{
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  {
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   "metadata": {},
   "source": [
    "# Ontological Differential Analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0b2a6bf8",
   "metadata": {},
   "source": [
    "## Summary"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3bed637b",
   "metadata": {},
   "source": [
    "Doing OGDA programatically is a two-step process. In the first step, sets of metadata triplets are created. In the second step, those sets are used as input to the actual calculator."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "303d550e",
   "metadata": {},
   "source": [
    "## Step 1 - Triplets"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "847e2367",
   "metadata": {},
   "source": [
    "Making a post request to "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0ac727a7",
   "metadata": {},
   "source": [
    "```\n",
    "http://bindiscover.metabolomics.us:4999/hgdametadataresource/\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cb3a44be",
   "metadata": {},
   "source": [
    "With the format "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d103ef0",
   "metadata": {},
   "source": [
    "```\n",
    "{\n",
    "    \"from_species\":\"10114\", #any NCBI species or parent ID\n",
    "    \"from_organ\":\"A03.620\", #any MeSH organ ID\n",
    "    \"from_disease\":\"No Disease\", #any MeSH disease ID\n",
    "    \"to_species\":\"314146\",\n",
    "    \"to_organ\":\"A03.556.875.500\",\n",
    "    \"to_disease\":\"No Disease\"\n",
    "}\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3275c5e5",
   "metadata": {},
   "source": [
    "Where values in this dictionary are nodes from the NCBI taxonomy and MeSH Hierarchies will yield a record-oriented metadata table, e.g."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "91c07de8",
   "metadata": {},
   "source": [
    "```\n",
    "\"[\n",
    "    {\\\"from_or_to\\\":\\\"from\\\",\\\"triplet_id\\\":\\\"rattus rattus - Liver - No Disease\\\",\\\"sample_count\\\":221},\n",
    "    {\\\"from_or_to\\\":\\\"to\\\",\\\"triplet_id\\\":\\\"mus musculus - Esophagus - No Disease\\\",\\\"sample_count\\\":24}\n",
    "]\"\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "beb1cf89",
   "metadata": {},
   "source": [
    "## Step 2 - OGDA "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "79b87016",
   "metadata": {},
   "source": [
    "Making a post request to "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3d0c0e3b",
   "metadata": {},
   "source": [
    "```\n",
    "http://bindiscover.metabolomics.us:4999/hgdaresource/\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2b5ffc72",
   "metadata": {},
   "source": [
    "with the format"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "89322be5",
   "metadata": {},
   "source": [
    "```\n",
    "{\n",
    "    \"metadata_datatable\":\n",
    "        [\n",
    "            {\"from_or_to\": \"from\", \"triplet_id\": \"citrus reticulata - Plant Leaves - No Disease\", \"sample_count\": 43}, \n",
    "            {\"from_or_to\": \"to\", \"triplet_id\": \"malus x domestica - Fruit - No Disease\", \"sample_count\": 17}\n",
    "        ],\n",
    "    \"bin_type\":\"known\" #values are 'known', 'unknown', and 'class' (compound classes)\n",
    "}\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3623d251",
   "metadata": {},
   "source": [
    "will yield the core information for the differential analysis, eg"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "eacd6c15",
   "metadata": {},
   "source": [
    "```\n",
    "\"[\n",
    "    {\\\"compound_id\\\": 14717, \\\"identifier\\\": \\\"OOWQBDFWEXAXPB-UHFFFAOYSA-N\\\", \\\"english_name\\\": \\\"hexadecylglycerol\\\", \\\"bin_type_dict\\\": \\\"known\\\", \\\"significance_welch\\\": 0.6109507199, \\\"fold_change_average\\\": 0.007302779200000001},\n",
    "    {\\\"compound_id\\\": 2214, \\\"identifier\\\": \\\"LOLKAJARZKDJTD-UHFFFAOYSA-N\\\", \\\"english_name\\\": \\\"ethylsuccinate\\\", \\\"bin_type_dict\\\": \\\"known\\\", \\\"significance_welch\\\": 0.1504452139, \\\"fold_change_average\\\": -0.031181263}...\n",
    "\"\n",
    "```"
   ]
  }
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