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  {
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   "source": [
    "# OBA tutorial\n",
    "\n",
    "* author: Harshad Hegde\n",
    "* created: 2023-01-25\n",
    "\n",
    "This tutorial walks through OBA."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6e93ee26",
   "metadata": {},
   "source": [
    "## Create an alias\n",
    "\n",
    "For convenience we will set a bash alias.\n",
    "\n",
    "This assumes you have built the sqlite version of oba in the `../../db` folder\n",
    "\n",
    "__NOTE__ an alternative is:\n",
    "\n",
    "`%alias oba runoak -i sqlite:obo:oba`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "43637cd0",
   "metadata": {},
   "outputs": [],
   "source": [
    "%alias oba runoak -i ../../db/oba.db"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e0925b63",
   "metadata": {},
   "source": [
    "### Basic lookup queries\n",
    "\n",
    "Let's check it's working:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "98923f51",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "OBA:1000076 ! attribute of cell\r\n"
     ]
    }
   ],
   "source": [
    "oba info OBA:1000076"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c12ee95d",
   "metadata": {},
   "source": [
    "## Exploring the structure of OBA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "20f0ed74",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "subject\tsubject_label\tpredicate\tpredicate_label\tobject\tobject_label\n",
      "UBERON:0004535\tcardiovascular system\tBFO:0000050\tpart of\tUBERON:0001009\tcirculatory system\n",
      "UBERON:0004535\tcardiovascular system\tBFO:0000051\thas part\tUBERON:0000948\theart\n",
      "UBERON:0004535\tcardiovascular system\tBFO:0000051\thas part\tUBERON:0001981\tblood vessel\n",
      "UBERON:0004535\tcardiovascular system\trdfs:subClassOf\tNone\tUBERON:0000467\tanatomical system\n",
      "UBERON:0004535\tcardiovascular system\towl:equivalentClass\tNone\t_:riog00287837\tNone\n"
     ]
    }
   ],
   "source": [
    "oba relationships UBERON:0004535"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "29edb128",
   "metadata": {},
   "source": [
    "Here we can see linkages to external ontologies using two relations\n",
    "\n",
    "### Querying ancestors\n",
    "\n",
    "We will try finding all ancestors of OBA:VT0010191 (immune system cell quantity)\n",
    "\n",
    "__IMPORTANT__ in OAK, all graph commands are parameterized by predicate lists. Consult the OAK docs if you\n",
    "don't understand what this means!\n",
    "\n",
    "To find all is-a ancestors (i.e. ancestors following SubClassOf between named classes) we use `-p i`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7d67c8dc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "id\tlabel\r",
      "\r\n",
      "BFO:0000001\tentity\r",
      "\r\n",
      "BFO:0000002\tcontinuant\r",
      "\r\n",
      "BFO:0000019\tquality\r",
      "\r\n",
      "BFO:0000019\tquality\r",
      "\r\n",
      "BFO:0000020\tspecifically dependent continuant\r",
      "\r\n",
      "OBA:0000001\tbiological attribute\r",
      "\r\n",
      "OBA:0100003\tanatomical entity attribute\r",
      "\r\n",
      "OBA:1000076\tattribute of cell\r",
      "\r\n",
      "OBA:VT0000237\tblood cell quantity\r",
      "\r\n",
      "OBA:VT0010191\timmune system cell quantity\r",
      "\r\n",
      "PATO:0000001\tquality\r",
      "\r\n",
      "PATO:0001241\tphysical object quality\r",
      "\r\n",
      "PATO:0001555\thas number of\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "oba ancestors -p i OBA:VT0010191"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "165efc59",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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