{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# ClassEnrichmentCalculationInterface Examples\n",
    "\n",
    "See also [Python docs](https://incatools.github.io/ontology-access-kit/packages/interfaces/class-enrichment.html)\n",
    "\n"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "37b92ff6d4a9d98c"
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "outputs": [],
   "source": [
    "from oaklib.datamodels.input_specification import InputSpecification\n",
    "from oaklib import get_adapter\n",
    "spec = InputSpecification(\n",
    "    ontology_resources={\n",
    "        \"hp\": {\n",
    "            \"selector\": \"sqlite:obo:hp\"\n",
    "        },\n",
    "    },\n",
    "    association_resources={\n",
    "        \"hpoa\": {\n",
    "            \"selector\": \"hpoa:\"\n",
    "        }\n",
    "    }\n",
    ")\n",
    "\n",
    "adapter = get_adapter(spec)"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:15.716905Z",
     "start_time": "2024-03-14T00:42:17.829253Z"
    }
   },
   "id": "d603fc57b88cc6b4"
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "outputs": [],
   "source": [
    "from oaklib.interfaces.association_provider_interface import AssociationProviderInterface\n",
    "\n",
    "if not isinstance(adapter, AssociationProviderInterface):\n",
    "    raise ValueError(\"Adapter is not an AssociationProviderInterface\")\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:15.721279Z",
     "start_time": "2024-03-14T00:43:15.717935Z"
    }
   },
   "id": "7e90e7b35311c8b0"
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "outputs": [],
   "source": [
    "from oaklib.datamodels.vocabulary import IS_A\n",
    "\n",
    "pinna_associations = list(adapter.associations(objects=[\"HP:0000377\"], object_closure_predicates=[IS_A]))"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:16.024951Z",
     "start_time": "2024-03-14T00:43:15.734336Z"
    }
   },
   "id": "935a60c956947ad2"
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "OMIM:619426 HP:0020206 Simple ear\n",
      "OMIM:619426 HP:0000400 Macrotia\n",
      "OMIM:619426 HP:0000369 Low-set ears\n",
      "OMIM:619354 HP:0100830 Round ear\n",
      "OMIM:117650 HP:0000358 Posteriorly rotated ears\n",
      "OMIM:117650 HP:0000369 Low-set ears\n",
      "OMIM:615546 HP:0008551 Microtia\n",
      "OMIM:618076 HP:0009748 Large earlobe\n",
      "OMIM:618076 HP:0000369 Low-set ears\n",
      "OMIM:618076 HP:0008551 Microtia\n"
     ]
    }
   ],
   "source": [
    "for assoc in pinna_associations[0:10]:\n",
    "    print(assoc.subject, assoc.object, adapter.label(assoc.object))"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:16.035600Z",
     "start_time": "2024-03-14T00:43:16.025992Z"
    }
   },
   "id": "b9fea431d59366fb"
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "outputs": [
    {
     "data": {
      "text/plain": "1885"
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "diseases = {assoc.subject for assoc in pinna_associations}\n",
    "len(diseases)"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:16.044305Z",
     "start_time": "2024-03-14T00:43:16.039789Z"
    }
   },
   "id": "5e7bc45185328732"
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "outputs": [],
   "source": [
    "from oaklib.interfaces.class_enrichment_calculation_interface import ClassEnrichmentCalculationInterface\n",
    "\n",
    "if not isinstance(adapter, ClassEnrichmentCalculationInterface):\n",
    "    raise ValueError(\"Adapter is not an AssociationProviderInterface\")\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:16.063572Z",
     "start_time": "2024-03-14T00:43:16.044169Z"
    }
   },
   "id": "ce52323e5f0c095b"
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "outputs": [],
   "source": [
    "results = list(adapter.enriched_classes(\n",
    "    subjects=diseases,\n",
    "    object_closure_predicates=[IS_A],\n",
    "))"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:38.162127Z",
     "start_time": "2024-03-14T00:43:16.052039Z"
    }
   },
   "id": "e397ed9448310f70"
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ClassEnrichmentResult(class_id='HP:0000347', class_label=None, rank=1, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=738, sample_total=1885, background_count=1138, background_total=12496, ancestor_of_more_informative_result=None, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0009118', class_label=None, rank=2, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=741, sample_total=1885, background_count=1142, background_total=12496, ancestor_of_more_informative_result=True, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0001167', class_label=None, rank=3, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=960, sample_total=1885, background_count=2064, background_total=12496, ancestor_of_more_informative_result=None, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0009116', class_label=None, rank=4, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=749, sample_total=1885, background_count=1161, background_total=12496, ancestor_of_more_informative_result=True, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0000277', class_label=None, rank=5, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=972, sample_total=1885, background_count=1611, background_total=12496, ancestor_of_more_informative_result=True, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0030791', class_label=None, rank=6, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=1008, sample_total=1885, background_count=1700, background_total=12496, ancestor_of_more_informative_result=True, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0000288', class_label=None, rank=7, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=690, sample_total=1885, background_count=991, background_total=12496, ancestor_of_more_informative_result=None, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0200006', class_label=None, rank=8, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=691, sample_total=1885, background_count=980, background_total=12496, ancestor_of_more_informative_result=None, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0000177', class_label=None, rank=9, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=903, sample_total=1885, background_count=1418, background_total=12496, ancestor_of_more_informative_result=True, descendant_of_more_informative_result=None)\n",
      "ClassEnrichmentResult(class_id='HP:0002683', class_label=None, rank=10, p_value=0.0, p_value_adjusted=0.0, false_discovery_rate=None, fold_enrichment=None, probability=None, sample_count=812, sample_total=1885, background_count=1475, background_total=12496, ancestor_of_more_informative_result=None, descendant_of_more_informative_result=None)\n"
     ]
    }
   ],
   "source": [
    "for r in results[0:10]:\n",
    "    print(r)"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-03-14T00:43:38.166018Z",
     "start_time": "2024-03-14T00:43:38.162557Z"
    }
   },
   "id": "3a4052bbf6960d51"
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   "execution_count": null,
   "outputs": [],
   "source": [],
   "metadata": {
    "collapsed": false
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   "id": "b69c08ab05ab268e"
  }
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