Updated tutorials & added tutorial for atopo, db translation and netw…

…ork comparison (#15) * Add network building tutorial * Add resource tutorial * Add atopo tutorial * Add upstream connection tutorial * Add phosphosite tutorial * Add phenotype tutorial * Add tissue mapping tutorial * Add network comparison tutorial
sysbio-curie · Jul 23, 2024 · f3cbb8c · f3cbb8c
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diff --git a/notebooks/1_network_building.ipynb b/notebooks/1_network_building.ipynb
diff --git a/notebooks/2_add_resources.ipynb b/notebooks/2_add_resources.ipynb
diff --git a/notebooks/3_stepwise_connection.ipynb b/notebooks/3_stepwise_connection.ipynb
diff --git a/notebooks/4_Connect_upstream.ipynb b/notebooks/4_Connect_upstream.ipynb
diff --git a/notebooks/5_build_phosphosite_network.ipynb b/notebooks/5_build_phosphosite_network.ipynb
diff --git a/notebooks/6_ontology.ipynb b/notebooks/6_ontology.ipynb
@@ -0,0 +1,385 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "55b5595c-fec9-41c3-b756-b95cd0c52048",
+   "metadata": {},
+   "source": [
+    "# Connect to downstream Gene Ontology terms.\n",
+    "\n",
+    "This notebook showcases the functionality of Omniflow that connects the existing nodes of a network to a phenotype of interest. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "3c317de8",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 34 µs, sys: 2 µs, total: 36 µs\n",
+      "Wall time: 41.2 µs\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "from neko.core.network import Network\n",
+    "from neko._visual.visualize_network import NetworkVisualizer\n",
+    "from neko._inputs.resources import Resources\n",
+    "from neko._annotations.gene_ontology import Ontology\n",
+    "import omnipath as op"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2910c871-fdfc-4d20-b76f-af213f06a3f0",
+   "metadata": {},
+   "source": [
+    "### 1. Build network\n",
+    "\n",
+    "Please see the [Network building](https://omniflow-project.readthedocs.io/en/latest/notebooks/network_building.html) tutorial for detailed explanations of each step."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "79c09e13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "genes = [\"SRC\", \"NOTCH1\", \"FAK\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "fcf68a99-8454-41e3-8816-c3f976d04c0b",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "c3540efecec947a5853420e3000ea9c4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "0.00B [00:00, ?B/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "new_net1 = Network(genes)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "370180cc",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 139 ms, sys: 3.96 ms, total: 143 ms\n",
+      "Wall time: 141 ms\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "new_net1.connect_nodes(only_signed=True, consensus_only=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8ed135d3-9f71-4cec-9381-96c63fba766e",
+   "metadata": {},
+   "source": [
+    "### 2. Connect to Gene Ontology (GO) term\n",
+    "\n",
+    "Connect the nodes of the Network with markers of a certain phenotype, from Gene Ontology. \n",
+    "\n",
+    "The _connect_genes_to_phenotype_ function will look for interactions between the nodes of the network and genes annotated with a GO term of interest. The argument _compress_ replaces the individual phenotype-specific genes into one phenotype node.\n",
+    "\n",
+    "<div class=\"alert alert-info\">\n",
+    "\n",
+    "**Note**\n",
+    "    \n",
+    "We suggest to the users to choose gene ontology terms lower in the hierarcy (e.g., execution phase of apoptosis _versus_ apoptosis) to avoid the inclusion of too many genes.\n",
+    "\n",
+    "</div>  "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "fa499a38-c22a-4a0e-b1d4-3ffb10e4a370",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Start requesting genes from Gene Ontology\n",
+      "Fetching from:  https://golr-aux.geneontology.io/solr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=bioentity_label&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&hl=true&hl.simple.pre=%3Cem%20class=%22hilite%22%3E&hl.snippets=1000&csv.encapsulator=&csv.separator=%09&csv.header=false&csv.mv.separator=%7C&fq=document_category:%22annotation%22&fq=isa_partof_closure:%22GO:0001837%22&fq=taxon_subset_closure_label:%22Homo%20sapiens%22&fq=type:%22protein%22&fq=annotation_class_label:%22epithelial%20to%20mesenchymal%20transition%22&facet.field=aspect&facet.field=taxon_subset_closure_label&facet.field=type&facet.field=evidence_subset_closure_label&facet.field=regulates_closure_label&facet.field=isa_partof_closure_label&facet.field=annotation_class_label&facet.field=qualifier&facet.field=annotation_extension_class_closure_label&facet.field=assigned_by&facet.field=panther_family_label&q=*:*\n",
+      "Done\n",
+      "Starting connecting network's nodes to:  ['WNT5A', 'WNT4', 'NOTCH1', 'RFLNB', 'SP6', 'AMELX', 'ROCK2', 'SLC39A6', 'PPP3R1', 'LEF1', 'FOXF2', 'ROCK1', 'S100A4', 'TGFB2', 'RBPJ', 'DLG5', 'DACT3', 'WNT11', 'HGF', 'CUL7', 'TGFB1', 'NOG', 'TRIM28', 'BMP2', 'TGFBR3', 'TGFBR1', 'FLNA', 'HMGA2', 'DDX17', 'TGFBR3L', 'EPB41L5', 'SNAI1', 'AKNA', 'IGF1', 'DDX5', 'SOX9', 'TGFBR2', 'HIF1A', 'BMP7', 'FGFR2', 'SMAD4', 'ENG', 'LOXL2', 'SNAI2', 'FGFR1', 'LIMS1', 'LOXL3', 'NCAM1', 'NOTCH4', 'GSK3B', 'SLC39A10', 'FAM83D', 'HNRNPAB', 'CTNNB1']\n",
+      "CPU times: user 3.2 s, sys: 35 µs, total: 3.2 s\n",
+      "Wall time: 4.07 s\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "new_net1.connect_genes_to_phenotype(id_accession=\"GO:0001837\", phenotype=\"epithelial to mesenchymal transition\", only_signed=True, compress=True, maxlen=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "33300268-bcf6-442b-97be-c7718922a939",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 2.43.0 (0)\n",
+       " -->\n",
+       "<!-- Title: %3 Pages: 1 -->\n",
+       "<svg width=\"378pt\" height=\"188pt\"\n",
+       " viewBox=\"0.00 0.00 378.47 188.00\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 184)\">\n",
+       "<title>%3</title>\n",
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+       "<!-- SRC -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>SRC</title>\n",
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+       "<text text-anchor=\"middle\" x=\"113.23\" y=\"-158.3\" font-family=\"Times,serif\" font-size=\"14.00\">SRC</text>\n",
+       "</g>\n",
+       "<!-- PTK2 -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>PTK2</title>\n",
+       "<ellipse fill=\"lightgray\" stroke=\"black\" cx=\"81.23\" cy=\"-90\" rx=\"36\" ry=\"18\"/>\n",
+       "<text text-anchor=\"middle\" x=\"81.23\" y=\"-86.3\" font-family=\"Times,serif\" font-size=\"14.00\">PTK2</text>\n",
+       "</g>\n",
+       "<!-- SRC&#45;&gt;PTK2 -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>SRC&#45;&gt;PTK2</title>\n",
+       "<path fill=\"none\" stroke=\"green\" d=\"M105.65,-144.41C101.92,-136.25 97.33,-126.22 93.15,-117.07\"/>\n",
+       "<polygon fill=\"green\" stroke=\"green\" points=\"96.33,-115.6 88.98,-107.96 89.96,-118.51 96.33,-115.6\"/>\n",
+       "</g>\n",
+       "<!-- epithelial_to_mesenchymal_transition -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>epithelial_to_mesenchymal_transition</title>\n",
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+       "<text text-anchor=\"middle\" x=\"185.23\" y=\"-14.3\" font-family=\"Times,serif\" font-size=\"14.00\">epithelial_to_mesenchymal_transition</text>\n",
+       "</g>\n",
+       "<!-- SRC&#45;&gt;epithelial_to_mesenchymal_transition -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>SRC&#45;&gt;epithelial_to_mesenchymal_transition</title>\n",
+       "<path fill=\"none\" stroke=\"red\" d=\"M121.63,-144.43C134.61,-118.84 159.54,-69.68 174.03,-41.09\"/>\n",
+       "<polygon fill=\"red\" stroke=\"red\" points=\"171.53,-34.98 180.45,-39.5 179.54,-41.28 170.62,-36.76 171.53,-34.98\"/>\n",
+       "<polyline fill=\"none\" stroke=\"red\" points=\"176.44,-36.35 174.18,-40.81 \"/>\n",
+       "</g>\n",
+       "<!-- PTK2&#45;&gt;epithelial_to_mesenchymal_transition -->\n",
+       "<g id=\"edge4\" class=\"edge\">\n",
+       "<title>PTK2&#45;&gt;epithelial_to_mesenchymal_transition</title>\n",
+       "<path fill=\"none\" stroke=\"purple\" d=\"M101.78,-75.17C115.47,-65.95 133.83,-53.6 149.84,-42.82\"/>\n",
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+       "</g>\n",
+       "<!-- NOTCH1 -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>NOTCH1</title>\n",
+       "<ellipse fill=\"lightgray\" stroke=\"black\" cx=\"225.23\" cy=\"-90\" rx=\"51.99\" ry=\"18\"/>\n",
+       "<text text-anchor=\"middle\" x=\"225.23\" y=\"-86.3\" font-family=\"Times,serif\" font-size=\"14.00\">NOTCH1</text>\n",
+       "</g>\n",
+       "<!-- NOTCH1&#45;&gt;epithelial_to_mesenchymal_transition -->\n",
+       "<g id=\"edge3\" class=\"edge\">\n",
+       "<title>NOTCH1&#45;&gt;epithelial_to_mesenchymal_transition</title>\n",
+       "<path fill=\"none\" stroke=\"green\" d=\"M210.16,-72.76C204.58,-64.61 198.57,-54.53 193.7,-45.31\"/>\n",
+       "<polygon fill=\"green\" stroke=\"green\" points=\"196.72,-43.51 189.12,-36.12 190.46,-46.63 196.72,-43.51\"/>\n",
+       "</g>\n",
+       "<!-- NOTCH1&#45;&gt;epithelial_to_mesenchymal_transition -->\n",
+       "<g id=\"edge5\" class=\"edge\">\n",
+       "<title>NOTCH1&#45;&gt;epithelial_to_mesenchymal_transition</title>\n",
+       "<path fill=\"none\" stroke=\"green\" d=\"M221.26,-71.7C217.45,-63.56 212.02,-53.69 206.45,-44.7\"/>\n",
+       "<polygon fill=\"green\" stroke=\"green\" points=\"209.27,-42.61 200.9,-36.1 203.39,-46.4 209.27,-42.61\"/>\n",
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+       "</g>\n",
+       "</svg>\n"
+      ],
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+       "<graphviz.graphs.Digraph at 0x7f640e187e20>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "#Visualize network\n",
+    "visualizer1 = NetworkVisualizer(new_net1, color_by='effect')\n",
+    "visualizer1.render()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "7ba750f3-8440-4bf6-a37b-5c917f334fc9",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>source</th>\n",
+       "      <th>target</th>\n",
+       "      <th>Type</th>\n",
+       "      <th>Effect</th>\n",
+       "      <th>References</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>P12931</td>\n",
+       "      <td>Q05397</td>\n",
+       "      <td>post_translational</td>\n",
+       "      <td>stimulation</td>\n",
+       "      <td>Adhesome:10085298;Adhesome:10592173;Adhesome:1...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>P12931</td>\n",
+       "      <td>epithelial_to_mesenchymal_transition</td>\n",
+       "      <td>post_translational</td>\n",
+       "      <td>inhibition</td>\n",
+       "      <td>ProtMapper:16859511;ProtMapper:17440088;ProtMa...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>P46531</td>\n",
+       "      <td>epithelial_to_mesenchymal_transition</td>\n",
+       "      <td>transcriptional, post_translational</td>\n",
+       "      <td>stimulation</td>\n",
+       "      <td>CollecTRI:22110751, ACSN:22330899;ACSN:2236313...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Q05397</td>\n",
+       "      <td>epithelial_to_mesenchymal_transition</td>\n",
+       "      <td>post_translational</td>\n",
+       "      <td>bimodal</td>\n",
+       "      <td>nan</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>P46531</td>\n",
+       "      <td>epithelial_to_mesenchymal_transition</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>stimulation</td>\n",
+       "      <td>Gene Ontology</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "   source                                target  \\\n",
+       "0  P12931                                Q05397   \n",
+       "1  P12931  epithelial_to_mesenchymal_transition   \n",
+       "2  P46531  epithelial_to_mesenchymal_transition   \n",
+       "3  Q05397  epithelial_to_mesenchymal_transition   \n",
+       "4  P46531  epithelial_to_mesenchymal_transition   \n",
+       "\n",
+       "                                  Type       Effect  \\\n",
+       "0                   post_translational  stimulation   \n",
+       "1                   post_translational   inhibition   \n",
+       "2  transcriptional, post_translational  stimulation   \n",
+       "3                   post_translational      bimodal   \n",
+       "4                                  NaN  stimulation   \n",
+       "\n",
+       "                                          References  \n",
+       "0  Adhesome:10085298;Adhesome:10592173;Adhesome:1...  \n",
+       "1  ProtMapper:16859511;ProtMapper:17440088;ProtMa...  \n",
+       "2  CollecTRI:22110751, ACSN:22330899;ACSN:2236313...  \n",
+       "3                                                nan  \n",
+       "4                                      Gene Ontology  "
+      ]
+     },
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+     "output_type": "execute_result"
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