{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "b3b0dbee",
   "metadata": {},
   "source": [
    "# NCIT tutorial\n",
    "\n",
    "* author: Chris Mungall\n",
    "* created: 2022-11-11\n",
    "\n",
    "This tutorial walks through NCIT-OBO, the goals are:\n",
    "\n",
    "- to help understand the structure of ncit\n",
    "- to show how to do advanced OAK queries (CLI and programmatic) on NCIT\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9aced0d9",
   "metadata": {},
   "source": [
    "## Create an alias\n",
    "\n",
    "For convenience we will set a bash alias.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "44bd10cd",
   "metadata": {},
   "outputs": [],
   "source": [
    "%alias ncit runoak -i sqlite:obo:ncit"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "09595dfc",
   "metadata": {},
   "source": [
    "### Basic lookup queries\n",
    "\n",
    "Let's check it's working:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "81399308",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NCIT:C4872 ! Breast Carcinoma\r\n"
     ]
    }
   ],
   "source": [
    "ncit info NCIT:C4872"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "fb640127",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NCIT:C4872 ! Breast Carcinoma\r\n"
     ]
    }
   ],
   "source": [
    "ncit info \"Breast Carcinoma\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f8b16045",
   "metadata": {},
   "source": [
    "## Exploring the structure of NCIT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "1e122ab2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "subject\tsubject_label\tpredicate\tpredicate_label\tobject\tobject_label\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R101\tDisease_Has_Primary_Anatomic_Site\tNCIT:C12971\tBreast\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R103\tDisease_Has_Normal_Tissue_Origin\tNCIT:C12937\tMammary Epithelium\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C2916\tCarcinoma\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C9335\tMalignant Breast Neoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\towl:equivalentClass\tNone\t_:riog00972235\tNone\n"
     ]
    }
   ],
   "source": [
    "phenio relationships NCIT:C4872"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "0162323e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "subject\tsubject_label\tpredicate\tpredicate_label\tobject\tobject_label\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R100\tDisease_Has_Associated_Anatomic_Site\tNCIT:C12219\tAnatomic Structure, System, or Substance\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R100\tDisease_Has_Associated_Anatomic_Site\tNCIT:C12971\tBreast\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R100\tDisease_Has_Associated_Anatomic_Site\tNCIT:C13018\tOrgan\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R105\tDisease_Has_Abnormal_Cell\tNCIT:C12913\tAbnormal Cell\n",
      "NCIT:C4872\tBreast Carcinoma\tNCIT:R105\tDisease_Has_Abnormal_Cell\tNCIT:C12922\tNeoplastic Cell\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C26709\tBreast Disorder\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C27551\tDisorder by Site\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C2910\tBreast Neoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C2916\tCarcinoma\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C2991\tDisease or Disorder\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C3262\tNeoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C3263\tNeoplasm by Site\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C3709\tEpithelial Neoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C4741\tNeoplasm by Morphology\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C4872\tBreast Carcinoma\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C7057\tDisease, Disorder or Finding\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C7062\tNeoplasm by Special Category\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C9305\tMalignant Neoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\trdfs:subClassOf\tNone\tNCIT:C9335\tMalignant Breast Neoplasm\n",
      "NCIT:C4872\tBreast Carcinoma\towl:equivalentClass\tNone\t_:riog00922295\tNone\n"
     ]
    }
   ],
   "source": [
    "phenio relationships --include-entailed NCIT:C4872"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b79f675d",
   "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 NCIT:C4872\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": 13,
   "id": "90d3806c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NCIT:C26709 ! Breast Disorder\n",
      "NCIT:C27551 ! Disorder by Site\n",
      "NCIT:C2910 ! Breast Neoplasm\n",
      "NCIT:C2916 ! Carcinoma\n",
      "NCIT:C2991 ! Disease or Disorder\n",
      "NCIT:C3262 ! Neoplasm\n",
      "NCIT:C3263 ! Neoplasm by Site\n",
      "NCIT:C3709 ! Epithelial Neoplasm\n",
      "NCIT:C4741 ! Neoplasm by Morphology\n",
      "NCIT:C4872 ! Breast Carcinoma\n",
      "NCIT:C7057 ! Disease, Disorder or Finding\n",
      "NCIT:C7062 ! Neoplasm by Special Category\n",
      "NCIT:C9305 ! Malignant Neoplasm\n",
      "NCIT:C9335 ! Malignant Breast Neoplasm\n"
     ]
    }
   ],
   "source": [
    "ncit ancestors -p i NCIT:C4872"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "58f23581",
   "metadata": {},
   "source": [
    "Next we will generate a visualization from this using the `viz` command:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "c10dc41f",
   "metadata": {},
   "outputs": [],
   "source": [
    "ncit viz -p i NCIT:C4872 -o output/NCIT_C4872.png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a354b6da",
   "metadata": {},
   "source": [
    "![img](output/NCIT_C4872.png)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "93d7083e",
   "metadata": {},
   "outputs": [],
   "source": [
    "ncit viz -p i,NCIT:R101,NCIT:R103,NCIT:R82 NCIT:C4872 -o output/NCIT_C4872_multirel.png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7e69abe3",
   "metadata": {},
   "source": [
    "![img](output/NCIT_C4872_multirel.png)"
   ]
  }
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