examples/dea_workflow.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example: Differentially Expressed Gene Analysis Workflow\n",
    "\n",
    "This notebook provides insights on how to use the tool if you have DEG file.\n",
    "Our current data sources include:\n",
    "* DisGeNet\n",
    "* MolMeDB\n",
    "* OpenTargets\n",
    "* WikiPathways\n",
    "* WikiData\n",
    "* STRING\n",
    "* Bgee"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import modules\n",
    "from pyBiodatafuse import data_loader, id_mapper\n",
    "from pyBiodatafuse.annotators import disgenet, molmedb  # Example with just two resource\n",
    "from pyBiodatafuse.utils import combine_sources"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load the DEA results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>F value</th>\n",
       "      <th>Pr(&gt;F)</th>\n",
       "      <th>FDR(&gt;F)</th>\n",
       "      <th>Log2FC</th>\n",
       "      <th>t.ratio</th>\n",
       "      <th>p.value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000000003</td>\n",
       "      <td>198663.0000</td>\n",
       "      <td>0.07389</td>\n",
       "      <td>0.11995</td>\n",
       "      <td>0.21672</td>\n",
       "      <td>267662.00000</td>\n",
       "      <td>0.10432</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000000005</td>\n",
       "      <td>532116.0000</td>\n",
       "      <td>0.00008</td>\n",
       "      <td>0.00041</td>\n",
       "      <td>-0.34276</td>\n",
       "      <td>-158217.00000</td>\n",
       "      <td>0.69388</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000000419</td>\n",
       "      <td>123704.0000</td>\n",
       "      <td>0.29357</td>\n",
       "      <td>0.36707</td>\n",
       "      <td>-0.03554</td>\n",
       "      <td>-0.68119</td>\n",
       "      <td>0.99364</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000000457</td>\n",
       "      <td>122821.0000</td>\n",
       "      <td>0.29781</td>\n",
       "      <td>0.37146</td>\n",
       "      <td>-0.10078</td>\n",
       "      <td>-168058.00000</td>\n",
       "      <td>0.62915</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000000460</td>\n",
       "      <td>0.7331</td>\n",
       "      <td>0.62400</td>\n",
       "      <td>0.67303</td>\n",
       "      <td>0.25185</td>\n",
       "      <td>134237.00000</td>\n",
       "      <td>0.83158</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        identifier      F value   Pr(>F)  FDR(>F)   Log2FC       t.ratio  \\\n",
       "0  ENSG00000000003  198663.0000  0.07389  0.11995  0.21672  267662.00000   \n",
       "1  ENSG00000000005  532116.0000  0.00008  0.00041 -0.34276 -158217.00000   \n",
       "2  ENSG00000000419  123704.0000  0.29357  0.36707 -0.03554      -0.68119   \n",
       "3  ENSG00000000457  122821.0000  0.29781  0.37146 -0.10078 -168058.00000   \n",
       "4  ENSG00000000460       0.7331  0.62400  0.67303  0.25185  134237.00000   \n",
       "\n",
       "   p.value  \n",
       "0  0.10432  \n",
       "1  0.69388  \n",
       "2  0.99364  \n",
       "3  0.62915  \n",
       "4  0.83158  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_input = data_loader.create_df_from_dea(\"dea_example.xls\")\n",
    "data_input.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Filtering the DEA table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>F value</th>\n",
       "      <th>Pr(&gt;F)</th>\n",
       "      <th>FDR(&gt;F)</th>\n",
       "      <th>Log2FC</th>\n",
       "      <th>t.ratio</th>\n",
       "      <th>p.value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>73</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>168</th>\n",
       "      <td>ENSG00000008226</td>\n",
       "      <td>1751.0</td>\n",
       "      <td>0.11493</td>\n",
       "      <td>0.17170</td>\n",
       "      <td>0.96160</td>\n",
       "      <td>254376.0</td>\n",
       "      <td>0.14795</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>181</th>\n",
       "      <td>ENSG00000008517</td>\n",
       "      <td>240722.0</td>\n",
       "      <td>0.03233</td>\n",
       "      <td>0.06086</td>\n",
       "      <td>-0.77406</td>\n",
       "      <td>-308262.0</td>\n",
       "      <td>0.03358</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>337</th>\n",
       "      <td>ENSG00000021826</td>\n",
       "      <td>189207.0</td>\n",
       "      <td>0.08899</td>\n",
       "      <td>0.13960</td>\n",
       "      <td>0.50922</td>\n",
       "      <td>304276.0</td>\n",
       "      <td>0.04013</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          identifier   F value   Pr(>F)  FDR(>F)   Log2FC   t.ratio  p.value\n",
       "70   ENSG00000005108  169738.0  0.12886  0.18847  0.59097  239599.0  0.20273\n",
       "73   ENSG00000005189  250342.0  0.02632  0.05167  0.70124  335289.0  0.01499\n",
       "168  ENSG00000008226    1751.0  0.11493  0.17170  0.96160  254376.0  0.14795\n",
       "181  ENSG00000008517  240722.0  0.03233  0.06086 -0.77406 -308262.0  0.03358\n",
       "337  ENSG00000021826  189207.0  0.08899  0.13960  0.50922  304276.0  0.04013"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_filtered = data_loader.filter_dea(data_input, column_name=\"FDR(>F)\", min_value=0.05)\n",
    "data_filtered = data_loader.filter_dea(data_filtered, column_name=\"Log2FC\", abs_value=0.5)\n",
    "data_filtered.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Entity resolution using BridgeDB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>identifier.source</th>\n",
       "      <th>target</th>\n",
       "      <th>target.source</th>\n",
       "      <th>F value_dea</th>\n",
       "      <th>Pr(&gt;F)_dea</th>\n",
       "      <th>FDR(&gt;F)_dea</th>\n",
       "      <th>Log2FC_dea</th>\n",
       "      <th>t.ratio_dea</th>\n",
       "      <th>p.value_dea</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>214920_PM_at</td>\n",
       "      <td>Affy</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>Hs.29900.0.S1_3p_at</td>\n",
       "      <td>Affy</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>221981</td>\n",
       "      <td>WikiGenes</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>GO:0016021</td>\n",
       "      <td>Gene Ontology</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>uc064bom.1</td>\n",
       "      <td>UCSC Genome Browser</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        identifier identifier.source               target  \\\n",
       "0  ENSG00000005108           Ensembl         214920_PM_at   \n",
       "1  ENSG00000005108           Ensembl  Hs.29900.0.S1_3p_at   \n",
       "2  ENSG00000005108           Ensembl               221981   \n",
       "3  ENSG00000005108           Ensembl           GO:0016021   \n",
       "4  ENSG00000005108           Ensembl           uc064bom.1   \n",
       "\n",
       "         target.source  F value_dea  Pr(>F)_dea  FDR(>F)_dea  Log2FC_dea  \\\n",
       "0                 Affy     169738.0     0.12886      0.18847     0.59097   \n",
       "1                 Affy     169738.0     0.12886      0.18847     0.59097   \n",
       "2            WikiGenes     169738.0     0.12886      0.18847     0.59097   \n",
       "3        Gene Ontology     169738.0     0.12886      0.18847     0.59097   \n",
       "4  UCSC Genome Browser     169738.0     0.12886      0.18847     0.59097   \n",
       "\n",
       "   t.ratio_dea  p.value_dea  \n",
       "0     239599.0      0.20273  \n",
       "1     239599.0      0.20273  \n",
       "2     239599.0      0.20273  \n",
       "3     239599.0      0.20273  \n",
       "4     239599.0      0.20273  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bridgdb_df, bridgdb_metadata = id_mapper.bridgedb_xref(\n",
    "    identifiers=data_filtered,\n",
    "    input_species=\"Human\",\n",
    "    input_datasource=\"Ensembl\",\n",
    "    output_datasource=\"All\",\n",
    ")\n",
    "bridgdb_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Disease annotating using DisGeNet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>identifier.source</th>\n",
       "      <th>target</th>\n",
       "      <th>target.source</th>\n",
       "      <th>F value_dea</th>\n",
       "      <th>Pr(&gt;F)_dea</th>\n",
       "      <th>FDR(&gt;F)_dea</th>\n",
       "      <th>Log2FC_dea</th>\n",
       "      <th>t.ratio_dea</th>\n",
       "      <th>p.value_dea</th>\n",
       "      <th>DisGeNET</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>221981</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>81691</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000008226</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>9940</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>1751.0</td>\n",
       "      <td>0.11493</td>\n",
       "      <td>0.17170</td>\n",
       "      <td>0.96160</td>\n",
       "      <td>254376.0</td>\n",
       "      <td>0.14795</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000008517</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>9235</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>240722.0</td>\n",
       "      <td>0.03233</td>\n",
       "      <td>0.06086</td>\n",
       "      <td>-0.77406</td>\n",
       "      <td>-308262.0</td>\n",
       "      <td>0.03358</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000021826</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>1373</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>189207.0</td>\n",
       "      <td>0.08899</td>\n",
       "      <td>0.13960</td>\n",
       "      <td>0.50922</td>\n",
       "      <td>304276.0</td>\n",
       "      <td>0.04013</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        identifier identifier.source  target target.source  F value_dea  \\\n",
       "0  ENSG00000005108           Ensembl  221981     NCBI Gene     169738.0   \n",
       "1  ENSG00000005189           Ensembl   81691     NCBI Gene     250342.0   \n",
       "2  ENSG00000008226           Ensembl    9940     NCBI Gene       1751.0   \n",
       "3  ENSG00000008517           Ensembl    9235     NCBI Gene     240722.0   \n",
       "4  ENSG00000021826           Ensembl    1373     NCBI Gene     189207.0   \n",
       "\n",
       "   Pr(>F)_dea  FDR(>F)_dea  Log2FC_dea  t.ratio_dea  p.value_dea  \\\n",
       "0     0.12886      0.18847     0.59097     239599.0      0.20273   \n",
       "1     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "2     0.11493      0.17170     0.96160     254376.0      0.14795   \n",
       "3     0.03233      0.06086    -0.77406    -308262.0      0.03358   \n",
       "4     0.08899      0.13960     0.50922     304276.0      0.04013   \n",
       "\n",
       "                                            DisGeNET  \n",
       "0  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...  \n",
       "1  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...  \n",
       "2  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...  \n",
       "3  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...  \n",
       "4  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "api_key = \"0209751bfa7b6a981a8f5fb5f062313067ecd36c\"  # TODO: add your key\n",
    "params = {\"source\": \"CURATED\", \"format\": \"json\"}  # only curated data\n",
    "disgenet_result, disgenet_metadata = disgenet.get_gene_disease(\n",
    "    bridgedb_df=bridgdb_df, api_key=api_key, params=params\n",
    ")\n",
    "disgenet_result.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'gene_dsi': nan,\n",
       "  'gene_dpi': nan,\n",
       "  'gene_pli': nan,\n",
       "  'protein_class': nan,\n",
       "  'protein_class_name': nan,\n",
       "  'diseaseid': nan,\n",
       "  'disease_name': nan,\n",
       "  'disease_class': nan,\n",
       "  'disease_class_name': nan,\n",
       "  'disease_type': nan,\n",
       "  'disease_semantic_type': nan,\n",
       "  'score': nan,\n",
       "  'ei': nan,\n",
       "  'el': nan,\n",
       "  'year_initial': nan,\n",
       "  'year_final': nan,\n",
       "  'source': nan}]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disgenet_result[\"DisGeNET\"][0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Inhibitors of trasporters encoded by genes annotation by MolMeDB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\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>identifier</th>\n",
       "      <th>identifier.source</th>\n",
       "      <th>target</th>\n",
       "      <th>target.source</th>\n",
       "      <th>F value_dea</th>\n",
       "      <th>Pr(&gt;F)_dea</th>\n",
       "      <th>FDR(&gt;F)_dea</th>\n",
       "      <th>Log2FC_dea</th>\n",
       "      <th>t.ratio_dea</th>\n",
       "      <th>p.value_dea</th>\n",
       "      <th>transporter_inhibitor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>Q9UPZ6</td>\n",
       "      <td>Uniprot-TrEMBL</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>A0A024R390</td>\n",
       "      <td>Uniprot-TrEMBL</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>H3BM72</td>\n",
       "      <td>Uniprot-TrEMBL</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>H3BPB2</td>\n",
       "      <td>Uniprot-TrEMBL</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>H3BQ98</td>\n",
       "      <td>Uniprot-TrEMBL</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        identifier identifier.source      target   target.source  F value_dea  \\\n",
       "0  ENSG00000005108           Ensembl      Q9UPZ6  Uniprot-TrEMBL     169738.0   \n",
       "1  ENSG00000005189           Ensembl  A0A024R390  Uniprot-TrEMBL     250342.0   \n",
       "2  ENSG00000005189           Ensembl      H3BM72  Uniprot-TrEMBL     250342.0   \n",
       "3  ENSG00000005189           Ensembl      H3BPB2  Uniprot-TrEMBL     250342.0   \n",
       "4  ENSG00000005189           Ensembl      H3BQ98  Uniprot-TrEMBL     250342.0   \n",
       "\n",
       "   Pr(>F)_dea  FDR(>F)_dea  Log2FC_dea  t.ratio_dea  p.value_dea  \\\n",
       "0     0.12886      0.18847     0.59097     239599.0      0.20273   \n",
       "1     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "2     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "3     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "4     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "\n",
       "                               transporter_inhibitor  \n",
       "0  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "1  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "2  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "3  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "4  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "inhibitor_df, inhibitor_metadata = molmedb.get_gene_mol_inhibitor(bridgedb_df=bridgdb_df)\n",
    "inhibitor_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'label': nan,\n",
       "  'InChIKey': nan,\n",
       "  'SMILES': nan,\n",
       "  'pubchem_compound_id': nan,\n",
       "  'molmedb_id': nan,\n",
       "  'source_doi': nan,\n",
       "  'source_pmid': nan,\n",
       "  'chebi_id': nan,\n",
       "  'drugbank_id': nan,\n",
       "  'pdb_ligand_id': nan}]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "inhibitor_df[\"transporter_inhibitor\"][72]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Combing all the results into single dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_df = combine_sources([disgenet_result, inhibitor_df])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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>identifier</th>\n",
       "      <th>identifier.source</th>\n",
       "      <th>target</th>\n",
       "      <th>target.source</th>\n",
       "      <th>F value_dea</th>\n",
       "      <th>Pr(&gt;F)_dea</th>\n",
       "      <th>FDR(&gt;F)_dea</th>\n",
       "      <th>Log2FC_dea</th>\n",
       "      <th>t.ratio_dea</th>\n",
       "      <th>p.value_dea</th>\n",
       "      <th>DisGeNET</th>\n",
       "      <th>transporter_inhibitor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000005108</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>221981</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>169738.0</td>\n",
       "      <td>0.12886</td>\n",
       "      <td>0.18847</td>\n",
       "      <td>0.59097</td>\n",
       "      <td>239599.0</td>\n",
       "      <td>0.20273</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000005189</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>81691</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>250342.0</td>\n",
       "      <td>0.02632</td>\n",
       "      <td>0.05167</td>\n",
       "      <td>0.70124</td>\n",
       "      <td>335289.0</td>\n",
       "      <td>0.01499</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000008226</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>9940</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>1751.0</td>\n",
       "      <td>0.11493</td>\n",
       "      <td>0.17170</td>\n",
       "      <td>0.96160</td>\n",
       "      <td>254376.0</td>\n",
       "      <td>0.14795</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000008517</td>\n",
       "      <td>Ensembl</td>\n",
       "      <td>9235</td>\n",
       "      <td>NCBI Gene</td>\n",
       "      <td>240722.0</td>\n",
       "      <td>0.03233</td>\n",
       "      <td>0.06086</td>\n",
       "      <td>-0.77406</td>\n",
       "      <td>-308262.0</td>\n",
       "      <td>0.03358</td>\n",
       "      <td>[{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...</td>\n",
       "      <td>[{'label': nan, 'InChIKey': nan, 'SMILES': nan...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        identifier identifier.source  target target.source  F value_dea  \\\n",
       "0  ENSG00000005108           Ensembl  221981     NCBI Gene     169738.0   \n",
       "1  ENSG00000005189           Ensembl   81691     NCBI Gene     250342.0   \n",
       "2  ENSG00000008226           Ensembl    9940     NCBI Gene       1751.0   \n",
       "3  ENSG00000008517           Ensembl    9235     NCBI Gene     240722.0   \n",
       "\n",
       "   Pr(>F)_dea  FDR(>F)_dea  Log2FC_dea  t.ratio_dea  p.value_dea  \\\n",
       "0     0.12886      0.18847     0.59097     239599.0      0.20273   \n",
       "1     0.02632      0.05167     0.70124     335289.0      0.01499   \n",
       "2     0.11493      0.17170     0.96160     254376.0      0.14795   \n",
       "3     0.03233      0.06086    -0.77406    -308262.0      0.03358   \n",
       "\n",
       "                                            DisGeNET  \\\n",
       "0  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...   \n",
       "1  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...   \n",
       "2  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...   \n",
       "3  [{'gene_dsi': nan, 'gene_dpi': nan, 'gene_pli'...   \n",
       "\n",
       "                               transporter_inhibitor  \n",
       "0  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "1  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "2  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  \n",
       "3  [{'label': nan, 'InChIKey': nan, 'SMILES': nan...  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_df.head(4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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