (or center of group of animals) and the vessel when the first sighting was made. This value is can be reported if 1) prior calibrations of radial distances have been made using the known observation height and the reticles on the specific types of binoculars used during the survey, and 2) sighting was detected by eye if ‘Naked Eye’ is specified in distanceEstimationMethod. *Optional use for aerial surveys: Typically these radial sighting distances are not recorded, but they can be calculated from clinometer readings (verticalAngle) and altitude (observationHeight). If distances between the plane and the animals are provided (e.g. using lasers, or calculating distance to the trackline using GPS locations above the initial animal sightings) this information can be included in this term.</td>\n",
       "      <td>http://rs.gbif.org/sandbox/extension/mbg-vlts.xml</td>\n",
       "      <td>http://mmisw.org/ont/ioos/marine_biogeography/sightingDistanceInMeters</td>\n",
       "      <td>sightingDistanceInMeters</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>The depth below the surface of the water, in meters, at which the observation was made. \"depth\" is expressed as a single value rather than the min and max as in DwC.  Work with a representative of the original data to determine what is the preferred way to represent single value and min/max, as necessary.  This single value named \"depth\" is required for ERDDAP and Climate and Forecast compatibility.</td>\n",
       "      <td>http://rs.gbif.org/sandbox/extension/mbg-common-terms.xml</td>\n",
       "      <td>http://mmisw.org/ont/ioos/marine_biogeography/depth</td>\n",
       "      <td>depth</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                def  \\\n",
       "0                                                                                                                                                                                                                                                                                                                                                                                                       Brief name of the type of binoculars used (e.g. BE = Big Eye) corresponding to the number of reticles recorded in the term reticles, or Naked Eye if sighting distance was estimated without binoculars. If codes for type of binoculars are used, they must be used consistently within a dataset and they must be explained in metadata. Metadata should also include additional information about the specific binoculars used, such as power (magnification X objective diameter in mm)   \n",
       "1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             This is a one-character string with enumerated values indicating what type of quantification this record represents. \"P\" for presence (and no quantification), \"Q\" for quantified or \"A\" for absence.   \n",
       "2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            The number of reticles below the horizon using a specified type of binoculars. Reticle 0 indicates the sighting is at the horizon. The type of binoculars must be specified in the term distanceEstimationMethod. If distanceEstimationMethod did not include binoculars with reticles then no values will be required for this field.   \n",
       "3  For boat-based surveys: Radial distance in meters between the animal (or center of group of animals) and the vessel when the first sighting was made. This value is can be reported if 1) prior calibrations of radial distances have been made using the known observation height and the reticles on the specific types of binoculars used during the survey, and 2) sighting was detected by eye if ‘Naked Eye’ is specified in distanceEstimationMethod. *Optional use for aerial surveys: Typically these radial sighting distances are not recorded, but they can be calculated from clinometer readings (verticalAngle) and altitude (observationHeight). If distances between the plane and the animals are provided (e.g. using lasers, or calculating distance to the trackline using GPS locations above the initial animal sightings) this information can be included in this term.   \n",
       "4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                The depth below the surface of the water, in meters, at which the observation was made. \"depth\" is expressed as a single value rather than the min and max as in DwC.  Work with a representative of the original data to determine what is the preferred way to represent single value and min/max, as necessary.  This single value named \"depth\" is required for ERDDAP and Climate and Forecast compatibility.   \n",
       "\n",
       "                                                         ref  \\\n",
       "0          http://rs.gbif.org/sandbox/extension/mbg-vlts.xml   \n",
       "1  http://rs.gbif.org/sandbox/extension/mbg-common-terms.xml   \n",
       "2          http://rs.gbif.org/sandbox/extension/mbg-vlts.xml   \n",
       "3          http://rs.gbif.org/sandbox/extension/mbg-vlts.xml   \n",
       "4  http://rs.gbif.org/sandbox/extension/mbg-common-terms.xml   \n",
       "\n",
       "                                                                  subject  \\\n",
       "0  http://mmisw.org/ont/ioos/marine_biogeography/distanceEstimationMethod   \n",
       "1      http://mmisw.org/ont/ioos/marine_biogeography/quantificationStatus   \n",
       "2                  http://mmisw.org/ont/ioos/marine_biogeography/reticles   \n",
       "3  http://mmisw.org/ont/ioos/marine_biogeography/sightingDistanceInMeters   \n",
       "4                     http://mmisw.org/ont/ioos/marine_biogeography/depth   \n",
       "\n",
       "                       term  \n",
       "0  distanceEstimationMethod  \n",
       "1      quantificationStatus  \n",
       "2                  reticles  \n",
       "3  sightingDistanceInMeters  \n",
       "4                     depth  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Retrieve MMI data via the SPARQL endpoint, display as dataframe\n",
    "# http://mmisw.org/ont/ioos/marine_biogeography\n",
    "\n",
    "# tag structure \n",
    "#<RDF>\n",
    "#<Description rdf:about=\"http://mmisw.org/ont/ioos/marine_biogeography/windDirectionRelativeToTrueNorth\">\n",
    "#  <ns0:Term>\n",
    "#    windDirectionRelativeToTrueNorth\n",
    "#  </ns0:Term>\n",
    "#  <ns0:Section>\n",
    "#    VLTS\n",
    "#  </ns0:Section>\n",
    "#  <ns0:Reference>\n",
    "#    http://rs.gbif.org/sandbox/extension/mbg-vlts.xml\n",
    "#  </ns0:Reference>\n",
    "#  <rdfs:label>\n",
    "#    windDirectionRelativeToTrueNorth\n",
    "#  </rdfs:label>\n",
    "#  <rdf:type rdf:resource=\"http://mmisw.org/ont/ioos/marine_biogeography/Parameter\"/>\n",
    "#  <ns0:Defintion>\n",
    "#    Wind direction in degrees relative to true North.</ns0:Defintion>\n",
    "#  <ns0:Darwin_Core_or_Extension>\n",
    "#    MBG VLTS Extension\n",
    "#  </ns0:Darwin_Core_or_Extension>\n",
    "#</Description></RDF>\n",
    "\n",
    "\n",
    "query_tag = \"\"\"\n",
    "PREFIX obis: <http://mmisw.org/ont/ioos/marine_biogeography>\n",
    "PREFIX owl:<http://www.w3.org/2002/07/owl#>\n",
    "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n",
    "SELECT ?subject ?def ?term ?ref\n",
    "WHERE {\n",
    "    ?subject ?pred1 ?def ; ?pred2 ?term ; ?pred3 ?ref  .\n",
    "    FILTER(regex(str(?subject), \"http://mmisw.org/ont/ioos/marine_biogeography\" )) . \n",
    "    FILTER(regex(str(?pred1),\"/Defintion\")) .\n",
    "    FILTER(regex(str(?pred2),\"/Term\")) .\n",
    "    FILTER(regex(str(?pred3),\"/Reference\")) .\n",
    "    }\n",
    "LIMIT 5\n",
    "\"\"\"\n",
    "\n",
    "sparql = SPARQLWrapper(\"https://mmisw.org/sparql\")\n",
    "sparql = SPARQLWrapper(\"http://cor.esipfed.org/sparql\")\n",
    "sparql.setQuery(query_tag)\n",
    "sparql.setReturnFormat(JSON)\n",
    "\n",
    "results = {}\n",
    "try :\n",
    "    results = sparql.query()\n",
    "    results = results.convert()\n",
    "except:\n",
    "    print('exception occurred - reconfigure query')\n",
    "\n",
    "# print results as dataframe or simple text (null or error)\n",
    "try:\n",
    "    proc_list = results['results']['bindings']\n",
    "    for i,j in enumerate(proc_list):\n",
    "        for k,v in j.items():\n",
    "            try:\n",
    "                proc_list[i][k] = v['value']\n",
    "            except:\n",
    "                pass\n",
    "    display(pd.DataFrame(proc_list))\n",
    "except:\n",
    "    pprint.pprint(results)\n",
    "\n"
   ]
  },
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   "outputs": [],
   "source": []
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