{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0f6c4513",
   "metadata": {},
   "source": [
    "# OAK obsoletes command\n",
    "\n",
    "This notebook is intended as a supplement to the [main OAK CLI docs](https://incatools.github.io/ontology-access-kit/cli.html).\n",
    "\n",
    "This notebook provides examples for the `obsoletes` command, which shows all obsolete entities in an ontology,\n",
    "plus associated metadata\n",
    "\n",
    "## Help Option\n",
    "\n",
    "You can get help on any OAK command using `--help`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "65db4b53",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Usage: runoak obsoletes [OPTIONS] [TERMS]...\n",
      "\n",
      "  Shows all obsolete entities.\n",
      "\n",
      "  Example:\n",
      "\n",
      "      runoak -i obolibrary:go.obo obsoletes\n",
      "\n",
      "  To exclude *merged terms*, use the ``--no-include-merged`` flag\n",
      "\n",
      "  Example:\n",
      "\n",
      "      runoak -i obolibrary:go.obo obsoletes --no-include-merged\n",
      "\n",
      "  To show migration relationships, use the ``--show-migration-relationships``\n",
      "  flag\n",
      "\n",
      "  Example:\n",
      "\n",
      "      runoak -i obolibrary:go.obo obsoletes --show-migration-relationships\n",
      "\n",
      "  You can also specify terms to show obsoletes for:\n",
      "\n",
      "  Example:\n",
      "\n",
      "      runoak -i obolibrary:go.obo obsoletes --show-migration-relationships\n",
      "      GO:0000187 GO:0000188\n",
      "\n",
      "Options:\n",
      "  --include-merged / --no-include-merged\n",
      "                                  Include merged terms in output  [default:\n",
      "                                  include-merged]\n",
      "  --show-migration-relationships / --no-show-migration-relationships\n",
      "                                  Show migration relationships (e.g.\n",
      "                                  replaced_by, consider)  [default: no-show-\n",
      "                                  migration-relationships]\n",
      "  -O, --output-type [obo|obojson|ofn|rdf|json|yaml|fhirjson|csv|nl]\n",
      "                                  Desired output type\n",
      "  -o, --output FILENAME           Output file, e.g. obo file\n",
      "  --help                          Show this message and exit.\n"
     ]
    }
   ],
   "source": [
    "!runoak obsoletes --help"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "803bc7b6",
   "metadata": {},
   "outputs": [],
   "source": [
    "alias cl runoak -i sqlite:obo:cl"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "97e6e346",
   "metadata": {},
   "outputs": [],
   "source": [
    "cl obsoletes > output/cl-obsoletes.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "c93883a0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "id\tlabel\r",
      "\r\n",
      "CL:0000002\tobsolete immortal cell line cell\r",
      "\r\n",
      "CL:0000004\tobsolete cell by organism\r",
      "\r\n",
      "CL:0000009\tobsolete fusiform initial\r",
      "\r\n",
      "CL:0000012\tobsolete cell by class\r",
      "\r\n",
      "CL:0000013\tobsolete dentine secreting cell\r",
      "\r\n",
      "CL:0000045\tobsolete thymus processed stem cell\r",
      "\r\n",
      "CL:0000046\tobsolete bursa processed stem cell\r",
      "\r\n",
      "CL:0000063\tobsolete cell by histology\r",
      "\r\n",
      "CL:0000070\tobsolete epithelial cell of gland\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!head output/cl-obsoletes.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "22c0636b",
   "metadata": {},
   "outputs": [],
   "source": [
    "cl obsoletes --show-migration-relationships > output/cl-obsoletes-full.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "7b49fb37",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "id\tlabel\tIAO:0100001\toio:consider\r",
      "\r\n",
      "CL:0000002\tobsolete immortal cell line cell\t['CLO:0000019']\t[]\r",
      "\r\n",
      "CL:0000004\tobsolete cell by organism\t[]\t['CL:0000000', 'CL:0000003', 'CL:0001034']\r",
      "\r\n",
      "CL:0000009\tobsolete fusiform initial\t['PO:0000079']\t[]\r",
      "\r\n",
      "CL:0000012\tobsolete cell by class\t[]\t['CL:0000000', 'CL:0000003', 'CL:0001034']\r",
      "\r\n",
      "CL:0000013\tobsolete dentine secreting cell\t[]\t['CL:0000140']\r",
      "\r\n",
      "CL:0000045\tobsolete thymus processed stem cell\t[]\t[]\r",
      "\r\n",
      "CL:0000046\tobsolete bursa processed stem cell\t[]\t[]\r",
      "\r\n",
      "CL:0000063\tobsolete cell by histology\t[]\t['CL:0000000', 'CL:0000003', 'CL:0001034']\r",
      "\r\n",
      "CL:0000070\tobsolete epithelial cell of gland\t[]\t[]\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!head output/cl-obsoletes-full.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1017c2b6",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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