pharmgkb.ipynb

{
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      "(8502, 131)\n",
      "id,accessionId,description,formatVersion,history,isAssociated,isPlural,objCls,pediatric,phenotypeCategories,populationPhenotypes,relatedChemicals,score,scoreDetails,sentence,studyParameters,useForCaScoring,connWords1.id,connWords1.resource,connWords1.term,connWords1.termId,drugsConnWord.id,drugsConnWord.resource,drugsConnWord.term,drugsConnWord.termId,literature.id,literature.title,literature._sameAs,literature.authors,literature.crossReferences,literature.journal,literature.month,literature.objCls,literature.page,literature.pediatric,literature.pgkbPublication,literature.pubDate,literature.terms,literature.volume,literature.year,location.id,location.copyNumber,location.diplotypes,location.displayName,location.genePhenotype.id,location.genePhenotype.resource,location.genePhenotype.term,location.genePhenotype.termId,location.genes,location.gpPosition,location.haplotypes,location.linkedObjects,location.refSeqPosition,location.tagGene,location.type,location.variant.objCls,location.variant.id,location.variant.name,metabolizer1.id,metabolizer1.resource,metabolizer1.term,metabolizer1.termId,metabolizer2.id,metabolizer2.resource,metabolizer2.term,metabolizer2.termId,polarity.id,polarity.resource,polarity.term,polarity.termId,populationTerm.id,populationTerm.resource,populationTerm.term,populationTerm.termId,significance.id,significance.resource,significance.term,significance.termId,alleleGenotype,assayType,comparison,objects,cell,phenotypes,connWords2.id,connWords2.resource,connWords2.term,connWords2.termId,phenotypeLinksConnWord.id,phenotypeLinksConnWord.resource,phenotypeLinksConnWord.term,phenotypeLinksConnWord.termId,populationPhenotypeLinksConnWord.id,populationPhenotypeLinksConnWord.resource,populationPhenotypeLinksConnWord.term,populationPhenotypeLinksConnWord.termId,geneSymbol,location.buildVersion,location.chromosomeId,location.chromosomeName,location.refSeqCrossReference.id,location.refSeqCrossReference.resource,location.refSeqCrossReference.resourceId,location.refSeqCrossReference._url,location.rsid,location.variant.symbol,sequenceLocation.id,sequenceLocation.assembly,sequenceLocation.begin,sequenceLocation.end,sequenceLocation.intronicOffset,sequenceLocation.referenceAllele,sequenceLocation.referenceHgvs,sequenceLocation.sequence.id,sequenceLocation.sequence.name,sequenceLocation.sequence.resource,sequenceLocation.sequence.resourceId,sequenceLocation.sequence._url,sequenceLocation.source,sequenceLocation.type,sequenceLocation.variantAlleles,sequenceLocation.variantHgvs,scoringRationale,location.refSeqCrossReference.name,sequenceLocation.altHgvs.c,sequenceLocation.altHgvs.g,sequenceLocation.altHgvs.name,sequenceLocation.altHgvs.p,alleleGroupingDescription,sequenceLocation.altHgvs.p.desc,sequenceLocation.notes\n"
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     "text": [
      "c:\\Users\\trent\\anaconda3\\envs\\Springboard\\lib\\site-packages\\IPython\\core\\interactiveshell.py:3437: DtypeWarning: Columns (38,63,64,65,124,125,126,127,128,129) have mixed types.Specify dtype option on import or set low_memory=False.\n",
      "  exec(code_obj, self.user_global_ns, self.user_ns)\n"
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>accessionId</th>\n",
       "      <th>description</th>\n",
       "      <th>formatVersion</th>\n",
       "      <th>history</th>\n",
       "      <th>isAssociated</th>\n",
       "      <th>isPlural</th>\n",
       "      <th>objCls</th>\n",
       "      <th>pediatric</th>\n",
       "      <th>phenotypeCategories</th>\n",
       "      <th>...</th>\n",
       "      <th>sequenceLocation.variantHgvs</th>\n",
       "      <th>scoringRationale</th>\n",
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       "      <td>PA166145182</td>\n",
       "      <td>Median (+)R,R-tramadol area under the curve wa...</td>\n",
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       "      <td>[{'id': 1450367381, 'date': '2019-01-29T09:19:...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Variant Drug Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 981344088, 'resource': 'Phenotype Cate...</td>\n",
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       "      <th>1</th>\n",
       "      <td>1183684661</td>\n",
       "      <td>PA166144530</td>\n",
       "      <td>Median (+)R,R-tramadol area under the curve wa...</td>\n",
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       "      <td>Variant Drug Annotation</td>\n",
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       "      <th>2</th>\n",
       "      <td>1450042177</td>\n",
       "      <td>PA166181190</td>\n",
       "      <td>Intrinsic clearance was 11.8% that of CYP2D6*1...</td>\n",
       "      <td>1</td>\n",
       "      <td>[{'id': 1450042184, 'date': '2018-11-14T11:30:...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Variant Functional Assay Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 981344088, 'resource': 'Phenotype Cate...</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>982047744</td>\n",
       "      <td>PA166143228</td>\n",
       "      <td>A 2 year old boy with an ultrarapid-metabolize...</td>\n",
       "      <td>1</td>\n",
       "      <td>[]</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Variant Drug Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 981344088, 'resource': 'Phenotype Cate...</td>\n",
       "      <td>...</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1451152848</td>\n",
       "      <td>PA166210941</td>\n",
       "      <td>Healthy volunteers were previously phenotyped ...</td>\n",
       "      <td>2</td>\n",
       "      <td>[]</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Variant Drug Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 981344088, 'resource': 'Phenotype Cate...</td>\n",
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       "<p>5 rows × 131 columns</p>\n",
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       "           id  accessionId                                        description  \\\n",
       "0  1183684657  PA166145182  Median (+)R,R-tramadol area under the curve wa...   \n",
       "1  1183684661  PA166144530  Median (+)R,R-tramadol area under the curve wa...   \n",
       "2  1450042177  PA166181190  Intrinsic clearance was 11.8% that of CYP2D6*1...   \n",
       "3   982047744  PA166143228  A 2 year old boy with an ultrarapid-metabolize...   \n",
       "4  1451152848  PA166210941  Healthy volunteers were previously phenotyped ...   \n",
       "\n",
       "   formatVersion                                            history  \\\n",
       "0              1  [{'id': 1450367381, 'date': '2019-01-29T09:19:...   \n",
       "1              1  [{'id': 1450367377, 'date': '2019-01-29T09:19:...   \n",
       "2              1  [{'id': 1450042184, 'date': '2018-11-14T11:30:...   \n",
       "3              1                                                 []   \n",
       "4              2                                                 []   \n",
       "\n",
       "   isAssociated  isPlural                               objCls  pediatric  \\\n",
       "0          True     False              Variant Drug Annotation      False   \n",
       "1          True     False              Variant Drug Annotation      False   \n",
       "2          True     False  Variant Functional Assay Annotation      False   \n",
       "3          True     False              Variant Drug Annotation      False   \n",
       "4          True     False              Variant Drug Annotation      False   \n",
       "\n",
       "                                 phenotypeCategories  ...  \\\n",
       "0  [{'id': 981344088, 'resource': 'Phenotype Cate...  ...   \n",
       "1  [{'id': 981344088, 'resource': 'Phenotype Cate...  ...   \n",
       "2  [{'id': 981344088, 'resource': 'Phenotype Cate...  ...   \n",
       "3  [{'id': 981344088, 'resource': 'Phenotype Cate...  ...   \n",
       "4  [{'id': 981344088, 'resource': 'Phenotype Cate...  ...   \n",
       "\n",
       "  sequenceLocation.variantHgvs scoringRationale  \\\n",
       "0                          NaN              NaN   \n",
       "1                          NaN              NaN   \n",
       "2                          NaN              NaN   \n",
       "3                          NaN              NaN   \n",
       "4                          NaN              NaN   \n",
       "\n",
       "   location.refSeqCrossReference.name sequenceLocation.altHgvs.c  \\\n",
       "0                                 NaN                        NaN   \n",
       "1                                 NaN                        NaN   \n",
       "2                                 NaN                        NaN   \n",
       "3                                 NaN                        NaN   \n",
       "4                                 NaN                        NaN   \n",
       "\n",
       "  sequenceLocation.altHgvs.g sequenceLocation.altHgvs.name  \\\n",
       "0                        NaN                           NaN   \n",
       "1                        NaN                           NaN   \n",
       "2                        NaN                           NaN   \n",
       "3                        NaN                           NaN   \n",
       "4                        NaN                           NaN   \n",
       "\n",
       "   sequenceLocation.altHgvs.p  alleleGroupingDescription  \\\n",
       "0                         NaN                        NaN   \n",
       "1                         NaN                        NaN   \n",
       "2                         NaN                        NaN   \n",
       "3                         NaN                        NaN   \n",
       "4                         NaN                        NaN   \n",
       "\n",
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       "4                             NaN                    NaN  \n",
       "\n",
       "[5 rows x 131 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
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    }
   ],
   "source": [
    "import requests\n",
    "import json\n",
    "import pandas as pd\n",
    "\n",
    "genes = ['CYP2D6', 'ESR1', 'COMT', \n",
    "         'CYP3A5', 'ABCB1', 'CYP2C19', \n",
    "         'UGT2B7', 'SLC22A16', 'TPMT', \n",
    "         'NR1I2', 'NAT2', 'CYP1A2', \n",
    "         'CYP2C9', 'SULT1A1', 'UGT1A4', \n",
    "         'UGT1A8', 'UGT1A9', 'UGT2B15', \n",
    "         'UGT2B15', 'DPYD', 'TYMS', \n",
    "         'RRM1']\n",
    "\n",
    "# variant annotation API\n",
    "def get_variant_data(genes, url):\n",
    "    # Create an empty DataFrame to hold the data\n",
    "    all_data = pd.DataFrame()\n",
    "\n",
    "    for gene in genes:\n",
    "        \n",
    "        # Make an API request for variant annotation data for the current gene\n",
    "        # Set the parameters for the API request\n",
    "        params = {\n",
    "            \"location.genes.symbol\": gene,\n",
    "            \"view\": \"base\"\n",
    "        }\n",
    "        \n",
    "        try:\n",
    "            # Make the API request\n",
    "            response = requests.get(url, params=params)\n",
    "            \n",
    "             #Parse the JSON response\n",
    "            data = response.json()\n",
    "            \n",
    "            # Convert the JSON response to a Pandas DataFrame\n",
    "            gene_data = pd.json_normalize(data[\"data\"])\n",
    "            \n",
    "            #print dimensions of the DataFrame\n",
    "            print(gene, \":\", gene_data.shape)\n",
    "\n",
    "            # Append the gene data to the master DataFrame\n",
    "            all_data = all_data.append(gene_data)\n",
    "        except:\n",
    "            print(\"Error: API request failed for gene \" + gene)\n",
    "\n",
    "        \n",
    "        \n",
    "    return all_data\n",
    "\n",
    "#all_data = get_variant_data(genes, \"https://api.pharmgkb.org/v1/data/variantAnnotation\")\n",
    "\n",
    "# Write the DataFrame to a CSV file\n",
    "#all_data.to_csv(\"pharmagkb_variant.csv\", index=False)\n",
    "\n",
    "# Load the CSV file into a pandas DataFrame\n",
    "all_data = pd.read_csv('pharmagkb_variant.csv')\n",
    "\n",
    "#print dimensions of the DataFrame\n",
    "print(all_data.shape)\n",
    "\n",
    "print(\",\".join(all_data.columns))\n",
    "\n",
    "all_data.head()\n"
   ]
  },
  {
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       "      <th></th>\n",
       "      <th>id</th>\n",
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       "      <th>alleleGenotype</th>\n",
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       "      <th>sequenceLocation.variantHgvs</th>\n",
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       "      <th>2</th>\n",
       "      <td>1450042177</td>\n",
       "      <td>PA166181190</td>\n",
       "      <td>*10</td>\n",
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       "      <td>or</td>\n",
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       "      <th>3</th>\n",
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       "      <th>4</th>\n",
       "      <td>1451152848</td>\n",
       "      <td>PA166210941</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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      "text/plain": [
       "           id  accessionId alleleGenotype geneSymbol drugsConnWord.term  \\\n",
       "0  1183684657  PA166145182            NaN        NaN                and   \n",
       "1  1183684661  PA166144530            NaN        NaN                and   \n",
       "2  1450042177  PA166181190            *10        NaN                 or   \n",
       "3   982047744  PA166143228           *1xN        NaN                and   \n",
       "4  1451152848  PA166210941            NaN        NaN                NaN   \n",
       "\n",
       "  phenotypes location.variant.symbol sequenceLocation.variantHgvs  \n",
       "0        NaN                     NaN                          NaN  \n",
       "1        NaN                     NaN                          NaN  \n",
       "2        NaN                     NaN                          NaN  \n",
       "3        NaN                     NaN                          NaN  \n",
       "4        NaN                     NaN                          NaN  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
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    }
   ],
   "source": [
    "# Create a list of the columns of interest\n",
    "cols_of_interest = [\"id\",\n",
    "                    \"accessionId\",\n",
    "                    \"alleleGenotype\", \n",
    "                    \"geneSymbol\", \n",
    "                    \"drugsConnWord.term\", \n",
    "                    \"phenotypes\", \n",
    "                    \"location.variant.symbol\", \n",
    "                    \"sequenceLocation.variantHgvs\"]\n",
    "\n",
    "# Use the loc method to keep only the columns of interest\n",
    "all_data_variant = all_data.loc[:, cols_of_interest]\n",
    "\n",
    "# Print the resulting DataFrame\n",
    "all_data_variant.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://api.pharmgkb.org/v1/data/label/\n",
      "(5, 28)\n"
     ]
    },
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>objCls</th>\n",
       "      <th>id</th>\n",
       "      <th>name</th>\n",
       "      <th>alternateDrugAvailable</th>\n",
       "      <th>biomarkerStatus</th>\n",
       "      <th>cancerGenome</th>\n",
       "      <th>crossReferences</th>\n",
       "      <th>dosingInformation</th>\n",
       "      <th>history</th>\n",
       "      <th>labelApplications</th>\n",
       "      <th>...</th>\n",
       "      <th>prescribingMarkdown.html</th>\n",
       "      <th>summaryMarkdown.id</th>\n",
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       "      <th>testing.id</th>\n",
       "      <th>testing.resource</th>\n",
       "      <th>testing.term</th>\n",
       "      <th>testing.termId</th>\n",
       "      <th>textMarkdown.id</th>\n",
       "      <th>textMarkdown.html</th>\n",
       "      <th>fdaPgxAssociation</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Label Annotation</td>\n",
       "      <td>PA166104819</td>\n",
       "      <td>Annotation of FDA Label for tamoxifen and ESR1...</td>\n",
       "      <td>True</td>\n",
       "      <td>On FDA Biomarker List</td>\n",
       "      <td>True</td>\n",
       "      <td>[]</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 1183681483, 'date': '2013-10-25T11:41:...</td>\n",
       "      <td>[{'id': 1449814265, 'onOpenFda': True, 'pgxPre...</td>\n",
       "      <td>...</td>\n",
       "      <td>&lt;p&gt;Excerpt from the tamoxifen (SOLTAMOX) drug ...</td>\n",
       "      <td>1447981618</td>\n",
       "      <td>&lt;p&gt;Tamoxifen (SOLTAMOX) is an anti-estrogen us...</td>\n",
       "      <td>1183672041</td>\n",
       "      <td>Genetic Testing Level</td>\n",
       "      <td>Testing required</td>\n",
       "      <td>geneTestLevel:1183672041</td>\n",
       "      <td>1447981617</td>\n",
       "      <td>&lt;p&gt;Excerpts from the tamoxifen (SOLTAMOX) drug...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Label Annotation</td>\n",
       "      <td>PA166184392</td>\n",
       "      <td>Annotation of Swissmedic Label for tamoxifen a...</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1450815403</td>\n",
       "      <td>&lt;p&gt;The Swiss drug label for tamoxifen (Nolvade...</td>\n",
       "      <td>1183672111</td>\n",
       "      <td>Genetic Testing Level</td>\n",
       "      <td>Actionable PGx</td>\n",
       "      <td>geneTestLevel:1183672111</td>\n",
       "      <td>1450815404</td>\n",
       "      <td>&lt;p&gt;&lt;strong&gt;Please note that the information co...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Label Annotation</td>\n",
       "      <td>PA166170936</td>\n",
       "      <td>Annotation of FDA Label for tamoxifen and F2, F5</td>\n",
       "      <td>False</td>\n",
       "      <td>On FDA Biomarker List</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1449814158, 'onOpenFda': True, 'pgxPre...</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1449052557</td>\n",
       "      <td>&lt;p&gt;Tamoxifen (SOLTAMOX) is indicated for the t...</td>\n",
       "      <td>1183672141</td>\n",
       "      <td>Genetic Testing Level</td>\n",
       "      <td>Informative PGx</td>\n",
       "      <td>geneTestLevel:1183672141</td>\n",
       "      <td>1449052556</td>\n",
       "      <td>&lt;p&gt;Excerpt from the tamoxifen (SOLTAMOX) drug ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Label Annotation</td>\n",
       "      <td>PA166181925</td>\n",
       "      <td>Annotation of FDA Label for tamoxifen and CYP2D6</td>\n",
       "      <td>False</td>\n",
       "      <td>On FDA Biomarker List</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'id': 1450821494, 'date': '2019-10-09T14:37:...</td>\n",
       "      <td>[{'id': 1450369807, 'onOpenFda': True, 'pgxPre...</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1450369804</td>\n",
       "      <td>&lt;p&gt;The FDA-approved drug label for tamoxifen (...</td>\n",
       "      <td>1183672111</td>\n",
       "      <td>Genetic Testing Level</td>\n",
       "      <td>Actionable PGx</td>\n",
       "      <td>geneTestLevel:1183672111</td>\n",
       "      <td>1450369805</td>\n",
       "      <td>&lt;p&gt;Excerpt from the tamoxifen (SOLTAMOX) drug ...</td>\n",
       "      <td>PK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Label Annotation</td>\n",
       "      <td>PA166127718</td>\n",
       "      <td>Annotation of HCSC Label for tamoxifen and CYP...</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>False</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1447982367</td>\n",
       "      <td>&lt;p&gt;The product monograph for tamoxifen states ...</td>\n",
       "      <td>1183672041</td>\n",
       "      <td>Genetic Testing Level</td>\n",
       "      <td>Testing required</td>\n",
       "      <td>geneTestLevel:1183672041</td>\n",
       "      <td>1447982366</td>\n",
       "      <td>&lt;p&gt;Excerpts from the tamoxifen product monogra...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 28 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             objCls           id  \\\n",
       "0  Label Annotation  PA166104819   \n",
       "1  Label Annotation  PA166184392   \n",
       "2  Label Annotation  PA166170936   \n",
       "3  Label Annotation  PA166181925   \n",
       "4  Label Annotation  PA166127718   \n",
       "\n",
       "                                                name  alternateDrugAvailable  \\\n",
       "0  Annotation of FDA Label for tamoxifen and ESR1...                    True   \n",
       "1  Annotation of Swissmedic Label for tamoxifen a...                   False   \n",
       "2   Annotation of FDA Label for tamoxifen and F2, F5                   False   \n",
       "3   Annotation of FDA Label for tamoxifen and CYP2D6                   False   \n",
       "4  Annotation of HCSC Label for tamoxifen and CYP...                   False   \n",
       "\n",
       "         biomarkerStatus  cancerGenome crossReferences  dosingInformation  \\\n",
       "0  On FDA Biomarker List          True              []              False   \n",
       "1                    NaN         False              []              False   \n",
       "2  On FDA Biomarker List         False              []              False   \n",
       "3  On FDA Biomarker List         False              []              False   \n",
       "4                    NaN         False              []              False   \n",
       "\n",
       "                                             history  \\\n",
       "0  [{'id': 1183681483, 'date': '2013-10-25T11:41:...   \n",
       "1                                                 []   \n",
       "2                                                 []   \n",
       "3  [{'id': 1450821494, 'date': '2019-10-09T14:37:...   \n",
       "4                                                 []   \n",
       "\n",
       "                                   labelApplications  ...  \\\n",
       "0  [{'id': 1449814265, 'onOpenFda': True, 'pgxPre...  ...   \n",
       "1                                                 []  ...   \n",
       "2  [{'id': 1449814158, 'onOpenFda': True, 'pgxPre...  ...   \n",
       "3  [{'id': 1450369807, 'onOpenFda': True, 'pgxPre...  ...   \n",
       "4                                                 []  ...   \n",
       "\n",
       "                            prescribingMarkdown.html  summaryMarkdown.id  \\\n",
       "0  <p>Excerpt from the tamoxifen (SOLTAMOX) drug ...          1447981618   \n",
       "1                                                NaN          1450815403   \n",
       "2                                                NaN          1449052557   \n",
       "3                                                NaN          1450369804   \n",
       "4                                                NaN          1447982367   \n",
       "\n",
       "                                summaryMarkdown.html  testing.id  \\\n",
       "0  <p>Tamoxifen (SOLTAMOX) is an anti-estrogen us...  1183672041   \n",
       "1  <p>The Swiss drug label for tamoxifen (Nolvade...  1183672111   \n",
       "2  <p>Tamoxifen (SOLTAMOX) is indicated for the t...  1183672141   \n",
       "3  <p>The FDA-approved drug label for tamoxifen (...  1183672111   \n",
       "4  <p>The product monograph for tamoxifen states ...  1183672041   \n",
       "\n",
       "        testing.resource      testing.term            testing.termId  \\\n",
       "0  Genetic Testing Level  Testing required  geneTestLevel:1183672041   \n",
       "1  Genetic Testing Level    Actionable PGx  geneTestLevel:1183672111   \n",
       "2  Genetic Testing Level   Informative PGx  geneTestLevel:1183672141   \n",
       "3  Genetic Testing Level    Actionable PGx  geneTestLevel:1183672111   \n",
       "4  Genetic Testing Level  Testing required  geneTestLevel:1183672041   \n",
       "\n",
       "   textMarkdown.id                                  textMarkdown.html  \\\n",
       "0       1447981617  <p>Excerpts from the tamoxifen (SOLTAMOX) drug...   \n",
       "1       1450815404  <p><strong>Please note that the information co...   \n",
       "2       1449052556  <p>Excerpt from the tamoxifen (SOLTAMOX) drug ...   \n",
       "3       1450369805  <p>Excerpt from the tamoxifen (SOLTAMOX) drug ...   \n",
       "4       1447982366  <p>Excerpts from the tamoxifen product monogra...   \n",
       "\n",
       "   fdaPgxAssociation  \n",
       "0                NaN  \n",
       "1                NaN  \n",
       "2                NaN  \n",
       "3                 PK  \n",
       "4                NaN  \n",
       "\n",
       "[5 rows x 28 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# drug label annotation API\n",
    "def get_drug_label_data(url):\n",
    "    # Create an empty DataFrame to hold the data\n",
    "    all_data = pd.DataFrame()\n",
    "\n",
    "    #for id in ids:\n",
    "        \n",
    "    #this_url = url + str(id)\n",
    "    this_url = url\n",
    "    print(this_url)\n",
    "        \n",
    "    # Make an API request for variant annotation data for the current gene\n",
    "    # Set the parameters for the API request\n",
    "    params = {\n",
    "        #\"relatedGenes.symbol\": id,\n",
    "        \"relatedChemicals.name\": \"tamoxifen\",\n",
    "        \"view\": \"base\"\n",
    "    }\n",
    "    \n",
    "    try:\n",
    "        # Make the API request\n",
    "        response = requests.get(this_url, params=params)\n",
    "\n",
    "        #Parse the JSON response\n",
    "        data = response.json()\n",
    "        \n",
    "        # Convert the JSON response to a Pandas DataFrame\n",
    "        gene_data = pd.json_normalize(data[\"data\"])\n",
    "        \n",
    "        #print dimensions of the DataFrame\n",
    "        #print(id, \":\", gene_data.shape)\n",
    "\n",
    "        # Append the gene data to the master DataFrame\n",
    "        all_data = all_data.append(gene_data)\n",
    "        \n",
    "    except:\n",
    "        print(\"Error: API request failed for gene \" + str(id))\n",
    "\n",
    "        \n",
    "        \n",
    "    return all_data\n",
    "\n",
    "all_data_drug_label = get_drug_label_data(\"https://api.pharmgkb.org/v1/data/label/\")    \n",
    "\n",
    "# Write the DataFrame to a CSV file\n",
    "all_data_drug_label.to_csv(\"pharmagkb_drug_label.csv\", index=False)\n",
    "\n",
    "#print dimensions of the DataFrame\n",
    "print(all_data_drug_label.shape)\n",
    "\n",
    "all_data_drug_label.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'response' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-11-95cf7eee0132>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mresponse\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtext\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m: name 'response' is not defined"
     ]
    }
   ],
   "source": [
    "response.text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['objCls', 'id', 'name', 'alternateDrugAvailable', 'biomarkerStatus',\n",
       "       'cancerGenome', 'crossReferences', 'dosingInformation',\n",
       "       'fdaPgxAssociation', 'history', 'labelApplications', 'literature',\n",
       "       'pediatric', 'prescribingGenes', 'relatedAlleles', 'relatedChemicals',\n",
       "       'relatedGenes', 'source', 'prescribingMarkdown.id',\n",
       "       'prescribingMarkdown.html', 'summaryMarkdown.id',\n",
       "       'summaryMarkdown.html', 'testing.id', 'testing.resource',\n",
       "       'testing.term', 'testing.termId', 'textMarkdown.id',\n",
       "       'textMarkdown.html', 'pediatricMarkdown.id', 'pediatricMarkdown.html',\n",
       "       'retirementReason.id', 'retirementReason.resource',\n",
       "       'retirementReason.term', 'retirementReason.termId', 'errors'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_data_drug_label.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DataFrame written to output.csv\n",
      "(289, 46)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>accessionId</th>\n",
       "      <th>allelePhenotypes</th>\n",
       "      <th>conflictingVariantAnnotationIds</th>\n",
       "      <th>history</th>\n",
       "      <th>name</th>\n",
       "      <th>objCls</th>\n",
       "      <th>overrideLevel</th>\n",
       "      <th>pediatric</th>\n",
       "      <th>relatedChemicals</th>\n",
       "      <th>...</th>\n",
       "      <th>location.refSeqCrossReference._url</th>\n",
       "      <th>location.refSeqPosition</th>\n",
       "      <th>location.rsid</th>\n",
       "      <th>location.tagGene</th>\n",
       "      <th>location.type</th>\n",
       "      <th>location.variant.objCls</th>\n",
       "      <th>location.variant.id</th>\n",
       "      <th>location.variant.symbol</th>\n",
       "      <th>location.variant.name</th>\n",
       "      <th>overrideLevelDescription</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1445117525</td>\n",
       "      <td>PA166136351</td>\n",
       "      <td>[{'id': 1451333059, 'allele': 'CC', 'limitedEv...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1445117526, 'date': '2015-07-23T14:19:...</td>\n",
       "      <td>Clinical Annotation for rs193922876 (RYR1); de...</td>\n",
       "      <td>Clinical Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>[{'objCls': 'Chemical', 'id': 'PA164749136', '...</td>\n",
       "      <td>...</td>\n",
       "      <td>https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10</td>\n",
       "      <td>38580114</td>\n",
       "      <td>rs193922876</td>\n",
       "      <td>False</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Variant</td>\n",
       "      <td>PA166155575</td>\n",
       "      <td>rs193922876</td>\n",
       "      <td>rs193922876</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1183705788</td>\n",
       "      <td>PA166135464</td>\n",
       "      <td>[{'id': 1451332933, 'allele': 'CC', 'limitedEv...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1447992478, 'date': '2016-05-27T16:43:...</td>\n",
       "      <td>Clinical Annotation for rs118192170 (RYR1); de...</td>\n",
       "      <td>Clinical Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>[{'objCls': 'Chemical', 'id': 'PA164749136', '...</td>\n",
       "      <td>...</td>\n",
       "      <td>https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10</td>\n",
       "      <td>38584989</td>\n",
       "      <td>rs118192170</td>\n",
       "      <td>False</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Variant</td>\n",
       "      <td>PA166155536</td>\n",
       "      <td>rs118192170</td>\n",
       "      <td>rs118192170</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1445400186</td>\n",
       "      <td>PA166135876</td>\n",
       "      <td>[{'id': 1451333191, 'allele': 'AA', 'limitedEv...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1445400187, 'date': '2015-07-30T16:02:...</td>\n",
       "      <td>Clinical Annotation for rs1801086 (RYR1); desf...</td>\n",
       "      <td>Clinical Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>[{'objCls': 'Chemical', 'id': 'PA164749136', '...</td>\n",
       "      <td>...</td>\n",
       "      <td>https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10</td>\n",
       "      <td>38446710</td>\n",
       "      <td>rs1801086</td>\n",
       "      <td>False</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Variant</td>\n",
       "      <td>PA166155375</td>\n",
       "      <td>rs1801086</td>\n",
       "      <td>rs1801086</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1451434920</td>\n",
       "      <td>PA166242001</td>\n",
       "      <td>[{'id': 1451461447, 'allele': 'A', 'limitedEvi...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1451434924, 'date': '2021-05-10T17:03:...</td>\n",
       "      <td>Clinical Annotation for rs267606617 (MT-RNR1);...</td>\n",
       "      <td>Clinical Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>[{'objCls': 'Chemical', 'id': 'PA164744372', '...</td>\n",
       "      <td>...</td>\n",
       "      <td>https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1</td>\n",
       "      <td>1555</td>\n",
       "      <td>rs267606617</td>\n",
       "      <td>False</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Variant</td>\n",
       "      <td>PA166159181</td>\n",
       "      <td>rs267606617</td>\n",
       "      <td>rs267606617</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1445400222</td>\n",
       "      <td>PA166136355</td>\n",
       "      <td>[{'id': 1451333198, 'allele': 'GG', 'limitedEv...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[{'id': 1445400223, 'date': '2015-07-30T16:36:...</td>\n",
       "      <td>Clinical Annotation for rs193922772 (RYR1); de...</td>\n",
       "      <td>Clinical Annotation</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>[{'objCls': 'Chemical', 'id': 'PA164749136', '...</td>\n",
       "      <td>...</td>\n",
       "      <td>https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10</td>\n",
       "      <td>38457546</td>\n",
       "      <td>rs193922772</td>\n",
       "      <td>False</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Variant</td>\n",
       "      <td>PA166155568</td>\n",
       "      <td>rs193922772</td>\n",
       "      <td>rs193922772</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 46 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           id  accessionId                                   allelePhenotypes  \\\n",
       "0  1445117525  PA166136351  [{'id': 1451333059, 'allele': 'CC', 'limitedEv...   \n",
       "1  1183705788  PA166135464  [{'id': 1451332933, 'allele': 'CC', 'limitedEv...   \n",
       "2  1445400186  PA166135876  [{'id': 1451333191, 'allele': 'AA', 'limitedEv...   \n",
       "3  1451434920  PA166242001  [{'id': 1451461447, 'allele': 'A', 'limitedEvi...   \n",
       "4  1445400222  PA166136355  [{'id': 1451333198, 'allele': 'GG', 'limitedEv...   \n",
       "\n",
       "  conflictingVariantAnnotationIds  \\\n",
       "0                              []   \n",
       "1                              []   \n",
       "2                              []   \n",
       "3                              []   \n",
       "4                              []   \n",
       "\n",
       "                                             history  \\\n",
       "0  [{'id': 1445117526, 'date': '2015-07-23T14:19:...   \n",
       "1  [{'id': 1447992478, 'date': '2016-05-27T16:43:...   \n",
       "2  [{'id': 1445400187, 'date': '2015-07-30T16:02:...   \n",
       "3  [{'id': 1451434924, 'date': '2021-05-10T17:03:...   \n",
       "4  [{'id': 1445400223, 'date': '2015-07-30T16:36:...   \n",
       "\n",
       "                                                name               objCls  \\\n",
       "0  Clinical Annotation for rs193922876 (RYR1); de...  Clinical Annotation   \n",
       "1  Clinical Annotation for rs118192170 (RYR1); de...  Clinical Annotation   \n",
       "2  Clinical Annotation for rs1801086 (RYR1); desf...  Clinical Annotation   \n",
       "3  Clinical Annotation for rs267606617 (MT-RNR1);...  Clinical Annotation   \n",
       "4  Clinical Annotation for rs193922772 (RYR1); de...  Clinical Annotation   \n",
       "\n",
       "   overrideLevel  pediatric  \\\n",
       "0          False       True   \n",
       "1          False      False   \n",
       "2          False       True   \n",
       "3          False       True   \n",
       "4          False       True   \n",
       "\n",
       "                                    relatedChemicals  ...  \\\n",
       "0  [{'objCls': 'Chemical', 'id': 'PA164749136', '...  ...   \n",
       "1  [{'objCls': 'Chemical', 'id': 'PA164749136', '...  ...   \n",
       "2  [{'objCls': 'Chemical', 'id': 'PA164749136', '...  ...   \n",
       "3  [{'objCls': 'Chemical', 'id': 'PA164744372', '...  ...   \n",
       "4  [{'objCls': 'Chemical', 'id': 'PA164749136', '...  ...   \n",
       "\n",
       "                  location.refSeqCrossReference._url location.refSeqPosition  \\\n",
       "0  https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10                38580114   \n",
       "1  https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10                38584989   \n",
       "2  https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10                38446710   \n",
       "3   https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1                    1555   \n",
       "4  https://www.ncbi.nlm.nih.gov/nuccore/NC_000019.10                38457546   \n",
       "\n",
       "  location.rsid location.tagGene  location.type location.variant.objCls  \\\n",
       "0   rs193922876            False            SNP                 Variant   \n",
       "1   rs118192170            False            SNP                 Variant   \n",
       "2     rs1801086            False            SNP                 Variant   \n",
       "3   rs267606617            False            SNP                 Variant   \n",
       "4   rs193922772            False            SNP                 Variant   \n",
       "\n",
       "  location.variant.id  location.variant.symbol location.variant.name  \\\n",
       "0         PA166155575              rs193922876           rs193922876   \n",
       "1         PA166155536              rs118192170           rs118192170   \n",
       "2         PA166155375                rs1801086             rs1801086   \n",
       "3         PA166159181              rs267606617           rs267606617   \n",
       "4         PA166155568              rs193922772           rs193922772   \n",
       "\n",
       "  overrideLevelDescription  \n",
       "0                      NaN  \n",
       "1                      NaN  \n",
       "2                      NaN  \n",
       "3                      NaN  \n",
       "4                      NaN  \n",
       "\n",
       "[5 rows x 46 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Set the API endpoint URL\n",
    "url = \"https://api.pharmgkb.org/v1/data/label\"\n",
    "\n",
    "# Set the parameters for the API request\n",
    "params = {\n",
    "    \"levelOfEvidence.term\": \"1A\",\n",
    "    \"view\": \"base\"\n",
    "}\n",
    "\n",
    "# Make the API request\n",
    "response = requests.get(url, params=params)\n",
    "\n",
    "# Parse the JSON response\n",
    "data = response.json()\n",
    "\n",
    "# Normalize the JSON data into a Pandas DataFrame\n",
    "df_clin = pd.json_normalize(data[\"data\"])\n",
    "\n",
    "# Write the DataFrame to a CSV file\n",
    "df_clin.to_csv(\"pharmagkb_clin.csv\", index=False)\n",
    "\n",
    "# Print a confirmation message\n",
    "print(\"DataFrame written to output.csv\")\n",
    "\n",
    "#print dimensions of the DataFrame\n",
    "print(df_clin.shape)\n",
    "\n",
    "df_clin.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['id', 'accessionId', 'allelePhenotypes',\n",
       "       'conflictingVariantAnnotationIds', 'history', 'name', 'objCls',\n",
       "       'overrideLevel', 'pediatric', 'relatedChemicals',\n",
       "       'relatedChemicalsLogic', 'relatedDiseases', 'relatedGuidelines',\n",
       "       'relatedLabels', 'score', 'scoreDetails', 'types', 'levelOfEvidence.id',\n",
       "       'levelOfEvidence.resource', 'levelOfEvidence.term',\n",
       "       'levelOfEvidence.termId', 'location.id', 'location.buildVersion',\n",
       "       'location.chromosomeId', 'location.chromosomeName',\n",
       "       'location.copyNumber', 'location.diplotypes', 'location.displayName',\n",
       "       'location.genes', 'location.gpPosition', 'location.haplotypes',\n",
       "       'location.linkedObjects', 'location.refSeqCrossReference.id',\n",
       "       'location.refSeqCrossReference.name',\n",
       "       'location.refSeqCrossReference.resource',\n",
       "       'location.refSeqCrossReference.resourceId',\n",
       "       'location.refSeqCrossReference._url', 'location.refSeqPosition',\n",
       "       'location.rsid', 'location.tagGene', 'location.type',\n",
       "       'location.variant.objCls', 'location.variant.id',\n",
       "       'location.variant.symbol', 'location.variant.name',\n",
       "       'overrideLevelDescription'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_clin.columns"
   ]
  }
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