diff --git a/docs/tutorials/virtual_db_tutorial.ipynb b/docs/tutorials/virtual_db_tutorial.ipynb
index 7305146..bb07e75 100644
--- a/docs/tutorials/virtual_db_tutorial.ipynb
+++ b/docs/tutorials/virtual_db_tutorial.ipynb
@@ -33,7 +33,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Config saved to: /tmp/tmpf610qghb/vdb_config.yaml\n"
+      "Config saved to: /tmp/tmp_krovt13/vdb_config.yaml\n"
      ]
     }
    ],
@@ -41,6 +41,10 @@
     "config_yaml = \"\"\"\n",
     "repositories:\n",
     "  BrentLab/harbison_2004:\n",
+    "    tags:\n",
+    "      assay: binding\n",
+    "      method: chip-chip\n",
+    "      organism: yeast\n",
     "    dataset:\n",
     "      harbison_2004:\n",
     "        db_name: harbison\n",
@@ -59,6 +63,10 @@
     "          field: regulator_symbol\n",
     "\n",
     "  BrentLab/kemmeren_2014:\n",
+    "    tags:\n",
+    "      assay: perturbation\n",
+    "      method: microarray\n",
+    "      organism: yeast\n",
     "    dataset:\n",
     "      kemmeren_2014:\n",
     "        db_name: kemmeren\n",
@@ -75,8 +83,17 @@
     "          field: regulator_symbol\n",
     "\n",
     "  BrentLab/hackett_2020:\n",
+    "    # Repo-level tags apply to all datasets in this repository\n",
+    "    tags:\n",
+    "      method: test_overwrite\n",
+    "      organism: yeast\n",
     "    dataset:\n",
     "      hackett_2020:\n",
+    "        # Dataset-level tags: 'assay' is new,\n",
+    "        # 'method' overrides the repo-level value\n",
+    "        tags:\n",
+    "          assay: perturbation\n",
+    "          method: overexpression\n",
     "        db_name: hackett\n",
     "        sample_id:\n",
     "          field: sample_id\n",
@@ -169,6 +186,56 @@
     "print(repr(vdb))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "0f10c138",
+   "metadata": {},
+   "source": [
+    "## Tags\n",
+    "\n",
+    "Tags are arbitrary key/value annotations defined in the configuration. They\n",
+    "follow the same hierarchy as property mappings: repo-level tags apply to all\n",
+    "datasets in that repository, and dataset-level tags override repo-level tags\n",
+    "with the same key.\n",
+    "\n",
+    "Use `config.get_tags(repo_id, config_name)` to retrieve the merged tags for\n",
+    "any dataset."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f7d73db0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "harbison tags: {'assay': 'binding', 'method': 'chip-chip', 'organism': 'yeast'}\n",
+      "kemmeren tags: {'assay': 'perturbation', 'method': 'microarray', 'organism': 'yeast'}\n",
+      "hackett tags: {'method': 'overexpression', 'organism': 'yeast', 'assay': 'perturbation'}\n",
+      "dto tags: {}\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "# Tags are accessible directly from the VirtualDB instance using the db_name.\n",
+    "# No need to import MetadataConfig or specify repo_id.\n",
+    "print(\"harbison tags:\", vdb.get_tags(\"harbison\"))\n",
+    "print(\"kemmeren tags:\", vdb.get_tags(\"kemmeren\"))\n",
+    "\n",
+    "# Hackett has tags at both levels:\n",
+    "# 'organism' comes from the repo level only,\n",
+    "# 'assay' is added at the dataset level only,\n",
+    "# 'method' is defined at both levels -- the dataset value wins.\n",
+    "print(\"hackett tags:\", vdb.get_tags(\"hackett\"))\n",
+    "\n",
+    "# Dataset with no tags returns empty dict\n",
+    "print(\"dto tags:\", vdb.get_tags(\"dto\"))"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "cell-5",
@@ -187,7 +254,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "cell-6",
    "metadata": {},
    "outputs": [
@@ -202,10 +269,11 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Fetching 1 files: 100%|██████████| 1/1 [00:00<00:00, 6374.32it/s]\n",
-      "Fetching 1 files: 100%|██████████| 1/1 [00:00<00:00, 12264.05it/s]\n",
-      "Fetching 1 files: 100%|██████████| 1/1 [00:00<00:00, 9731.56it/s]\n",
-      "Fetching 6 files: 100%|██████████| 6/6 [00:00<00:00, 21883.33it/s]\n",
+      "Fetching 1 files: 100%|██████████| 1/1 [00:00<00:00, 10407.70it/s]\n",
+      "Fetching 1 files: 100%|██████████| 1/1 [00:00<00:00, 1770.50it/s]\n",
+      "Fetching 1 files: 100%|██████████| 1/1 [00:20<00:00, 20.31s/it]\n",
+      "No metadata fields found for data config 'dto' in repo 'BrentLab/yeast_comparative_analysis' -- no embedded metadata_fields and no metadata config with applies_to\n",
+      "Fetching 30 files: 100%|██████████| 30/30 [00:00<00:00, 55091.56it/s]\n",
       "Key 'carbon_source' not found at path 'media.carbon_source' (current keys: ['name'])\n",
       "Key 'carbon_source' not found at path 'media.carbon_source' (current keys: ['name'])\n",
       "Key 'carbon_source' not found at path 'media.carbon_source' (current keys: ['name'])\n",
@@ -235,7 +303,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "pdebujnqb9q",
    "metadata": {},
    "outputs": [
@@ -284,7 +352,7 @@
          "type": "unknown"
         }
        ],
-       "ref": "8720a362-ea0c-4293-9656-ba6725dcaa3d",
+       "ref": "955566a4-2a55-483f-a0d4-11f1757f6a28",
        "rows": [
         [
          "0",
@@ -299,7 +367,7 @@
         [
          "1",
          "harbison_meta",
-         "regulator_locus_tag",
+         "condition",
          "VARCHAR",
          "YES",
          null,
@@ -309,7 +377,7 @@
         [
          "2",
          "harbison_meta",
-         "regulator_symbol",
+         "regulator_locus_tag",
          "VARCHAR",
          "YES",
          null,
@@ -319,7 +387,7 @@
         [
          "3",
          "harbison_meta",
-         "condition",
+         "regulator_symbol",
          "VARCHAR",
          "YES",
          null,
@@ -394,7 +462,7 @@
        "    <tr>\n",
        "      <th>1</th>\n",
        "      <td>harbison_meta</td>\n",
-       "      <td>regulator_locus_tag</td>\n",
+       "      <td>condition</td>\n",
        "      <td>VARCHAR</td>\n",
        "      <td>YES</td>\n",
        "      <td>None</td>\n",
@@ -404,7 +472,7 @@
        "    <tr>\n",
        "      <th>2</th>\n",
        "      <td>harbison_meta</td>\n",
-       "      <td>regulator_symbol</td>\n",
+       "      <td>regulator_locus_tag</td>\n",
        "      <td>VARCHAR</td>\n",
        "      <td>YES</td>\n",
        "      <td>None</td>\n",
@@ -414,7 +482,7 @@
        "    <tr>\n",
        "      <th>3</th>\n",
        "      <td>harbison_meta</td>\n",
-       "      <td>condition</td>\n",
+       "      <td>regulator_symbol</td>\n",
        "      <td>VARCHAR</td>\n",
        "      <td>YES</td>\n",
        "      <td>None</td>\n",
@@ -448,14 +516,14 @@
       "text/plain": [
        "           table          column_name column_type null   key default extra\n",
        "0  harbison_meta            sample_id     INTEGER  YES  None    None  None\n",
-       "1  harbison_meta  regulator_locus_tag     VARCHAR  YES  None    None  None\n",
-       "2  harbison_meta     regulator_symbol     VARCHAR  YES  None    None  None\n",
-       "3  harbison_meta            condition     VARCHAR  YES  None    None  None\n",
+       "1  harbison_meta            condition     VARCHAR  YES  None    None  None\n",
+       "2  harbison_meta  regulator_locus_tag     VARCHAR  YES  None    None  None\n",
+       "3  harbison_meta     regulator_symbol     VARCHAR  YES  None    None  None\n",
        "4  harbison_meta        carbon_source     VARCHAR  YES  None    None  None\n",
        "5  harbison_meta  temperature_celsius      DOUBLE  YES  None    None  None"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -468,7 +536,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "id": "9deee334",
    "metadata": {},
    "outputs": [
@@ -517,7 +585,7 @@
          "type": "unknown"
         }
        ],
-       "ref": "001db2c7-a5c2-4561-9b12-35733ce1b2e6",
+       "ref": "012ff714-cded-469d-9c53-642872a5d487",
        "rows": [
         [
          "0",
@@ -793,7 +861,7 @@
        "10  harbison  temperature_celsius      DOUBLE  YES  None    None  None"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -805,7 +873,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "id": "cell-9",
    "metadata": {},
    "outputs": [
@@ -839,7 +907,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "id": "1a705f1c",
    "metadata": {},
    "outputs": [
@@ -858,17 +926,17 @@
          "type": "integer"
         },
         {
-         "name": "regulator_locus_tag",
+         "name": "condition",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "regulator_symbol",
+         "name": "regulator_locus_tag",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "condition",
+         "name": "regulator_symbol",
          "rawType": "object",
          "type": "string"
         },
@@ -883,50 +951,50 @@
          "type": "float"
         }
        ],
-       "ref": "e5bb4909-b231-44d7-85b8-5219b51f4a4b",
+       "ref": "b5c797e5-c834-4f9d-a8fc-89789ef0cc68",
        "rows": [
         [
          "0",
-         "166",
-         "YIL131C",
-         "FKH1",
+         "300",
          "YPD",
+         "YOL116W",
+         "MSN1",
          "glucose",
          "30.0"
         ],
         [
          "1",
-         "3",
-         "YBL005W",
-         "PDR3",
+         "113",
          "YPD",
+         "YGL035C",
+         "MIG1",
          "glucose",
          "30.0"
         ],
         [
          "2",
-         "173",
-         "YIR023W",
-         "DAL81",
-         "YPD",
+         "81",
+         "RAPA",
+         "YEL009C",
+         "GCN4",
          "glucose",
          "30.0"
         ],
         [
          "3",
-         "220",
-         "YLR014C",
-         "PPR1",
+         "279",
          "YPD",
+         "YNL139C",
+         "THO2",
          "glucose",
          "30.0"
         ],
         [
          "4",
-         "83",
-         "YEL009C",
-         "GCN4",
-         "YPD",
+         "73",
+         "H2O2Hi",
+         "YDR423C",
+         "CAD1",
          "glucose",
          "30.0"
         ]
@@ -956,9 +1024,9 @@
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>sample_id</th>\n",
+       "      <th>condition</th>\n",
        "      <th>regulator_locus_tag</th>\n",
        "      <th>regulator_symbol</th>\n",
-       "      <th>condition</th>\n",
        "      <th>carbon_source</th>\n",
        "      <th>temperature_celsius</th>\n",
        "    </tr>\n",
@@ -966,46 +1034,46 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>166</td>\n",
-       "      <td>YIL131C</td>\n",
-       "      <td>FKH1</td>\n",
+       "      <td>300</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YOL116W</td>\n",
+       "      <td>MSN1</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>3</td>\n",
-       "      <td>YBL005W</td>\n",
-       "      <td>PDR3</td>\n",
+       "      <td>113</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YGL035C</td>\n",
+       "      <td>MIG1</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>173</td>\n",
-       "      <td>YIR023W</td>\n",
-       "      <td>DAL81</td>\n",
-       "      <td>YPD</td>\n",
+       "      <td>81</td>\n",
+       "      <td>RAPA</td>\n",
+       "      <td>YEL009C</td>\n",
+       "      <td>GCN4</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>220</td>\n",
-       "      <td>YLR014C</td>\n",
-       "      <td>PPR1</td>\n",
+       "      <td>279</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YNL139C</td>\n",
+       "      <td>THO2</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>83</td>\n",
-       "      <td>YEL009C</td>\n",
-       "      <td>GCN4</td>\n",
-       "      <td>YPD</td>\n",
+       "      <td>73</td>\n",
+       "      <td>H2O2Hi</td>\n",
+       "      <td>YDR423C</td>\n",
+       "      <td>CAD1</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
@@ -1014,12 +1082,12 @@
        "</div>"
       ],
       "text/plain": [
-       "   sample_id regulator_locus_tag regulator_symbol condition carbon_source  \\\n",
-       "0        166             YIL131C             FKH1       YPD       glucose   \n",
-       "1          3             YBL005W             PDR3       YPD       glucose   \n",
-       "2        173             YIR023W            DAL81       YPD       glucose   \n",
-       "3        220             YLR014C             PPR1       YPD       glucose   \n",
-       "4         83             YEL009C             GCN4       YPD       glucose   \n",
+       "   sample_id condition regulator_locus_tag regulator_symbol carbon_source  \\\n",
+       "0        300       YPD             YOL116W             MSN1       glucose   \n",
+       "1        113       YPD             YGL035C             MIG1       glucose   \n",
+       "2         81      RAPA             YEL009C             GCN4       glucose   \n",
+       "3        279       YPD             YNL139C             THO2       glucose   \n",
+       "4         73    H2O2Hi             YDR423C             CAD1       glucose   \n",
        "\n",
        "   temperature_celsius  \n",
        "0                 30.0  \n",
@@ -1029,7 +1097,7 @@
        "4                 30.0  "
       ]
      },
-     "execution_count": 7,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1055,7 +1123,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "id": "cell-17",
    "metadata": {},
    "outputs": [
@@ -1124,75 +1192,75 @@
          "type": "float"
         }
        ],
-       "ref": "a6cb8a91-c1c2-4bc8-af51-12e900d7a4bf",
+       "ref": "06d7e391-9665-4a5f-9276-359ff8e71c3e",
        "rows": [
         [
          "0",
-         "14",
-         "13.0",
+         "15",
+         "14.0",
          "YBR049C",
          "REB1",
-         "H2O2Lo",
+         "YPD",
          "YPR204W",
          "YPR204W",
-         "0.78449615",
-         "0.53566521",
+         "0.85288861",
+         "0.76943045",
          "glucose",
          "30.0"
         ],
         [
          "1",
-         "14",
-         "13.0",
+         "15",
+         "14.0",
          "YBR049C",
          "REB1",
-         "H2O2Lo",
+         "YPD",
          "YPR203W",
          "YPR203W",
-         "1.4509147",
-         "0.95955603",
+         "1.2490028",
+         "0.11237602",
          "glucose",
          "30.0"
         ],
         [
          "2",
-         "14",
-         "13.0",
+         "15",
+         "14.0",
          "YBR049C",
          "REB1",
-         "H2O2Lo",
+         "YPD",
          "YPR202W",
          "YPR202W",
-         "1.4509147",
-         "0.95955603",
+         "1.2490028",
+         "0.11237602",
          "glucose",
          "30.0"
         ],
         [
          "3",
-         "14",
-         "13.0",
+         "15",
+         "14.0",
          "YBR049C",
          "REB1",
-         "H2O2Lo",
+         "YPD",
          "YPR201W",
          "ARR3",
-         "0.92586339",
-         "0.45367192",
+         "1.5137073",
+         "0.1681333",
          "glucose",
          "30.0"
         ],
         [
          "4",
-         "14",
-         "13.0",
+         "15",
+         "14.0",
          "YBR049C",
          "REB1",
-         "H2O2Lo",
+         "YPD",
          "YPR200C",
          "ARR2",
-         "0.92586339",
-         "0.45367192",
+         "1.5137073",
+         "0.1681333",
          "glucose",
          "30.0"
         ]
@@ -1237,71 +1305,71 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>14</td>\n",
-       "      <td>13.0</td>\n",
+       "      <td>15</td>\n",
+       "      <td>14.0</td>\n",
        "      <td>YBR049C</td>\n",
        "      <td>REB1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>YPD</td>\n",
        "      <td>YPR204W</td>\n",
        "      <td>YPR204W</td>\n",
-       "      <td>0.784496</td>\n",
-       "      <td>0.535665</td>\n",
+       "      <td>0.852889</td>\n",
+       "      <td>0.769430</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>14</td>\n",
-       "      <td>13.0</td>\n",
+       "      <td>15</td>\n",
+       "      <td>14.0</td>\n",
        "      <td>YBR049C</td>\n",
        "      <td>REB1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>YPD</td>\n",
        "      <td>YPR203W</td>\n",
        "      <td>YPR203W</td>\n",
-       "      <td>1.450915</td>\n",
-       "      <td>0.959556</td>\n",
+       "      <td>1.249003</td>\n",
+       "      <td>0.112376</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>14</td>\n",
-       "      <td>13.0</td>\n",
+       "      <td>15</td>\n",
+       "      <td>14.0</td>\n",
        "      <td>YBR049C</td>\n",
        "      <td>REB1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>YPD</td>\n",
        "      <td>YPR202W</td>\n",
        "      <td>YPR202W</td>\n",
-       "      <td>1.450915</td>\n",
-       "      <td>0.959556</td>\n",
+       "      <td>1.249003</td>\n",
+       "      <td>0.112376</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>14</td>\n",
-       "      <td>13.0</td>\n",
+       "      <td>15</td>\n",
+       "      <td>14.0</td>\n",
        "      <td>YBR049C</td>\n",
        "      <td>REB1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>YPD</td>\n",
        "      <td>YPR201W</td>\n",
        "      <td>ARR3</td>\n",
-       "      <td>0.925863</td>\n",
-       "      <td>0.453672</td>\n",
+       "      <td>1.513707</td>\n",
+       "      <td>0.168133</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>14</td>\n",
-       "      <td>13.0</td>\n",
+       "      <td>15</td>\n",
+       "      <td>14.0</td>\n",
        "      <td>YBR049C</td>\n",
        "      <td>REB1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>YPD</td>\n",
        "      <td>YPR200C</td>\n",
        "      <td>ARR2</td>\n",
-       "      <td>0.925863</td>\n",
-       "      <td>0.453672</td>\n",
+       "      <td>1.513707</td>\n",
+       "      <td>0.168133</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
@@ -1311,18 +1379,18 @@
       ],
       "text/plain": [
        "   sample_id  db_id regulator_locus_tag regulator_symbol condition  \\\n",
-       "0         14   13.0             YBR049C             REB1    H2O2Lo   \n",
-       "1         14   13.0             YBR049C             REB1    H2O2Lo   \n",
-       "2         14   13.0             YBR049C             REB1    H2O2Lo   \n",
-       "3         14   13.0             YBR049C             REB1    H2O2Lo   \n",
-       "4         14   13.0             YBR049C             REB1    H2O2Lo   \n",
+       "0         15   14.0             YBR049C             REB1       YPD   \n",
+       "1         15   14.0             YBR049C             REB1       YPD   \n",
+       "2         15   14.0             YBR049C             REB1       YPD   \n",
+       "3         15   14.0             YBR049C             REB1       YPD   \n",
+       "4         15   14.0             YBR049C             REB1       YPD   \n",
        "\n",
        "  target_locus_tag target_symbol    effect    pvalue carbon_source  \\\n",
-       "0          YPR204W       YPR204W  0.784496  0.535665       glucose   \n",
-       "1          YPR203W       YPR203W  1.450915  0.959556       glucose   \n",
-       "2          YPR202W       YPR202W  1.450915  0.959556       glucose   \n",
-       "3          YPR201W          ARR3  0.925863  0.453672       glucose   \n",
-       "4          YPR200C          ARR2  0.925863  0.453672       glucose   \n",
+       "0          YPR204W       YPR204W  0.852889  0.769430       glucose   \n",
+       "1          YPR203W       YPR203W  1.249003  0.112376       glucose   \n",
+       "2          YPR202W       YPR202W  1.249003  0.112376       glucose   \n",
+       "3          YPR201W          ARR3  1.513707  0.168133       glucose   \n",
+       "4          YPR200C          ARR2  1.513707  0.168133       glucose   \n",
        "\n",
        "   temperature_celsius  \n",
        "0                 30.0  \n",
@@ -1332,7 +1400,7 @@
        "4                 30.0  "
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1361,7 +1429,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "id": "cell-19",
    "metadata": {},
    "outputs": [
@@ -1385,7 +1453,7 @@
          "type": "integer"
         }
        ],
-       "ref": "9234aaf4-a313-42c2-838a-a13568eed01d",
+       "ref": "6d8b4d37-3b6b-40f1-833d-aa6711694bcb",
        "rows": [
         [
          "0",
@@ -1399,17 +1467,17 @@
         ],
         [
          "2",
-         "HSF1",
+         "STE12",
          "4"
         ],
         [
          "3",
-         "STE12",
+         "RTG3",
          "4"
         ],
         [
          "4",
-         "RTG3",
+         "DIG1",
          "4"
         ],
         [
@@ -1419,62 +1487,62 @@
         ],
         [
          "6",
-         "SKN7",
+         "HSF1",
          "4"
         ],
         [
          "7",
-         "DIG1",
+         "SKN7",
          "4"
         ],
         [
          "8",
-         "GAT1",
+         "RPN4",
          "3"
         ],
         [
          "9",
-         "RPN4",
+         "GAT1",
          "3"
         ],
         [
          "10",
-         "YAP7",
+         "AFT2",
          "3"
         ],
         [
          "11",
-         "TEC1",
+         "YAP7",
          "3"
         ],
         [
          "12",
-         "AFT1",
+         "TEC1",
          "3"
         ],
         [
          "13",
-         "MAL33",
+         "MOT3",
          "3"
         ],
         [
          "14",
-         "PHO2",
+         "ROX1",
          "3"
         ],
         [
          "15",
-         "MBP1",
+         "GZF3",
          "3"
         ],
         [
          "16",
-         "KSS1",
+         "PHO2",
          "3"
         ],
         [
          "17",
-         "SFP1",
+         "MAL33",
          "3"
         ],
         [
@@ -1484,37 +1552,37 @@
         ],
         [
          "19",
-         "YJL206C",
+         "SFP1",
          "3"
         ],
         [
          "20",
-         "GZF3",
+         "KSS1",
          "3"
         ],
         [
          "21",
-         "MOT3",
+         "YAP6",
          "3"
         ],
         [
          "22",
-         "FHL1",
+         "RPH1",
          "3"
         ],
         [
          "23",
-         "ROX1",
+         "NRG1",
          "3"
         ],
         [
          "24",
-         "FKH2",
+         "PHD1",
          "3"
         ],
         [
          "25",
-         "AFT2",
+         "FHL1",
          "3"
         ],
         [
@@ -1524,117 +1592,117 @@
         ],
         [
          "27",
-         "RIM101",
+         "FKH2",
          "3"
         ],
         [
          "28",
-         "YAP6",
+         "MBP1",
          "3"
         ],
         [
          "29",
-         "RPH1",
+         "RIM101",
          "3"
         ],
         [
          "30",
-         "PHD1",
+         "YJL206C",
          "3"
         ],
         [
          "31",
-         "NRG1",
+         "AFT1",
          "3"
         ],
         [
          "32",
-         "MGA1",
+         "RLM1",
          "2"
         ],
         [
          "33",
-         "UME1",
+         "XBP1",
          "2"
         ],
         [
          "34",
-         "YAP3",
+         "IME4",
          "2"
         ],
         [
          "35",
-         "XBP1",
+         "MCM1",
          "2"
         ],
         [
          "36",
-         "RDS1",
+         "DAL80",
          "2"
         ],
         [
          "37",
-         "MSS11",
+         "YAP3",
          "2"
         ],
         [
          "38",
-         "HAP2",
+         "YAP5",
          "2"
         ],
         [
          "39",
-         "MCM1",
+         "MAC1",
          "2"
         ],
         [
          "40",
-         "ADR1",
+         "UME6",
          "2"
         ],
         [
          "41",
-         "GCN4",
+         "PDR1",
          "2"
         ],
         [
          "42",
-         "MIG2",
+         "UME1",
          "2"
         ],
         [
          "43",
-         "SOK2",
+         "CAD1",
          "2"
         ],
         [
          "44",
-         "RTG1",
+         "MGA1",
          "2"
         ],
         [
          "45",
-         "MOT2",
+         "HAP4",
          "2"
         ],
         [
          "46",
-         "UGA3",
+         "MIG2",
          "2"
         ],
         [
          "47",
-         "PUT3",
+         "GCN4",
          "2"
         ],
         [
          "48",
-         "YAP5",
+         "RTG1",
          "2"
         ],
         [
          "49",
-         "UME6",
+         "PUT3",
          "2"
         ]
        ],
@@ -1679,17 +1747,17 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>HSF1</td>\n",
+       "      <td>STE12</td>\n",
        "      <td>4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>STE12</td>\n",
+       "      <td>RTG3</td>\n",
        "      <td>4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>RTG3</td>\n",
+       "      <td>DIG1</td>\n",
        "      <td>4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
@@ -1699,27 +1767,27 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>58</th>\n",
-       "      <td>DAL82</td>\n",
+       "      <td>IME1</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>59</th>\n",
-       "      <td>DAL80</td>\n",
+       "      <td>RDS1</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>60</th>\n",
-       "      <td>HAP4</td>\n",
+       "      <td>MSS11</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>61</th>\n",
-       "      <td>PDR1</td>\n",
+       "      <td>HAP2</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>62</th>\n",
-       "      <td>RLM1</td>\n",
+       "      <td>ARR1</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
@@ -1731,20 +1799,20 @@
        "   regulator_symbol  n\n",
        "0              MSN2  6\n",
        "1              MSN4  5\n",
-       "2              HSF1  4\n",
-       "3             STE12  4\n",
-       "4              RTG3  4\n",
+       "2             STE12  4\n",
+       "3              RTG3  4\n",
+       "4              DIG1  4\n",
        "..              ... ..\n",
-       "58            DAL82  2\n",
-       "59            DAL80  2\n",
-       "60             HAP4  2\n",
-       "61             PDR1  2\n",
-       "62             RLM1  2\n",
+       "58             IME1  2\n",
+       "59             RDS1  2\n",
+       "60            MSS11  2\n",
+       "61             HAP2  2\n",
+       "62             ARR1  2\n",
        "\n",
        "[63 rows x 2 columns]"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1785,7 +1853,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "id": "cell-21",
    "metadata": {},
    "outputs": [
@@ -1838,6 +1906,11 @@
          "rawType": "float64",
          "type": "float"
         },
+        {
+         "name": "pr_ranking_column",
+         "rawType": "object",
+         "type": "string"
+        },
         {
          "name": "binding_repo_dataset",
          "rawType": "object",
@@ -1869,62 +1942,65 @@
          "type": "string"
         }
        ],
-       "ref": "3464c093-78d3-4dde-9a28-850a7be5d032",
+       "ref": "1ce4dce9-5191-4116-b848-394fcdb3b5fc",
        "rows": [
         [
          "0",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;85",
-         "2.0",
-         "2.0",
-         "3.0",
-         "2.0",
-         "0.0002250900360144",
-         "0.004",
+         "BrentLab/harbison_2004;harbison_2004;105",
+         "BrentLab/hughes_2006;overexpression;10",
+         "11.0",
+         "206.0",
+         "12.0",
+         "206.0",
+         "0.041292917490562644",
+         "0.017",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "105",
          "harbison",
-         "85",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "10",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "1",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;83",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;108",
+         "BrentLab/hughes_2006;overexpression;11",
+         "60.0",
+         "67.0",
+         "60.0",
+         "67.0",
+         "0.05428351009647073",
+         "0.0",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "108",
          "harbison",
-         "83",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "11",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "2",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;84",
-         "2.0",
-         "1.0",
-         "3.0",
-         "1.0",
-         "0.0",
-         "0.011",
+         "BrentLab/harbison_2004;harbison_2004;109",
+         "BrentLab/hughes_2006;overexpression;11",
+         "27.0",
+         "1265.0",
+         "27.0",
+         "1265.0",
+         "0.12321364371741866",
+         "0.057",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "109",
          "harbison",
-         "84",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "11",
+         "BrentLab/hughes_2006;overexpression"
         ]
        ],
        "shape": {
-        "columns": 14,
+        "columns": 15,
         "rows": 3
        }
       },
@@ -1955,6 +2031,7 @@
        "      <th>perturbation_set_size</th>\n",
        "      <th>dto_fdr</th>\n",
        "      <th>dto_empirical_pvalue</th>\n",
+       "      <th>pr_ranking_column</th>\n",
        "      <th>binding_repo_dataset</th>\n",
        "      <th>perturbation_repo_dataset</th>\n",
        "      <th>binding_id_id</th>\n",
@@ -1966,92 +2043,95 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>BrentLab/harbison_2004;harbison_2004;3</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020;85</td>\n",
-       "      <td>2.0</td>\n",
-       "      <td>2.0</td>\n",
-       "      <td>3.0</td>\n",
-       "      <td>2.0</td>\n",
-       "      <td>0.000225</td>\n",
-       "      <td>0.004</td>\n",
+       "      <td>BrentLab/harbison_2004;harbison_2004;105</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression;10</td>\n",
+       "      <td>11.0</td>\n",
+       "      <td>206.0</td>\n",
+       "      <td>12.0</td>\n",
+       "      <td>206.0</td>\n",
+       "      <td>0.041293</td>\n",
+       "      <td>0.017</td>\n",
+       "      <td>log2fc</td>\n",
        "      <td>harbison_2004-harbison_2004</td>\n",
-       "      <td>Hackett_2020-hackett_2020</td>\n",
-       "      <td>3</td>\n",
+       "      <td>hughes_2006-overexpression</td>\n",
+       "      <td>105</td>\n",
        "      <td>harbison</td>\n",
-       "      <td>85</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020</td>\n",
+       "      <td>10</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>BrentLab/harbison_2004;harbison_2004;3</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020;83</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",
+       "      <td>BrentLab/harbison_2004;harbison_2004;108</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression;11</td>\n",
+       "      <td>60.0</td>\n",
+       "      <td>67.0</td>\n",
+       "      <td>60.0</td>\n",
+       "      <td>67.0</td>\n",
+       "      <td>0.054284</td>\n",
+       "      <td>0.000</td>\n",
+       "      <td>log2fc</td>\n",
        "      <td>harbison_2004-harbison_2004</td>\n",
-       "      <td>Hackett_2020-hackett_2020</td>\n",
-       "      <td>3</td>\n",
+       "      <td>hughes_2006-overexpression</td>\n",
+       "      <td>108</td>\n",
        "      <td>harbison</td>\n",
-       "      <td>83</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020</td>\n",
+       "      <td>11</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>BrentLab/harbison_2004;harbison_2004;3</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020;84</td>\n",
-       "      <td>2.0</td>\n",
-       "      <td>1.0</td>\n",
-       "      <td>3.0</td>\n",
-       "      <td>1.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.011</td>\n",
+       "      <td>BrentLab/harbison_2004;harbison_2004;109</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression;11</td>\n",
+       "      <td>27.0</td>\n",
+       "      <td>1265.0</td>\n",
+       "      <td>27.0</td>\n",
+       "      <td>1265.0</td>\n",
+       "      <td>0.123214</td>\n",
+       "      <td>0.057</td>\n",
+       "      <td>log2fc</td>\n",
        "      <td>harbison_2004-harbison_2004</td>\n",
-       "      <td>Hackett_2020-hackett_2020</td>\n",
-       "      <td>3</td>\n",
+       "      <td>hughes_2006-overexpression</td>\n",
+       "      <td>109</td>\n",
        "      <td>harbison</td>\n",
-       "      <td>84</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020</td>\n",
+       "      <td>11</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "                               binding_id  \\\n",
-       "0  BrentLab/harbison_2004;harbison_2004;3   \n",
-       "1  BrentLab/harbison_2004;harbison_2004;3   \n",
-       "2  BrentLab/harbison_2004;harbison_2004;3   \n",
+       "                                 binding_id  \\\n",
+       "0  BrentLab/harbison_2004;harbison_2004;105   \n",
+       "1  BrentLab/harbison_2004;harbison_2004;108   \n",
+       "2  BrentLab/harbison_2004;harbison_2004;109   \n",
        "\n",
-       "                         perturbation_id  binding_rank_threshold  \\\n",
-       "0  BrentLab/Hackett_2020;hackett_2020;85                     2.0   \n",
-       "1  BrentLab/Hackett_2020;hackett_2020;83                     NaN   \n",
-       "2  BrentLab/Hackett_2020;hackett_2020;84                     2.0   \n",
+       "                          perturbation_id  binding_rank_threshold  \\\n",
+       "0  BrentLab/hughes_2006;overexpression;10                    11.0   \n",
+       "1  BrentLab/hughes_2006;overexpression;11                    60.0   \n",
+       "2  BrentLab/hughes_2006;overexpression;11                    27.0   \n",
        "\n",
        "   perturbation_rank_threshold  binding_set_size  perturbation_set_size  \\\n",
-       "0                          2.0               3.0                    2.0   \n",
-       "1                          NaN               NaN                    NaN   \n",
-       "2                          1.0               3.0                    1.0   \n",
+       "0                        206.0              12.0                  206.0   \n",
+       "1                         67.0              60.0                   67.0   \n",
+       "2                       1265.0              27.0                 1265.0   \n",
        "\n",
-       "    dto_fdr  dto_empirical_pvalue         binding_repo_dataset  \\\n",
-       "0  0.000225                 0.004  harbison_2004-harbison_2004   \n",
-       "1       NaN                   NaN  harbison_2004-harbison_2004   \n",
-       "2  0.000000                 0.011  harbison_2004-harbison_2004   \n",
+       "    dto_fdr  dto_empirical_pvalue pr_ranking_column  \\\n",
+       "0  0.041293                 0.017            log2fc   \n",
+       "1  0.054284                 0.000            log2fc   \n",
+       "2  0.123214                 0.057            log2fc   \n",
        "\n",
-       "   perturbation_repo_dataset binding_id_id binding_id_source  \\\n",
-       "0  Hackett_2020-hackett_2020             3          harbison   \n",
-       "1  Hackett_2020-hackett_2020             3          harbison   \n",
-       "2  Hackett_2020-hackett_2020             3          harbison   \n",
+       "          binding_repo_dataset   perturbation_repo_dataset binding_id_id  \\\n",
+       "0  harbison_2004-harbison_2004  hughes_2006-overexpression           105   \n",
+       "1  harbison_2004-harbison_2004  hughes_2006-overexpression           108   \n",
+       "2  harbison_2004-harbison_2004  hughes_2006-overexpression           109   \n",
        "\n",
-       "  perturbation_id_id              perturbation_id_source  \n",
-       "0                 85  BrentLab/Hackett_2020;hackett_2020  \n",
-       "1                 83  BrentLab/Hackett_2020;hackett_2020  \n",
-       "2                 84  BrentLab/Hackett_2020;hackett_2020  "
+       "  binding_id_source perturbation_id_id               perturbation_id_source  \n",
+       "0          harbison                 10  BrentLab/hughes_2006;overexpression  \n",
+       "1          harbison                 11  BrentLab/hughes_2006;overexpression  \n",
+       "2          harbison                 11  BrentLab/hughes_2006;overexpression  "
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2063,7 +2143,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "id": "cell-22",
    "metadata": {},
    "outputs": [
@@ -2082,17 +2162,17 @@
          "type": "integer"
         },
         {
-         "name": "regulator_locus_tag",
+         "name": "condition",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "regulator_symbol",
+         "name": "regulator_locus_tag",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "condition",
+         "name": "regulator_symbol",
          "rawType": "object",
          "type": "string"
         },
@@ -2117,117 +2197,117 @@
          "type": "float"
         }
        ],
-       "ref": "58c1f0ca-b0a7-4ce7-b29f-f4e789b74707",
+       "ref": "8e604dcf-efad-42a8-a049-7bf684faa9b6",
        "rows": [
         [
          "0",
-         "50",
-         "YDR043C",
-         "NRG1",
-         "H2O2Lo",
+         "18",
+         "YPD",
+         "YBR083W",
+         "TEC1",
          "glucose",
          "30.0",
          "0.0",
-         "0.081863152643831"
+         "0.08188235294117648"
         ],
         [
          "1",
-         "213",
-         "YKL222C",
-         "YKL222C",
-         "YPD",
+         "157",
+         "H2O2Hi",
+         "YHR206W",
+         "SKN7",
          "glucose",
          "30.0",
          "0.0",
-         "0.0"
+         "0.13931986462735127"
         ],
         [
          "2",
-         "18",
-         "YBR083W",
-         "TEC1",
+         "93",
          "YPD",
+         "YER111C",
+         "SWI4",
          "glucose",
          "30.0",
          "0.0",
-         "0.0620669105826265"
+         "0.17005078106191404"
         ],
         [
          "3",
-         "7",
-         "YBL103C",
-         "RTG3",
-         "H2O2Hi",
+         "72",
+         "YPD",
+         "YDR421W",
+         "ARO80",
          "glucose",
          "30.0",
          "0.0",
-         "0.1577232390460343"
+         "0.00011392635800218739"
         ],
         [
          "4",
-         "277",
-         "YNL103W",
-         "MET4",
-         "YPD",
-         "glucose",
+         "71",
+         "SM",
+         "YDR421W",
+         "ARO80",
+         "unspecified",
          "30.0",
          "0.0",
-         "0.016281512605042"
+         "0.00011392635800218739"
         ],
         [
          "5",
-         "281",
-         "YNL199C",
-         "GCR2",
-         "SM",
-         "unspecified",
+         "346",
+         "RAPA",
+         "YPR104C",
+         "FHL1",
+         "glucose",
          "30.0",
          "0.0",
-         "0.0296346442259623"
+         "0.019746237283784218"
         ],
         [
          "6",
-         "86",
-         "YER040W",
-         "GLN3",
-         "SM",
-         "unspecified",
+         "226",
+         "YPD",
+         "YLR182W",
+         "SWI6",
+         "glucose",
          "30.0",
          "0.0",
-         "0.2298889521004841"
+         "0.07368989186287292"
         ],
         [
          "7",
-         "225",
-         "YLR176C",
-         "RFX1",
+         "286",
          "YPD",
+         "YNL309W",
+         "STB1",
          "glucose",
          "30.0",
          "0.0",
-         "0.0144559001906082"
+         "0.1821470588235294"
         ],
         [
          "8",
-         "86",
-         "YER040W",
-         "GLN3",
+         "172",
          "SM",
+         "YIR023W",
+         "DAL81",
          "unspecified",
          "30.0",
          "0.0",
-         "0.0961169019780866"
+         "0.21656240134694307"
         ],
         [
          "9",
-         "225",
-         "YLR176C",
-         "RFX1",
+         "320",
          "YPD",
+         "YPL038W",
+         "MET31",
          "glucose",
          "30.0",
          "0.0",
-         "0.0335260614428719"
+         "0.0661219662690251"
         ]
        ],
        "shape": {
@@ -2255,9 +2335,9 @@
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>sample_id</th>\n",
+       "      <th>condition</th>\n",
        "      <th>regulator_locus_tag</th>\n",
        "      <th>regulator_symbol</th>\n",
-       "      <th>condition</th>\n",
        "      <th>carbon_source</th>\n",
        "      <th>temperature_celsius</th>\n",
        "      <th>dto_empirical_pvalue</th>\n",
@@ -2267,145 +2347,145 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>50</td>\n",
-       "      <td>YDR043C</td>\n",
-       "      <td>NRG1</td>\n",
-       "      <td>H2O2Lo</td>\n",
+       "      <td>18</td>\n",
+       "      <td>YPD</td>\n",
+       "      <td>YBR083W</td>\n",
+       "      <td>TEC1</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.081863</td>\n",
+       "      <td>0.081882</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>213</td>\n",
-       "      <td>YKL222C</td>\n",
-       "      <td>YKL222C</td>\n",
-       "      <td>YPD</td>\n",
+       "      <td>157</td>\n",
+       "      <td>H2O2Hi</td>\n",
+       "      <td>YHR206W</td>\n",
+       "      <td>SKN7</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
+       "      <td>0.139320</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>18</td>\n",
-       "      <td>YBR083W</td>\n",
-       "      <td>TEC1</td>\n",
+       "      <td>93</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YER111C</td>\n",
+       "      <td>SWI4</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.062067</td>\n",
+       "      <td>0.170051</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>7</td>\n",
-       "      <td>YBL103C</td>\n",
-       "      <td>RTG3</td>\n",
-       "      <td>H2O2Hi</td>\n",
+       "      <td>72</td>\n",
+       "      <td>YPD</td>\n",
+       "      <td>YDR421W</td>\n",
+       "      <td>ARO80</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.157723</td>\n",
+       "      <td>0.000114</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>277</td>\n",
-       "      <td>YNL103W</td>\n",
-       "      <td>MET4</td>\n",
-       "      <td>YPD</td>\n",
-       "      <td>glucose</td>\n",
+       "      <td>71</td>\n",
+       "      <td>SM</td>\n",
+       "      <td>YDR421W</td>\n",
+       "      <td>ARO80</td>\n",
+       "      <td>unspecified</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.016282</td>\n",
+       "      <td>0.000114</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>5</th>\n",
-       "      <td>281</td>\n",
-       "      <td>YNL199C</td>\n",
-       "      <td>GCR2</td>\n",
-       "      <td>SM</td>\n",
-       "      <td>unspecified</td>\n",
+       "      <td>346</td>\n",
+       "      <td>RAPA</td>\n",
+       "      <td>YPR104C</td>\n",
+       "      <td>FHL1</td>\n",
+       "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.029635</td>\n",
+       "      <td>0.019746</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>6</th>\n",
-       "      <td>86</td>\n",
-       "      <td>YER040W</td>\n",
-       "      <td>GLN3</td>\n",
-       "      <td>SM</td>\n",
-       "      <td>unspecified</td>\n",
+       "      <td>226</td>\n",
+       "      <td>YPD</td>\n",
+       "      <td>YLR182W</td>\n",
+       "      <td>SWI6</td>\n",
+       "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.229889</td>\n",
+       "      <td>0.073690</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>7</th>\n",
-       "      <td>225</td>\n",
-       "      <td>YLR176C</td>\n",
-       "      <td>RFX1</td>\n",
+       "      <td>286</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YNL309W</td>\n",
+       "      <td>STB1</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.014456</td>\n",
+       "      <td>0.182147</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>8</th>\n",
-       "      <td>86</td>\n",
-       "      <td>YER040W</td>\n",
-       "      <td>GLN3</td>\n",
+       "      <td>172</td>\n",
        "      <td>SM</td>\n",
+       "      <td>YIR023W</td>\n",
+       "      <td>DAL81</td>\n",
        "      <td>unspecified</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.096117</td>\n",
+       "      <td>0.216562</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>9</th>\n",
-       "      <td>225</td>\n",
-       "      <td>YLR176C</td>\n",
-       "      <td>RFX1</td>\n",
+       "      <td>320</td>\n",
        "      <td>YPD</td>\n",
+       "      <td>YPL038W</td>\n",
+       "      <td>MET31</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>0.033526</td>\n",
+       "      <td>0.066122</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "   sample_id regulator_locus_tag regulator_symbol condition carbon_source  \\\n",
-       "0         50             YDR043C             NRG1    H2O2Lo       glucose   \n",
-       "1        213             YKL222C          YKL222C       YPD       glucose   \n",
-       "2         18             YBR083W             TEC1       YPD       glucose   \n",
-       "3          7             YBL103C             RTG3    H2O2Hi       glucose   \n",
-       "4        277             YNL103W             MET4       YPD       glucose   \n",
-       "5        281             YNL199C             GCR2        SM   unspecified   \n",
-       "6         86             YER040W             GLN3        SM   unspecified   \n",
-       "7        225             YLR176C             RFX1       YPD       glucose   \n",
-       "8         86             YER040W             GLN3        SM   unspecified   \n",
-       "9        225             YLR176C             RFX1       YPD       glucose   \n",
+       "   sample_id condition regulator_locus_tag regulator_symbol carbon_source  \\\n",
+       "0         18       YPD             YBR083W             TEC1       glucose   \n",
+       "1        157    H2O2Hi             YHR206W             SKN7       glucose   \n",
+       "2         93       YPD             YER111C             SWI4       glucose   \n",
+       "3         72       YPD             YDR421W            ARO80       glucose   \n",
+       "4         71        SM             YDR421W            ARO80   unspecified   \n",
+       "5        346      RAPA             YPR104C             FHL1       glucose   \n",
+       "6        226       YPD             YLR182W             SWI6       glucose   \n",
+       "7        286       YPD             YNL309W             STB1       glucose   \n",
+       "8        172        SM             YIR023W            DAL81   unspecified   \n",
+       "9        320       YPD             YPL038W            MET31       glucose   \n",
        "\n",
        "   temperature_celsius  dto_empirical_pvalue   dto_fdr  \n",
-       "0                 30.0                   0.0  0.081863  \n",
-       "1                 30.0                   0.0  0.000000  \n",
-       "2                 30.0                   0.0  0.062067  \n",
-       "3                 30.0                   0.0  0.157723  \n",
-       "4                 30.0                   0.0  0.016282  \n",
-       "5                 30.0                   0.0  0.029635  \n",
-       "6                 30.0                   0.0  0.229889  \n",
-       "7                 30.0                   0.0  0.014456  \n",
-       "8                 30.0                   0.0  0.096117  \n",
-       "9                 30.0                   0.0  0.033526  "
+       "0                 30.0                   0.0  0.081882  \n",
+       "1                 30.0                   0.0  0.139320  \n",
+       "2                 30.0                   0.0  0.170051  \n",
+       "3                 30.0                   0.0  0.000114  \n",
+       "4                 30.0                   0.0  0.000114  \n",
+       "5                 30.0                   0.0  0.019746  \n",
+       "6                 30.0                   0.0  0.073690  \n",
+       "7                 30.0                   0.0  0.182147  \n",
+       "8                 30.0                   0.0  0.216562  \n",
+       "9                 30.0                   0.0  0.066122  "
       ]
      },
-     "execution_count": 11,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2426,7 +2506,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "id": "cell-23",
    "metadata": {},
    "outputs": [
@@ -2460,77 +2540,77 @@
          "type": "string"
         }
        ],
-       "ref": "b916ca80-75d1-448d-82a5-c82086ca1ed9",
+       "ref": "18363370-be4d-4693-8836-96409a2ac869",
        "rows": [
         [
          "0",
-         "289",
-         "DAL82",
+         "15",
+         "REB1",
          "0.0",
-         "1208"
+         "100_242"
         ],
         [
          "1",
-         "251",
-         "MAC1",
+         "303",
+         "CIN5",
          "0.0",
-         "1103"
+         "1280"
         ],
         [
          "2",
-         "321",
-         "DIG1",
+         "330",
+         "CUP9",
          "0.0",
-         "1372"
+         "256"
         ],
         [
          "3",
-         "238",
-         "YAP1",
+         "114",
+         "AFT1",
          "0.0",
-         "996"
+         "87"
         ],
         [
          "4",
-         "303",
-         "CIN5",
+         "9",
+         "RTG3",
          "0.0",
-         "1365"
+         "57"
         ],
         [
          "5",
-         "245",
-         "ARG81",
+         "118",
+         "HSF1",
          "0.0",
-         "1023"
+         "88"
         ],
         [
          "6",
-         "184",
-         "CBF1",
+         "15",
+         "REB1",
          "0.0",
-         "754"
+         "100_242"
         ],
         [
          "7",
-         "252",
-         "MAC1",
+         "162",
+         "XBP1",
          "0.0",
-         "1103"
+         "24"
         ],
         [
          "8",
-         "200",
-         "PHD1",
+         "240",
+         "YAP1",
          "0.0",
-         "890"
+         "182"
         ],
         [
          "9",
-         "251",
-         "MAC1",
+         "150",
+         "STP2",
          "0.0",
-         "1110"
+         "604"
         ]
        ],
        "shape": {
@@ -2566,73 +2646,73 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>289</td>\n",
-       "      <td>DAL82</td>\n",
+       "      <td>15</td>\n",
+       "      <td>REB1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1208</td>\n",
+       "      <td>100_242</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>251</td>\n",
-       "      <td>MAC1</td>\n",
+       "      <td>303</td>\n",
+       "      <td>CIN5</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1103</td>\n",
+       "      <td>1280</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>321</td>\n",
-       "      <td>DIG1</td>\n",
+       "      <td>330</td>\n",
+       "      <td>CUP9</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1372</td>\n",
+       "      <td>256</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>238</td>\n",
-       "      <td>YAP1</td>\n",
+       "      <td>114</td>\n",
+       "      <td>AFT1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>996</td>\n",
+       "      <td>87</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>303</td>\n",
-       "      <td>CIN5</td>\n",
+       "      <td>9</td>\n",
+       "      <td>RTG3</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1365</td>\n",
+       "      <td>57</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>5</th>\n",
-       "      <td>245</td>\n",
-       "      <td>ARG81</td>\n",
+       "      <td>118</td>\n",
+       "      <td>HSF1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1023</td>\n",
+       "      <td>88</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>6</th>\n",
-       "      <td>184</td>\n",
-       "      <td>CBF1</td>\n",
+       "      <td>15</td>\n",
+       "      <td>REB1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>754</td>\n",
+       "      <td>100_242</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>7</th>\n",
-       "      <td>252</td>\n",
-       "      <td>MAC1</td>\n",
+       "      <td>162</td>\n",
+       "      <td>XBP1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1103</td>\n",
+       "      <td>24</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>8</th>\n",
-       "      <td>200</td>\n",
-       "      <td>PHD1</td>\n",
+       "      <td>240</td>\n",
+       "      <td>YAP1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>890</td>\n",
+       "      <td>182</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>9</th>\n",
-       "      <td>251</td>\n",
-       "      <td>MAC1</td>\n",
+       "      <td>150</td>\n",
+       "      <td>STP2</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>1110</td>\n",
+       "      <td>604</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -2640,19 +2720,19 @@
       ],
       "text/plain": [
        "   harbison_sample_id regulator_symbol  dto_empirical_pvalue hackett_sample_id\n",
-       "0                 289            DAL82                   0.0              1208\n",
-       "1                 251             MAC1                   0.0              1103\n",
-       "2                 321             DIG1                   0.0              1372\n",
-       "3                 238             YAP1                   0.0               996\n",
-       "4                 303             CIN5                   0.0              1365\n",
-       "5                 245            ARG81                   0.0              1023\n",
-       "6                 184             CBF1                   0.0               754\n",
-       "7                 252             MAC1                   0.0              1103\n",
-       "8                 200             PHD1                   0.0               890\n",
-       "9                 251             MAC1                   0.0              1110"
+       "0                  15             REB1                   0.0           100_242\n",
+       "1                 303             CIN5                   0.0              1280\n",
+       "2                 330             CUP9                   0.0               256\n",
+       "3                 114             AFT1                   0.0                87\n",
+       "4                   9             RTG3                   0.0                57\n",
+       "5                 118             HSF1                   0.0                88\n",
+       "6                  15             REB1                   0.0           100_242\n",
+       "7                 162             XBP1                   0.0                24\n",
+       "8                 240             YAP1                   0.0               182\n",
+       "9                 150             STP2                   0.0               604"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2690,7 +2770,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "id": "f03e942a",
    "metadata": {},
    "outputs": [
@@ -2729,12 +2809,12 @@
          "type": "integer"
         }
        ],
-       "ref": "1185b490-3375-41d0-b61c-0f35dae2b815",
+       "ref": "0736a331-fb06-4ba3-abe4-dff7ac0e65a3",
        "rows": [
         [
          "0",
          "SWI1",
-         "15.0",
+         "5.0",
          "ZEV",
          "P",
          "3"
@@ -2750,7 +2830,7 @@
         [
          "2",
          "SWI1",
-         "45.0",
+         "20.0",
          "ZEV",
          "P",
          "3"
@@ -2758,7 +2838,7 @@
         [
          "3",
          "SWI1",
-         "5.0",
+         "10.0",
          "ZEV",
          "P",
          "3"
@@ -2766,7 +2846,7 @@
         [
          "4",
          "SWI1",
-         "0.0",
+         "90.0",
          "ZEV",
          "P",
          "3"
@@ -2774,7 +2854,7 @@
         [
          "5",
          "SWI1",
-         "90.0",
+         "0.0",
          "ZEV",
          "P",
          "3"
@@ -2782,7 +2862,7 @@
         [
          "6",
          "SWI1",
-         "10.0",
+         "15.0",
          "ZEV",
          "P",
          "3"
@@ -2790,31 +2870,31 @@
         [
          "7",
          "SWI1",
-         "20.0",
+         "45.0",
          "ZEV",
          "P",
          "3"
         ],
         [
          "8",
-         "GCN4",
-         "0.0",
+         "RDS2",
+         "10.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "9",
-         "GCN4",
-         "30.0",
-         "ZEV",
+         "MAC1",
+         "90.0",
+         "GEV",
          "P",
          "2"
         ],
         [
          "10",
          "MAC1",
-         "0.0",
+         "15.0",
          "GEV",
          "P",
          "2"
@@ -2822,22 +2902,22 @@
         [
          "11",
          "RDS2",
-         "5.0",
+         "20.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "12",
-         "RDS2",
+         "MAC1",
          "45.0",
-         "ZEV",
+         "GEV",
          "P",
          "2"
         ],
         [
          "13",
-         "Z3EV",
+         "RDS2",
          "30.0",
          "ZEV",
          "P",
@@ -2846,46 +2926,46 @@
         [
          "14",
          "GCN4",
-         "90.0",
+         "15.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "15",
-         "Z3EV",
-         "15.0",
-         "ZEV",
+         "MAC1",
+         "30.0",
+         "GEV",
          "P",
          "2"
         ],
         [
          "16",
-         "GCN4",
-         "45.0",
-         "ZEV",
+         "MAC1",
+         "5.0",
+         "GEV",
          "P",
          "2"
         ],
         [
          "17",
-         "MAC1",
-         "5.0",
-         "GEV",
+         "GCN4",
+         "45.0",
+         "ZEV",
          "P",
          "2"
         ],
         [
          "18",
-         "MAC1",
+         "GCN4",
          "90.0",
-         "GEV",
+         "ZEV",
          "P",
          "2"
         ],
         [
          "19",
-         "Z3EV",
+         "RDS2",
          "45.0",
          "ZEV",
          "P",
@@ -2894,38 +2974,38 @@
         [
          "20",
          "RDS2",
-         "10.0",
+         "0.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "21",
-         "GCN4",
-         "15.0",
+         "RDS2",
+         "90.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "22",
-         "RDS2",
-         "90.0",
+         "GCN4",
+         "30.0",
          "ZEV",
          "P",
          "2"
         ],
         [
          "23",
-         "RDS2",
+         "MAC1",
          "0.0",
-         "ZEV",
+         "GEV",
          "P",
          "2"
         ],
         [
          "24",
-         "Z3EV",
+         "RDS2",
          "5.0",
          "ZEV",
          "P",
@@ -2933,88 +3013,24 @@
         ],
         [
          "25",
-         "Z3EV",
-         "90.0",
-         "ZEV",
-         "P",
-         "2"
-        ],
-        [
-         "26",
-         "Z3EV",
-         "20.0",
-         "ZEV",
-         "P",
-         "2"
-        ],
-        [
-         "27",
-         "RDS2",
-         "30.0",
-         "ZEV",
-         "P",
-         "2"
-        ],
-        [
-         "28",
-         "Z3EV",
+         "GCN4",
          "0.0",
          "ZEV",
          "P",
          "2"
         ],
         [
-         "29",
+         "26",
          "RDS2",
          "15.0",
          "ZEV",
          "P",
          "2"
-        ],
-        [
-         "30",
-         "Z3EV",
-         "10.0",
-         "ZEV",
-         "P",
-         "2"
-        ],
-        [
-         "31",
-         "RDS2",
-         "20.0",
-         "ZEV",
-         "P",
-         "2"
-        ],
-        [
-         "32",
-         "MAC1",
-         "45.0",
-         "GEV",
-         "P",
-         "2"
-        ],
-        [
-         "33",
-         "MAC1",
-         "15.0",
-         "GEV",
-         "P",
-         "2"
-        ],
-        [
-         "34",
-         "MAC1",
-         "30.0",
-         "GEV",
-         "P",
-         "2"
         ]
        ],
        "shape": {
         "columns": 5,
-        "rows": 35
+        "rows": 27
        }
       },
       "text/html": [
@@ -3047,7 +3063,7 @@
        "    <tr>\n",
        "      <th>0</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>15.0</td>\n",
+       "      <td>5.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3063,7 +3079,7 @@
        "    <tr>\n",
        "      <th>2</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>45.0</td>\n",
+       "      <td>20.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3071,7 +3087,7 @@
        "    <tr>\n",
        "      <th>3</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>5.0</td>\n",
+       "      <td>10.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3079,7 +3095,7 @@
        "    <tr>\n",
        "      <th>4</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>0.0</td>\n",
+       "      <td>90.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3087,7 +3103,7 @@
        "    <tr>\n",
        "      <th>5</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>90.0</td>\n",
+       "      <td>0.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3095,7 +3111,7 @@
        "    <tr>\n",
        "      <th>6</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>10.0</td>\n",
+       "      <td>15.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
@@ -3103,31 +3119,31 @@
        "    <tr>\n",
        "      <th>7</th>\n",
        "      <td>SWI1</td>\n",
-       "      <td>20.0</td>\n",
+       "      <td>45.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>3</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>8</th>\n",
-       "      <td>GCN4</td>\n",
-       "      <td>0.0</td>\n",
+       "      <td>RDS2</td>\n",
+       "      <td>10.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>9</th>\n",
-       "      <td>GCN4</td>\n",
-       "      <td>30.0</td>\n",
-       "      <td>ZEV</td>\n",
+       "      <td>MAC1</td>\n",
+       "      <td>90.0</td>\n",
+       "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>10</th>\n",
        "      <td>MAC1</td>\n",
-       "      <td>0.0</td>\n",
+       "      <td>15.0</td>\n",
        "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
@@ -3135,22 +3151,22 @@
        "    <tr>\n",
        "      <th>11</th>\n",
        "      <td>RDS2</td>\n",
-       "      <td>5.0</td>\n",
+       "      <td>20.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>12</th>\n",
-       "      <td>RDS2</td>\n",
+       "      <td>MAC1</td>\n",
        "      <td>45.0</td>\n",
-       "      <td>ZEV</td>\n",
+       "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>13</th>\n",
-       "      <td>Z3EV</td>\n",
+       "      <td>RDS2</td>\n",
        "      <td>30.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
@@ -3159,46 +3175,46 @@
        "    <tr>\n",
        "      <th>14</th>\n",
        "      <td>GCN4</td>\n",
-       "      <td>90.0</td>\n",
+       "      <td>15.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>15</th>\n",
-       "      <td>Z3EV</td>\n",
-       "      <td>15.0</td>\n",
-       "      <td>ZEV</td>\n",
+       "      <td>MAC1</td>\n",
+       "      <td>30.0</td>\n",
+       "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>16</th>\n",
-       "      <td>GCN4</td>\n",
-       "      <td>45.0</td>\n",
-       "      <td>ZEV</td>\n",
+       "      <td>MAC1</td>\n",
+       "      <td>5.0</td>\n",
+       "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>17</th>\n",
-       "      <td>MAC1</td>\n",
-       "      <td>5.0</td>\n",
-       "      <td>GEV</td>\n",
+       "      <td>GCN4</td>\n",
+       "      <td>45.0</td>\n",
+       "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>18</th>\n",
-       "      <td>MAC1</td>\n",
+       "      <td>GCN4</td>\n",
        "      <td>90.0</td>\n",
-       "      <td>GEV</td>\n",
+       "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>19</th>\n",
-       "      <td>Z3EV</td>\n",
+       "      <td>RDS2</td>\n",
        "      <td>45.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
@@ -3207,38 +3223,38 @@
        "    <tr>\n",
        "      <th>20</th>\n",
        "      <td>RDS2</td>\n",
-       "      <td>10.0</td>\n",
+       "      <td>0.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>21</th>\n",
-       "      <td>GCN4</td>\n",
-       "      <td>15.0</td>\n",
+       "      <td>RDS2</td>\n",
+       "      <td>90.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>22</th>\n",
-       "      <td>RDS2</td>\n",
-       "      <td>90.0</td>\n",
+       "      <td>GCN4</td>\n",
+       "      <td>30.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>23</th>\n",
-       "      <td>RDS2</td>\n",
+       "      <td>MAC1</td>\n",
        "      <td>0.0</td>\n",
-       "      <td>ZEV</td>\n",
+       "      <td>GEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>24</th>\n",
-       "      <td>Z3EV</td>\n",
+       "      <td>RDS2</td>\n",
        "      <td>5.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
@@ -3246,128 +3262,56 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>25</th>\n",
-       "      <td>Z3EV</td>\n",
-       "      <td>90.0</td>\n",
-       "      <td>ZEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>26</th>\n",
-       "      <td>Z3EV</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>ZEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>27</th>\n",
-       "      <td>RDS2</td>\n",
-       "      <td>30.0</td>\n",
-       "      <td>ZEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>28</th>\n",
-       "      <td>Z3EV</td>\n",
+       "      <td>GCN4</td>\n",
        "      <td>0.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>29</th>\n",
+       "      <th>26</th>\n",
        "      <td>RDS2</td>\n",
        "      <td>15.0</td>\n",
        "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
        "      <td>2</td>\n",
        "    </tr>\n",
-       "    <tr>\n",
-       "      <th>30</th>\n",
-       "      <td>Z3EV</td>\n",
-       "      <td>10.0</td>\n",
-       "      <td>ZEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>31</th>\n",
-       "      <td>RDS2</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>ZEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>32</th>\n",
-       "      <td>MAC1</td>\n",
-       "      <td>45.0</td>\n",
-       "      <td>GEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>33</th>\n",
-       "      <td>MAC1</td>\n",
-       "      <td>15.0</td>\n",
-       "      <td>GEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>34</th>\n",
-       "      <td>MAC1</td>\n",
-       "      <td>30.0</td>\n",
-       "      <td>GEV</td>\n",
-       "      <td>P</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
        "   regulator_symbol  time mechanism restriction  n\n",
-       "0              SWI1  15.0       ZEV           P  3\n",
+       "0              SWI1   5.0       ZEV           P  3\n",
        "1              SWI1  30.0       ZEV           P  3\n",
-       "2              SWI1  45.0       ZEV           P  3\n",
-       "3              SWI1   5.0       ZEV           P  3\n",
-       "4              SWI1   0.0       ZEV           P  3\n",
-       "5              SWI1  90.0       ZEV           P  3\n",
-       "6              SWI1  10.0       ZEV           P  3\n",
-       "7              SWI1  20.0       ZEV           P  3\n",
-       "8              GCN4   0.0       ZEV           P  2\n",
-       "9              GCN4  30.0       ZEV           P  2\n",
-       "10             MAC1   0.0       GEV           P  2\n",
-       "11             RDS2   5.0       ZEV           P  2\n",
-       "12             RDS2  45.0       ZEV           P  2\n",
-       "13             Z3EV  30.0       ZEV           P  2\n",
-       "14             GCN4  90.0       ZEV           P  2\n",
-       "15             Z3EV  15.0       ZEV           P  2\n",
-       "16             GCN4  45.0       ZEV           P  2\n",
-       "17             MAC1   5.0       GEV           P  2\n",
-       "18             MAC1  90.0       GEV           P  2\n",
-       "19             Z3EV  45.0       ZEV           P  2\n",
-       "20             RDS2  10.0       ZEV           P  2\n",
-       "21             GCN4  15.0       ZEV           P  2\n",
-       "22             RDS2  90.0       ZEV           P  2\n",
-       "23             RDS2   0.0       ZEV           P  2\n",
-       "24             Z3EV   5.0       ZEV           P  2\n",
-       "25             Z3EV  90.0       ZEV           P  2\n",
-       "26             Z3EV  20.0       ZEV           P  2\n",
-       "27             RDS2  30.0       ZEV           P  2\n",
-       "28             Z3EV   0.0       ZEV           P  2\n",
-       "29             RDS2  15.0       ZEV           P  2\n",
-       "30             Z3EV  10.0       ZEV           P  2\n",
-       "31             RDS2  20.0       ZEV           P  2\n",
-       "32             MAC1  45.0       GEV           P  2\n",
-       "33             MAC1  15.0       GEV           P  2\n",
-       "34             MAC1  30.0       GEV           P  2"
+       "2              SWI1  20.0       ZEV           P  3\n",
+       "3              SWI1  10.0       ZEV           P  3\n",
+       "4              SWI1  90.0       ZEV           P  3\n",
+       "5              SWI1   0.0       ZEV           P  3\n",
+       "6              SWI1  15.0       ZEV           P  3\n",
+       "7              SWI1  45.0       ZEV           P  3\n",
+       "8              RDS2  10.0       ZEV           P  2\n",
+       "9              MAC1  90.0       GEV           P  2\n",
+       "10             MAC1  15.0       GEV           P  2\n",
+       "11             RDS2  20.0       ZEV           P  2\n",
+       "12             MAC1  45.0       GEV           P  2\n",
+       "13             RDS2  30.0       ZEV           P  2\n",
+       "14             GCN4  15.0       ZEV           P  2\n",
+       "15             MAC1  30.0       GEV           P  2\n",
+       "16             MAC1   5.0       GEV           P  2\n",
+       "17             GCN4  45.0       ZEV           P  2\n",
+       "18             GCN4  90.0       ZEV           P  2\n",
+       "19             RDS2  45.0       ZEV           P  2\n",
+       "20             RDS2   0.0       ZEV           P  2\n",
+       "21             RDS2  90.0       ZEV           P  2\n",
+       "22             GCN4  30.0       ZEV           P  2\n",
+       "23             MAC1   0.0       GEV           P  2\n",
+       "24             RDS2   5.0       ZEV           P  2\n",
+       "25             GCN4   0.0       ZEV           P  2\n",
+       "26             RDS2  15.0       ZEV           P  2"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3386,7 +3330,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "id": "4d869036",
    "metadata": {},
    "outputs": [
@@ -3405,32 +3349,27 @@
          "type": "integer"
         },
         {
-         "name": "regulator_locus_tag",
+         "name": "date",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "regulator_symbol",
+         "name": "mechanism",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "time",
-         "rawType": "float64",
-         "type": "float"
-        },
-        {
-         "name": "mechanism",
+         "name": "regulator_locus_tag",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "restriction",
+         "name": "regulator_symbol",
          "rawType": "object",
          "type": "string"
         },
         {
-         "name": "date",
+         "name": "restriction",
          "rawType": "object",
          "type": "string"
         },
@@ -3439,6 +3378,11 @@
          "rawType": "object",
          "type": "string"
         },
+        {
+         "name": "time",
+         "rawType": "float64",
+         "type": "float"
+        },
         {
          "name": "carbon_source",
          "rawType": "object",
@@ -3450,44 +3394,44 @@
          "type": "float"
         }
        ],
-       "ref": "440ab0a2-f84a-4505-8380-e218512394f7",
+       "ref": "0f36c45d-0bab-4761-98f1-0e2a625be2df",
        "rows": [
         [
          "0",
-         "1620",
+         "1636",
+         "20161117",
+         "ZEV",
          "YPL016W",
          "SWI1",
-         "20.0",
-         "ZEV",
          "P",
-         "20161117",
-         "SMY2266a",
+         "SMY2266c",
+         "20.0",
          "glucose",
          "30.0"
         ],
         [
          "1",
          "1628",
+         "20161117",
+         "ZEV",
          "YPL016W",
          "SWI1",
-         "20.0",
-         "ZEV",
          "P",
-         "20161117",
          "SMY2266b",
+         "20.0",
          "glucose",
          "30.0"
         ],
         [
          "2",
-         "1636",
+         "1620",
+         "20161117",
+         "ZEV",
          "YPL016W",
          "SWI1",
-         "20.0",
-         "ZEV",
          "P",
-         "20161117",
-         "SMY2266c",
+         "SMY2266a",
+         "20.0",
          "glucose",
          "30.0"
         ]
@@ -3517,13 +3461,13 @@
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>sample_id</th>\n",
+       "      <th>date</th>\n",
+       "      <th>mechanism</th>\n",
        "      <th>regulator_locus_tag</th>\n",
        "      <th>regulator_symbol</th>\n",
-       "      <th>time</th>\n",
-       "      <th>mechanism</th>\n",
        "      <th>restriction</th>\n",
-       "      <th>date</th>\n",
        "      <th>strain</th>\n",
+       "      <th>time</th>\n",
        "      <th>carbon_source</th>\n",
        "      <th>temperature_celsius</th>\n",
        "    </tr>\n",
@@ -3531,40 +3475,40 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>1620</td>\n",
+       "      <td>1636</td>\n",
+       "      <td>20161117</td>\n",
+       "      <td>ZEV</td>\n",
        "      <td>YPL016W</td>\n",
        "      <td>SWI1</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
-       "      <td>20161117</td>\n",
-       "      <td>SMY2266a</td>\n",
+       "      <td>SMY2266c</td>\n",
+       "      <td>20.0</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
        "      <td>1628</td>\n",
+       "      <td>20161117</td>\n",
+       "      <td>ZEV</td>\n",
        "      <td>YPL016W</td>\n",
        "      <td>SWI1</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
-       "      <td>20161117</td>\n",
        "      <td>SMY2266b</td>\n",
+       "      <td>20.0</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>1636</td>\n",
+       "      <td>1620</td>\n",
+       "      <td>20161117</td>\n",
+       "      <td>ZEV</td>\n",
        "      <td>YPL016W</td>\n",
        "      <td>SWI1</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>ZEV</td>\n",
        "      <td>P</td>\n",
-       "      <td>20161117</td>\n",
-       "      <td>SMY2266c</td>\n",
+       "      <td>SMY2266a</td>\n",
+       "      <td>20.0</td>\n",
        "      <td>glucose</td>\n",
        "      <td>30.0</td>\n",
        "    </tr>\n",
@@ -3573,18 +3517,18 @@
        "</div>"
       ],
       "text/plain": [
-       "   sample_id regulator_locus_tag regulator_symbol  time mechanism restriction  \\\n",
-       "0       1620             YPL016W             SWI1  20.0       ZEV           P   \n",
-       "1       1628             YPL016W             SWI1  20.0       ZEV           P   \n",
-       "2       1636             YPL016W             SWI1  20.0       ZEV           P   \n",
+       "   sample_id      date mechanism regulator_locus_tag regulator_symbol  \\\n",
+       "0       1636  20161117       ZEV             YPL016W             SWI1   \n",
+       "1       1628  20161117       ZEV             YPL016W             SWI1   \n",
+       "2       1620  20161117       ZEV             YPL016W             SWI1   \n",
        "\n",
-       "       date    strain carbon_source  temperature_celsius  \n",
-       "0  20161117  SMY2266a       glucose                 30.0  \n",
-       "1  20161117  SMY2266b       glucose                 30.0  \n",
-       "2  20161117  SMY2266c       glucose                 30.0  "
+       "  restriction    strain  time carbon_source  temperature_celsius  \n",
+       "0           P  SMY2266c  20.0       glucose                 30.0  \n",
+       "1           P  SMY2266b  20.0       glucose                 30.0  \n",
+       "2           P  SMY2266a  20.0       glucose                 30.0  "
       ]
      },
-     "execution_count": 14,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3602,7 +3546,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "89408d2b",
    "metadata": {},
    "outputs": [
@@ -3610,7 +3554,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['GCN4', 'MAC1', 'SWI1', 'Z3EV', 'RDS2']\n"
+      "['MAC1', 'SWI1', 'GCN4', 'RDS2']\n"
      ]
     }
    ],
@@ -3630,7 +3574,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "id": "5a3b802b",
    "metadata": {},
    "outputs": [
@@ -3638,7 +3582,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['GCN4', 'MAC1', 'SWI1', 'Z3EV', 'RDS2', 'GEV']\n"
+      "['MAC1', 'SWI1', 'GCN4', 'RDS2', 'GEV']\n"
      ]
     }
    ],
@@ -3650,7 +3594,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "id": "abed8bc2",
    "metadata": {},
    "outputs": [
@@ -3703,6 +3647,11 @@
          "rawType": "float64",
          "type": "float"
         },
+        {
+         "name": "pr_ranking_column",
+         "rawType": "object",
+         "type": "string"
+        },
         {
          "name": "binding_repo_dataset",
          "rawType": "object",
@@ -3734,862 +3683,912 @@
          "type": "string"
         }
        ],
-       "ref": "b9dead21-45e7-491d-82d4-a2358af05efe",
+       "ref": "b0a3d538-3af3-4f72-8610-7722a73a7a4f",
        "rows": [
         [
          "0",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;85",
-         "2.0",
-         "2.0",
-         "3.0",
-         "2.0",
-         "0.0002250900360144",
-         "0.004",
+         "BrentLab/harbison_2004;harbison_2004;105",
+         "BrentLab/hughes_2006;overexpression;10",
+         "11.0",
+         "206.0",
+         "12.0",
+         "206.0",
+         "0.041292917490562644",
+         "0.017",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "105",
          "harbison",
-         "85",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "10",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "1",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;83",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;108",
+         "BrentLab/hughes_2006;overexpression;11",
+         "60.0",
+         "67.0",
+         "60.0",
+         "67.0",
+         "0.05428351009647073",
+         "0.0",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "108",
          "harbison",
-         "83",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "11",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "2",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;84",
-         "2.0",
-         "1.0",
-         "3.0",
-         "1.0",
-         "0.0",
-         "0.011",
+         "BrentLab/harbison_2004;harbison_2004;109",
+         "BrentLab/hughes_2006;overexpression;11",
+         "27.0",
+         "1265.0",
+         "27.0",
+         "1265.0",
+         "0.12321364371741866",
+         "0.057",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "109",
          "harbison",
-         "84",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "11",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "3",
-         "BrentLab/harbison_2004;harbison_2004;4",
-         "BrentLab/Hackett_2020;hackett_2020;78",
-         "487.0",
-         "96.0",
-         "479.0",
-         "92.0",
-         "0.4121918908550328",
-         "0.576",
+         "BrentLab/harbison_2004;harbison_2004;112",
+         "BrentLab/hughes_2006;overexpression;12",
+         "532.0",
+         "1093.0",
+         "532.0",
+         "1093.0",
+         "0.4363046674390623",
+         "0.092",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "4",
+         "hughes_2006-overexpression",
+         "112",
          "harbison",
-         "78",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "12",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "4",
-         "BrentLab/harbison_2004;harbison_2004;3",
-         "BrentLab/Hackett_2020;hackett_2020;81",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;113",
+         "BrentLab/hughes_2006;overexpression;12",
+         "10.0",
+         "556.0",
+         "10.0",
+         "556.0",
+         "0.01756663927480034",
+         "0.002",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "3",
+         "hughes_2006-overexpression",
+         "113",
          "harbison",
-         "81",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "12",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "5",
-         "BrentLab/harbison_2004;harbison_2004;2",
-         "BrentLab/Hackett_2020;hackett_2020;33",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;118",
+         "BrentLab/hughes_2006;overexpression;13",
+         "574.0",
+         "354.0",
+         "574.0",
+         "354.0",
+         "0.13894295437217577",
+         "0.0",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "2",
+         "hughes_2006-overexpression",
+         "118",
          "harbison",
-         "33",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "13",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "6",
-         "BrentLab/harbison_2004;harbison_2004;4",
-         "BrentLab/Hackett_2020;hackett_2020;73",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;119",
+         "BrentLab/hughes_2006;overexpression;13",
+         "251.0",
+         "492.0",
+         "251.0",
+         "492.0",
+         "0.11808548603694578",
+         "0.0",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "4",
+         "hughes_2006-overexpression",
+         "119",
          "harbison",
-         "73",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "13",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "7",
-         "BrentLab/harbison_2004;harbison_2004;7",
-         "BrentLab/Hackett_2020;hackett_2020;47",
-         "407.0",
-         "310.0",
-         "378.0",
-         "306.0",
-         "0.2038622347205313",
-         "0.441",
+         "BrentLab/harbison_2004;harbison_2004;120",
+         "BrentLab/hughes_2006;overexpression;13",
+         "14.0",
+         "2954.0",
+         "14.0",
+         "2954.0",
+         "0.1616346595561947",
+         "1.0",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "7",
+         "hughes_2006-overexpression",
+         "120",
          "harbison",
-         "47",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "13",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "8",
-         "BrentLab/harbison_2004;harbison_2004;7",
-         "BrentLab/Hackett_2020;hackett_2020;46",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;121",
+         "BrentLab/hughes_2006;overexpression;13",
+         "422.0",
+         "544.0",
+         "423.0",
+         "544.0",
+         "0.401585299611564",
+         "0.001",
+         "log2fc",
          "harbison_2004-harbison_2004",
-         "Hackett_2020-hackett_2020",
-         "7",
+         "hughes_2006-overexpression",
+         "121",
          "harbison",
-         "46",
-         "BrentLab/Hackett_2020;hackett_2020"
+         "13",
+         "BrentLab/hughes_2006;overexpression"
         ],
         [
          "9",
-         "BrentLab/harbison_2004;harbison_2004;7",
-         "BrentLab/Hackett_2020;hackett_2020;45",
-         null,
-         null,
-         null,
-         null,
-         null,
-         null,
+         "BrentLab/harbison_2004;harbison_2004;122",
+         "BrentLab/hughes_2006;overexpression;14",
+         "842.0",
+         "152.0",
+         "842.0",
+         "152.0",
+         "0.37750827352885596",
+         "0.106",
+         "log2fc",
          "harbison_2004-harbison_2004",
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@@ -4619,6 +4618,7 @@
        "      <th>perturbation_set_size</th>\n",
        "      <th>dto_fdr</th>\n",
        "      <th>dto_empirical_pvalue</th>\n",
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        "      <th>binding_repo_dataset</th>\n",
        "      <th>perturbation_repo_dataset</th>\n",
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+       "      <td>BrentLab/harbison_2004;harbison_2004;112</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression;12</td>\n",
+       "      <td>532.0</td>\n",
+       "      <td>1093.0</td>\n",
+       "      <td>532.0</td>\n",
+       "      <td>1093.0</td>\n",
+       "      <td>0.436305</td>\n",
+       "      <td>0.092</td>\n",
+       "      <td>log2fc</td>\n",
        "      <td>harbison_2004-harbison_2004</td>\n",
-       "      <td>Hackett_2020-hackett_2020</td>\n",
-       "      <td>4</td>\n",
+       "      <td>hughes_2006-overexpression</td>\n",
+       "      <td>112</td>\n",
        "      <td>harbison</td>\n",
-       "      <td>78</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020</td>\n",
+       "      <td>12</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>BrentLab/harbison_2004;harbison_2004;3</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020;81</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",
+       "      <td>BrentLab/harbison_2004;harbison_2004;113</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression;12</td>\n",
+       "      <td>10.0</td>\n",
+       "      <td>556.0</td>\n",
+       "      <td>10.0</td>\n",
+       "      <td>556.0</td>\n",
+       "      <td>0.017567</td>\n",
+       "      <td>0.002</td>\n",
+       "      <td>log2fc</td>\n",
        "      <td>harbison_2004-harbison_2004</td>\n",
-       "      <td>Hackett_2020-hackett_2020</td>\n",
-       "      <td>3</td>\n",
+       "      <td>hughes_2006-overexpression</td>\n",
+       "      <td>113</td>\n",
        "      <td>harbison</td>\n",
-       "      <td>81</td>\n",
-       "      <td>BrentLab/Hackett_2020;hackett_2020</td>\n",
+       "      <td>12</td>\n",
+       "      <td>BrentLab/hughes_2006;overexpression</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>...</th>\n",
@@ -4729,193 +4734,199 @@
        "      <td>...</td>\n",
        "      <td>...</td>\n",
        "      <td>...</td>\n",
+       "      <td>...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>9599</th>\n",
-       "      <td>BrentLab/callingcards;annotated_features;804</td>\n",
-       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;901</td>\n",
-       "      <td>14.0</td>\n",
-       "      <td>39.0</td>\n",
-       "      <td>13.0</td>\n",
-       "      <td>39.0</td>\n",
-       "      <td>0.000879</td>\n",
+       "      <th>29799</th>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combi...</td>\n",
+       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;784</td>\n",
+       "      <td>154.0</td>\n",
+       "      <td>905.0</td>\n",
+       "      <td>154.0</td>\n",
+       "      <td>905.0</td>\n",
+       "      <td>0.090665</td>\n",
        "      <td>0.000</td>\n",
-       "      <td>callingcards-annotated_features</td>\n",
+       "      <td>pvalue</td>\n",
+       "      <td>callingcards-annotated_features_combined</td>\n",
        "      <td>kemmeren_2014-kemmeren_2014</td>\n",
-       "      <td>804</td>\n",
-       "      <td>BrentLab/callingcards;annotated_features</td>\n",
-       "      <td>901</td>\n",
+       "      <td>724-692-688</td>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combined</td>\n",
+       "      <td>784</td>\n",
        "      <td>kemmeren</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>9600</th>\n",
-       "      <td>BrentLab/callingcards;annotated_features;805</td>\n",
-       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;1053</td>\n",
-       "      <td>18.0</td>\n",
-       "      <td>278.0</td>\n",
-       "      <td>17.0</td>\n",
-       "      <td>171.0</td>\n",
-       "      <td>0.001455</td>\n",
-       "      <td>0.000</td>\n",
-       "      <td>callingcards-annotated_features</td>\n",
+       "      <th>29800</th>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combi...</td>\n",
+       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;666</td>\n",
+       "      <td>215.0</td>\n",
+       "      <td>108.0</td>\n",
+       "      <td>215.0</td>\n",
+       "      <td>108.0</td>\n",
+       "      <td>0.075036</td>\n",
+       "      <td>0.005</td>\n",
+       "      <td>pvalue</td>\n",
+       "      <td>callingcards-annotated_features_combined</td>\n",
        "      <td>kemmeren_2014-kemmeren_2014</td>\n",
-       "      <td>805</td>\n",
-       "      <td>BrentLab/callingcards;annotated_features</td>\n",
-       "      <td>1053</td>\n",
+       "      <td>725-435-395</td>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combined</td>\n",
+       "      <td>666</td>\n",
        "      <td>kemmeren</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>9601</th>\n",
-       "      <td>BrentLab/callingcards;annotated_features;808</td>\n",
-       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;218</td>\n",
-       "      <td>20.0</td>\n",
-       "      <td>57.0</td>\n",
-       "      <td>19.0</td>\n",
-       "      <td>27.0</td>\n",
-       "      <td>0.003116</td>\n",
-       "      <td>0.000</td>\n",
-       "      <td>callingcards-annotated_features</td>\n",
+       "      <th>29801</th>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combi...</td>\n",
+       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;271</td>\n",
+       "      <td>221.0</td>\n",
+       "      <td>925.0</td>\n",
+       "      <td>221.0</td>\n",
+       "      <td>925.0</td>\n",
+       "      <td>0.403484</td>\n",
+       "      <td>0.126</td>\n",
+       "      <td>pvalue</td>\n",
+       "      <td>callingcards-annotated_features_combined</td>\n",
        "      <td>kemmeren_2014-kemmeren_2014</td>\n",
-       "      <td>808</td>\n",
-       "      <td>BrentLab/callingcards;annotated_features</td>\n",
-       "      <td>218</td>\n",
+       "      <td>726-445-424</td>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combined</td>\n",
+       "      <td>271</td>\n",
        "      <td>kemmeren</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>9602</th>\n",
-       "      <td>BrentLab/callingcards;annotated_features;806</td>\n",
-       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;1023</td>\n",
-       "      <td>10.0</td>\n",
-       "      <td>9.0</td>\n",
-       "      <td>11.0</td>\n",
-       "      <td>9.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000</td>\n",
-       "      <td>callingcards-annotated_features</td>\n",
+       "      <th>29802</th>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combi...</td>\n",
+       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;1077</td>\n",
+       "      <td>281.0</td>\n",
+       "      <td>73.0</td>\n",
+       "      <td>283.0</td>\n",
+       "      <td>77.0</td>\n",
+       "      <td>0.095948</td>\n",
+       "      <td>0.174</td>\n",
+       "      <td>pvalue</td>\n",
+       "      <td>callingcards-annotated_features_combined</td>\n",
        "      <td>kemmeren_2014-kemmeren_2014</td>\n",
-       "      <td>806</td>\n",
-       "      <td>BrentLab/callingcards;annotated_features</td>\n",
-       "      <td>1023</td>\n",
+       "      <td>79-33</td>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combined</td>\n",
+       "      <td>1077</td>\n",
        "      <td>kemmeren</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>9603</th>\n",
-       "      <td>BrentLab/callingcards;annotated_features;809</td>\n",
-       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;913</td>\n",
-       "      <td>150.0</td>\n",
-       "      <td>221.0</td>\n",
-       "      <td>140.0</td>\n",
-       "      <td>206.0</td>\n",
-       "      <td>0.116890</td>\n",
+       "      <th>29803</th>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combi...</td>\n",
+       "      <td>BrentLab/kemmeren_2014;kemmeren_2014;963</td>\n",
+       "      <td>526.0</td>\n",
+       "      <td>227.0</td>\n",
+       "      <td>527.0</td>\n",
+       "      <td>227.0</td>\n",
+       "      <td>0.064919</td>\n",
        "      <td>0.000</td>\n",
-       "      <td>callingcards-annotated_features</td>\n",
+       "      <td>pvalue</td>\n",
+       "      <td>callingcards-annotated_features_combined</td>\n",
        "      <td>kemmeren_2014-kemmeren_2014</td>\n",
-       "      <td>809</td>\n",
-       "      <td>BrentLab/callingcards;annotated_features</td>\n",
-       "      <td>913</td>\n",
+       "      <td>96-49</td>\n",
+       "      <td>BrentLab/callingcards;annotated_features_combined</td>\n",
+       "      <td>963</td>\n",
        "      <td>kemmeren</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
-       "<p>9604 rows × 14 columns</p>\n",
+       "<p>29804 rows × 15 columns</p>\n",
        "</div>"
       ],
       "text/plain": [
-       "                                        binding_id  \\\n",
-       "0           BrentLab/harbison_2004;harbison_2004;3   \n",
-       "1           BrentLab/harbison_2004;harbison_2004;3   \n",
-       "2           BrentLab/harbison_2004;harbison_2004;3   \n",
-       "3           BrentLab/harbison_2004;harbison_2004;4   \n",
-       "4           BrentLab/harbison_2004;harbison_2004;3   \n",
-       "...                                            ...   \n",
-       "9599  BrentLab/callingcards;annotated_features;804   \n",
-       "9600  BrentLab/callingcards;annotated_features;805   \n",
-       "9601  BrentLab/callingcards;annotated_features;808   \n",
-       "9602  BrentLab/callingcards;annotated_features;806   \n",
-       "9603  BrentLab/callingcards;annotated_features;809   \n",
+       "                                              binding_id  \\\n",
+       "0               BrentLab/harbison_2004;harbison_2004;105   \n",
+       "1               BrentLab/harbison_2004;harbison_2004;108   \n",
+       "2               BrentLab/harbison_2004;harbison_2004;109   \n",
+       "3               BrentLab/harbison_2004;harbison_2004;112   \n",
+       "4               BrentLab/harbison_2004;harbison_2004;113   \n",
+       "...                                                  ...   \n",
+       "29799  BrentLab/callingcards;annotated_features_combi...   \n",
+       "29800  BrentLab/callingcards;annotated_features_combi...   \n",
+       "29801  BrentLab/callingcards;annotated_features_combi...   \n",
+       "29802  BrentLab/callingcards;annotated_features_combi...   \n",
+       "29803  BrentLab/callingcards;annotated_features_combi...   \n",
        "\n",
-       "                                perturbation_id  binding_rank_threshold  \\\n",
-       "0         BrentLab/Hackett_2020;hackett_2020;85                     2.0   \n",
-       "1         BrentLab/Hackett_2020;hackett_2020;83                     NaN   \n",
-       "2         BrentLab/Hackett_2020;hackett_2020;84                     2.0   \n",
-       "3         BrentLab/Hackett_2020;hackett_2020;78                   487.0   \n",
-       "4         BrentLab/Hackett_2020;hackett_2020;81                     NaN   \n",
-       "...                                         ...                     ...   \n",
-       "9599   BrentLab/kemmeren_2014;kemmeren_2014;901                    14.0   \n",
-       "9600  BrentLab/kemmeren_2014;kemmeren_2014;1053                    18.0   \n",
-       "9601   BrentLab/kemmeren_2014;kemmeren_2014;218                    20.0   \n",
-       "9602  BrentLab/kemmeren_2014;kemmeren_2014;1023                    10.0   \n",
-       "9603   BrentLab/kemmeren_2014;kemmeren_2014;913                   150.0   \n",
+       "                                 perturbation_id  binding_rank_threshold  \\\n",
+       "0         BrentLab/hughes_2006;overexpression;10                    11.0   \n",
+       "1         BrentLab/hughes_2006;overexpression;11                    60.0   \n",
+       "2         BrentLab/hughes_2006;overexpression;11                    27.0   \n",
+       "3         BrentLab/hughes_2006;overexpression;12                   532.0   \n",
+       "4         BrentLab/hughes_2006;overexpression;12                    10.0   \n",
+       "...                                          ...                     ...   \n",
+       "29799   BrentLab/kemmeren_2014;kemmeren_2014;784                   154.0   \n",
+       "29800   BrentLab/kemmeren_2014;kemmeren_2014;666                   215.0   \n",
+       "29801   BrentLab/kemmeren_2014;kemmeren_2014;271                   221.0   \n",
+       "29802  BrentLab/kemmeren_2014;kemmeren_2014;1077                   281.0   \n",
+       "29803   BrentLab/kemmeren_2014;kemmeren_2014;963                   526.0   \n",
        "\n",
-       "      perturbation_rank_threshold  binding_set_size  perturbation_set_size  \\\n",
-       "0                             2.0               3.0                    2.0   \n",
-       "1                             NaN               NaN                    NaN   \n",
-       "2                             1.0               3.0                    1.0   \n",
-       "3                            96.0             479.0                   92.0   \n",
-       "4                             NaN               NaN                    NaN   \n",
-       "...                           ...               ...                    ...   \n",
-       "9599                         39.0              13.0                   39.0   \n",
-       "9600                        278.0              17.0                  171.0   \n",
-       "9601                         57.0              19.0                   27.0   \n",
-       "9602                          9.0              11.0                    9.0   \n",
-       "9603                        221.0             140.0                  206.0   \n",
+       "       perturbation_rank_threshold  binding_set_size  perturbation_set_size  \\\n",
+       "0                            206.0              12.0                  206.0   \n",
+       "1                             67.0              60.0                   67.0   \n",
+       "2                           1265.0              27.0                 1265.0   \n",
+       "3                           1093.0             532.0                 1093.0   \n",
+       "4                            556.0              10.0                  556.0   \n",
+       "...                            ...               ...                    ...   \n",
+       "29799                        905.0             154.0                  905.0   \n",
+       "29800                        108.0             215.0                  108.0   \n",
+       "29801                        925.0             221.0                  925.0   \n",
+       "29802                         73.0             283.0                   77.0   \n",
+       "29803                        227.0             527.0                  227.0   \n",
        "\n",
-       "       dto_fdr  dto_empirical_pvalue             binding_repo_dataset  \\\n",
-       "0     0.000225                 0.004      harbison_2004-harbison_2004   \n",
-       "1          NaN                   NaN      harbison_2004-harbison_2004   \n",
-       "2     0.000000                 0.011      harbison_2004-harbison_2004   \n",
-       "3     0.412192                 0.576      harbison_2004-harbison_2004   \n",
-       "4          NaN                   NaN      harbison_2004-harbison_2004   \n",
-       "...        ...                   ...                              ...   \n",
-       "9599  0.000879                 0.000  callingcards-annotated_features   \n",
-       "9600  0.001455                 0.000  callingcards-annotated_features   \n",
-       "9601  0.003116                 0.000  callingcards-annotated_features   \n",
-       "9602  0.000000                 0.000  callingcards-annotated_features   \n",
-       "9603  0.116890                 0.000  callingcards-annotated_features   \n",
+       "        dto_fdr  dto_empirical_pvalue pr_ranking_column  \\\n",
+       "0      0.041293                 0.017            log2fc   \n",
+       "1      0.054284                 0.000            log2fc   \n",
+       "2      0.123214                 0.057            log2fc   \n",
+       "3      0.436305                 0.092            log2fc   \n",
+       "4      0.017567                 0.002            log2fc   \n",
+       "...         ...                   ...               ...   \n",
+       "29799  0.090665                 0.000            pvalue   \n",
+       "29800  0.075036                 0.005            pvalue   \n",
+       "29801  0.403484                 0.126            pvalue   \n",
+       "29802  0.095948                 0.174            pvalue   \n",
+       "29803  0.064919                 0.000            pvalue   \n",
        "\n",
-       "        perturbation_repo_dataset binding_id_id  \\\n",
-       "0       Hackett_2020-hackett_2020             3   \n",
-       "1       Hackett_2020-hackett_2020             3   \n",
-       "2       Hackett_2020-hackett_2020             3   \n",
-       "3       Hackett_2020-hackett_2020             4   \n",
-       "4       Hackett_2020-hackett_2020             3   \n",
-       "...                           ...           ...   \n",
-       "9599  kemmeren_2014-kemmeren_2014           804   \n",
-       "9600  kemmeren_2014-kemmeren_2014           805   \n",
-       "9601  kemmeren_2014-kemmeren_2014           808   \n",
-       "9602  kemmeren_2014-kemmeren_2014           806   \n",
-       "9603  kemmeren_2014-kemmeren_2014           809   \n",
+       "                           binding_repo_dataset    perturbation_repo_dataset  \\\n",
+       "0                   harbison_2004-harbison_2004   hughes_2006-overexpression   \n",
+       "1                   harbison_2004-harbison_2004   hughes_2006-overexpression   \n",
+       "2                   harbison_2004-harbison_2004   hughes_2006-overexpression   \n",
+       "3                   harbison_2004-harbison_2004   hughes_2006-overexpression   \n",
+       "4                   harbison_2004-harbison_2004   hughes_2006-overexpression   \n",
+       "...                                         ...                          ...   \n",
+       "29799  callingcards-annotated_features_combined  kemmeren_2014-kemmeren_2014   \n",
+       "29800  callingcards-annotated_features_combined  kemmeren_2014-kemmeren_2014   \n",
+       "29801  callingcards-annotated_features_combined  kemmeren_2014-kemmeren_2014   \n",
+       "29802  callingcards-annotated_features_combined  kemmeren_2014-kemmeren_2014   \n",
+       "29803  callingcards-annotated_features_combined  kemmeren_2014-kemmeren_2014   \n",
        "\n",
-       "                             binding_id_source perturbation_id_id  \\\n",
-       "0                                     harbison                 85   \n",
-       "1                                     harbison                 83   \n",
-       "2                                     harbison                 84   \n",
-       "3                                     harbison                 78   \n",
-       "4                                     harbison                 81   \n",
-       "...                                        ...                ...   \n",
-       "9599  BrentLab/callingcards;annotated_features                901   \n",
-       "9600  BrentLab/callingcards;annotated_features               1053   \n",
-       "9601  BrentLab/callingcards;annotated_features                218   \n",
-       "9602  BrentLab/callingcards;annotated_features               1023   \n",
-       "9603  BrentLab/callingcards;annotated_features                913   \n",
+       "      binding_id_id                                  binding_id_source  \\\n",
+       "0               105                                           harbison   \n",
+       "1               108                                           harbison   \n",
+       "2               109                                           harbison   \n",
+       "3               112                                           harbison   \n",
+       "4               113                                           harbison   \n",
+       "...             ...                                                ...   \n",
+       "29799   724-692-688  BrentLab/callingcards;annotated_features_combined   \n",
+       "29800   725-435-395  BrentLab/callingcards;annotated_features_combined   \n",
+       "29801   726-445-424  BrentLab/callingcards;annotated_features_combined   \n",
+       "29802         79-33  BrentLab/callingcards;annotated_features_combined   \n",
+       "29803         96-49  BrentLab/callingcards;annotated_features_combined   \n",
        "\n",
-       "                  perturbation_id_source  \n",
-       "0     BrentLab/Hackett_2020;hackett_2020  \n",
-       "1     BrentLab/Hackett_2020;hackett_2020  \n",
-       "2     BrentLab/Hackett_2020;hackett_2020  \n",
-       "3     BrentLab/Hackett_2020;hackett_2020  \n",
-       "4     BrentLab/Hackett_2020;hackett_2020  \n",
-       "...                                  ...  \n",
-       "9599                            kemmeren  \n",
-       "9600                            kemmeren  \n",
-       "9601                            kemmeren  \n",
-       "9602                            kemmeren  \n",
-       "9603                            kemmeren  \n",
+       "      perturbation_id_id               perturbation_id_source  \n",
+       "0                     10  BrentLab/hughes_2006;overexpression  \n",
+       "1                     11  BrentLab/hughes_2006;overexpression  \n",
+       "2                     11  BrentLab/hughes_2006;overexpression  \n",
+       "3                     12  BrentLab/hughes_2006;overexpression  \n",
+       "4                     12  BrentLab/hughes_2006;overexpression  \n",
+       "...                  ...                                  ...  \n",
+       "29799                784                             kemmeren  \n",
+       "29800                666                             kemmeren  \n",
+       "29801                271                             kemmeren  \n",
+       "29802               1077                             kemmeren  \n",
+       "29803                963                             kemmeren  \n",
        "\n",
-       "[9604 rows x 14 columns]"
+       "[29804 rows x 15 columns]"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -4926,7 +4937,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 19,
    "id": "cell-25",
    "metadata": {},
    "outputs": [
@@ -4942,53 +4953,53 @@
       "4        448             ACA1  15.0       ZEV   \n",
       "\n",
       "                                     binding_id  \\\n",
-      "0  BrentLab/callingcards;annotated_features;803   \n",
+      "0  BrentLab/callingcards;annotated_features;146   \n",
       "1  BrentLab/callingcards;annotated_features;156   \n",
-      "2  BrentLab/callingcards;annotated_features;126   \n",
-      "3  BrentLab/callingcards;annotated_features;189   \n",
-      "4  BrentLab/callingcards;annotated_features;146   \n",
+      "2       BrentLab/harbison_2004;harbison_2004;88   \n",
+      "3  BrentLab/callingcards;annotated_features;146   \n",
+      "4  BrentLab/callingcards;annotated_features;803   \n",
       "\n",
       "                          perturbation_id  binding_rank_threshold  \\\n",
-      "0  BrentLab/Hackett_2020;hackett_2020;448                   112.0   \n",
-      "1  BrentLab/Hackett_2020;hackett_2020;448                    31.0   \n",
-      "2  BrentLab/Hackett_2020;hackett_2020;448                    21.0   \n",
-      "3  BrentLab/Hackett_2020;hackett_2020;448                   164.0   \n",
-      "4  BrentLab/Hackett_2020;hackett_2020;448                    23.0   \n",
+      "0  BrentLab/hackett_2020;hackett_2020;448                   452.0   \n",
+      "1  BrentLab/hackett_2020;hackett_2020;448                   296.0   \n",
+      "2  BrentLab/hackett_2020;hackett_2020;448                   122.0   \n",
+      "3  BrentLab/hackett_2020;hackett_2020;448                    35.0   \n",
+      "4  BrentLab/hackett_2020;hackett_2020;448                   544.0   \n",
       "\n",
       "   perturbation_rank_threshold  binding_set_size  perturbation_set_size  \\\n",
-      "0                         98.0             108.0                   90.0   \n",
-      "1                         98.0              26.0                   90.0   \n",
-      "2                         98.0              17.0                   90.0   \n",
-      "3                        154.0             150.0                  144.0   \n",
-      "4                         98.0              18.0                   90.0   \n",
+      "0                          1.0             454.0                 5591.0   \n",
+      "1                        346.0             297.0                  346.0   \n",
+      "2                        218.0             122.0                  218.0   \n",
+      "3                        407.0              35.0                  407.0   \n",
+      "4                          1.0             544.0                 5591.0   \n",
       "\n",
-      "    dto_fdr  dto_empirical_pvalue             binding_repo_dataset  \\\n",
-      "0  0.187319                 0.074  callingcards-annotated_features   \n",
-      "1  0.072561                 0.047  callingcards-annotated_features   \n",
-      "2  0.061941                 0.071  callingcards-annotated_features   \n",
-      "3  0.213716                 0.011  callingcards-annotated_features   \n",
-      "4  0.066616                 0.171  callingcards-annotated_features   \n",
+      "    dto_fdr  dto_empirical_pvalue pr_ranking_column  \\\n",
+      "0  0.000000                 1.000            pvalue   \n",
+      "1  0.277211                 0.000            log2fc   \n",
+      "2  0.612736                 0.917            log2fc   \n",
+      "3  0.116834                 0.000            log2fc   \n",
+      "4  0.000000                 1.000            pvalue   \n",
       "\n",
-      "   perturbation_repo_dataset binding_id_id  \\\n",
-      "0  Hackett_2020-hackett_2020           803   \n",
-      "1  Hackett_2020-hackett_2020           156   \n",
-      "2  Hackett_2020-hackett_2020           126   \n",
-      "3  Hackett_2020-hackett_2020           189   \n",
-      "4  Hackett_2020-hackett_2020           146   \n",
+      "              binding_repo_dataset  perturbation_repo_dataset binding_id_id  \\\n",
+      "0  callingcards-annotated_features  hackett_2020-hackett_2020           146   \n",
+      "1  callingcards-annotated_features  hackett_2020-hackett_2020           156   \n",
+      "2      harbison_2004-harbison_2004  hackett_2020-hackett_2020            88   \n",
+      "3  callingcards-annotated_features  hackett_2020-hackett_2020           146   \n",
+      "4  callingcards-annotated_features  hackett_2020-hackett_2020           803   \n",
       "\n",
       "                          binding_id_source perturbation_id_id  \\\n",
       "0  BrentLab/callingcards;annotated_features                448   \n",
       "1  BrentLab/callingcards;annotated_features                448   \n",
-      "2  BrentLab/callingcards;annotated_features                448   \n",
+      "2                                  harbison                448   \n",
       "3  BrentLab/callingcards;annotated_features                448   \n",
       "4  BrentLab/callingcards;annotated_features                448   \n",
       "\n",
-      "               perturbation_id_source  \n",
-      "0  BrentLab/Hackett_2020;hackett_2020  \n",
-      "1  BrentLab/Hackett_2020;hackett_2020  \n",
-      "2  BrentLab/Hackett_2020;hackett_2020  \n",
-      "3  BrentLab/Hackett_2020;hackett_2020  \n",
-      "4  BrentLab/Hackett_2020;hackett_2020  \n"
+      "  perturbation_id_source  \n",
+      "0                hackett  \n",
+      "1                hackett  \n",
+      "2                hackett  \n",
+      "3                hackett  \n",
+      "4                hackett  \n"
      ]
     }
    ],
@@ -5016,7 +5027,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 20,
    "id": "cell-26",
    "metadata": {},
    "outputs": [],
diff --git a/docs/virtual_db.md b/docs/virtual_db.md
index 3ec4b45..9062618 100644
--- a/docs/virtual_db.md
+++ b/docs/virtual_db.md
@@ -23,6 +23,66 @@ For comparative analysis datasets, VirtualDB creates:
 See the [configuration guide](virtual_db_configuration.md) for setup details
 and the [tutorial](tutorials/virtual_db_tutorial.ipynb) for usage examples.
 
+## Advanced Usage
+
+After any public method is called (e.g. `vdb.tables()`), the underlying DuckDB
+connection is available as `vdb._db`. You can use `_db` to execute any SQL
+on the database, eg creating more views, or creating a table in memory
+
+Custom **views** created this way appear in `tables()`, `describe()`, and
+`get_fields()` automatically because those methods query DuckDB's
+`information_schema`. Custom **tables** do not appear in `tables()` (which
+only lists views), but are fully queryable via `vdb.query()`.
+
+Call at least one public method first to ensure the connection is initialized
+before accessing `_db` directly.
+
+Example -- create a materialized analysis table::
+
+    # Trigger view registration
+    vdb.tables()
+
+    # Create a persistent in-memory table from a complex query.
+    # This example selects one "best" Hackett-2020 sample per regulator
+    # using a priority system: ZEV+P > GEV+P > GEV+M.
+    vdb._db.execute("""
+        CREATE OR REPLACE TABLE hackett_analysis_set AS
+        WITH regulator_tiers AS (
+            SELECT
+                regulator_locus_tag,
+                CASE
+                    WHEN BOOL_OR(mechanism = 'ZEV' AND restriction = 'P') THEN 1
+                    WHEN BOOL_OR(mechanism = 'GEV' AND restriction = 'P') THEN 2
+                    ELSE 3
+                END AS tier
+            FROM hackett_meta
+            WHERE regulator_locus_tag NOT IN ('Z3EV', 'GEV')
+            GROUP BY regulator_locus_tag
+        ),
+        tier_filter AS (
+            SELECT
+                h.sample_id, h.regulator_locus_tag, h.regulator_symbol,
+                h.mechanism, h.restriction, h.date, h.strain, t.tier
+            FROM hackett_meta h
+            JOIN regulator_tiers t USING (regulator_locus_tag)
+            WHERE
+                (t.tier = 1 AND h.mechanism = 'ZEV' AND h.restriction = 'P')
+                OR (t.tier = 2 AND h.mechanism = 'GEV' AND h.restriction = 'P')
+                OR (t.tier = 3 AND h.mechanism = 'GEV' AND h.restriction = 'M')
+        )
+        SELECT DISTINCT
+            sample_id, regulator_locus_tag, regulator_symbol,
+            mechanism, restriction, date, strain
+        FROM tier_filter
+        WHERE regulator_symbol NOT IN ('GCN4', 'RDS2', 'SWI1', 'MAC1')
+        ORDER BY regulator_locus_tag, sample_id
+    """)
+
+    df = vdb.query("SELECT * FROM hackett_analysis_set")
+
+Tables and views created this way are in-memory only and do not persist across
+VirtualDB instances. They exist for the lifetime of the DuckDB connection.
+
 ## API Reference
 
 ::: tfbpapi.virtual_db.VirtualDB
diff --git a/docs/virtual_db_configuration.md b/docs/virtual_db_configuration.md
index 45320d4..42316d5 100644
--- a/docs/virtual_db_configuration.md
+++ b/docs/virtual_db_configuration.md
@@ -10,8 +10,10 @@ levels.
 repositories:
   # Each repository defines a "table" in the virtual database
   BrentLab/harbison_2004:
-    # REQUIRED: Specify which field is the sample identifier. At this level, it means
-    # that all datasets have a field `sample_id` that uniquely identifies samples.
+    # REQUIRED: Specify which column is the sample identifier. The `field`
+    # value is the actual column name in the parquet data. At the repo level,
+    # it applies to all datasets in this repository. If not specified at
+    # either level, the default column name "sample_id" is assumed.
     sample_id:
       field: sample_id
     # Repository-wide properties (apply to all datasets in this repository)
@@ -47,8 +49,9 @@ repositories:
       kemmeren_2014:
         # optional -- see the note for `db_name` in harbison above
         db_name: kemmeren
-        # REQUIRED: If `sample_id` isn't defined at the repo level, then it must be
-        # defined at the dataset level for each dataset in the repo
+        # REQUIRED: If `sample_id` isn't defined at the repo level, it must be
+        # defined at the dataset level. The `field` value is the actual column
+        # name in the parquet data (does not need to be literally "sample_id").
         sample_id:
           field: sample_id
         # Same logical fields, different physical paths
@@ -144,6 +147,62 @@ during metadata extraction and query filtering.
 2. **Type consistency**: When source data might be extracted with incorrect type
 3. **Performance**: Helps with query optimization and prevents type mismatches
 
+## Tags
+
+Tags are arbitrary string key/value pairs for annotating datasets. They follow
+the same hierarchy as property mappings: repo-level tags apply to all datasets
+in the repository, dataset-level tags apply only to that dataset, and
+dataset-level tags override repo-level tags with the same key.
+
+```yaml
+repositories:
+  BrentLab/harbison_2004:
+    # Repo-level tags apply to all datasets in this repository
+    tags:
+      assay: binding
+      organism: yeast
+    dataset:
+      harbison_2004:
+        sample_id:
+          field: sample_id
+        # Dataset-level tags override repo-level tags with the same key
+        tags:
+          assay: chip-chip
+
+  BrentLab/kemmeren_2014:
+    tags:
+      assay: perturbation
+      organism: yeast
+    dataset:
+      kemmeren_2014:
+        sample_id:
+          field: sample_id
+```
+
+Access merged tags via `vdb.get_tags(db_name)`, identifying datasets by
+their name as it appears in `vdb.tables()`:
+
+```python
+from tfbpapi.virtual_db import VirtualDB
+
+vdb = VirtualDB("datasets.yaml")
+
+# Returns {"assay": "chip-chip", "organism": "yeast"}
+# (dataset-level assay overrides repo-level)
+vdb.get_tags("harbison")
+
+# Returns {"assay": "perturbation", "organism": "yeast"}
+vdb.get_tags("kemmeren")
+```
+
+The underlying `MetadataConfig` (available as `vdb.config`) exposes the same
+data via `(repo_id, config_name)` pairs for programmatic or developer use:
+
+```python
+# Equivalent to vdb.get_tags("harbison") above
+vdb.config.get_tags("BrentLab/harbison_2004", "harbison_2004")
+```
+
 ## Comparative Datasets
 
 Comparative datasets differ from other dataset types in that they represent
@@ -152,9 +211,10 @@ Each row relates 2+ samples from other datasets.
 
 ### Structure
 
-Comparative datasets use `source_sample` fields instead of a single `sample_id`:
+Comparative datasets use `source_sample` fields instead of a single sample
+identifier column:
 - Multiple fields with `role: source_sample`
-- Each contains composite identifier: `"repo_id;config_name;sample_id"`
+- Each contains composite identifier: `"repo_id;config_name;sample_id_value"`
 - Example: `binding_id = "BrentLab/harbison_2004;harbison_2004;42"`
 
 ### Fields
@@ -206,10 +266,11 @@ build on each other. Using `harbison` as an example primary dataset and
 
 **1. Metadata view**
 
-One row per unique `sample_id`. Derived columns from the configuration
-(e.g., `carbon_source`, `temperature_celsius`) are resolved here using
-datacard definitions, factor aliases, and missing value labels. This is
-the primary view for querying sample-level metadata.
+One row per unique sample identifier (the column configured via
+`sample_id: {field: <column_name>}`). Derived columns from the
+configuration (e.g., `carbon_source`, `temperature_celsius`) are resolved
+here using datacard definitions, factor aliases, and missing value labels.
+This is the primary view for querying sample-level metadata.
 
 **2. Raw data view**
 
@@ -239,7 +300,7 @@ or filter by source dataset without parsing composite IDs in SQL.
 ```
 __harbison_parquet  (raw parquet, not directly exposed)
   |
-  +-> harbison_meta  (deduplicated, one row per sample_id,
+  +-> harbison_meta  (deduplicated, one row per sample identifier,
   |                   with derived columns from config)
   |
   +-> harbison  (full parquet joined to harbison_meta)
diff --git a/tfbpapi/datacard.py b/tfbpapi/datacard.py
index abf94dd..734a5f3 100644
--- a/tfbpapi/datacard.py
+++ b/tfbpapi/datacard.py
@@ -17,6 +17,7 @@
 """
 
 import logging
+from dataclasses import dataclass
 from typing import Any
 
 from pydantic import ValidationError
@@ -36,6 +37,34 @@
 )
 
 
+@dataclass
+class DatasetSchema:
+    """
+    Complete schema summary for a data configuration.
+
+    Derived entirely from the DataCard YAML -- no DuckDB introspection needed. Used by
+    VirtualDB to determine column partitioning between data and metadata parquets.
+
+    :ivar data_columns: Column names present in the data parquet.
+    :ivar metadata_columns: Column names that are metadata.
+    :ivar join_columns: Columns common to both data and metadata parquets (used as JOIN
+        keys for external metadata). Empty for embedded metadata (same parquet, no JOIN
+        needed).
+    :ivar metadata_source: One of ``"embedded"``, ``"external"``, or ``"none"``.
+    :ivar external_metadata_config: Config name of the external metadata config, or
+        ``None`` if metadata is embedded or absent.
+    :ivar is_partitioned: Whether the data parquet is partitioned.
+
+    """
+
+    data_columns: set[str]
+    metadata_columns: set[str]
+    join_columns: set[str]
+    metadata_source: str
+    external_metadata_config: str | None
+    is_partitioned: bool
+
+
 class DataCard:
     """
     Parser and explorer for HuggingFace dataset metadata.
@@ -91,6 +120,7 @@ def __init__(self, repo_id: str, token: str | None = None):
         # Cache for parsed card
         self._dataset_card: DatasetCard | None = None
         self._metadata_cache: dict[str, list[ExtractedMetadata]] = {}
+        self._metadata_fields_map: dict[str, list[str]] = {}
 
     @property
     def dataset_card(self) -> DatasetCard:
@@ -115,6 +145,7 @@ def _load_and_validate_card(self) -> None:
 
             # Validate using Pydantic model
             self._dataset_card = DatasetCard(**card_data)
+            self._build_metadata_fields_map()
             self.logger.debug(f"Successfully validated dataset card for {self.repo_id}")
 
         except ValidationError as e:
@@ -241,6 +272,186 @@ def get_metadata_relationships(
 
         return relationships
 
+    def _build_metadata_fields_map(self) -> None:
+        """
+        Build a mapping from data config names to their metadata fields.
+
+        Called during card loading. For each data config, resolves metadata
+        fields from two sources:
+
+        1. Embedded: the data config has ``metadata_fields`` listing which
+           of its own columns are metadata.
+        2. External: a separate metadata-type config has ``applies_to``
+           including this config name. The metadata fields are the feature
+           names from that metadata config.
+
+        Embedded takes priority. For external, the first matching metadata
+        config wins.
+
+        """
+        assert self._dataset_card is not None
+        self._metadata_fields_map = {}
+        meta_configs = self._dataset_card.get_metadata_configs()
+
+        for data_cfg in self._dataset_card.get_data_configs():
+            name = data_cfg.config_name
+            # Embedded case
+            if data_cfg.metadata_fields:
+                self._metadata_fields_map[name] = list(data_cfg.metadata_fields)
+                continue
+            # External case: find metadata config with applies_to
+            for meta_cfg in meta_configs:
+                if meta_cfg.applies_to and name in meta_cfg.applies_to:
+                    self._metadata_fields_map[name] = [
+                        f.name for f in meta_cfg.dataset_info.features
+                    ]
+                    break
+            else:
+                self.logger.warning(
+                    "No metadata fields found for data config '%s' "
+                    "in repo '%s' -- no embedded metadata_fields and "
+                    "no metadata config with applies_to",
+                    name,
+                    self.repo_id,
+                )
+
+    def get_metadata_fields(self, config_name: str) -> list[str] | None:
+        """
+        Get metadata field names for a data configuration.
+
+        Returns pre-computed metadata fields resolved during card loading.
+        Handles both embedded metadata (``metadata_fields`` on the data
+        config) and external metadata (separate metadata config with
+        ``applies_to``).
+
+        :param config_name: Name of the data configuration
+        :return: List of metadata field names, or None if no metadata
+
+        """
+        # Ensure card is loaded (triggers _build_metadata_fields_map)
+        _ = self.dataset_card
+        return self._metadata_fields_map.get(config_name)
+
+    def get_data_col_names(self, config_name: str) -> set[str]:
+        """
+        Return the column names from the data config's feature list.
+
+        These are the columns present in the data parquet file, derived directly from
+        the DataCard feature definitions without any DuckDB introspection.
+
+        :param config_name: Name of the data configuration
+        :return: Set of column names, empty if config not found
+
+        """
+        _ = self.dataset_card  # ensure loaded
+        config = self.get_config(config_name)
+        if not config:
+            return set()
+        return {f.name for f in config.dataset_info.features}
+
+    def get_metadata_config_name(self, config_name: str) -> str | None:
+        """
+        Return the config_name of the external metadata config, if any.
+
+        If the data config has embedded ``metadata_fields``, or if no
+        metadata config with ``applies_to`` references this config,
+        returns None.
+
+        :param config_name: Name of the data configuration
+        :return: The metadata config name, or None
+
+        """
+        _ = self.dataset_card  # ensure loaded
+        data_cfg = self.get_config(config_name)
+        if not data_cfg:
+            return None
+        # Embedded metadata -- no external config needed
+        if data_cfg.metadata_fields:
+            return None
+        # Find external metadata config with applies_to
+        for meta_cfg in self.dataset_card.get_metadata_configs():
+            if meta_cfg.applies_to and config_name in meta_cfg.applies_to:
+                return meta_cfg.config_name
+        return None
+
+    def get_dataset_schema(self, config_name: str) -> DatasetSchema | None:
+        """
+        Return schema summary for a data configuration.
+
+        Determines whether metadata is embedded or external, which
+        columns belong to data vs metadata parquets, and which columns
+        are shared between them (join keys for external metadata).
+        All information is derived from the DataCard YAML -- no DuckDB
+        introspection is needed.
+
+        :param config_name: Name of the data configuration
+        :return: DatasetSchema instance, or None if config not found
+
+        Example -- embedded metadata::
+
+            schema = card.get_dataset_schema("harbison_2004")
+            # schema.metadata_source == "embedded"
+            # schema.join_columns == set()  (same parquet, no JOIN)
+
+        Example -- external metadata::
+
+            schema = card.get_dataset_schema("annotated_features")
+            # schema.metadata_source == "external"
+            # schema.external_metadata_config == "annotated_features_meta"
+            # schema.join_columns == {"id"}  (common to both parquets)
+
+        """
+        _ = self.dataset_card  # ensure loaded
+        config = self.get_config(config_name)
+        if not config:
+            return None
+
+        is_partitioned = bool(
+            config.dataset_info.partitioning
+            and config.dataset_info.partitioning.enabled
+        )
+
+        # Embedded: metadata_fields lists which of the config's own
+        # columns are metadata; all live in the same parquet
+        if config.metadata_fields:
+            all_cols = {f.name for f in config.dataset_info.features}
+            meta_cols = set(config.metadata_fields)
+            data_cols = all_cols - meta_cols
+            return DatasetSchema(
+                data_columns=data_cols,
+                metadata_columns=meta_cols,
+                join_columns=set(),
+                metadata_source="embedded",
+                external_metadata_config=None,
+                is_partitioned=is_partitioned,
+            )
+
+        # External: find metadata config with applies_to
+        for meta_cfg in self.dataset_card.get_metadata_configs():
+            if meta_cfg.applies_to and config_name in meta_cfg.applies_to:
+                data_cols = {f.name for f in config.dataset_info.features}
+                meta_cols = {f.name for f in meta_cfg.dataset_info.features}
+                join_cols = data_cols & meta_cols
+                return DatasetSchema(
+                    data_columns=data_cols,
+                    metadata_columns=meta_cols,
+                    join_columns=join_cols,
+                    metadata_source="external",
+                    external_metadata_config=meta_cfg.config_name,
+                    is_partitioned=is_partitioned,
+                )
+
+        # No metadata relationship -- treat all columns as data
+        all_cols = {f.name for f in config.dataset_info.features}
+        return DatasetSchema(
+            data_columns=all_cols,
+            metadata_columns=set(),
+            join_columns=set(),
+            metadata_source="none",
+            external_metadata_config=None,
+            is_partitioned=is_partitioned,
+        )
+
     def get_repository_info(self) -> dict[str, Any]:
         """Get general repository information."""
         card = self.dataset_card
@@ -315,12 +526,13 @@ def extract_metadata_schema(self, config_name: str) -> dict[str, Any]:
             raise DataCardError(f"Configuration '{config_name}' not found")
 
         schema: dict[str, Any] = {
-            "regulator_fields": [],  # Fields with role=regulator_identifier
-            "target_fields": [],  # Fields with role=target_identifier
-            "condition_fields": [],  # Fields with role=experimental_condition
-            "condition_definitions": {},  # Field-level condition details
-            "top_level_conditions": None,  # Repo-level conditions
-            "config_level_conditions": None,  # Config-level conditions
+            "regulator_fields": [],
+            "target_fields": [],
+            "condition_fields": [],
+            "condition_definitions": {},
+            "metadata_fields": None,
+            "top_level_conditions": None,
+            "config_level_conditions": None,
         }
 
         for feature in config.dataset_info.features:
@@ -333,15 +545,32 @@ def extract_metadata_schema(self, config_name: str) -> dict[str, Any]:
                 if feature.definitions:
                     schema["condition_definitions"][feature.name] = feature.definitions
 
+        # Include features from external metadata config
+        meta_fields = self.get_metadata_fields(config_name)
+        schema["metadata_fields"] = meta_fields
+        if meta_fields is not None and not config.metadata_fields:
+            for meta_cfg in self.dataset_card.get_metadata_configs():
+                if meta_cfg.applies_to and config_name in meta_cfg.applies_to:
+                    for feature in meta_cfg.dataset_info.features:
+                        if feature.role == "regulator_identifier":
+                            schema["regulator_fields"].append(feature.name)
+                        elif feature.role == "target_identifier":
+                            schema["target_fields"].append(feature.name)
+                        elif feature.role == "experimental_condition":
+                            schema["condition_fields"].append(feature.name)
+                            if feature.definitions:
+                                schema["condition_definitions"][
+                                    feature.name
+                                ] = feature.definitions
+                    break
+
         # Add top-level conditions (applies to all configs/samples)
-        # Stored in model_extra as dict
         if self.dataset_card.model_extra:
             top_level = self.dataset_card.model_extra.get("experimental_conditions")
             if top_level:
                 schema["top_level_conditions"] = top_level
 
         # Add config-level conditions (applies to this config's samples)
-        # Stored in model_extra as dict
         if config.model_extra:
             config_level = config.model_extra.get("experimental_conditions")
             if config_level:
diff --git a/tfbpapi/models.py b/tfbpapi/models.py
index a8660a1..4d77f02 100644
--- a/tfbpapi/models.py
+++ b/tfbpapi/models.py
@@ -458,6 +458,10 @@ class DatasetVirtualDBConfig(BaseModel):
         description="For comparative datasets: map link_field -> "
         "[repo_id, config_name] pairs",
     )
+    tags: dict[str, str] = Field(
+        default_factory=dict,
+        description="Arbitrary key/value annotations for this dataset",
+    )
 
     model_config = ConfigDict(extra="allow")
 
@@ -526,7 +530,7 @@ def parse_property_mappings(cls, data: Any) -> dict[str, Any]:
         result = {}
         for key, value in data.items():
             # Known typed fields - let Pydantic handle them
-            if key in ("sample_id", "links", "db_name"):
+            if key in ("sample_id", "links", "db_name", "tags"):
                 result[key] = value
             # Dict values should be PropertyMappings
             elif isinstance(value, dict):
@@ -591,6 +595,10 @@ class RepositoryConfig(BaseModel):
     dataset: dict[str, DatasetVirtualDBConfig] | None = Field(
         None, description="Dataset-specific configurations"
     )
+    tags: dict[str, str] = Field(
+        default_factory=dict,
+        description="Arbitrary key/value annotations for all datasets in this repo",
+    )
 
     @model_validator(mode="before")
     @classmethod
@@ -628,10 +636,10 @@ def parse_structure(cls, data: Any) -> dict[str, Any]:
                         f"Invalid configuration for dataset '{dataset_name}': {e}"
                     ) from e
 
-        # Parse repo-wide properties (all keys except 'dataset')
+        # Parse repo-wide properties (all keys except 'dataset' and 'tags')
         parsed_properties = {}
         for key, value in data.items():
-            if key == "dataset":
+            if key in ("dataset", "tags"):
                 continue
 
             try:
@@ -639,7 +647,11 @@ def parse_structure(cls, data: Any) -> dict[str, Any]:
             except Exception as e:
                 raise ValueError(f"Invalid repo-wide property '{key}': {e}") from e
 
-        return {"properties": parsed_properties, "dataset": parsed_datasets}
+        return {
+            "properties": parsed_properties,
+            "dataset": parsed_datasets,
+            "tags": data.get("tags") or {},
+        }
 
 
 class MetadataConfig(BaseModel):
@@ -876,3 +888,55 @@ def get_property_mappings(
             mappings.update(dataset_config.property_mappings)
 
         return mappings
+
+    def get_tags(self, repo_id: str, config_name: str) -> dict[str, str]:
+        """
+        Get merged tags for a repo/dataset combination.
+
+        Merges repo-level and dataset-level tags, with dataset-level tags taking
+        precedence for the same key.
+
+        :param repo_id: Repository ID
+        :param config_name: Dataset/config name
+        :return: Dict of merged tags
+
+        """
+        repo_config = self.get_repository_config(repo_id)
+        if not repo_config:
+            return {}
+
+        merged: dict[str, str] = dict(repo_config.tags)
+
+        if repo_config.dataset and config_name in repo_config.dataset:
+            merged.update(repo_config.dataset[config_name].tags)
+
+        return merged
+
+    def get_sample_id_field(self, repo_id: str, config_name: str) -> str:
+        """
+        Resolve the actual column name for the sample identifier.
+
+        Checks dataset-level ``sample_id`` first, then repo-level,
+        falling back to ``"sample_id"`` if neither is configured.
+
+        :param repo_id: Repository ID
+        :param config_name: Dataset/config name
+        :return: Column name for the sample identifier
+
+        """
+        repo_cfg = self.get_repository_config(repo_id)
+        if not repo_cfg:
+            return "sample_id"
+
+        # Dataset-level takes precedence
+        if repo_cfg.dataset and config_name in repo_cfg.dataset:
+            ds_cfg = repo_cfg.dataset[config_name]
+            if ds_cfg.sample_id is not None and ds_cfg.sample_id.field:
+                return ds_cfg.sample_id.field
+
+        # Repo-level fallback
+        repo_sample_id = repo_cfg.properties.get("sample_id")
+        if repo_sample_id is not None and repo_sample_id.field is not None:
+            return repo_sample_id.field
+
+        return "sample_id"
diff --git a/tfbpapi/tests/test_datacard.py b/tfbpapi/tests/test_datacard.py
index 5f098de..b9228d1 100644
--- a/tfbpapi/tests/test_datacard.py
+++ b/tfbpapi/tests/test_datacard.py
@@ -5,10 +5,80 @@
 import pytest
 
 from tfbpapi import DataCard
+from tfbpapi.datacard import DatasetSchema
 from tfbpapi.errors import DataCardError, DataCardValidationError, HfDataFetchError
 from tfbpapi.models import DatasetType
 
 
+def _external_metadata_card_data():
+    """Card data with external metadata (no embedded metadata_fields)."""
+    return {
+        "configs": [
+            {
+                "config_name": "coverage_data",
+                "description": "Coverage measurements",
+                "dataset_type": "genome_map",
+                "default": True,
+                "data_files": [{"split": "train", "path": "coverage.parquet"}],
+                "dataset_info": {
+                    "features": [
+                        {
+                            "name": "sample_id",
+                            "dtype": "integer",
+                            "description": "Sample ID",
+                        },
+                        {
+                            "name": "chr",
+                            "dtype": "string",
+                            "description": "Chromosome",
+                            "role": "genomic_coordinate",
+                        },
+                        {
+                            "name": "coverage",
+                            "dtype": "float32",
+                            "description": "Coverage value",
+                            "role": "quantitative_measure",
+                        },
+                    ]
+                },
+            },
+            {
+                "config_name": "sample_metadata",
+                "description": "Sample metadata",
+                "dataset_type": "metadata",
+                "applies_to": ["coverage_data"],
+                "data_files": [{"split": "train", "path": "metadata.parquet"}],
+                "dataset_info": {
+                    "features": [
+                        {
+                            "name": "sample_id",
+                            "dtype": "integer",
+                            "description": "Sample ID",
+                        },
+                        {
+                            "name": "batch",
+                            "dtype": "string",
+                            "description": "Batch ID",
+                        },
+                        {
+                            "name": "regulator_locus_tag",
+                            "dtype": "string",
+                            "description": "TF locus tag",
+                            "role": "regulator_identifier",
+                        },
+                        {
+                            "name": "regulator_symbol",
+                            "dtype": "string",
+                            "description": "TF symbol",
+                            "role": "regulator_identifier",
+                        },
+                    ]
+                },
+            },
+        ],
+    }
+
+
 class TestDataCard:
     """Test suite for DataCard class."""
 
@@ -30,6 +100,7 @@ def test_init(
         assert datacard.token == test_token
         assert datacard._dataset_card is None
         assert datacard._metadata_cache == {}
+        assert datacard._metadata_fields_map == {}
 
         # Check that fetchers were initialized
         mock_card_fetcher.assert_called_once_with(token=test_token)
@@ -447,3 +518,393 @@ def test_extract_partition_values_fetch_error(
 
         # Should return empty set on error
         assert values == set()
+
+
+class TestGetMetadataFields:
+    """Tests for DataCard.get_metadata_fields()."""
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_embedded_metadata_fields(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Embedded metadata_fields on the data config are returned."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_fields("binding_data")
+
+        assert result == ["regulator_symbol", "experimental_condition"]
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_external_metadata_fields(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+    ):
+        """External metadata via applies_to returns feature names."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = _external_metadata_card_data()
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_fields("coverage_data")
+
+        assert result == [
+            "sample_id",
+            "batch",
+            "regulator_locus_tag",
+            "regulator_symbol",
+        ]
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_no_metadata_returns_none(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Config with no metadata returns None."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_fields("genomic_features")
+
+        assert result is None
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_unknown_config_returns_none(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Unknown config name returns None."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_fields("nonexistent")
+
+        assert result is None
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_extract_schema_includes_external_features(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+    ):
+        """extract_metadata_schema includes roles from external metadata."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = _external_metadata_card_data()
+
+        datacard = DataCard(test_repo_id)
+        schema = datacard.extract_metadata_schema("coverage_data")
+
+        # External metadata features with role=regulator_identifier
+        assert "regulator_locus_tag" in schema["regulator_fields"]
+        assert "regulator_symbol" in schema["regulator_fields"]
+        # metadata_fields key populated
+        assert schema["metadata_fields"] is not None
+        assert "sample_id" in schema["metadata_fields"]
+
+
+class TestGetMetadataConfigName:
+    """Tests for DataCard.get_metadata_config_name()."""
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_external_metadata_returns_config_name(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+    ):
+        """Returns metadata config name when applies_to matches."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = _external_metadata_card_data()
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_config_name("coverage_data")
+
+        assert result == "sample_metadata"
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_embedded_metadata_returns_none(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Returns None when metadata is embedded."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_config_name("binding_data")
+
+        assert result is None
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_unknown_config_returns_none(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Returns None for unknown config name."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_metadata_config_name("nonexistent")
+
+        assert result is None
+
+
+class TestGetDataColNames:
+    """Tests for DataCard.get_data_col_names()."""
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_returns_feature_names(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Returns column names from the data config's features."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_data_col_names("binding_data")
+
+        # binding_data features: regulator_symbol, target_gene,
+        # experimental_condition, binding_score
+        assert isinstance(result, set)
+        assert result == {
+            "regulator_symbol",
+            "target_gene",
+            "experimental_condition",
+            "binding_score",
+        }
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_external_metadata_config_returns_data_features(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+    ):
+        """For external metadata, returns data config features only."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = _external_metadata_card_data()
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_data_col_names("coverage_data")
+
+        # coverage_data features: sample_id, chr, coverage
+        assert result == {"sample_id", "chr", "coverage"}
+        # Must NOT include metadata-only columns
+        assert "batch" not in result
+        assert "regulator_locus_tag" not in result
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_unknown_config_returns_empty_set(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Returns empty set for unknown config name."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_data_col_names("nonexistent")
+
+        assert result == set()
+
+
+class TestGetDatasetSchema:
+    """Tests for DataCard.get_dataset_schema()."""
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_embedded_metadata_returns_correct_schema(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Embedded metadata produces correct data/metadata column split."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        # binding_data has metadata_fields: [regulator_symbol,
+        # experimental_condition] and features: regulator_symbol,
+        # target_gene, experimental_condition, binding_score
+        result = datacard.get_dataset_schema("binding_data")
+
+        assert result is not None
+        assert isinstance(result, DatasetSchema)
+        assert result.metadata_source == "embedded"
+        assert result.external_metadata_config is None
+        assert result.join_columns == set()
+        assert result.metadata_columns == {
+            "regulator_symbol",
+            "experimental_condition",
+        }
+        # data_columns = all features minus metadata_columns
+        assert result.data_columns == {
+            "target_gene",
+            "binding_score",
+        }
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_external_metadata_returns_correct_schema(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+    ):
+        """External metadata produces correct split and join columns."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = _external_metadata_card_data()
+
+        datacard = DataCard(test_repo_id)
+        # coverage_data features: sample_id, chr, coverage
+        # sample_metadata features: sample_id, batch, regulator_locus_tag,
+        #   regulator_symbol
+        # join_columns = intersection = {sample_id}
+        result = datacard.get_dataset_schema("coverage_data")
+
+        assert result is not None
+        assert result.metadata_source == "external"
+        assert result.external_metadata_config == "sample_metadata"
+        assert result.data_columns == {"sample_id", "chr", "coverage"}
+        assert result.metadata_columns == {
+            "sample_id",
+            "batch",
+            "regulator_locus_tag",
+            "regulator_symbol",
+        }
+        assert result.join_columns == {"sample_id"}
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_no_metadata_returns_all_cols_as_data(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Config with no metadata relationship has all cols as data."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        # genomic_features has no metadata_fields and no applies_to
+        result = datacard.get_dataset_schema("genomic_features")
+
+        assert result is not None
+        assert result.metadata_source == "none"
+        assert result.external_metadata_config is None
+        assert result.metadata_columns == set()
+        assert result.join_columns == set()
+        assert result.data_columns == {
+            "gene_id",
+            "gene_symbol",
+            "chromosome",
+            "start",
+            "end",
+        }
+
+    @patch("tfbpapi.datacard.HfDataCardFetcher")
+    @patch("tfbpapi.datacard.HfRepoStructureFetcher")
+    @patch("tfbpapi.datacard.HfSizeInfoFetcher")
+    def test_unknown_config_returns_none(
+        self,
+        mock_size_fetcher,
+        mock_structure_fetcher,
+        mock_card_fetcher,
+        test_repo_id,
+        sample_dataset_card_data,
+    ):
+        """Returns None for an unknown config name."""
+        mock_fetcher_instance = Mock()
+        mock_card_fetcher.return_value = mock_fetcher_instance
+        mock_fetcher_instance.fetch.return_value = sample_dataset_card_data
+
+        datacard = DataCard(test_repo_id)
+        result = datacard.get_dataset_schema("nonexistent")
+
+        assert result is None
diff --git a/tfbpapi/tests/test_virtual_db.py b/tfbpapi/tests/test_virtual_db.py
index e62b840..cb64592 100644
--- a/tfbpapi/tests/test_virtual_db.py
+++ b/tfbpapi/tests/test_virtual_db.py
@@ -14,6 +14,8 @@
 import pytest
 import yaml  # type: ignore
 
+from tfbpapi.datacard import DatasetSchema
+from tfbpapi.models import MetadataConfig
 from tfbpapi.virtual_db import VirtualDB
 
 # ------------------------------------------------------------------
@@ -313,27 +315,87 @@ def _make_mock_datacard(repo_id):
         card.get_config.return_value = config_mock
         card.get_field_definitions.return_value = HARBISON_CONDITION_DEFS
         card.get_experimental_conditions.return_value = {}
+        card.get_metadata_fields.return_value = METADATA_FIELDS["harbison_2004"]
+        card.get_metadata_config_name.return_value = None
+        # Harbison: embedded metadata, condition is data col used for
+        # derived properties; metadata_cols are the three metadata fields
+        harbison_meta_cols = set(METADATA_FIELDS["harbison_2004"])
+        harbison_data_cols = {
+            "sample_id",
+            "condition",
+            "target_locus_tag",
+            "effect",
+            "pvalue",
+        } - harbison_meta_cols
+        card.get_data_col_names.return_value = {
+            "sample_id",
+            "regulator_locus_tag",
+            "regulator_symbol",
+            "condition",
+            "target_locus_tag",
+            "effect",
+            "pvalue",
+        }
+        card.get_dataset_schema.return_value = DatasetSchema(
+            data_columns=harbison_data_cols
+            | {
+                "sample_id",
+                "condition",
+                "target_locus_tag",
+                "effect",
+                "pvalue",
+            },
+            metadata_columns=harbison_meta_cols,
+            join_columns=set(),
+            metadata_source="embedded",
+            external_metadata_config=None,
+            is_partitioned=False,
+        )
     elif repo_id == "BrentLab/kemmeren":
         config_mock = MagicMock()
         config_mock.metadata_fields = METADATA_FIELDS["kemmeren_2014"]
-        # model_extra at config level (no experimental_conditions
-        # at this level for kemmeren)
         config_mock.model_extra = {}
         card.get_config.return_value = config_mock
         card.get_field_definitions.return_value = {}
-        # model_extra at top level with experimental_conditions
-        # wrapper -- matches real DataCard structure
         dataset_card_mock = MagicMock()
         dataset_card_mock.model_extra = {
             "experimental_conditions": KEMMEREN_EXP_CONDITIONS,
         }
         card.dataset_card = dataset_card_mock
+        card.get_metadata_fields.return_value = METADATA_FIELDS["kemmeren_2014"]
+        card.get_metadata_config_name.return_value = None
+        kemmeren_meta_cols = set(METADATA_FIELDS["kemmeren_2014"])
+        card.get_data_col_names.return_value = {
+            "sample_id",
+            "regulator_locus_tag",
+            "regulator_symbol",
+            "target_locus_tag",
+            "effect",
+            "pvalue",
+        }
+        card.get_dataset_schema.return_value = DatasetSchema(
+            data_columns={
+                "sample_id",
+                "target_locus_tag",
+                "effect",
+                "pvalue",
+            },
+            metadata_columns=kemmeren_meta_cols,
+            join_columns=set(),
+            metadata_source="embedded",
+            external_metadata_config=None,
+            is_partitioned=False,
+        )
     else:
         config_mock = MagicMock()
         config_mock.metadata_fields = None
         card.get_config.return_value = config_mock
         card.get_field_definitions.return_value = {}
         card.get_experimental_conditions.return_value = {}
+        card.get_metadata_fields.return_value = None
+        card.get_metadata_config_name.return_value = None
+        card.get_data_col_names.return_value = set()
+        card.get_dataset_schema.return_value = None
 
     return card
 
@@ -408,6 +470,201 @@ def test_db_name_map(self, config_path):
         )
 
 
+# ------------------------------------------------------------------
+# Tests: Tags
+# ------------------------------------------------------------------
+
+
+class TestTags:
+    """Tests for get_tags() hierarchical merging."""
+
+    def _make_config(self, yaml_str: str) -> MetadataConfig:
+        import yaml as _yaml
+
+        return MetadataConfig.model_validate(_yaml.safe_load(yaml_str))
+
+    def test_repo_level_tags_only(self):
+        """Repo-level tags propagate when dataset has none."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/harbison:
+                tags:
+                  assay: binding
+                  organism: yeast
+                dataset:
+                  harbison_2004:
+                    sample_id:
+                      field: sample_id
+            """
+        )
+        tags = config.get_tags("BrentLab/harbison", "harbison_2004")
+        assert tags == {"assay": "binding", "organism": "yeast"}
+
+    def test_dataset_level_tags_only(self):
+        """Dataset-level tags are returned when repo has none."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/harbison:
+                dataset:
+                  harbison_2004:
+                    sample_id:
+                      field: sample_id
+                    tags:
+                      assay: chip-chip
+            """
+        )
+        tags = config.get_tags("BrentLab/harbison", "harbison_2004")
+        assert tags == {"assay": "chip-chip"}
+
+    def test_dataset_overrides_repo_tags(self):
+        """Dataset-level tags override repo-level for the same key."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/harbison:
+                tags:
+                  assay: binding
+                  organism: yeast
+                dataset:
+                  harbison_2004:
+                    sample_id:
+                      field: sample_id
+                    tags:
+                      assay: chip-chip
+            """
+        )
+        tags = config.get_tags("BrentLab/harbison", "harbison_2004")
+        assert tags["assay"] == "chip-chip"
+        assert tags["organism"] == "yeast"
+
+    def test_no_tags(self):
+        """Returns empty dict when neither level has tags."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/harbison:
+                dataset:
+                  harbison_2004:
+                    sample_id:
+                      field: sample_id
+            """
+        )
+        tags = config.get_tags("BrentLab/harbison", "harbison_2004")
+        assert tags == {}
+
+    def test_unknown_repo_returns_empty(self):
+        """Unknown repo_id returns empty dict."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/harbison:
+                dataset:
+                  harbison_2004:
+                    sample_id:
+                      field: sample_id
+            """
+        )
+        assert config.get_tags("BrentLab/nonexistent", "harbison_2004") == {}
+
+    def test_yaml_round_trip(self):
+        """Tags parsed from YAML produce correct merged result."""
+        config = self._make_config(
+            """
+            repositories:
+              BrentLab/repo_a:
+                tags:
+                  type: primary
+                  organism: yeast
+                dataset:
+                  dataset_a:
+                    sample_id:
+                      field: sample_id
+                    tags:
+                      type: binding
+                      version: "2024"
+              BrentLab/repo_b:
+                tags:
+                  type: perturbation
+                dataset:
+                  dataset_b:
+                    sample_id:
+                      field: sample_id
+            """
+        )
+        tags_a = config.get_tags("BrentLab/repo_a", "dataset_a")
+        assert tags_a == {"type": "binding", "organism": "yeast", "version": "2024"}
+
+        tags_b = config.get_tags("BrentLab/repo_b", "dataset_b")
+        assert tags_b == {"type": "perturbation"}
+
+    def _make_vdb(self, yaml_str: str, tmp_path) -> VirtualDB:
+
+        p = tmp_path / "config.yaml"
+        p.write_text(yaml_str)
+        return VirtualDB(str(p))
+
+    def test_vdb_get_tags_returns_merged(self, tmp_path):
+        """VirtualDB.get_tags() returns merged repo+dataset tags by db_name."""
+        vdb = self._make_vdb(
+            """
+            repositories:
+              BrentLab/harbison:
+                tags:
+                  assay: binding
+                  organism: yeast
+                dataset:
+                  harbison_2004:
+                    db_name: harbison
+                    sample_id:
+                      field: sample_id
+                    tags:
+                      assay: chip-chip
+            """,
+            tmp_path,
+        )
+        tags = vdb.get_tags("harbison")
+        assert tags == {"assay": "chip-chip", "organism": "yeast"}
+
+    def test_vdb_get_tags_unknown_name_returns_empty(self, tmp_path):
+        """VirtualDB.get_tags() returns empty dict for unknown db_name."""
+        vdb = self._make_vdb(
+            """
+            repositories:
+              BrentLab/harbison:
+                dataset:
+                  harbison_2004:
+                    db_name: harbison
+                    sample_id:
+                      field: sample_id
+            """,
+            tmp_path,
+        )
+        assert vdb.get_tags("nonexistent") == {}
+
+    def test_vdb_get_tags_no_views_needed(self, tmp_path):
+        """VirtualDB.get_tags() works before any views are registered."""
+        vdb = self._make_vdb(
+            """
+            repositories:
+              BrentLab/harbison:
+                tags:
+                  assay: binding
+                dataset:
+                  harbison_2004:
+                    db_name: harbison
+                    sample_id:
+                      field: sample_id
+            """,
+            tmp_path,
+        )
+        assert not vdb._views_registered
+        tags = vdb.get_tags("harbison")
+        assert tags == {"assay": "binding"}
+        assert not vdb._views_registered
+
+
 # ------------------------------------------------------------------
 # Tests: View registration
 # ------------------------------------------------------------------
@@ -780,3 +1037,283 @@ def test_lazy_init(self, config_path):
         v = VirtualDB(config_path)
         assert v._conn is None
         assert not v._views_registered
+
+
+# ------------------------------------------------------------------
+# Tests: dynamic sample_id column
+# ------------------------------------------------------------------
+
+
+class TestDynamicSampleId:
+    """Tests that the sample identifier column is resolved from config."""
+
+    def test_non_default_sample_id(self, tmp_path, monkeypatch):
+        """Views work when sample_id maps to a non-default column."""
+        import tfbpapi.virtual_db as vdb_module
+
+        # Config uses experiment_id as the sample identifier
+        config = {
+            "repositories": {
+                "TestOrg/custom_id": {
+                    "dataset": {
+                        "custom_data": {
+                            "db_name": "custom",
+                            "sample_id": {
+                                "field": "experiment_id",
+                            },
+                            "regulator": {
+                                "field": "regulator",
+                            },
+                        }
+                    }
+                }
+            }
+        }
+        config_path = tmp_path / "config.yaml"
+        with open(config_path, "w") as f:
+            yaml.dump(config, f)
+
+        # Parquet uses experiment_id (not sample_id)
+        df = pd.DataFrame(
+            {
+                "experiment_id": [100, 100, 200, 200],
+                "regulator": ["TF1", "TF1", "TF2", "TF2"],
+                "target": ["G1", "G2", "G1", "G2"],
+                "score": [1.5, 0.8, 2.1, 0.3],
+            }
+        )
+        parquet_path = tmp_path / "custom.parquet"
+        files = {
+            ("TestOrg/custom_id", "custom_data"): [_write_parquet(parquet_path, df)],
+        }
+
+        # Mock datacard
+        mock_card = MagicMock()
+        mock_card.get_metadata_fields.return_value = [
+            "regulator",
+        ]
+        mock_card.get_field_definitions.return_value = {}
+        mock_card.get_experimental_conditions.return_value = {}
+        mock_card.get_dataset_schema.return_value = DatasetSchema(
+            data_columns={"experiment_id", "target", "score"},
+            metadata_columns={"regulator"},
+            join_columns=set(),
+            metadata_source="embedded",
+            external_metadata_config=None,
+            is_partitioned=False,
+        )
+
+        v = VirtualDB(config_path)
+
+        monkeypatch.setattr(
+            VirtualDB,
+            "_resolve_parquet_files",
+            lambda self, repo_id, cn: files.get((repo_id, cn), []),
+        )
+        monkeypatch.setattr(
+            vdb_module,
+            "_cached_datacard",
+            lambda repo_id, token=None: mock_card,
+        )
+
+        # Meta view should have experiment_id + regulator
+        meta_df = v.query("SELECT * FROM custom_meta")
+        assert "experiment_id" in meta_df.columns
+        assert len(meta_df) == 2  # 2 distinct samples
+
+        # Enriched raw view should JOIN on experiment_id
+        raw_df = v.query("SELECT * FROM custom")
+        assert "experiment_id" in raw_df.columns
+        assert len(raw_df) == 4  # all rows
+
+    def test_get_sample_id_field_dataset_level(self):
+        """Dataset-level sample_id takes precedence."""
+        config = MetadataConfig.model_validate(
+            {
+                "repositories": {
+                    "Org/repo": {
+                        "dataset": {
+                            "ds": {
+                                "sample_id": {
+                                    "field": "my_id",
+                                },
+                            }
+                        }
+                    }
+                }
+            }
+        )
+        assert config.get_sample_id_field("Org/repo", "ds") == "my_id"
+
+    def test_get_sample_id_field_repo_level(self):
+        """Repo-level sample_id used when dataset has none."""
+        config = MetadataConfig.model_validate(
+            {
+                "repositories": {
+                    "Org/repo": {
+                        "sample_id": {"field": "repo_sid"},
+                        "dataset": {"ds": {}},
+                    }
+                }
+            }
+        )
+        assert config.get_sample_id_field("Org/repo", "ds") == "repo_sid"
+
+    def test_get_sample_id_field_default(self):
+        """Falls back to 'sample_id' when not configured."""
+        config = MetadataConfig.model_validate(
+            {"repositories": {"Org/repo": {"dataset": {"ds": {}}}}}
+        )
+        assert config.get_sample_id_field("Org/repo", "ds") == "sample_id"
+
+    def test_get_sample_id_field_dataset_overrides_repo(self):
+        """Dataset-level overrides repo-level."""
+        config = MetadataConfig.model_validate(
+            {
+                "repositories": {
+                    "Org/repo": {
+                        "sample_id": {"field": "repo_id_col"},
+                        "dataset": {
+                            "ds": {
+                                "sample_id": {
+                                    "field": "ds_id_col",
+                                },
+                            }
+                        },
+                    }
+                }
+            }
+        )
+        assert config.get_sample_id_field("Org/repo", "ds") == "ds_id_col"
+
+
+class TestExternalMetadata:
+    """Tests for datasets with external metadata parquet files."""
+
+    def test_external_metadata_join(self, tmp_path, monkeypatch):
+        """Meta view JOINs data and metadata parquet when metadata is in a separate
+        config."""
+        import tfbpapi.virtual_db as vdb_module
+
+        # Data parquet: measurements with sample_id but no
+        # metadata columns like db_id or batch
+        data_df = pd.DataFrame(
+            {
+                "sample_id": [1, 1, 2, 2],
+                "target_locus_tag": [
+                    "YAL001C",
+                    "YAL002W",
+                    "YAL001C",
+                    "YAL002W",
+                ],
+                "effect": [1.5, 0.8, 2.1, 0.3],
+            }
+        )
+        # Metadata parquet: sample-level metadata
+        meta_df = pd.DataFrame(
+            {
+                "sample_id": [1, 2],
+                "db_id": [101, 102],
+                "regulator_locus_tag": ["YBR049C", "YDR463W"],
+                "background_hops": [500, 600],
+            }
+        )
+
+        data_path = _write_parquet(tmp_path / "data.parquet", data_df)
+        meta_path = _write_parquet(tmp_path / "meta.parquet", meta_df)
+
+        parquet_files = {
+            ("TestOrg/repo", "chip_data"): [data_path],
+            ("TestOrg/repo", "sample_metadata"): [meta_path],
+        }
+
+        config = {
+            "repositories": {
+                "TestOrg/repo": {
+                    "sample_id": {"field": "sample_id"},
+                    "dataset": {
+                        "chip_data": {
+                            "db_name": "chip",
+                            "regulator_locus_tag": {
+                                "field": "regulator_locus_tag",
+                            },
+                        }
+                    },
+                }
+            }
+        }
+        config_file = tmp_path / "config.yaml"
+        with open(config_file, "w") as f:
+            yaml.dump(config, f)
+
+        # Mock DataCard: external metadata via applies_to
+        card = MagicMock()
+        config_mock = MagicMock()
+        config_mock.metadata_fields = None  # no embedded
+        card.get_config.return_value = config_mock
+        card.get_metadata_fields.return_value = [
+            "sample_id",
+            "db_id",
+            "regulator_locus_tag",
+            "background_hops",
+        ]
+        card.get_metadata_config_name.return_value = "sample_metadata"
+        # Data parquet columns (from chip_data features)
+        card.get_data_col_names.return_value = {
+            "sample_id",
+            "target_locus_tag",
+            "effect",
+        }
+        card.get_field_definitions.return_value = {}
+        card.get_experimental_conditions.return_value = {}
+        # External metadata schema: data cols in data parquet,
+        # metadata cols in metadata parquet, joined on sample_id
+        card.get_dataset_schema.return_value = DatasetSchema(
+            data_columns={"sample_id", "target_locus_tag", "effect"},
+            metadata_columns={
+                "sample_id",
+                "db_id",
+                "regulator_locus_tag",
+                "background_hops",
+            },
+            join_columns={"sample_id"},
+            metadata_source="external",
+            external_metadata_config="sample_metadata",
+            is_partitioned=False,
+        )
+
+        v = VirtualDB(config_file)
+        monkeypatch.setattr(
+            VirtualDB,
+            "_resolve_parquet_files",
+            lambda self, repo_id, cfg: parquet_files.get((repo_id, cfg), []),
+        )
+        monkeypatch.setattr(
+            vdb_module,
+            "_cached_datacard",
+            lambda repo_id, token=None: card,
+        )
+
+        # Trigger view registration
+        tables = v.tables()
+        assert "chip" in tables
+        assert "chip_meta" in tables
+
+        # Meta view should have columns from both parquets
+        meta_result = v.query("SELECT * FROM chip_meta ORDER BY sample_id")
+        meta_cols = set(meta_result.columns)
+        assert "sample_id" in meta_cols
+        assert "db_id" in meta_cols
+        assert "regulator_locus_tag" in meta_cols
+        assert "background_hops" in meta_cols
+
+        # Verify data is correct (joined properly)
+        assert len(meta_result) == 2
+        row1 = meta_result[meta_result["sample_id"] == 1].iloc[0]
+        assert row1["db_id"] == 101
+        assert row1["regulator_locus_tag"] == "YBR049C"
+
+        # Enriched raw view should also work
+        raw_result = v.query("SELECT * FROM chip ORDER BY sample_id")
+        assert "db_id" in raw_result.columns
+        assert len(raw_result) == 4  # 4 data rows
diff --git a/tfbpapi/virtual_db.py b/tfbpapi/virtual_db.py
index 96097a3..1ac968c 100644
--- a/tfbpapi/virtual_db.py
+++ b/tfbpapi/virtual_db.py
@@ -11,8 +11,8 @@
 views (one row per sample with derived columns) and full data views (measurement-level
 data joined to metadata). For comparative analysis datasets, VirtualDB creates expanded
 views that parse composite ID fields into ``_source`` (aliased to the configured
-db_name) and ``_id`` (sample_id) columns. The expectation is that a developer will
-use this interface to write SQL queries against the views to provide an API to
+db_name) and ``_id`` (sample identifier) columns. The expectation is that a developer
+will use this interface to write SQL queries against the views to provide an API to
 downstream users and applications.
 
 Example Usage::
@@ -49,8 +49,9 @@
 
 import duckdb
 import pandas as pd
+from duckdb import BinderException
 
-from tfbpapi.datacard import DataCard
+from tfbpapi.datacard import DataCard, DatasetSchema
 from tfbpapi.models import MetadataConfig
 
 logger = logging.getLogger(__name__)
@@ -389,6 +390,27 @@ def get_common_fields(self) -> list[str]:
         common = set.intersection(*sets)
         return sorted(common)
 
+    def get_tags(self, db_name: str) -> dict[str, str]:
+        """
+        Return the merged tags for a dataset.
+
+        Tags are defined in the configuration at the repository and/or
+        dataset level. Dataset-level tags override repository-level tags
+        with the same key. See the ``tags`` section of the configuration
+        guide for details.
+
+        :param db_name: Dataset name as it appears in :meth:`tables` (the
+            resolved ``db_name`` from the configuration, or the
+            ``config_name`` if ``db_name`` was not explicitly set).
+        :return: Dict of merged tags, or empty dict if the dataset has no
+            tags or the name is not found.
+
+        """
+        if db_name not in self._db_name_map:
+            return {}
+        repo_id, config_name = self._db_name_map[db_name]
+        return self.config.get_tags(repo_id, config_name)
+
     # ------------------------------------------------------------------
     # Lazy initialisation
     # ------------------------------------------------------------------
@@ -414,6 +436,62 @@ def _register_all_views(self) -> None:
                 parquet_only=comparative,
             )
 
+        # 1b. Resolve external metadata parquet views.
+        # When a data config's metadata lives in a separate HF config
+        # (applies_to), register its parquet as __<db_name>_metadata_parquet.
+        # All information is derived from DataCard YAML -- no DuckDB
+        # introspection needed.
+        self._dataset_schemas: dict[str, DatasetSchema] = {}
+        self._external_meta_views: dict[str, str] = {}
+        for db_name, (repo_id, config_name) in self._db_name_map.items():
+            if self._is_comparative(repo_id, config_name):
+                continue
+            try:
+                card = _cached_datacard(repo_id, token=self.token)
+                schema = card.get_dataset_schema(config_name)
+            except Exception as exc:
+                logger.warning(
+                    "Could not get dataset schema for %s/%s: %s",
+                    repo_id,
+                    config_name,
+                    exc,
+                )
+                continue
+            if schema is not None:
+                self._dataset_schemas[db_name] = schema
+            if (
+                schema is None
+                or schema.metadata_source != "external"
+                or not schema.external_metadata_config
+            ):
+                continue
+            meta_view = f"__{db_name}_metadata_parquet"
+            files = self._resolve_parquet_files(
+                repo_id, schema.external_metadata_config
+            )
+            if not files:
+                logger.warning(
+                    "No parquet files for external metadata config "
+                    "'%s' in repo '%s'",
+                    schema.external_metadata_config,
+                    repo_id,
+                )
+                continue
+            files_sql = ", ".join(f"'{f}'" for f in files)
+            try:
+                self._db.execute(
+                    f"CREATE OR REPLACE VIEW {meta_view} AS "
+                    f"SELECT * FROM read_parquet([{files_sql}])"
+                )
+            except Exception as exc:
+                logger.warning(
+                    "Failed to create external metadata view '%s': %s",
+                    meta_view,
+                    exc,
+                )
+                continue
+            self._external_meta_views[db_name] = meta_view
+
         # 2. Metadata views for primary datasets (<db_name>_meta)
         # This is based on the metadata defined in the datacard,
         # and includes any additional derived columns based on the
@@ -567,62 +645,150 @@ def _register_raw_view(
 
     def _register_meta_view(self, db_name: str, repo_id: str, config_name: str) -> None:
         """
-        Register a ``<db_name>_meta`` view with one row per sample_id.
+        Register a ``<db_name>_meta`` view with one row per sample.
+
+        Includes metadata columns from the DataCard plus any derived columns
+        from config property mappings (resolved against DataCard definitions
+        with factor aliases applied).
 
-        Includes raw metadata columns from the DataCard plus any derived columns from
-        config property mappings (resolved against DataCard definitions with factor
-        aliases applied).
+        For datasets with external metadata (a separate HF config with
+        ``applies_to``), JOINs the data parquet to the metadata parquet
+        on the configured sample_id column. The actual columns in the metadata
+        parquet are determined by DuckDB introspection (``DESCRIBE``) rather
+        than the DataCard feature list, because DataCard feature lists are
+        conceptual schemas that may include columns not physically present
+        in the parquet files.
 
         :param db_name: Base view name for the primary dataset
         :param repo_id: Repository ID
         :param config_name: Configuration name
 
+        raises ValueError: If no metadata fields are found.
+        raises BinderException: If view creation fails, with SQL details.
+
         """
         parquet_view = f"__{db_name}_parquet"
         if not self._view_exists(parquet_view):
             return
 
-        meta_cols = self._resolve_metadata_fields(repo_id, config_name)
-        prop_result = self._resolve_property_columns(repo_id, config_name)
+        sample_col = self._get_sample_id_col(db_name)
 
-        if prop_result is not None:
-            derived_exprs, prop_raw_cols = prop_result
-            # Raw cols = metadata_fields + any source fields needed
-            # by property mappings
-            if meta_cols is not None:
-                raw = list(dict.fromkeys(["sample_id"] + meta_cols + prop_raw_cols))
-            else:
-                raw = list(dict.fromkeys(["sample_id"] + prop_raw_cols))
+        # Pull ext_meta_view early -- needed for both meta_cols and
+        # FROM clause construction.
+        schema: DatasetSchema | None = getattr(self, "_dataset_schemas", {}).get(
+            db_name
+        )
+        ext_meta_view: str | None = getattr(self, "_external_meta_views", {}).get(
+            db_name
+        )
 
-            raw_sql = ", ".join(raw)
+        is_external = (
+            ext_meta_view is not None
+            and schema is not None
+            and schema.metadata_source == "external"
+        )
 
-            # Outer SELECT: raw cols + derived expressions
-            outer_parts = list(raw) + derived_exprs
-            outer_sql = ", ".join(outer_parts)
+        if is_external:
+            # DataCard feature lists are conceptual -- columns listed there
+            # may not be physically present in the parquet file. Use DuckDB
+            # introspection to get the actual columns in the metadata parquet.
+            assert ext_meta_view is not None
+            actual_meta_cols: set[str] = set(self._get_view_columns(ext_meta_view))
+            meta_cols: list[str] = sorted(actual_meta_cols)
+        elif schema is not None:
+            actual_meta_cols = schema.metadata_columns
+            meta_cols = sorted(actual_meta_cols)
+        else:
+            meta_cols = self._resolve_metadata_fields(repo_id, config_name) or []
+            actual_meta_cols = set(meta_cols)
 
-            self._db.execute(
-                f"CREATE OR REPLACE VIEW {db_name}_meta AS "
-                f"SELECT DISTINCT {outer_sql} "
-                f"FROM ("
-                f"SELECT DISTINCT {raw_sql} "
-                f"FROM {parquet_view}"
-                f") AS __raw"
+        if not meta_cols:
+            raise ValueError(
+                f"No metadata fields found for {repo_id}/{config_name}. "
+                f"Cannot create meta view '{db_name}_meta'."
             )
-        elif meta_cols is not None:
-            # Fallback: metadata_fields only, no property mappings
-            cols = list(dict.fromkeys(["sample_id"] + meta_cols))
-            cols_sql = ", ".join(cols)
-            self._db.execute(
-                f"CREATE OR REPLACE VIEW {db_name}_meta AS "
-                f"SELECT DISTINCT {cols_sql} "
-                f"FROM {parquet_view}"
+
+        # FROM clause: JOIN data + metadata parquets when external,
+        # plain parquet view otherwise.
+        if is_external:
+            assert ext_meta_view is not None
+            # Use the configured sample_id column as the join key.
+            # The DataCard feature intersection (schema.join_columns)
+            # is unreliable because a data config's feature list may
+            # document columns that are physically only in the metadata
+            # parquet (present conceptually after a join, not in the
+            # physical data parquet file).
+            from_clause = (
+                f"{parquet_view} d " f"JOIN {ext_meta_view} m " f"USING ({sample_col})"
             )
+            is_join = True
         else:
-            # No metadata_fields at all -- all columns are metadata
-            self._db.execute(
-                f"CREATE OR REPLACE VIEW {db_name}_meta AS "
-                f"SELECT DISTINCT * FROM {parquet_view}"
-            )
+            from_clause = parquet_view
+            is_join = False
+
+        def qualify(col: str) -> str:
+            """Return qualified column name for JOIN context."""
+            if not is_join:
+                return col
+            if col == sample_col:
+                return col  # USING makes join key unqualified
+            # Use the actual metadata parquet columns (from DuckDB
+            # introspection) to decide qualification, not the DataCard
+            # feature list which may be inaccurate.
+            if col in actual_meta_cols:
+                return f"m.{col}"
+            return f"d.{col}"
+
+        # Build SELECT: sample_id + metadata cols (deduplicated)
+        seen: set[str] = set()
+        select_parts: list[str] = []
+
+        def add_col(col: str) -> None:
+            if col not in seen:
+                seen.add(col)
+                select_parts.append(qualify(col))
+
+        add_col(sample_col)
+        for col in meta_cols:
+            add_col(col)
+
+        # Add derived property expressions from the VirtualDB config
+        prop_result = self._resolve_property_columns(repo_id, config_name)
+        if prop_result is not None:
+            derived_exprs, prop_raw_cols = prop_result
+            # Ensure source columns needed by expressions are selected
+            for col in prop_raw_cols:
+                add_col(col)
+            # Qualify source column references inside CASE WHEN expressions
+            if is_join:
+                qualified_exprs = []
+                for expr in derived_exprs:
+                    for raw_col in prop_raw_cols:
+                        q = qualify(raw_col)
+                        if q != raw_col:
+                            # Replace bare column name in CASE WHEN patterns
+                            expr = expr.replace(
+                                f"CASE {raw_col} ", f"CASE {q} "
+                            ).replace(f" {raw_col} = ", f" {q} = ")
+                    qualified_exprs.append(expr)
+                derived_exprs = qualified_exprs
+            select_parts.extend(derived_exprs)
+
+        cols_sql = ", ".join(select_parts)
+        sql = (
+            f"CREATE OR REPLACE VIEW {db_name}_meta AS "
+            f"SELECT DISTINCT {cols_sql} FROM {from_clause}"
+        )
+        try:
+            self._db.execute(sql)
+        except BinderException as exc:
+            raise BinderException(
+                f"Failed to create meta view '{db_name}_meta'.\n"
+                f"  schema: {schema}\n"
+                f"  from_clause: {from_clause}\n"
+                f"  SQL: {sql}\n"
+                f"  error: {exc}"
+            ) from exc
 
     def _enrich_raw_view(self, db_name: str) -> None:
         """
@@ -648,40 +814,58 @@ def _enrich_raw_view(self, db_name: str) -> None:
         if not extra_cols:
             return
 
+        sample_col = self._get_sample_id_col(db_name)
         extra_select = ", ".join(f"m.{c}" for c in sorted(extra_cols))
         self._db.execute(
             f"CREATE OR REPLACE VIEW {db_name} AS "
             f"SELECT r.*, {extra_select} "
             f"FROM {parquet_name} r "
-            f"JOIN {meta_name} m USING (sample_id)"
+            f"JOIN {meta_name} m USING ({sample_col})"
         )
 
     def _get_view_columns(self, view: str) -> list[str]:
-        """Return column names for a view."""
-        df = self._db.execute(
-            f"SELECT column_name FROM information_schema.columns "
-            f"WHERE table_name = '{view}'"
-        ).fetchdf()
+        """
+        Return column names for a view.
+
+        Uses ``DESCRIBE`` rather than ``information_schema`` to force
+        eager schema resolution for ``read_parquet``-backed views,
+        which DuckDB may evaluate lazily.
+
+        """
+        df = self._db.execute(f"DESCRIBE {view}").fetchdf()
         return df["column_name"].tolist()
 
+    def _get_sample_id_col(self, db_name: str) -> str:
+        """
+        Resolve the sample identifier column name for a dataset.
+
+        :param db_name: Resolved database view name
+        :return: Actual column name for the sample identifier
+
+        """
+        repo_id, config_name = self._db_name_map[db_name]
+        return self.config.get_sample_id_field(repo_id, config_name)
+
     def _resolve_metadata_fields(
         self, repo_id: str, config_name: str
     ) -> list[str] | None:
         """
-        Get the metadata_fields list from the DataCard config.
+        Get metadata field names from the DataCard.
+
+        Delegates to ``DataCard.get_metadata_fields()`` which handles
+        both embedded metadata_fields and external metadata configs
+        (via applies_to).
 
         :param repo_id: Repository ID
         :param config_name: Configuration name
-        :return: List of metadata field names, or None if not specified
+        :return: List of metadata field names, or None if not found
 
         """
         try:
             card = _cached_datacard(repo_id, token=self.token)
-            config = card.get_config(config_name)
-            if config and config.metadata_fields:
-                return list(config.metadata_fields)
+            return card.get_metadata_fields(config_name)
         except Exception:
-            logger.debug(
+            logger.error(
                 "Could not resolve metadata_fields for %s/%s",
                 repo_id,
                 config_name,
@@ -975,7 +1159,7 @@ def _register_comparative_expanded_view(
 
         - ``<link_field>_source`` -- the ``repo_id;config_name`` prefix,
           aliased to the configured ``db_name`` when available.
-        - ``<link_field>_id`` -- the sample_id component.
+        - ``<link_field>_id`` -- the sample identifier component.
 
         :param db_name: Base view name for the comparative dataset
         :param ds_cfg: DatasetVirtualDBConfig with ``links``