ontology_mapping.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "47bcd090-0737-4c94-91f9-a021efd73f18",
   "metadata": {},
   "source": [
    "# Ontology mapping"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "62dc1484-a7eb-4f5b-aedc-b57ce865c920",
   "metadata": {},
   "source": [
    "Ontologies are structured and standardized representations of knowledge in a specific domain, defining the concepts, relationships, and properties within that domain. They matter for Electronic Health Records (EHR) as they provide a common vocabulary and framework for organizing and integrating healthcare data. By using ontologies, EHR systems can improve interoperability, semantic understanding, and facilitate effective data exchange, leading to enhanced decision support, data analysis, and collaboration among healthcare providers and also analysts."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "86af2499-df15-4dac-b80d-7db600eba205",
   "metadata": {},
   "source": [
    "ehrapy is compatible with [Bionty](https://github.com/laminlabs/bionty) which provides access to public ontologies and functionality to map values against them.\n",
    "\n",
    "Here, we'll create an artificial AnnData object containing different diseases that we will map against to ensure that all of our annotations adhere to ontologies."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "d7579faa-c9a8-48aa-b385-8ab0c9f52ddf",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import anndata as ad\n",
    "import numpy as np\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9223258c-cded-49ed-8380-93e3870b3182",
   "metadata": {},
   "source": [
    "Create an AnnData object with disease annotations in the `obs` slot."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "79e34af4-bb5d-420c-b284-66a72168d611",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/zeth/miniconda3/envs/ehrapy/lib/python3.11/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
      "  warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 3 × 3\n",
       "    obs: 'Immune system disorders', 'nervous system disorder', 'injury'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = ad.AnnData(\n",
    "    X=np.random.random((3, 3)),\n",
    "    var=pd.DataFrame(index=[f\"Lab value {val}\" for val in range(3)]),\n",
    "    obs=pd.DataFrame(\n",
    "        columns=[\"Immune system disorders\", \"nervous system disorder\", \"injury\"],\n",
    "        data=[\n",
    "            [\"Rheumatoid arthritis\", \"Alzheimer's disease\", \"Fracture\"],\n",
    "            [\"Celiac disease\", \"Parkinson's disease\", \"Traumatic brain injury\"],\n",
    "            [\"Multipla sclurosis\", \"Epilepsy\", \"Fractured Femur\"],\n",
    "        ],\n",
    "    ),\n",
    ")\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bffd9a56-8127-45cb-bd8b-ab86cdb54d1f",
   "metadata": {
    "tags": []
   },
   "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>Immune system disorders</th>\n",
       "      <th>nervous system disorder</th>\n",
       "      <th>injury</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Rheumatoid arthritis</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>Fracture</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Celiac disease</td>\n",
       "      <td>Parkinson's disease</td>\n",
       "      <td>Traumatic brain injury</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Multipla sclurosis</td>\n",
       "      <td>Epilepsy</td>\n",
       "      <td>Fractured Femur</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Immune system disorders nervous system disorder                  injury\n",
       "0    Rheumatoid arthritis     Alzheimer's disease                Fracture\n",
       "1          Celiac disease     Parkinson's disease  Traumatic brain injury\n",
       "2      Multipla sclurosis                Epilepsy         Fractured Femur"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "716fc989-1f56-428c-8c97-6c74e1a3b3a1",
   "metadata": {},
   "source": [
    "We notice that one of our injuries does not exist and we expect to have to correct it later."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "900b48e8-3785-46fe-8659-8ecc0c9fecd5",
   "metadata": {},
   "source": [
    "## Introduction to Bionty"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7c267a1f-5e68-4761-ab6f-c704c7207479",
   "metadata": {},
   "source": [
    "First we import Bionty."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "f5b2634e-b809-4115-9440-7ef40399e38e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ wrote new records from public sources.yaml to /home/zeth/.lamin/bionty/versions/sources_local.yaml!\n",
      "\n",
      "if you see this message repeatedly, run: import bionty_base; bionty_base.reset_sources()\n"
     ]
    }
   ],
   "source": [
    "import bionty_base as bt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "abca4350-8799-41fe-a955-0ea96201fc7b",
   "metadata": {},
   "source": [
    "Bionty provides support for several ontologies related to diseases."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "60d2a5b4-3a89-4dc7-9101-8d0ddb1705b7",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
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       "\n",
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       "    }\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>organism</th>\n",
       "      <th>version</th>\n",
       "      <th>url</th>\n",
       "      <th>md5</th>\n",
       "      <th>source_name</th>\n",
       "      <th>source_website</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>entity</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>mondo</td>\n",
       "      <td>all</td>\n",
       "      <td>2024-02-06</td>\n",
       "      <td>http://purl.obolibrary.org/obo/mondo/releases/...</td>\n",
       "      <td>78914fa236773c5ea6605f7570df6245</td>\n",
       "      <td>Mondo Disease Ontology</td>\n",
       "      <td>https://mondo.monarchinitiative.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>mondo</td>\n",
       "      <td>all</td>\n",
       "      <td>2023-08-02</td>\n",
       "      <td>http://purl.obolibrary.org/obo/mondo/releases/...</td>\n",
       "      <td>7f33767422042eec29f08b501fc851db</td>\n",
       "      <td>Mondo Disease Ontology</td>\n",
       "      <td>https://mondo.monarchinitiative.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>mondo</td>\n",
       "      <td>all</td>\n",
       "      <td>2023-04-04</td>\n",
       "      <td>http://purl.obolibrary.org/obo/mondo/releases/...</td>\n",
       "      <td>700c43dd9ba51aecc7a8edfc3bc2dab1</td>\n",
       "      <td>Mondo Disease Ontology</td>\n",
       "      <td>https://mondo.monarchinitiative.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>mondo</td>\n",
       "      <td>all</td>\n",
       "      <td>2023-02-06</td>\n",
       "      <td>http://purl.obolibrary.org/obo/mondo/releases/...</td>\n",
       "      <td>2b7d479d4bd02a94eab47d1c9e64c5db</td>\n",
       "      <td>Mondo Disease Ontology</td>\n",
       "      <td>https://mondo.monarchinitiative.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>mondo</td>\n",
       "      <td>all</td>\n",
       "      <td>2022-10-11</td>\n",
       "      <td>http://purl.obolibrary.org/obo/mondo/releases/...</td>\n",
       "      <td>04b808d05c2c2e81430b20a0e87552bb</td>\n",
       "      <td>Mondo Disease Ontology</td>\n",
       "      <td>https://mondo.monarchinitiative.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>doid</td>\n",
       "      <td>human</td>\n",
       "      <td>2024-01-31</td>\n",
       "      <td>http://purl.obolibrary.org/obo/doid/releases/2...</td>\n",
       "      <td>b36c15a4610757094f8db64b78ae2693</td>\n",
       "      <td>Human Disease Ontology</td>\n",
       "      <td>https://disease-ontology.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>doid</td>\n",
       "      <td>human</td>\n",
       "      <td>2023-03-31</td>\n",
       "      <td>http://purl.obolibrary.org/obo/doid/releases/2...</td>\n",
       "      <td>64f083a1e47867c307c8eae308afc3bb</td>\n",
       "      <td>Human Disease Ontology</td>\n",
       "      <td>https://disease-ontology.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>doid</td>\n",
       "      <td>human</td>\n",
       "      <td>2023-01-30</td>\n",
       "      <td>http://purl.obolibrary.org/obo/doid/releases/2...</td>\n",
       "      <td>9f0c92ad2896dda82195e9226a06dc36</td>\n",
       "      <td>Human Disease Ontology</td>\n",
       "      <td>https://disease-ontology.org</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>icd</td>\n",
       "      <td>human</td>\n",
       "      <td>icd-11-2023</td>\n",
       "      <td>s3://bionty-assets/df_human__icd__icd-11-2023_...</td>\n",
       "      <td>16263aef644d2c62c47b7b1ecfbad9d6</td>\n",
       "      <td>International Classification of Diseases (ICD)</td>\n",
       "      <td>https://www.cdc.gov/nchs/icd/icd9cm.htm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>icd</td>\n",
       "      <td>human</td>\n",
       "      <td>icd-10-2020</td>\n",
       "      <td>s3://bionty-assets/df_human__icd__icd-10-2020_...</td>\n",
       "      <td>93ec5734fcc2edd64686d5ffc6f6105f</td>\n",
       "      <td>International Classification of Diseases (ICD)</td>\n",
       "      <td>https://www.cdc.gov/nchs/icd/icd9cm.htm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>icd</td>\n",
       "      <td>human</td>\n",
       "      <td>icd-9-2011</td>\n",
       "      <td>s3://bionty-assets/df_human__icd__icd-9-2011__...</td>\n",
       "      <td>cb3aefb3c4f7b2c47bf3de38453350c7</td>\n",
       "      <td>International Classification of Diseases (ICD)</td>\n",
       "      <td>https://www.cdc.gov/nchs/icd/icd9cm.htm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Disease</th>\n",
       "      <td>icd</td>\n",
       "      <td>human</td>\n",
       "      <td>icd-10-2024</td>\n",
       "      <td>s3://bionty-assets/df_human__icd__icd-10-2024_...</td>\n",
       "      <td>None</td>\n",
       "      <td>International Classification of Diseases (ICD)</td>\n",
       "      <td>https://www.cdc.gov/nchs/icd/icd9cm.htm</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        source organism      version  \\\n",
       "entity                                 \n",
       "Disease  mondo      all   2024-02-06   \n",
       "Disease  mondo      all   2023-08-02   \n",
       "Disease  mondo      all   2023-04-04   \n",
       "Disease  mondo      all   2023-02-06   \n",
       "Disease  mondo      all   2022-10-11   \n",
       "Disease   doid    human   2024-01-31   \n",
       "Disease   doid    human   2023-03-31   \n",
       "Disease   doid    human   2023-01-30   \n",
       "Disease    icd    human  icd-11-2023   \n",
       "Disease    icd    human  icd-10-2020   \n",
       "Disease    icd    human   icd-9-2011   \n",
       "Disease    icd    human  icd-10-2024   \n",
       "\n",
       "                                                       url  \\\n",
       "entity                                                       \n",
       "Disease  http://purl.obolibrary.org/obo/mondo/releases/...   \n",
       "Disease  http://purl.obolibrary.org/obo/mondo/releases/...   \n",
       "Disease  http://purl.obolibrary.org/obo/mondo/releases/...   \n",
       "Disease  http://purl.obolibrary.org/obo/mondo/releases/...   \n",
       "Disease  http://purl.obolibrary.org/obo/mondo/releases/...   \n",
       "Disease  http://purl.obolibrary.org/obo/doid/releases/2...   \n",
       "Disease  http://purl.obolibrary.org/obo/doid/releases/2...   \n",
       "Disease  http://purl.obolibrary.org/obo/doid/releases/2...   \n",
       "Disease  s3://bionty-assets/df_human__icd__icd-11-2023_...   \n",
       "Disease  s3://bionty-assets/df_human__icd__icd-10-2020_...   \n",
       "Disease  s3://bionty-assets/df_human__icd__icd-9-2011__...   \n",
       "Disease  s3://bionty-assets/df_human__icd__icd-10-2024_...   \n",
       "\n",
       "                                      md5  \\\n",
       "entity                                      \n",
       "Disease  78914fa236773c5ea6605f7570df6245   \n",
       "Disease  7f33767422042eec29f08b501fc851db   \n",
       "Disease  700c43dd9ba51aecc7a8edfc3bc2dab1   \n",
       "Disease  2b7d479d4bd02a94eab47d1c9e64c5db   \n",
       "Disease  04b808d05c2c2e81430b20a0e87552bb   \n",
       "Disease  b36c15a4610757094f8db64b78ae2693   \n",
       "Disease  64f083a1e47867c307c8eae308afc3bb   \n",
       "Disease  9f0c92ad2896dda82195e9226a06dc36   \n",
       "Disease  16263aef644d2c62c47b7b1ecfbad9d6   \n",
       "Disease  93ec5734fcc2edd64686d5ffc6f6105f   \n",
       "Disease  cb3aefb3c4f7b2c47bf3de38453350c7   \n",
       "Disease                              None   \n",
       "\n",
       "                                            source_name  \\\n",
       "entity                                                    \n",
       "Disease                          Mondo Disease Ontology   \n",
       "Disease                          Mondo Disease Ontology   \n",
       "Disease                          Mondo Disease Ontology   \n",
       "Disease                          Mondo Disease Ontology   \n",
       "Disease                          Mondo Disease Ontology   \n",
       "Disease                          Human Disease Ontology   \n",
       "Disease                          Human Disease Ontology   \n",
       "Disease                          Human Disease Ontology   \n",
       "Disease  International Classification of Diseases (ICD)   \n",
       "Disease  International Classification of Diseases (ICD)   \n",
       "Disease  International Classification of Diseases (ICD)   \n",
       "Disease  International Classification of Diseases (ICD)   \n",
       "\n",
       "                                  source_website  \n",
       "entity                                            \n",
       "Disease      https://mondo.monarchinitiative.org  \n",
       "Disease      https://mondo.monarchinitiative.org  \n",
       "Disease      https://mondo.monarchinitiative.org  \n",
       "Disease      https://mondo.monarchinitiative.org  \n",
       "Disease      https://mondo.monarchinitiative.org  \n",
       "Disease             https://disease-ontology.org  \n",
       "Disease             https://disease-ontology.org  \n",
       "Disease             https://disease-ontology.org  \n",
       "Disease  https://www.cdc.gov/nchs/icd/icd9cm.htm  \n",
       "Disease  https://www.cdc.gov/nchs/icd/icd9cm.htm  \n",
       "Disease  https://www.cdc.gov/nchs/icd/icd9cm.htm  \n",
       "Disease  https://www.cdc.gov/nchs/icd/icd9cm.htm  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bt.display_available_sources().loc[\"Disease\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b345b269-6b21-42ed-86a3-fa3e8d468b77",
   "metadata": {},
   "source": [
    "Bionty provides three key functionalities:\n",
    "\n",
    "1. `inspect`: Check whether any of our values (here diseases) are mappable against a specified ontology.\n",
    "2. `map_synonyms`: Map values against synonyms. This is not relevant for our diseases.\n",
    "3. `curate`: Curate ontology values against the ontology to ensure compliance."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "81d67ba7-b8b1-4b6b-ad42-3fe122c60705",
   "metadata": {},
   "source": [
    "## Mapping against the MONDO Disease Ontology with Bionty"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "35e32be9-4ade-411d-9e0f-fff64357a338",
   "metadata": {},
   "source": [
    "We will now showcase how to access the [Mondo Disease Ontology](https://mondo.monarchinitiative.org/) with Bionty.\n",
    "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world.\n",
    "\n",
    "There are several different sources available that provide definitions and data models for diseases, such as [HPO](https://hpo.jax.org/app), [OMIM](https://omim.org/), [SNOMED CT](http://www.snomed.org/), [ICD](https://www.cdc.gov/nchs/icd/icd10cm.htm), [PhenoDB](https://phenodb.org/), [MedDRA](https://www.meddra.org/), [MedGen](https://www.ncbi.nlm.nih.gov/medgen/), [ORDO](https://www.orpha.net/consor/cgi-bin/index.php?lng=EN), [DO](http://disease-ontology.org/), [GARD](https://rarediseases.info.nih.gov/), and others. However, these sources often overlap and sometimes conflict with each other, making it challenging to understand how they are related.\n",
    "\n",
    "To address the need for a unified disease terminology that offers precise equivalences between disease concepts, Mondo was developed. Mondo is designed to unify multiple disease resources using a logic-based structure."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "427cc9fe-ca9c-45ae-8670-a491fbac609c",
   "metadata": {},
   "source": [
    "Bionty is centered around Bionty entity objects that provide the above introduced functionality. We'll now create a Bionty Disease object with the MONDO ontology as our source and a specific version for reproducibility."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "2cb0a9c2-0f75-448e-858d-f93f73b6cd9a",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "PublicOntology\n",
       "Entity: Disease\n",
       "Organism: all\n",
       "Source: mondo, 2023-02-06\n",
       "#terms: 25913\n"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty = bt.Disease(source=\"mondo\", version=\"2023-02-06\")\n",
    "disease_bionty"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d6cd8893-bc5d-424d-872e-80242ba26c68",
   "metadata": {},
   "source": [
    "We can access the DataFrame that contains all ontology terms:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "8bf7ef19-aea8-4fc7-9360-8e544f59d3b7",
   "metadata": {
    "tags": []
   },
   "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>name</th>\n",
       "      <th>definition</th>\n",
       "      <th>synonyms</th>\n",
       "      <th>parents</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ontology_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>MONDO:0000001</th>\n",
       "      <td>disease or disorder</td>\n",
       "      <td>A Disease Is A Disposition To Undergo Patholog...</td>\n",
       "      <td>disorders|medical condition|other disease|dise...</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:0000002</th>\n",
       "      <td>obsolete 46,XX sex reversal</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:0000003</th>\n",
       "      <td>obsolete 17-hydroxysteroid dehydrogenase defic...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:0000004</th>\n",
       "      <td>adrenocortical insufficiency</td>\n",
       "      <td>An Endocrine Or Hormonal Disorder That Occurs ...</td>\n",
       "      <td>adrenal gland insufficiency|adrenal cortical i...</td>\n",
       "      <td>[MONDO:0002816]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:0000005</th>\n",
       "      <td>alopecia, isolated</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0021034]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:8000030</th>\n",
       "      <td>obsolete morphological anomaly</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:8000031</th>\n",
       "      <td>obsolete subtype of a disorder</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:8000032</th>\n",
       "      <td>obsolete malformation syndrome</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:8000033</th>\n",
       "      <td>obsolete group of disorders</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MONDO:8000034</th>\n",
       "      <td>obsolete disorder</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>25913 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                            name  \\\n",
       "ontology_id                                                        \n",
       "MONDO:0000001                                disease or disorder   \n",
       "MONDO:0000002                        obsolete 46,XX sex reversal   \n",
       "MONDO:0000003  obsolete 17-hydroxysteroid dehydrogenase defic...   \n",
       "MONDO:0000004                       adrenocortical insufficiency   \n",
       "MONDO:0000005                                 alopecia, isolated   \n",
       "...                                                          ...   \n",
       "MONDO:8000030                     obsolete morphological anomaly   \n",
       "MONDO:8000031                     obsolete subtype of a disorder   \n",
       "MONDO:8000032                     obsolete malformation syndrome   \n",
       "MONDO:8000033                        obsolete group of disorders   \n",
       "MONDO:8000034                                  obsolete disorder   \n",
       "\n",
       "                                                      definition  \\\n",
       "ontology_id                                                        \n",
       "MONDO:0000001  A Disease Is A Disposition To Undergo Patholog...   \n",
       "MONDO:0000002                                               None   \n",
       "MONDO:0000003                                               None   \n",
       "MONDO:0000004  An Endocrine Or Hormonal Disorder That Occurs ...   \n",
       "MONDO:0000005                                               None   \n",
       "...                                                          ...   \n",
       "MONDO:8000030                                               None   \n",
       "MONDO:8000031                                               None   \n",
       "MONDO:8000032                                               None   \n",
       "MONDO:8000033                                               None   \n",
       "MONDO:8000034                                               None   \n",
       "\n",
       "                                                        synonyms  \\\n",
       "ontology_id                                                        \n",
       "MONDO:0000001  disorders|medical condition|other disease|dise...   \n",
       "MONDO:0000002                                               None   \n",
       "MONDO:0000003                                               None   \n",
       "MONDO:0000004  adrenal gland insufficiency|adrenal cortical i...   \n",
       "MONDO:0000005                                               None   \n",
       "...                                                          ...   \n",
       "MONDO:8000030                                               None   \n",
       "MONDO:8000031                                               None   \n",
       "MONDO:8000032                                               None   \n",
       "MONDO:8000033                                               None   \n",
       "MONDO:8000034                                               None   \n",
       "\n",
       "                       parents  \n",
       "ontology_id                     \n",
       "MONDO:0000001               []  \n",
       "MONDO:0000002               []  \n",
       "MONDO:0000003               []  \n",
       "MONDO:0000004  [MONDO:0002816]  \n",
       "MONDO:0000005  [MONDO:0021034]  \n",
       "...                        ...  \n",
       "MONDO:8000030               []  \n",
       "MONDO:8000031               []  \n",
       "MONDO:8000032               []  \n",
       "MONDO:8000033               []  \n",
       "MONDO:8000034               []  \n",
       "\n",
       "[25913 rows x 4 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty.df()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c2dc951a-5e92-4753-a364-0bc5a87e0dd5",
   "metadata": {},
   "source": [
    "Let's inspect all of our \"Immune system disorders\" to learn which terms map against the MONDO Disease ontology."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "60563f60-b573-4182-9bae-9825ada8f943",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "❗ \u001b[1;93m3 terms\u001b[0m (100.00%) are not validated for \u001b[3mname\u001b[0m: \u001b[1;93mRheumatoid arthritis, Celiac disease, Multipla sclurosis\u001b[0m\n",
      "   detected \u001b[1;93m2 terms with inconsistent casing/synonyms\u001b[0m: \u001b[1;93mRheumatoid arthritis, Celiac disease\u001b[0m\n",
      "→  standardize terms via \u001b[3m.standardize()\u001b[0m\n"
     ]
    },
    {
     "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>__validated__</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Rheumatoid arthritis</th>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Celiac disease</th>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Multipla sclurosis</th>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                      __validated__\n",
       "Rheumatoid arthritis          False\n",
       "Celiac disease                False\n",
       "Multipla sclurosis            False"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty.inspect(\n",
    "    adata.obs[\"Immune system disorders\"], field=disease_bionty.name, return_df=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6d0383e6-09db-43f8-a52d-471046ebacdc",
   "metadata": {},
   "source": [
    "None of the values can be validated immediately, but \"Rheumatoid arthritis\" and \"Celiac disease\" have synonyms and can be standardized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "d868811c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "💡 standardized 2/3 terms\n"
     ]
    }
   ],
   "source": [
    "adata.obs[\"Immune system disorders\"] = disease_bionty.standardize(adata.obs[\"Immune system disorders\"], field=disease_bionty.name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "f533ceb7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ \u001b[1;92m2 terms\u001b[0m (66.70%) are validated for \u001b[3mname\u001b[0m\n",
      "❗ \u001b[1;93m1 term\u001b[0m (33.30%) is not validated for \u001b[3mname\u001b[0m: \u001b[1;93mMultipla sclurosis\u001b[0m\n"
     ]
    },
    {
     "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>__validated__</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>rheumatoid arthritis</th>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>celiac disease</th>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Multipla sclurosis</th>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                      __validated__\n",
       "rheumatoid arthritis           True\n",
       "celiac disease                 True\n",
       "Multipla sclurosis            False"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty.inspect(\n",
    "    adata.obs[\"Immune system disorders\"], field=disease_bionty.name, return_df=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "de59a7a1-8ccf-4b7c-a6e5-16bd2ca2e126",
   "metadata": {},
   "source": [
    "We can use Bionty's lookup functionality to try to find the corresponding term in the MONDO Disease ontology for the terms that could not be mapped using auto-complete.\n",
    "For this purpose we create a lookup object."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "5a570f24-44b4-43ad-b7ee-f1ba3bf922c9",
   "metadata": {},
   "outputs": [],
   "source": [
    "disease_bionty_lookup = disease_bionty.lookup()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "aa16c040-961d-4905-affc-297d66cc1a9c",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Disease(ontology_id='MONDO:0005301', name='multiple sclerosis', definition='A Progressive Autoimmune Disorder Affecting The Central Nervous System Resulting In Demyelination. Patients Develop Physical And Cognitive Impairments That Correspond With The Affected Nerve Fibers.', synonyms=None, parents=array(['MONDO:0006704', 'MONDO:0000568', 'MONDO:0002562', 'MONDO:0005560'],\n",
       "      dtype=object), _5='multiple sclerosis')"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty_lookup.multiple_sclerosis"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "53000247-6061-47c8-8f7d-794d9b8fc650",
   "metadata": {},
   "source": [
    "We found a match! Let's look at the definition of our result."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "87ef3eba-be0c-4816-95eb-5175d78250d9",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'A Progressive Autoimmune Disorder Affecting The Central Nervous System Resulting In Demyelination. Patients Develop Physical And Cognitive Impairments That Correspond With The Affected Nerve Fibers.'"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty_lookup.multiple_sclerosis.definition"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "168311ef-c77c-42cb-9faf-587150c152cd",
   "metadata": {},
   "source": [
    "This is exactly what we've been looking for. We can also search directly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "cdb65c6e-92b9-494e-96fd-f566cd68074d",
   "metadata": {
    "tags": []
   },
   "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>ontology_id</th>\n",
       "      <th>definition</th>\n",
       "      <th>synonyms</th>\n",
       "      <th>parents</th>\n",
       "      <th>__agg__</th>\n",
       "      <th>__ratio__</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>multiple sclerosis</th>\n",
       "      <td>MONDO:0005301</td>\n",
       "      <td>A Progressive Autoimmune Disorder Affecting Th...</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0006704, MONDO:0000568, MONDO:0002562, ...</td>\n",
       "      <td>multiple sclerosis</td>\n",
       "      <td>88.888889</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>multiple sclerosis variant</th>\n",
       "      <td>MONDO:0016428</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0005071]</td>\n",
       "      <td>multiple sclerosis variant</td>\n",
       "      <td>72.727273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pediatric multiple sclerosis</th>\n",
       "      <td>MONDO:0018784</td>\n",
       "      <td>Pediatric Multiple Sclerosis (Ms) Is A Rare Mu...</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0016428]</td>\n",
       "      <td>pediatric multiple sclerosis</td>\n",
       "      <td>69.565217</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>lateral sclerosis</th>\n",
       "      <td>MONDO:0018155</td>\n",
       "      <td>Primary Lateral Sclerosis (Pls) Is An Idiopath...</td>\n",
       "      <td>primary lateral sclerosis|adult-onset PLS|PLS|...</td>\n",
       "      <td>[MONDO:0024257]</td>\n",
       "      <td>lateral sclerosis</td>\n",
       "      <td>68.571429</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>glomerulosclerosis</th>\n",
       "      <td>MONDO:0000490</td>\n",
       "      <td>A Hardening Of The Kidney Glomerulus Caused By...</td>\n",
       "      <td>glomerular sclerosis</td>\n",
       "      <td>[MONDO:0019722]</td>\n",
       "      <td>glomerulosclerosis</td>\n",
       "      <td>68.421053</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>BAFopathy</th>\n",
       "      <td>MONDO:0700120</td>\n",
       "      <td>Disorder Caused By Mutations In The Various Su...</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0003847]</td>\n",
       "      <td>bafopathy</td>\n",
       "      <td>14.814815</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hydrocele</th>\n",
       "      <td>MONDO:0004920</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0003150]</td>\n",
       "      <td>hydrocele</td>\n",
       "      <td>14.814815</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>XH antigen</th>\n",
       "      <td>MONDO:0010760</td>\n",
       "      <td>None</td>\n",
       "      <td>XH antigen</td>\n",
       "      <td>[MONDO:0003847]</td>\n",
       "      <td>xh antigen</td>\n",
       "      <td>14.285714</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>angiomyxoma</th>\n",
       "      <td>MONDO:0006086</td>\n",
       "      <td>A Benign Soft Tissue Neoplasm Characterized By...</td>\n",
       "      <td>None</td>\n",
       "      <td>[MONDO:0021581, MONDO:0044335]</td>\n",
       "      <td>angiomyxoma</td>\n",
       "      <td>13.793103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Pygmy</th>\n",
       "      <td>MONDO:0009941</td>\n",
       "      <td>None</td>\n",
       "      <td>Pygmy</td>\n",
       "      <td>[MONDO:0003847]</td>\n",
       "      <td>pygmy</td>\n",
       "      <td>8.695652</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>25913 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ontology_id  \\\n",
       "name                                          \n",
       "multiple sclerosis            MONDO:0005301   \n",
       "multiple sclerosis variant    MONDO:0016428   \n",
       "pediatric multiple sclerosis  MONDO:0018784   \n",
       "lateral sclerosis             MONDO:0018155   \n",
       "glomerulosclerosis            MONDO:0000490   \n",
       "...                                     ...   \n",
       "BAFopathy                     MONDO:0700120   \n",
       "hydrocele                     MONDO:0004920   \n",
       "XH antigen                    MONDO:0010760   \n",
       "angiomyxoma                   MONDO:0006086   \n",
       "Pygmy                         MONDO:0009941   \n",
       "\n",
       "                                                                     definition  \\\n",
       "name                                                                              \n",
       "multiple sclerosis            A Progressive Autoimmune Disorder Affecting Th...   \n",
       "multiple sclerosis variant                                                 None   \n",
       "pediatric multiple sclerosis  Pediatric Multiple Sclerosis (Ms) Is A Rare Mu...   \n",
       "lateral sclerosis             Primary Lateral Sclerosis (Pls) Is An Idiopath...   \n",
       "glomerulosclerosis            A Hardening Of The Kidney Glomerulus Caused By...   \n",
       "...                                                                         ...   \n",
       "BAFopathy                     Disorder Caused By Mutations In The Various Su...   \n",
       "hydrocele                                                                  None   \n",
       "XH antigen                                                                 None   \n",
       "angiomyxoma                   A Benign Soft Tissue Neoplasm Characterized By...   \n",
       "Pygmy                                                                      None   \n",
       "\n",
       "                                                                       synonyms  \\\n",
       "name                                                                              \n",
       "multiple sclerosis                                                         None   \n",
       "multiple sclerosis variant                                                 None   \n",
       "pediatric multiple sclerosis                                               None   \n",
       "lateral sclerosis             primary lateral sclerosis|adult-onset PLS|PLS|...   \n",
       "glomerulosclerosis                                         glomerular sclerosis   \n",
       "...                                                                         ...   \n",
       "BAFopathy                                                                  None   \n",
       "hydrocele                                                                  None   \n",
       "XH antigen                                                           XH antigen   \n",
       "angiomyxoma                                                                None   \n",
       "Pygmy                                                                     Pygmy   \n",
       "\n",
       "                                                                        parents  \\\n",
       "name                                                                              \n",
       "multiple sclerosis            [MONDO:0006704, MONDO:0000568, MONDO:0002562, ...   \n",
       "multiple sclerosis variant                                      [MONDO:0005071]   \n",
       "pediatric multiple sclerosis                                    [MONDO:0016428]   \n",
       "lateral sclerosis                                               [MONDO:0024257]   \n",
       "glomerulosclerosis                                              [MONDO:0019722]   \n",
       "...                                                                         ...   \n",
       "BAFopathy                                                       [MONDO:0003847]   \n",
       "hydrocele                                                       [MONDO:0003150]   \n",
       "XH antigen                                                      [MONDO:0003847]   \n",
       "angiomyxoma                                      [MONDO:0021581, MONDO:0044335]   \n",
       "Pygmy                                                           [MONDO:0003847]   \n",
       "\n",
       "                                                   __agg__  __ratio__  \n",
       "name                                                                   \n",
       "multiple sclerosis                      multiple sclerosis  88.888889  \n",
       "multiple sclerosis variant      multiple sclerosis variant  72.727273  \n",
       "pediatric multiple sclerosis  pediatric multiple sclerosis  69.565217  \n",
       "lateral sclerosis                        lateral sclerosis  68.571429  \n",
       "glomerulosclerosis                      glomerulosclerosis  68.421053  \n",
       "...                                                    ...        ...  \n",
       "BAFopathy                                        bafopathy  14.814815  \n",
       "hydrocele                                        hydrocele  14.814815  \n",
       "XH antigen                                      xh antigen  14.285714  \n",
       "angiomyxoma                                    angiomyxoma  13.793103  \n",
       "Pygmy                                                pygmy   8.695652  \n",
       "\n",
       "[25913 rows x 6 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty.search(\n",
    "    \"Multipla sclurosis\", field=disease_bionty.name, case_sensitive=False\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b71eb051-d388-4587-8def-54cbad53d6ed",
   "metadata": {},
   "source": [
    "Now we can finally replace the values of our obs column with the MONDO Disease ontology values."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "0a862857-929f-4e0a-97b4-2e84a695a2a8",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_305804/3382110660.py:1: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.\n",
      "The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.\n",
      "\n",
      "For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.\n",
      "\n",
      "\n",
      "  adata.obs[\"Immune system disorders\"].replace({\"Multipla sclurosis\": disease_bionty_lookup.multiple_sclerosis.name},\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0    rheumatoid arthritis\n",
       "1          celiac disease\n",
       "2      multiple sclerosis\n",
       "Name: Immune system disorders, dtype: object"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs[\"Immune system disorders\"].replace({\"Multipla sclurosis\": disease_bionty_lookup.multiple_sclerosis.name},\n",
    "                                             inplace=True)\n",
    "adata.obs[\"Immune system disorders\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "c70b961d-d483-44ed-8f7b-575cb18265a3",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ \u001b[1;92m3 terms\u001b[0m (100.00%) are validated for \u001b[3mname\u001b[0m\n"
     ]
    },
    {
     "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>__validated__</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>rheumatoid arthritis</th>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>celiac disease</th>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>multiple sclerosis</th>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                      __validated__\n",
       "rheumatoid arthritis           True\n",
       "celiac disease                 True\n",
       "multiple sclerosis             True"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty.inspect(\n",
    "    adata.obs[\"Immune system disorders\"], field=disease_bionty.name, return_df=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c7a08e5e-039e-40ba-bf5d-2997a3a16c52",
   "metadata": {},
   "source": [
    "Voilà, all of our immune system disorders are mapped against the ontology. We could now repeat this process for all other columns."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8974c126-55c0-4d97-8889-39e396fc21ea",
   "metadata": {},
   "source": [
    "## Mapping against other Disease ontologies"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9bb095a1-da4f-4f71-a8e6-d08459b27a8c",
   "metadata": {},
   "source": [
    "Bionty supports other ontologies besides the MONDO Disease Ontology like the [Disease Ontology](https://disease-ontology.org/) or [ICD](https://www.who.int/standards/classifications/classification-of-diseases). The workflow is the same.\n",
    "\n",
    "We solely need to adapt the source and the version."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "1227ca5f-80b9-491c-a7e4-dd309c599fd9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "PublicOntology\n",
       "Entity: Disease\n",
       "Organism: human\n",
       "Source: icd, icd-11-2023\n",
       "#terms: 35574\n"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_bionty = bt.Disease(source=\"icd\", version=\"icd-11-2023\")\n",
    "disease_bionty"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "226ad0a8-bd1e-4eb3-baf9-11402123a57c",
   "metadata": {},
   "source": [
    "The remaining workflow would be the same as above."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "19bc232b-cd44-4505-a31f-ee65e37d29f6",
   "metadata": {},
   "source": [
    "## Conclusion"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7a15db25-70ea-4d0a-b7a4-49f2d4e35e1f",
   "metadata": {},
   "source": [
    "ehrapy provides support for ontology management, inspection and mapping through [Bionty](https://github.com/laminlabs/bionty).\n",
    "Bionty provide access to ontologies such as the [Mondo Disease Ontology](https://mondo.monarchinitiative.org/), [Disease Ontology](https://disease-ontology.org/) and many others.\n",
    "To access these ontologies we create a Bionty Disease objects that have class functions to map synonyms and to inspect data for adherence against ontologies.\n",
    "Mismatches can be remedied by finding the actual correct ontology name using lookup objects or fuzzy matching."
   ]
  }
 ],
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