Rodam_demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                       levelName SetID Identifier WSEntry\n",
      "1  plants                            1    PlantID   plant\n",
      "2   °--samples                       2   SampleID  sample\n",
      "3       ¦--aliquots                  3  AliquotID aliquot\n",
      "4       ¦   ¦--cellwall_metabo       4  AliquotID aliquot\n",
      "5       ¦   ¦--cellwall_metaboFW     5  AliquotID aliquot\n",
      "6       ¦   ¦--activome              6  AliquotID aliquot\n",
      "7       ¦   ¦--plato_hexosesP       10  AliquotID aliquot\n",
      "8       ¦   ¦--lipids_AG            11  AliquotID aliquot\n",
      "9       ¦   °--AminoAcid            12  AliquotID aliquot\n",
      "10      °--pools                     7     PoolID    pool\n",
      "11          ¦--qMS_metabo            8     PoolID    pool\n",
      "12          °--qNMR_metabo           9     PoolID    pool\n",
      "                               Description Count\n",
      "1                           Plant features   552\n",
      "2                          Sample features  1288\n",
      "3                        Aliquots features   530\n",
      "4       Cell wall Compound quantifications    75\n",
      "5  Cell Wall Compound quantifications (FW)    75\n",
      "6                        Activome Features   266\n",
      "7                        Hexoses Phosphate   266\n",
      "8                                Lipids AG    57\n",
      "9                              Amino Acids    69\n",
      "10                Pools of remaining pools   195\n",
      "11             MS Compounds quantification    25\n",
      "12            NMR Compounds quantification    64\n"
     ]
    }
   ],
   "source": [
    "library(Rodam)\n",
    "\n",
    "# Initialize the 'ODAM' object \n",
    "dh <- new('odamws', 'http://pmb-bordeaux.fr/getdata/', 'frim1')\n",
    "\n",
    "# Get the Data Tree\n",
    "show(dh)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'plants'</li>\n",
       "\t<li>'samples'</li>\n",
       "\t<li>'aliquots'</li>\n",
       "\t<li>'cellwall_metabo'</li>\n",
       "\t<li>'cellwall_metaboFW'</li>\n",
       "\t<li>'activome'</li>\n",
       "\t<li>'pools'</li>\n",
       "\t<li>'qMS_metabo'</li>\n",
       "\t<li>'qNMR_metabo'</li>\n",
       "\t<li>'plato_hexosesP'</li>\n",
       "\t<li>'lipids_AG'</li>\n",
       "\t<li>'AminoAcid'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'plants'\n",
       "\\item 'samples'\n",
       "\\item 'aliquots'\n",
       "\\item 'cellwall\\_metabo'\n",
       "\\item 'cellwall\\_metaboFW'\n",
       "\\item 'activome'\n",
       "\\item 'pools'\n",
       "\\item 'qMS\\_metabo'\n",
       "\\item 'qNMR\\_metabo'\n",
       "\\item 'plato\\_hexosesP'\n",
       "\\item 'lipids\\_AG'\n",
       "\\item 'AminoAcid'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'plants'\n",
       "2. 'samples'\n",
       "3. 'aliquots'\n",
       "4. 'cellwall_metabo'\n",
       "5. 'cellwall_metaboFW'\n",
       "6. 'activome'\n",
       "7. 'pools'\n",
       "8. 'qMS_metabo'\n",
       "9. 'qNMR_metabo'\n",
       "10. 'plato_hexosesP'\n",
       "11. 'lipids_AG'\n",
       "12. 'AminoAcid'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"plants\"            \"samples\"           \"aliquots\"         \n",
       " [4] \"cellwall_metabo\"   \"cellwall_metaboFW\" \"activome\"         \n",
       " [7] \"pools\"             \"qMS_metabo\"        \"qNMR_metabo\"      \n",
       "[10] \"plato_hexosesP\"    \"lipids_AG\"         \"AminoAcid\"        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Get the data subsets list\n",
    "dh$subsetNames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.frame: 42 × 6</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Subset</th><th scope=col>Attribute</th><th scope=col>Description</th><th scope=col>Type</th><th scope=col>CV_Term_ID </th><th scope=col>CV_Term_Name</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>activome</td><td>AliquotID      </td><td>Aliquot Identifier                              </td><td>Identifier</td><td>http://edamontology.org/data_0842        </td><td>identifier                                               </td></tr>\n",
       "\t<tr><td>plants  </td><td>Treatment      </td><td>Treatment applied on plants                     </td><td>Factor    </td><td>http://www.ebi.ac.uk/efo/EFO_0000469     </td><td>environmental factor                                     </td></tr>\n",
       "\t<tr><td>samples </td><td>DevStage       </td><td>fruit development stage                         </td><td>Factor    </td><td>http://purl.obolibrary.org/obo/PO_0001002</td><td>fruit development stage                                  </td></tr>\n",
       "\t<tr><td>samples </td><td>FruitAge       </td><td>fruit age (dpa)                                 </td><td>Factor    </td><td>http://purl.obolibrary.org/obo/PO_0001002</td><td>fruit development stage                                  </td></tr>\n",
       "\t<tr><td>activome</td><td>PGM            </td><td>Phosphoglucomutase (nmol/gFW/min)               </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004614</td><td>EC 5.4.2.2 Phosphoglucomutase                            </td></tr>\n",
       "\t<tr><td>activome</td><td>cFBPase        </td><td>cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0042132</td><td>EC 3.1.3.11 fructose-bisphosphatase                      </td></tr>\n",
       "\t<tr><td>activome</td><td>PyrK           </td><td>Pyruvate Kinase (nmol/gFW/min)                  </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004743</td><td>EC 2.7.1.40 pyruvate kinase                              </td></tr>\n",
       "\t<tr><td>activome</td><td>CitS           </td><td>Citrate Synthase Total (nmol/gFW/min)           </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0036440</td><td>EC 2.3.3.1 citrate synthase                              </td></tr>\n",
       "\t<tr><td>activome</td><td>PPI            </td><td>PPI (nmol/gFW/min)                              </td><td>Variable  </td><td>                                         </td><td>                                                         </td></tr>\n",
       "\t<tr><td>activome</td><td>Aconitase      </td><td>Aconitase (nmol/gFW/min)                        </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_000394 </td><td>EC 4.2.1.3 Aconitase                                     </td></tr>\n",
       "\t<tr><td>activome</td><td>PFK            </td><td>ATP-Phosphofructokinase (nmol/gFW/min)          </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0008443</td><td>EC 2.7.1.11 phosphofructokinase                          </td></tr>\n",
       "\t<tr><td>activome</td><td>FruK           </td><td>Fructokinase (nmol/gFW/min)                     </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0008865</td><td>EC 2.7.1.4 fructokinase                                  </td></tr>\n",
       "\t<tr><td>activome</td><td>pFBPase        </td><td>plastidial Fru-1,6-bisphosphatase (nmol/gFW/min)</td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0042132</td><td>EC 3.1.3.11 fructose-bisphosphatase                      </td></tr>\n",
       "\t<tr><td>activome</td><td>GluK           </td><td>Glucokinase (nmol/gFW/min)                      </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004340</td><td>EC 2.7.1.2 Glucokinase                                   </td></tr>\n",
       "\t<tr><td>activome</td><td>NAD_ISODH      </td><td>Isocitrate DH - NADP (nmol/gFW/min)             </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004450</td><td>EC 1.1.1.42 isocitrate dehydrogenase                     </td></tr>\n",
       "\t<tr><td>activome</td><td>Enolase        </td><td>Enolase (nmol/gFW/min)                          </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0000015</td><td>EC 4.2.1.11 Enolase                                      </td></tr>\n",
       "\t<tr><td>activome</td><td>NADP_ISODH     </td><td>Isocitrate DH - NAD (nmol/gFW/min)              </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004448</td><td>EC 1.1.1.41 isocitrate dehydrogenase                     </td></tr>\n",
       "\t<tr><td>activome</td><td>PEPC           </td><td>PEP Carboxylase (nmol/gFW/min)                  </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0008964</td><td>EC 4.1.1.31 PEP Carboxylase                              </td></tr>\n",
       "\t<tr><td>activome</td><td>Aldolase       </td><td>FBP-Aldolase (nmol/gFW/min)                     </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004332</td><td>EC 4.1.2.13 fructose-bisphosphate aldolase               </td></tr>\n",
       "\t<tr><td>activome</td><td>Succ_CoA_ligase</td><td>Succinate CoA ligase (nmol/gFW/min)             </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0042709</td><td>EC 6.2.1.5 Succinate CoA ligase                          </td></tr>\n",
       "\t<tr><td>activome</td><td>NAD_MalDH      </td><td>Malate DH - NAD (nmol/gFW/min)                  </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0016615</td><td>EC 1.1.1.37 malate dehydrogenase                         </td></tr>\n",
       "\t<tr><td>activome</td><td>AlaAT          </td><td>Alanine aminotransferase (nmol/gFW/min)         </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004021</td><td>EC 2.6.1.2 alanine transaminase                          </td></tr>\n",
       "\t<tr><td>activome</td><td>Fumarase       </td><td>Fumarase (nmol/gFW/min)                         </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004333</td><td>EC 4.2.1.2 fumarase                                      </td></tr>\n",
       "\t<tr><td>activome</td><td>AspAT          </td><td>Aspartate aminotransferase (nmol/gFW/min)       </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004069</td><td>EC 2.6.1.1 aspartate aminotransferase                    </td></tr>\n",
       "\t<tr><td>activome</td><td>NADP_GluDH     </td><td>Glutamate DH - NADP (nmol/gFW/min)              </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004354</td><td>EC 1.4.1.4 glutamate dehydrogenase NADP                  </td></tr>\n",
       "\t<tr><td>activome</td><td>NAD_GAPDH      </td><td>GAPDH - NAD (nmol/gFW/min)                      </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004365</td><td>EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD </td></tr>\n",
       "\t<tr><td>activome</td><td>NADP_GAPDH     </td><td>GAPDH - NADP (nmol/gFW/min)                     </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0047100</td><td>EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP</td></tr>\n",
       "\t<tr><td>activome</td><td>NAD_GluDH      </td><td>Glutamate DH - NAD (nmol/gFW/min)               </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004352</td><td>EC 1.4.1.2 glutamate dehydrogenase NAP                   </td></tr>\n",
       "\t<tr><td>activome</td><td>TPI            </td><td>Triose Phosphate Isomerase (nmol/gFW/min)       </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004807</td><td>EC 5.3.1.1 triose-phosphate isomerase                    </td></tr>\n",
       "\t<tr><td>activome</td><td>PGK            </td><td>Phosphoglycerokinase (nmol/gFW/min)             </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004618</td><td>EC 2.7.2.3 phosphoglycerate kinase                       </td></tr>\n",
       "\t<tr><td>activome</td><td>Neutral_Inv    </td><td>Neutral invertase (nmol/gFW/min)                </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004564</td><td>EC 3.2.1.26 invertase                                    </td></tr>\n",
       "\t<tr><td>activome</td><td>Acid_Inv       </td><td>Acid invertase (nmol/gFW/min)                   </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004564</td><td>EC 3.2.1.26 invertase                                    </td></tr>\n",
       "\t<tr><td>activome</td><td>G6PDH          </td><td>Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min)</td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004345</td><td>EC 1.1.1.49 glucose-6-phosphate dehydrogenase            </td></tr>\n",
       "\t<tr><td>activome</td><td>UGPase         </td><td>UDP-Glucose Pyrophosphorylase (nmol/gFW/min)    </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0003983</td><td>EC 2.7.7.9 UDPG phosphorylase                            </td></tr>\n",
       "\t<tr><td>activome</td><td>SuSy           </td><td>Sucrose Synthase (nmol/gFW/min)                 </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0016157</td><td>EC 2.4.1.13 sucrose synthase                             </td></tr>\n",
       "\t<tr><td>activome</td><td>NAD_ME         </td><td>Malic Enzyme NAD (nmol/gFW/min)                 </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0009763</td><td>EC 1.1.1.38 NAD+-malic enzyme                            </td></tr>\n",
       "\t<tr><td>activome</td><td>ShiDH          </td><td>Shikimate dehydrogenase (nmol/gFW/min)          </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0033706</td><td>EC 1.1.1.282 shikimate dehydrogenase                     </td></tr>\n",
       "\t<tr><td>activome</td><td>NADP_ME        </td><td>Malic Enzyme NADP (nmol/gFW/min)                </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0009762</td><td>EC 1.1.1.40 NADP+-malic enzyme                           </td></tr>\n",
       "\t<tr><td>activome</td><td>PGI            </td><td>Phosphoglucose Isomerase (nmol/gFW/min)         </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0004347</td><td>EC 5.3.1.9 phosphohexose isomerase                       </td></tr>\n",
       "\t<tr><td>activome</td><td>StarchS        </td><td>Soluble Starch Synthase (nmol/gFW/min)          </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0009011</td><td>EC 2.4.1.21 starch synthase                              </td></tr>\n",
       "\t<tr><td>activome</td><td>AGPase         </td><td>AGPase (nmol/gFW/min)                           </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0080042</td><td>EC 2.7.7.27 ADP-glucose synthase                         </td></tr>\n",
       "\t<tr><td>activome</td><td>SPS            </td><td>Sucrose Phosphate Synthase (nmol/gFW/min)       </td><td>Variable  </td><td>http://purl.obolibrary.org/obo/GO_0046524</td><td>EC 2.4.1.14 sucrose-phosphate synthase                   </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 42 × 6\n",
       "\\begin{tabular}{llllll}\n",
       " Subset & Attribute & Description & Type & CV\\_Term\\_ID  & CV\\_Term\\_Name\\\\\n",
       " <chr> & <chr> & <chr> & <chr> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t activome & AliquotID       & Aliquot Identifier                               & Identifier & http://edamontology.org/data\\_0842         & identifier                                               \\\\\n",
       "\t plants   & Treatment       & Treatment applied on plants                      & Factor     & http://www.ebi.ac.uk/efo/EFO\\_0000469      & environmental factor                                     \\\\\n",
       "\t samples  & DevStage        & fruit development stage                          & Factor     & http://purl.obolibrary.org/obo/PO\\_0001002 & fruit development stage                                  \\\\\n",
       "\t samples  & FruitAge        & fruit age (dpa)                                  & Factor     & http://purl.obolibrary.org/obo/PO\\_0001002 & fruit development stage                                  \\\\\n",
       "\t activome & PGM             & Phosphoglucomutase (nmol/gFW/min)                & Variable   & http://purl.obolibrary.org/obo/GO\\_0004614 & EC 5.4.2.2 Phosphoglucomutase                            \\\\\n",
       "\t activome & cFBPase         & cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min)  & Variable   & http://purl.obolibrary.org/obo/GO\\_0042132 & EC 3.1.3.11 fructose-bisphosphatase                      \\\\\n",
       "\t activome & PyrK            & Pyruvate Kinase (nmol/gFW/min)                   & Variable   & http://purl.obolibrary.org/obo/GO\\_0004743 & EC 2.7.1.40 pyruvate kinase                              \\\\\n",
       "\t activome & CitS            & Citrate Synthase Total (nmol/gFW/min)            & Variable   & http://purl.obolibrary.org/obo/GO\\_0036440 & EC 2.3.3.1 citrate synthase                              \\\\\n",
       "\t activome & PPI             & PPI (nmol/gFW/min)                               & Variable   &                                           &                                                          \\\\\n",
       "\t activome & Aconitase       & Aconitase (nmol/gFW/min)                         & Variable   & http://purl.obolibrary.org/obo/GO\\_000394  & EC 4.2.1.3 Aconitase                                     \\\\\n",
       "\t activome & PFK             & ATP-Phosphofructokinase (nmol/gFW/min)           & Variable   & http://purl.obolibrary.org/obo/GO\\_0008443 & EC 2.7.1.11 phosphofructokinase                          \\\\\n",
       "\t activome & FruK            & Fructokinase (nmol/gFW/min)                      & Variable   & http://purl.obolibrary.org/obo/GO\\_0008865 & EC 2.7.1.4 fructokinase                                  \\\\\n",
       "\t activome & pFBPase         & plastidial Fru-1,6-bisphosphatase (nmol/gFW/min) & Variable   & http://purl.obolibrary.org/obo/GO\\_0042132 & EC 3.1.3.11 fructose-bisphosphatase                      \\\\\n",
       "\t activome & GluK            & Glucokinase (nmol/gFW/min)                       & Variable   & http://purl.obolibrary.org/obo/GO\\_0004340 & EC 2.7.1.2 Glucokinase                                   \\\\\n",
       "\t activome & NAD\\_ISODH       & Isocitrate DH - NADP (nmol/gFW/min)              & Variable   & http://purl.obolibrary.org/obo/GO\\_0004450 & EC 1.1.1.42 isocitrate dehydrogenase                     \\\\\n",
       "\t activome & Enolase         & Enolase (nmol/gFW/min)                           & Variable   & http://purl.obolibrary.org/obo/GO\\_0000015 & EC 4.2.1.11 Enolase                                      \\\\\n",
       "\t activome & NADP\\_ISODH      & Isocitrate DH - NAD (nmol/gFW/min)               & Variable   & http://purl.obolibrary.org/obo/GO\\_0004448 & EC 1.1.1.41 isocitrate dehydrogenase                     \\\\\n",
       "\t activome & PEPC            & PEP Carboxylase (nmol/gFW/min)                   & Variable   & http://purl.obolibrary.org/obo/GO\\_0008964 & EC 4.1.1.31 PEP Carboxylase                              \\\\\n",
       "\t activome & Aldolase        & FBP-Aldolase (nmol/gFW/min)                      & Variable   & http://purl.obolibrary.org/obo/GO\\_0004332 & EC 4.1.2.13 fructose-bisphosphate aldolase               \\\\\n",
       "\t activome & Succ\\_CoA\\_ligase & Succinate CoA ligase (nmol/gFW/min)              & Variable   & http://purl.obolibrary.org/obo/GO\\_0042709 & EC 6.2.1.5 Succinate CoA ligase                          \\\\\n",
       "\t activome & NAD\\_MalDH       & Malate DH - NAD (nmol/gFW/min)                   & Variable   & http://purl.obolibrary.org/obo/GO\\_0016615 & EC 1.1.1.37 malate dehydrogenase                         \\\\\n",
       "\t activome & AlaAT           & Alanine aminotransferase (nmol/gFW/min)          & Variable   & http://purl.obolibrary.org/obo/GO\\_0004021 & EC 2.6.1.2 alanine transaminase                          \\\\\n",
       "\t activome & Fumarase        & Fumarase (nmol/gFW/min)                          & Variable   & http://purl.obolibrary.org/obo/GO\\_0004333 & EC 4.2.1.2 fumarase                                      \\\\\n",
       "\t activome & AspAT           & Aspartate aminotransferase (nmol/gFW/min)        & Variable   & http://purl.obolibrary.org/obo/GO\\_0004069 & EC 2.6.1.1 aspartate aminotransferase                    \\\\\n",
       "\t activome & NADP\\_GluDH      & Glutamate DH - NADP (nmol/gFW/min)               & Variable   & http://purl.obolibrary.org/obo/GO\\_0004354 & EC 1.4.1.4 glutamate dehydrogenase NADP                  \\\\\n",
       "\t activome & NAD\\_GAPDH       & GAPDH - NAD (nmol/gFW/min)                       & Variable   & http://purl.obolibrary.org/obo/GO\\_0004365 & EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD \\\\\n",
       "\t activome & NADP\\_GAPDH      & GAPDH - NADP (nmol/gFW/min)                      & Variable   & http://purl.obolibrary.org/obo/GO\\_0047100 & EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP\\\\\n",
       "\t activome & NAD\\_GluDH       & Glutamate DH - NAD (nmol/gFW/min)                & Variable   & http://purl.obolibrary.org/obo/GO\\_0004352 & EC 1.4.1.2 glutamate dehydrogenase NAP                   \\\\\n",
       "\t activome & TPI             & Triose Phosphate Isomerase (nmol/gFW/min)        & Variable   & http://purl.obolibrary.org/obo/GO\\_0004807 & EC 5.3.1.1 triose-phosphate isomerase                    \\\\\n",
       "\t activome & PGK             & Phosphoglycerokinase (nmol/gFW/min)              & Variable   & http://purl.obolibrary.org/obo/GO\\_0004618 & EC 2.7.2.3 phosphoglycerate kinase                       \\\\\n",
       "\t activome & Neutral\\_Inv     & Neutral invertase (nmol/gFW/min)                 & Variable   & http://purl.obolibrary.org/obo/GO\\_0004564 & EC 3.2.1.26 invertase                                    \\\\\n",
       "\t activome & Acid\\_Inv        & Acid invertase (nmol/gFW/min)                    & Variable   & http://purl.obolibrary.org/obo/GO\\_0004564 & EC 3.2.1.26 invertase                                    \\\\\n",
       "\t activome & G6PDH           & Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min) & Variable   & http://purl.obolibrary.org/obo/GO\\_0004345 & EC 1.1.1.49 glucose-6-phosphate dehydrogenase            \\\\\n",
       "\t activome & UGPase          & UDP-Glucose Pyrophosphorylase (nmol/gFW/min)     & Variable   & http://purl.obolibrary.org/obo/GO\\_0003983 & EC 2.7.7.9 UDPG phosphorylase                            \\\\\n",
       "\t activome & SuSy            & Sucrose Synthase (nmol/gFW/min)                  & Variable   & http://purl.obolibrary.org/obo/GO\\_0016157 & EC 2.4.1.13 sucrose synthase                             \\\\\n",
       "\t activome & NAD\\_ME          & Malic Enzyme NAD (nmol/gFW/min)                  & Variable   & http://purl.obolibrary.org/obo/GO\\_0009763 & EC 1.1.1.38 NAD+-malic enzyme                            \\\\\n",
       "\t activome & ShiDH           & Shikimate dehydrogenase (nmol/gFW/min)           & Variable   & http://purl.obolibrary.org/obo/GO\\_0033706 & EC 1.1.1.282 shikimate dehydrogenase                     \\\\\n",
       "\t activome & NADP\\_ME         & Malic Enzyme NADP (nmol/gFW/min)                 & Variable   & http://purl.obolibrary.org/obo/GO\\_0009762 & EC 1.1.1.40 NADP+-malic enzyme                           \\\\\n",
       "\t activome & PGI             & Phosphoglucose Isomerase (nmol/gFW/min)          & Variable   & http://purl.obolibrary.org/obo/GO\\_0004347 & EC 5.3.1.9 phosphohexose isomerase                       \\\\\n",
       "\t activome & StarchS         & Soluble Starch Synthase (nmol/gFW/min)           & Variable   & http://purl.obolibrary.org/obo/GO\\_0009011 & EC 2.4.1.21 starch synthase                              \\\\\n",
       "\t activome & AGPase          & AGPase (nmol/gFW/min)                            & Variable   & http://purl.obolibrary.org/obo/GO\\_0080042 & EC 2.7.7.27 ADP-glucose synthase                         \\\\\n",
       "\t activome & SPS             & Sucrose Phosphate Synthase (nmol/gFW/min)        & Variable   & http://purl.obolibrary.org/obo/GO\\_0046524 & EC 2.4.1.14 sucrose-phosphate synthase                   \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 42 × 6\n",
       "\n",
       "| Subset &lt;chr&gt; | Attribute &lt;chr&gt; | Description &lt;chr&gt; | Type &lt;chr&gt; | CV_Term_ID  &lt;chr&gt; | CV_Term_Name &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|\n",
       "| activome | AliquotID       | Aliquot Identifier                               | Identifier | http://edamontology.org/data_0842         | identifier                                                |\n",
       "| plants   | Treatment       | Treatment applied on plants                      | Factor     | http://www.ebi.ac.uk/efo/EFO_0000469      | environmental factor                                      |\n",
       "| samples  | DevStage        | fruit development stage                          | Factor     | http://purl.obolibrary.org/obo/PO_0001002 | fruit development stage                                   |\n",
       "| samples  | FruitAge        | fruit age (dpa)                                  | Factor     | http://purl.obolibrary.org/obo/PO_0001002 | fruit development stage                                   |\n",
       "| activome | PGM             | Phosphoglucomutase (nmol/gFW/min)                | Variable   | http://purl.obolibrary.org/obo/GO_0004614 | EC 5.4.2.2 Phosphoglucomutase                             |\n",
       "| activome | cFBPase         | cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min)  | Variable   | http://purl.obolibrary.org/obo/GO_0042132 | EC 3.1.3.11 fructose-bisphosphatase                       |\n",
       "| activome | PyrK            | Pyruvate Kinase (nmol/gFW/min)                   | Variable   | http://purl.obolibrary.org/obo/GO_0004743 | EC 2.7.1.40 pyruvate kinase                               |\n",
       "| activome | CitS            | Citrate Synthase Total (nmol/gFW/min)            | Variable   | http://purl.obolibrary.org/obo/GO_0036440 | EC 2.3.3.1 citrate synthase                               |\n",
       "| activome | PPI             | PPI (nmol/gFW/min)                               | Variable   | <!----> | <!----> |\n",
       "| activome | Aconitase       | Aconitase (nmol/gFW/min)                         | Variable   | http://purl.obolibrary.org/obo/GO_000394  | EC 4.2.1.3 Aconitase                                      |\n",
       "| activome | PFK             | ATP-Phosphofructokinase (nmol/gFW/min)           | Variable   | http://purl.obolibrary.org/obo/GO_0008443 | EC 2.7.1.11 phosphofructokinase                           |\n",
       "| activome | FruK            | Fructokinase (nmol/gFW/min)                      | Variable   | http://purl.obolibrary.org/obo/GO_0008865 | EC 2.7.1.4 fructokinase                                   |\n",
       "| activome | pFBPase         | plastidial Fru-1,6-bisphosphatase (nmol/gFW/min) | Variable   | http://purl.obolibrary.org/obo/GO_0042132 | EC 3.1.3.11 fructose-bisphosphatase                       |\n",
       "| activome | GluK            | Glucokinase (nmol/gFW/min)                       | Variable   | http://purl.obolibrary.org/obo/GO_0004340 | EC 2.7.1.2 Glucokinase                                    |\n",
       "| activome | NAD_ISODH       | Isocitrate DH - NADP (nmol/gFW/min)              | Variable   | http://purl.obolibrary.org/obo/GO_0004450 | EC 1.1.1.42 isocitrate dehydrogenase                      |\n",
       "| activome | Enolase         | Enolase (nmol/gFW/min)                           | Variable   | http://purl.obolibrary.org/obo/GO_0000015 | EC 4.2.1.11 Enolase                                       |\n",
       "| activome | NADP_ISODH      | Isocitrate DH - NAD (nmol/gFW/min)               | Variable   | http://purl.obolibrary.org/obo/GO_0004448 | EC 1.1.1.41 isocitrate dehydrogenase                      |\n",
       "| activome | PEPC            | PEP Carboxylase (nmol/gFW/min)                   | Variable   | http://purl.obolibrary.org/obo/GO_0008964 | EC 4.1.1.31 PEP Carboxylase                               |\n",
       "| activome | Aldolase        | FBP-Aldolase (nmol/gFW/min)                      | Variable   | http://purl.obolibrary.org/obo/GO_0004332 | EC 4.1.2.13 fructose-bisphosphate aldolase                |\n",
       "| activome | Succ_CoA_ligase | Succinate CoA ligase (nmol/gFW/min)              | Variable   | http://purl.obolibrary.org/obo/GO_0042709 | EC 6.2.1.5 Succinate CoA ligase                           |\n",
       "| activome | NAD_MalDH       | Malate DH - NAD (nmol/gFW/min)                   | Variable   | http://purl.obolibrary.org/obo/GO_0016615 | EC 1.1.1.37 malate dehydrogenase                          |\n",
       "| activome | AlaAT           | Alanine aminotransferase (nmol/gFW/min)          | Variable   | http://purl.obolibrary.org/obo/GO_0004021 | EC 2.6.1.2 alanine transaminase                           |\n",
       "| activome | Fumarase        | Fumarase (nmol/gFW/min)                          | Variable   | http://purl.obolibrary.org/obo/GO_0004333 | EC 4.2.1.2 fumarase                                       |\n",
       "| activome | AspAT           | Aspartate aminotransferase (nmol/gFW/min)        | Variable   | http://purl.obolibrary.org/obo/GO_0004069 | EC 2.6.1.1 aspartate aminotransferase                     |\n",
       "| activome | NADP_GluDH      | Glutamate DH - NADP (nmol/gFW/min)               | Variable   | http://purl.obolibrary.org/obo/GO_0004354 | EC 1.4.1.4 glutamate dehydrogenase NADP                   |\n",
       "| activome | NAD_GAPDH       | GAPDH - NAD (nmol/gFW/min)                       | Variable   | http://purl.obolibrary.org/obo/GO_0004365 | EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD  |\n",
       "| activome | NADP_GAPDH      | GAPDH - NADP (nmol/gFW/min)                      | Variable   | http://purl.obolibrary.org/obo/GO_0047100 | EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP |\n",
       "| activome | NAD_GluDH       | Glutamate DH - NAD (nmol/gFW/min)                | Variable   | http://purl.obolibrary.org/obo/GO_0004352 | EC 1.4.1.2 glutamate dehydrogenase NAP                    |\n",
       "| activome | TPI             | Triose Phosphate Isomerase (nmol/gFW/min)        | Variable   | http://purl.obolibrary.org/obo/GO_0004807 | EC 5.3.1.1 triose-phosphate isomerase                     |\n",
       "| activome | PGK             | Phosphoglycerokinase (nmol/gFW/min)              | Variable   | http://purl.obolibrary.org/obo/GO_0004618 | EC 2.7.2.3 phosphoglycerate kinase                        |\n",
       "| activome | Neutral_Inv     | Neutral invertase (nmol/gFW/min)                 | Variable   | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase                                     |\n",
       "| activome | Acid_Inv        | Acid invertase (nmol/gFW/min)                    | Variable   | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase                                     |\n",
       "| activome | G6PDH           | Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min) | Variable   | http://purl.obolibrary.org/obo/GO_0004345 | EC 1.1.1.49 glucose-6-phosphate dehydrogenase             |\n",
       "| activome | UGPase          | UDP-Glucose Pyrophosphorylase (nmol/gFW/min)     | Variable   | http://purl.obolibrary.org/obo/GO_0003983 | EC 2.7.7.9 UDPG phosphorylase                             |\n",
       "| activome | SuSy            | Sucrose Synthase (nmol/gFW/min)                  | Variable   | http://purl.obolibrary.org/obo/GO_0016157 | EC 2.4.1.13 sucrose synthase                              |\n",
       "| activome | NAD_ME          | Malic Enzyme NAD (nmol/gFW/min)                  | Variable   | http://purl.obolibrary.org/obo/GO_0009763 | EC 1.1.1.38 NAD+-malic enzyme                             |\n",
       "| activome | ShiDH           | Shikimate dehydrogenase (nmol/gFW/min)           | Variable   | http://purl.obolibrary.org/obo/GO_0033706 | EC 1.1.1.282 shikimate dehydrogenase                      |\n",
       "| activome | NADP_ME         | Malic Enzyme NADP (nmol/gFW/min)                 | Variable   | http://purl.obolibrary.org/obo/GO_0009762 | EC 1.1.1.40 NADP+-malic enzyme                            |\n",
       "| activome | PGI             | Phosphoglucose Isomerase (nmol/gFW/min)          | Variable   | http://purl.obolibrary.org/obo/GO_0004347 | EC 5.3.1.9 phosphohexose isomerase                        |\n",
       "| activome | StarchS         | Soluble Starch Synthase (nmol/gFW/min)           | Variable   | http://purl.obolibrary.org/obo/GO_0009011 | EC 2.4.1.21 starch synthase                               |\n",
       "| activome | AGPase          | AGPase (nmol/gFW/min)                            | Variable   | http://purl.obolibrary.org/obo/GO_0080042 | EC 2.7.7.27 ADP-glucose synthase                          |\n",
       "| activome | SPS             | Sucrose Phosphate Synthase (nmol/gFW/min)        | Variable   | http://purl.obolibrary.org/obo/GO_0046524 | EC 2.4.1.14 sucrose-phosphate synthase                    |\n",
       "\n"
      ],
      "text/plain": [
       "   Subset   Attribute       Description                                     \n",
       "1  activome AliquotID       Aliquot Identifier                              \n",
       "2  plants   Treatment       Treatment applied on plants                     \n",
       "3  samples  DevStage        fruit development stage                         \n",
       "4  samples  FruitAge        fruit age (dpa)                                 \n",
       "5  activome PGM             Phosphoglucomutase (nmol/gFW/min)               \n",
       "6  activome cFBPase         cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) \n",
       "7  activome PyrK            Pyruvate Kinase (nmol/gFW/min)                  \n",
       "8  activome CitS            Citrate Synthase Total (nmol/gFW/min)           \n",
       "9  activome PPI             PPI (nmol/gFW/min)                              \n",
       "10 activome Aconitase       Aconitase (nmol/gFW/min)                        \n",
       "11 activome PFK             ATP-Phosphofructokinase (nmol/gFW/min)          \n",
       "12 activome FruK            Fructokinase (nmol/gFW/min)                     \n",
       "13 activome pFBPase         plastidial Fru-1,6-bisphosphatase (nmol/gFW/min)\n",
       "14 activome GluK            Glucokinase (nmol/gFW/min)                      \n",
       "15 activome NAD_ISODH       Isocitrate DH - NADP (nmol/gFW/min)             \n",
       "16 activome Enolase         Enolase (nmol/gFW/min)                          \n",
       "17 activome NADP_ISODH      Isocitrate DH - NAD (nmol/gFW/min)              \n",
       "18 activome PEPC            PEP Carboxylase (nmol/gFW/min)                  \n",
       "19 activome Aldolase        FBP-Aldolase (nmol/gFW/min)                     \n",
       "20 activome Succ_CoA_ligase Succinate CoA ligase (nmol/gFW/min)             \n",
       "21 activome NAD_MalDH       Malate DH - NAD (nmol/gFW/min)                  \n",
       "22 activome AlaAT           Alanine aminotransferase (nmol/gFW/min)         \n",
       "23 activome Fumarase        Fumarase (nmol/gFW/min)                         \n",
       "24 activome AspAT           Aspartate aminotransferase (nmol/gFW/min)       \n",
       "25 activome NADP_GluDH      Glutamate DH - NADP (nmol/gFW/min)              \n",
       "26 activome NAD_GAPDH       GAPDH - NAD (nmol/gFW/min)                      \n",
       "27 activome NADP_GAPDH      GAPDH - NADP (nmol/gFW/min)                     \n",
       "28 activome NAD_GluDH       Glutamate DH - NAD (nmol/gFW/min)               \n",
       "29 activome TPI             Triose Phosphate Isomerase (nmol/gFW/min)       \n",
       "30 activome PGK             Phosphoglycerokinase (nmol/gFW/min)             \n",
       "31 activome Neutral_Inv     Neutral invertase (nmol/gFW/min)                \n",
       "32 activome Acid_Inv        Acid invertase (nmol/gFW/min)                   \n",
       "33 activome G6PDH           Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min)\n",
       "34 activome UGPase          UDP-Glucose Pyrophosphorylase (nmol/gFW/min)    \n",
       "35 activome SuSy            Sucrose Synthase (nmol/gFW/min)                 \n",
       "36 activome NAD_ME          Malic Enzyme NAD (nmol/gFW/min)                 \n",
       "37 activome ShiDH           Shikimate dehydrogenase (nmol/gFW/min)          \n",
       "38 activome NADP_ME         Malic Enzyme NADP (nmol/gFW/min)                \n",
       "39 activome PGI             Phosphoglucose Isomerase (nmol/gFW/min)         \n",
       "40 activome StarchS         Soluble Starch Synthase (nmol/gFW/min)          \n",
       "41 activome AGPase          AGPase (nmol/gFW/min)                           \n",
       "42 activome SPS             Sucrose Phosphate Synthase (nmol/gFW/min)       \n",
       "   Type       CV_Term_ID                               \n",
       "1  Identifier http://edamontology.org/data_0842        \n",
       "2  Factor     http://www.ebi.ac.uk/efo/EFO_0000469     \n",
       "3  Factor     http://purl.obolibrary.org/obo/PO_0001002\n",
       "4  Factor     http://purl.obolibrary.org/obo/PO_0001002\n",
       "5  Variable   http://purl.obolibrary.org/obo/GO_0004614\n",
       "6  Variable   http://purl.obolibrary.org/obo/GO_0042132\n",
       "7  Variable   http://purl.obolibrary.org/obo/GO_0004743\n",
       "8  Variable   http://purl.obolibrary.org/obo/GO_0036440\n",
       "9  Variable                                            \n",
       "10 Variable   http://purl.obolibrary.org/obo/GO_000394 \n",
       "11 Variable   http://purl.obolibrary.org/obo/GO_0008443\n",
       "12 Variable   http://purl.obolibrary.org/obo/GO_0008865\n",
       "13 Variable   http://purl.obolibrary.org/obo/GO_0042132\n",
       "14 Variable   http://purl.obolibrary.org/obo/GO_0004340\n",
       "15 Variable   http://purl.obolibrary.org/obo/GO_0004450\n",
       "16 Variable   http://purl.obolibrary.org/obo/GO_0000015\n",
       "17 Variable   http://purl.obolibrary.org/obo/GO_0004448\n",
       "18 Variable   http://purl.obolibrary.org/obo/GO_0008964\n",
       "19 Variable   http://purl.obolibrary.org/obo/GO_0004332\n",
       "20 Variable   http://purl.obolibrary.org/obo/GO_0042709\n",
       "21 Variable   http://purl.obolibrary.org/obo/GO_0016615\n",
       "22 Variable   http://purl.obolibrary.org/obo/GO_0004021\n",
       "23 Variable   http://purl.obolibrary.org/obo/GO_0004333\n",
       "24 Variable   http://purl.obolibrary.org/obo/GO_0004069\n",
       "25 Variable   http://purl.obolibrary.org/obo/GO_0004354\n",
       "26 Variable   http://purl.obolibrary.org/obo/GO_0004365\n",
       "27 Variable   http://purl.obolibrary.org/obo/GO_0047100\n",
       "28 Variable   http://purl.obolibrary.org/obo/GO_0004352\n",
       "29 Variable   http://purl.obolibrary.org/obo/GO_0004807\n",
       "30 Variable   http://purl.obolibrary.org/obo/GO_0004618\n",
       "31 Variable   http://purl.obolibrary.org/obo/GO_0004564\n",
       "32 Variable   http://purl.obolibrary.org/obo/GO_0004564\n",
       "33 Variable   http://purl.obolibrary.org/obo/GO_0004345\n",
       "34 Variable   http://purl.obolibrary.org/obo/GO_0003983\n",
       "35 Variable   http://purl.obolibrary.org/obo/GO_0016157\n",
       "36 Variable   http://purl.obolibrary.org/obo/GO_0009763\n",
       "37 Variable   http://purl.obolibrary.org/obo/GO_0033706\n",
       "38 Variable   http://purl.obolibrary.org/obo/GO_0009762\n",
       "39 Variable   http://purl.obolibrary.org/obo/GO_0004347\n",
       "40 Variable   http://purl.obolibrary.org/obo/GO_0009011\n",
       "41 Variable   http://purl.obolibrary.org/obo/GO_0080042\n",
       "42 Variable   http://purl.obolibrary.org/obo/GO_0046524\n",
       "   CV_Term_Name                                             \n",
       "1  identifier                                               \n",
       "2  environmental factor                                     \n",
       "3  fruit development stage                                  \n",
       "4  fruit development stage                                  \n",
       "5  EC 5.4.2.2 Phosphoglucomutase                            \n",
       "6  EC 3.1.3.11 fructose-bisphosphatase                      \n",
       "7  EC 2.7.1.40 pyruvate kinase                              \n",
       "8  EC 2.3.3.1 citrate synthase                              \n",
       "9                                                           \n",
       "10 EC 4.2.1.3 Aconitase                                     \n",
       "11 EC 2.7.1.11 phosphofructokinase                          \n",
       "12 EC 2.7.1.4 fructokinase                                  \n",
       "13 EC 3.1.3.11 fructose-bisphosphatase                      \n",
       "14 EC 2.7.1.2 Glucokinase                                   \n",
       "15 EC 1.1.1.42 isocitrate dehydrogenase                     \n",
       "16 EC 4.2.1.11 Enolase                                      \n",
       "17 EC 1.1.1.41 isocitrate dehydrogenase                     \n",
       "18 EC 4.1.1.31 PEP Carboxylase                              \n",
       "19 EC 4.1.2.13 fructose-bisphosphate aldolase               \n",
       "20 EC 6.2.1.5 Succinate CoA ligase                          \n",
       "21 EC 1.1.1.37 malate dehydrogenase                         \n",
       "22 EC 2.6.1.2 alanine transaminase                          \n",
       "23 EC 4.2.1.2 fumarase                                      \n",
       "24 EC 2.6.1.1 aspartate aminotransferase                    \n",
       "25 EC 1.4.1.4 glutamate dehydrogenase NADP                  \n",
       "26 EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD \n",
       "27 EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP\n",
       "28 EC 1.4.1.2 glutamate dehydrogenase NAP                   \n",
       "29 EC 5.3.1.1 triose-phosphate isomerase                    \n",
       "30 EC 2.7.2.3 phosphoglycerate kinase                       \n",
       "31 EC 3.2.1.26 invertase                                    \n",
       "32 EC 3.2.1.26 invertase                                    \n",
       "33 EC 1.1.1.49 glucose-6-phosphate dehydrogenase            \n",
       "34 EC 2.7.7.9 UDPG phosphorylase                            \n",
       "35 EC 2.4.1.13 sucrose synthase                             \n",
       "36 EC 1.1.1.38 NAD+-malic enzyme                            \n",
       "37 EC 1.1.1.282 shikimate dehydrogenase                     \n",
       "38 EC 1.1.1.40 NADP+-malic enzyme                           \n",
       "39 EC 5.3.1.9 phosphohexose isomerase                       \n",
       "40 EC 2.4.1.21 starch synthase                              \n",
       "41 EC 2.7.7.27 ADP-glucose synthase                         \n",
       "42 EC 2.4.1.14 sucrose-phosphate synthase                   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Get 'activome' data subset\n",
    "ds <- dh$getSubsetByName('activome')\n",
    "\n",
    "# Show all descriptions of variables\n",
    "ds$LABELS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'Treatment'</li>\n",
       "\t<li>'DevStage'</li>\n",
       "\t<li>'FruitAge'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'Treatment'\n",
       "\\item 'DevStage'\n",
       "\\item 'FruitAge'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'Treatment'\n",
       "2. 'DevStage'\n",
       "3. 'FruitAge'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"Treatment\" \"DevStage\"  \"FruitAge\" "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show all factors defined in the data subset\n",
    "ds$facnames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'PGM'</li>\n",
       "\t<li>'cFBPase'</li>\n",
       "\t<li>'PyrK'</li>\n",
       "\t<li>'CitS'</li>\n",
       "\t<li>'PPI'</li>\n",
       "\t<li>'Aconitase'</li>\n",
       "\t<li>'PFK'</li>\n",
       "\t<li>'FruK'</li>\n",
       "\t<li>'pFBPase'</li>\n",
       "\t<li>'GluK'</li>\n",
       "\t<li>'NAD_ISODH'</li>\n",
       "\t<li>'Enolase'</li>\n",
       "\t<li>'NADP_ISODH'</li>\n",
       "\t<li>'PEPC'</li>\n",
       "\t<li>'Aldolase'</li>\n",
       "\t<li>'Succ_CoA_ligase'</li>\n",
       "\t<li>'NAD_MalDH'</li>\n",
       "\t<li>'AlaAT'</li>\n",
       "\t<li>'Fumarase'</li>\n",
       "\t<li>'AspAT'</li>\n",
       "\t<li>'NADP_GluDH'</li>\n",
       "\t<li>'NAD_GAPDH'</li>\n",
       "\t<li>'NADP_GAPDH'</li>\n",
       "\t<li>'NAD_GluDH'</li>\n",
       "\t<li>'TPI'</li>\n",
       "\t<li>'PGK'</li>\n",
       "\t<li>'Neutral_Inv'</li>\n",
       "\t<li>'Acid_Inv'</li>\n",
       "\t<li>'G6PDH'</li>\n",
       "\t<li>'UGPase'</li>\n",
       "\t<li>'SuSy'</li>\n",
       "\t<li>'NAD_ME'</li>\n",
       "\t<li>'ShiDH'</li>\n",
       "\t<li>'NADP_ME'</li>\n",
       "\t<li>'PGI'</li>\n",
       "\t<li>'StarchS'</li>\n",
       "\t<li>'AGPase'</li>\n",
       "\t<li>'SPS'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'PGM'\n",
       "\\item 'cFBPase'\n",
       "\\item 'PyrK'\n",
       "\\item 'CitS'\n",
       "\\item 'PPI'\n",
       "\\item 'Aconitase'\n",
       "\\item 'PFK'\n",
       "\\item 'FruK'\n",
       "\\item 'pFBPase'\n",
       "\\item 'GluK'\n",
       "\\item 'NAD\\_ISODH'\n",
       "\\item 'Enolase'\n",
       "\\item 'NADP\\_ISODH'\n",
       "\\item 'PEPC'\n",
       "\\item 'Aldolase'\n",
       "\\item 'Succ\\_CoA\\_ligase'\n",
       "\\item 'NAD\\_MalDH'\n",
       "\\item 'AlaAT'\n",
       "\\item 'Fumarase'\n",
       "\\item 'AspAT'\n",
       "\\item 'NADP\\_GluDH'\n",
       "\\item 'NAD\\_GAPDH'\n",
       "\\item 'NADP\\_GAPDH'\n",
       "\\item 'NAD\\_GluDH'\n",
       "\\item 'TPI'\n",
       "\\item 'PGK'\n",
       "\\item 'Neutral\\_Inv'\n",
       "\\item 'Acid\\_Inv'\n",
       "\\item 'G6PDH'\n",
       "\\item 'UGPase'\n",
       "\\item 'SuSy'\n",
       "\\item 'NAD\\_ME'\n",
       "\\item 'ShiDH'\n",
       "\\item 'NADP\\_ME'\n",
       "\\item 'PGI'\n",
       "\\item 'StarchS'\n",
       "\\item 'AGPase'\n",
       "\\item 'SPS'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'PGM'\n",
       "2. 'cFBPase'\n",
       "3. 'PyrK'\n",
       "4. 'CitS'\n",
       "5. 'PPI'\n",
       "6. 'Aconitase'\n",
       "7. 'PFK'\n",
       "8. 'FruK'\n",
       "9. 'pFBPase'\n",
       "10. 'GluK'\n",
       "11. 'NAD_ISODH'\n",
       "12. 'Enolase'\n",
       "13. 'NADP_ISODH'\n",
       "14. 'PEPC'\n",
       "15. 'Aldolase'\n",
       "16. 'Succ_CoA_ligase'\n",
       "17. 'NAD_MalDH'\n",
       "18. 'AlaAT'\n",
       "19. 'Fumarase'\n",
       "20. 'AspAT'\n",
       "21. 'NADP_GluDH'\n",
       "22. 'NAD_GAPDH'\n",
       "23. 'NADP_GAPDH'\n",
       "24. 'NAD_GluDH'\n",
       "25. 'TPI'\n",
       "26. 'PGK'\n",
       "27. 'Neutral_Inv'\n",
       "28. 'Acid_Inv'\n",
       "29. 'G6PDH'\n",
       "30. 'UGPase'\n",
       "31. 'SuSy'\n",
       "32. 'NAD_ME'\n",
       "33. 'ShiDH'\n",
       "34. 'NADP_ME'\n",
       "35. 'PGI'\n",
       "36. 'StarchS'\n",
       "37. 'AGPase'\n",
       "38. 'SPS'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"PGM\"             \"cFBPase\"         \"PyrK\"            \"CitS\"           \n",
       " [5] \"PPI\"             \"Aconitase\"       \"PFK\"             \"FruK\"           \n",
       " [9] \"pFBPase\"         \"GluK\"            \"NAD_ISODH\"       \"Enolase\"        \n",
       "[13] \"NADP_ISODH\"      \"PEPC\"            \"Aldolase\"        \"Succ_CoA_ligase\"\n",
       "[17] \"NAD_MalDH\"       \"AlaAT\"           \"Fumarase\"        \"AspAT\"          \n",
       "[21] \"NADP_GluDH\"      \"NAD_GAPDH\"       \"NADP_GAPDH\"      \"NAD_GluDH\"      \n",
       "[25] \"TPI\"             \"PGK\"             \"Neutral_Inv\"     \"Acid_Inv\"       \n",
       "[29] \"G6PDH\"           \"UGPase\"          \"SuSy\"            \"NAD_ME\"         \n",
       "[33] \"ShiDH\"           \"NADP_ME\"         \"PGI\"             \"StarchS\"        \n",
       "[37] \"AGPase\"          \"SPS\"            "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show all quantitative variables defined in the data subset\n",
    "ds$varnames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [],
      "text/latex": [],
      "text/markdown": [],
      "text/plain": [
       "character(0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show all qualitative variables defined in the data subset\n",
    "ds$qualnames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "      PGM             cFBPase           PyrK              CitS       \n",
       " Min.   :   4.11   Min.   : 0.02   Min.   :   5.25   Min.   :  0.20  \n",
       " 1st Qu.: 934.62   1st Qu.: 7.32   1st Qu.: 172.04   1st Qu.: 19.03  \n",
       " Median :1609.69   Median :10.97   Median : 276.78   Median : 33.08  \n",
       " Mean   :2156.69   Mean   :12.81   Mean   : 472.99   Mean   : 41.71  \n",
       " 3rd Qu.:3064.04   3rd Qu.:16.64   3rd Qu.: 556.97   3rd Qu.: 59.91  \n",
       " Max.   :8054.61   Max.   :85.02   Max.   :3053.11   Max.   :171.99  \n",
       " NA's   :46        NA's   :37                        NA's   :227     \n",
       "      PPI            Aconitase            PFK              FruK        \n",
       " Min.   :  60.49   Min.   :  12.06   Min.   :  8.59   Min.   :   5.60  \n",
       " 1st Qu.: 395.51   1st Qu.:  88.30   1st Qu.: 49.27   1st Qu.:  55.94  \n",
       " Median : 637.17   Median : 164.71   Median : 72.59   Median :  97.51  \n",
       " Mean   : 973.64   Mean   : 308.42   Mean   : 89.60   Mean   : 242.68  \n",
       " 3rd Qu.:1364.62   3rd Qu.: 344.83   3rd Qu.:118.84   3rd Qu.: 344.62  \n",
       " Max.   :3373.46   Max.   :2014.02   Max.   :270.30   Max.   :1223.19  \n",
       "                   NA's   :29                         NA's   :7        \n",
       "    pFBPase            GluK           NAD_ISODH         Enolase      \n",
       " Min.   :  5.28   Min.   :   0.01   Min.   : 52.67   Min.   :  2.21  \n",
       " 1st Qu.: 46.90   1st Qu.:  33.44   1st Qu.:122.94   1st Qu.:226.35  \n",
       " Median :102.46   Median :  83.51   Median :182.58   Median :320.36  \n",
       " Mean   :162.53   Mean   : 186.81   Mean   :231.85   Mean   :348.46  \n",
       " 3rd Qu.:209.70   3rd Qu.: 271.34   3rd Qu.:284.48   3rd Qu.:503.27  \n",
       " Max.   :778.47   Max.   :1271.77   Max.   :975.77   Max.   :766.52  \n",
       " NA's   :17       NA's   :60        NA's   :4        NA's   :99      \n",
       "   NADP_ISODH          PEPC            Aldolase       Succ_CoA_ligase  \n",
       " Min.   :  0.27   Min.   :   3.09   Min.   :  215.6   Min.   :  12.27  \n",
       " 1st Qu.: 23.32   1st Qu.: 214.94   1st Qu.: 1861.7   1st Qu.: 172.61  \n",
       " Median : 44.24   Median : 397.33   Median : 2683.7   Median : 268.17  \n",
       " Mean   : 59.45   Mean   : 457.07   Mean   : 3440.4   Mean   : 391.75  \n",
       " 3rd Qu.: 86.79   3rd Qu.: 672.65   3rd Qu.: 4620.1   3rd Qu.: 539.01  \n",
       " Max.   :231.52   Max.   :1414.29   Max.   :11538.5   Max.   :1528.87  \n",
       " NA's   :265      NA's   :16                          NA's   :14       \n",
       "   NAD_MalDH         AlaAT            Fumarase           AspAT      \n",
       " Min.   : 2178   Min.   :   7.14   Min.   :  10.33   Min.   :  378  \n",
       " 1st Qu.: 8879   1st Qu.: 829.48   1st Qu.: 142.42   1st Qu.: 1828  \n",
       " Median :18530   Median :1263.87   Median : 290.33   Median : 2800  \n",
       " Mean   :25507   Mean   :1329.22   Mean   : 420.92   Mean   : 4935  \n",
       " 3rd Qu.:38895   3rd Qu.:1777.71   3rd Qu.: 548.57   3rd Qu.: 6471  \n",
       " Max.   :78412   Max.   :4605.69   Max.   :1753.96   Max.   :19862  \n",
       "                 NA's   :94        NA's   :241       NA's   :216    \n",
       "   NADP_GluDH       NAD_GAPDH        NADP_GAPDH        NAD_GluDH     \n",
       " Min.   : 0.030   Min.   : 244.6   Min.   :   6.82   Min.   :  1.16  \n",
       " 1st Qu.: 2.660   1st Qu.:1187.2   1st Qu.: 500.82   1st Qu.: 27.57  \n",
       " Median : 5.410   Median :1905.9   Median : 798.36   Median : 48.62  \n",
       " Mean   : 5.978   Mean   :2539.9   Mean   :1007.51   Mean   : 76.32  \n",
       " 3rd Qu.: 8.107   3rd Qu.:3245.1   3rd Qu.:1307.23   3rd Qu.: 81.40  \n",
       " Max.   :22.790   Max.   :9000.0   Max.   :9647.29   Max.   :336.56  \n",
       " NA's   :222      NA's   :26       NA's   :36        NA's   :115     \n",
       "      TPI              PGK           Neutral_Inv        Acid_Inv      \n",
       " Min.   :  2946   Min.   :  301.1   Min.   :  4.81   Min.   :-2083.6  \n",
       " 1st Qu.: 27346   1st Qu.: 3635.4   1st Qu.: 57.97   1st Qu.:   40.5  \n",
       " Median : 51122   Median : 5492.4   Median :123.70   Median :  398.1  \n",
       " Mean   : 77922   Mean   : 7634.1   Mean   :131.10   Mean   :  540.6  \n",
       " 3rd Qu.:115730   3rd Qu.: 9884.5   3rd Qu.:190.59   3rd Qu.:  823.3  \n",
       " Max.   :299124   Max.   :27041.3   Max.   :402.54   Max.   : 4236.6  \n",
       " NA's   :5                                                            \n",
       "     G6PDH           UGPase          SuSy             NAD_ME      \n",
       " Min.   : 17.8   Min.   :1102   Min.   :   2.01   Min.   :   5.3  \n",
       " 1st Qu.:101.8   1st Qu.:2984   1st Qu.: 228.90   1st Qu.: 414.8  \n",
       " Median :131.2   Median :3275   Median : 353.76   Median : 986.9  \n",
       " Mean   :183.5   Mean   :3198   Mean   : 427.21   Mean   :1086.3  \n",
       " 3rd Qu.:250.3   3rd Qu.:3538   3rd Qu.: 587.89   3rd Qu.:1608.5  \n",
       " Max.   :678.3   Max.   :4145   Max.   :3130.57   Max.   :3893.2  \n",
       " NA's   :38      NA's   :9      NA's   :125       NA's   :100     \n",
       "     ShiDH           NADP_ME            PGI             StarchS      \n",
       " Min.   :  3.55   Min.   :  1.38   Min.   :  31.37   Min.   :  1.23  \n",
       " 1st Qu.: 67.48   1st Qu.: 89.87   1st Qu.: 356.56   1st Qu.: 40.44  \n",
       " Median : 98.97   Median :172.36   Median : 520.14   Median : 66.16  \n",
       " Mean   :190.91   Mean   :181.01   Mean   : 702.01   Mean   : 83.89  \n",
       " 3rd Qu.:180.13   3rd Qu.:263.44   3rd Qu.: 941.90   3rd Qu.:116.13  \n",
       " Max.   :944.64   Max.   :560.68   Max.   :2392.79   Max.   :256.72  \n",
       " NA's   :4        NA's   :64                         NA's   :57      \n",
       "     AGPase             SPS        \n",
       " Min.   :   0.73   Min.   :  1.47  \n",
       " 1st Qu.: 257.81   1st Qu.: 52.23  \n",
       " Median : 409.79   Median : 83.12  \n",
       " Mean   : 498.92   Mean   :101.27  \n",
       " 3rd Qu.: 726.49   3rd Qu.:124.63  \n",
       " Max.   :1372.63   Max.   :678.33  \n",
       " NA's   :35        NA's   :168     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Display a summary for each quantitative variable\n",
    "summary(ds$data[, ds$varnames ])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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F4Emj5VCPR0W0FluRbh6tLdAt2n2LwINH2qEejLcg3vxVeWvBpNbF4Emj61DPTT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\nRU5ErkJggg==",
      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 600,
       "width": 720
      },
      "text/plain": {
       "height": 600,
       "width": 720
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Boxplot of all variables defined in ds$varnames\n",
    "Rank <- simplify2array(lapply(ds$varnames, function(x) { round(mean(log10(ds$data[ , x]), na.rm=T)) }))\n",
    "Rank[!is.finite(Rank)] <- 0\n",
    "colRank <- Rank - min(Rank) + 1\n",
    "cols <- c('red', 'orange', 'darkgreen', 'blue', 'purple', 'brown')\n",
    "options(repr.plot.width=12, repr.plot.height=10)\n",
    "boxplot(log10(ds$data[, ds$varnames]), outline=F, horizontal=T, border=cols[colRank], las=2, cex.axis=0.5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "R",
   "language": "R",
   "name": "ir"
  },
  "language_info": {
   "codemirror_mode": "r",
   "file_extension": ".r",
   "mimetype": "text/x-r-source",
   "name": "R",
   "pygments_lexer": "r",
   "version": "3.5.1"
  },
  "nteract": {
   "version": "0.15.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}