{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# How to query Solr using the Command Line\n",
    "\n",
    "For this we will use the Golr endpoint: https://golr.geneontology.org/solr\n",
    "\n",
    "Note this endpoint doesn't use Solr cores - all collections are in a single core and are differentiated by the `document_category` field.\n",
    "\n",
    "## Specifying a Solr backend on the command line:\n",
    "\n",
    "We can specify this directly on the CLI. Following does a facet count query on the `source` slot:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "eb82e1256fef74d6"
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"source\": {\n",
      "    \"ncbi_taxonomy\": 30916,\n",
      "    \"biological_process\": 30715,\n",
      "    \"molecular_function\": 12597,\n",
      "    \"cellular_component\": 4513,\n",
      "    \"eco\": 2004,\n",
      "    \"sequence\": 106,\n",
      "    \"go/extensions/gorel\": 74,\n",
      "    \"external\": 66,\n",
      "    \"gene_ontology\": 3,\n",
      "    \"AGI_LocusCode\": 0,\n",
      "    \"CGD\": 0,\n",
      "    \"ComplexPortal\": 0,\n",
      "    \"FB\": 0,\n",
      "    \"GeneDB\": 0,\n",
      "    \"JaponicusDB\": 0,\n",
      "    \"MGI\": 0,\n",
      "    \"PR\": 0,\n",
      "    \"PlasmoDB\": 0,\n",
      "    \"PomBase\": 0,\n",
      "    \"PseudoCAP\": 0,\n",
      "    \"RGD\": 0,\n",
      "    \"RNAcentral\": 0,\n",
      "    \"RefSeq\": 0,\n",
      "    \"SGD\": 0,\n",
      "    \"SGN\": 0,\n",
      "    \"TAIR\": 0,\n",
      "    \"TriTrypDB\": 0,\n",
      "    \"UniProtKB\": 0,\n",
      "    \"WB\": 0,\n",
      "    \"Xenbase\": 0,\n",
      "    \"ZFIN\": 0,\n",
      "    \"dictyBase\": 0\n",
      "  }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "linkml-store -d solr:https://golr.geneontology.org/solr --set collection_type_slot=document_category -c ontology_class fq -S source"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-05-11T02:04:45.596784Z",
     "start_time": "2024-05-11T02:04:43.379311Z"
    }
   },
   "id": "initial_id"
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Using a configuration\n",
    "\n",
    "Rather than specifying the same information again each time, we can use a configuration.\n",
    "\n",
    "See [input/golr.config.yaml](input/golr.config.yaml)."
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "c82427e2edb5d318"
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"source\": {\n",
      "    \"ncbi_taxonomy\": 30916,\n",
      "    \"biological_process\": 30712,\n",
      "    \"molecular_function\": 12596,\n",
      "    \"cellular_component\": 4513,\n",
      "    \"eco\": 2004,\n",
      "    \"sequence\": 106,\n",
      "    \"go/extensions/gorel\": 74,\n",
      "    \"external\": 66,\n",
      "    \"gene_ontology\": 3,\n",
      "    \"AGI_LocusCode\": 0,\n",
      "    \"CGD\": 0,\n",
      "    \"ComplexPortal\": 0,\n",
      "    \"FB\": 0,\n",
      "    \"GeneDB\": 0,\n",
      "    \"JaponicusDB\": 0,\n",
      "    \"MGI\": 0,\n",
      "    \"PR\": 0,\n",
      "    \"PlasmoDB\": 0,\n",
      "    \"PomBase\": 0,\n",
      "    \"PseudoCAP\": 0,\n",
      "    \"RGD\": 0,\n",
      "    \"RNAcentral\": 0,\n",
      "    \"RefSeq\": 0,\n",
      "    \"SGD\": 0,\n",
      "    \"SGN\": 0,\n",
      "    \"TAIR\": 0,\n",
      "    \"TriTrypDB\": 0,\n",
      "    \"UniProtKB\": 0,\n",
      "    \"WB\": 0,\n",
      "    \"Xenbase\": 0,\n",
      "    \"ZFIN\": 0,\n",
      "    \"dictyBase\": 0\n",
      "  }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "linkml-store -C input/golr.config.yaml -c ontology_class fq -S source"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-04-24T02:00:52.476138Z",
     "start_time": "2024-04-24T02:00:51.315573Z"
    }
   },
   "id": "417b61df945d440b"
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Search\n",
    "\n",
    "With some engines, a search index needs to be explicitly constructed. This is not necessary with Solr, as it is done automatically."
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "e76e7f9c807415b8"
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'fq': 'document_category:\"ontology_class\"', 'wt': 'json', 'q': 'nucleus*', 'defType': 'edismax', 'qf': ['entity_label_searchable', 'general_blob_searchable', 'annotation_class_label_searchable']}\n",
      "[\n",
      "  {\n",
      "    \"score\": 1.0,\n",
      "    \"document_category\": \"ontology_class\",\n",
      "    \"id\": \"GO:1905754\",\n",
      "    \"annotation_class\": \"GO:1905754\",\n",
      "    \"annotation_class_label\": \"ascospore-type prospore nucleus\",\n",
      "    \"annotation_class_label_searchable\": \"ascospore-type prospore nucleus\",\n",
      "    \"description\": \"Any nucleus that is part of a ascospore-type prospore.\",\n",
      "    \"description_searchable\": \"Any nucleus that is part of a ascospore-type prospore.\",\n",
      "    \"source\": \"cellular_component\",\n",
      "    \"idspace\": \"GO\",\n",
      "    \"is_obsolete\": false,\n",
      "    \"topology_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"CARO:0030000\\\",\\\"lbl\\\":\\\"biological entity\\\"},{\\\"id\\\":\\\"CL:0000000\\\",\\\"lbl\\\":\\\"cell\\\"},{\\\"id\\\":\\\"GO:1905754\\\",\\\"lbl\\\":\\\"ascospore-type prospore nucleus\\\"},{\\\"id\\\":\\\"GO:0005575\\\",\\\"lbl\\\":\\\"cellular_component\\\"},{\\\"id\\\":\\\"GO:0042763\\\",\\\"lbl\\\":\\\"intracellular immature spore\\\"},{\\\"id\\\":\\\"GO:0042764\\\",\\\"lbl\\\":\\\"ascospore-type prospore\\\"},{\\\"id\\\":\\\"UBERON:0000061\\\",\\\"lbl\\\":\\\"anatomical structure\\\"},{\\\"id\\\":\\\"UBERON:0001062\\\",\\\"lbl\\\":\\\"anatomical entity\\\"},{\\\"id\\\":\\\"GO:0043227\\\",\\\"lbl\\\":\\\"membrane-bounded organelle\\\"},{\\\"id\\\":\\\"GO:0043226\\\",\\\"lbl\\\":\\\"organelle\\\"},{\\\"id\\\":\\\"GO:0005634\\\",\\\"lbl\\\":\\\"nucleus\\\"},{\\\"id\\\":\\\"GO:0043229\\\",\\\"lbl\\\":\\\"intracellular organelle\\\"},{\\\"id\\\":\\\"GO:0110165\\\",\\\"lbl\\\":\\\"cellular anatomical entity\\\"},{\\\"id\\\":\\\"GO:0005622\\\",\\\"lbl\\\":\\\"intracellular anatomical structure\\\"},{\\\"id\\\":\\\"CARO:0000006\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"UBERON:0000465\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"CARO:0000003\\\",\\\"lbl\\\":\\\"connected anatomical structure\\\"},{\\\"id\\\":\\\"CARO:0000000\\\",\\\"lbl\\\":\\\"anatomical entity\\\"},{\\\"id\\\":\\\"GO:0043231\\\",\\\"lbl\\\":\\\"intracellular membrane-bounded organelle\\\"}],\\\"edges\\\":[{\\\"sub\\\":\\\"CL:0000000\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0043226\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0042763\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0110165\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0005622\\\",\\\"obj\\\":\\\"CL:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:0043231\\\",\\\"obj\\\":\\\"GO:0043229\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0043231\\\",\\\"obj\\\":\\\"GO:0043227\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0043227\\\",\\\"obj\\\":\\\"GO:0043226\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005634\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0005634\\\",\\\"obj\\\":\\\"GO:0043231\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0005622\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"CARO:0000003\\\",\\\"obj\\\":\\\"CARO:0000006\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"UBERON:0000061\\\",\\\"obj\\\":\\\"UBERON:0000465\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0043229\\\",\\\"obj\\\":\\\"GO:0043226\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0110165\\\",\\\"obj\\\":\\\"GO:0005575\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"CARO:0000006\\\",\\\"obj\\\":\\\"CARO:0000000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"UBERON:0000465\\\",\\\"obj\\\":\\\"UBERON:0001062\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042764\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:0043229\\\",\\\"obj\\\":\\\"GO:0005622\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"CARO:0000000\\\",\\\"obj\\\":\\\"CARO:0030000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:0042763\\\",\\\"obj\\\":\\\"CL:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:0042764\\\",\\\"obj\\\":\\\"GO:0042763\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"UBERON:0000061\\\",\\\"obj\\\":\\\"CARO:0000003\\\",\\\"pred\\\":\\\"is_a\\\"}],\\\"meta\\\":{}}\",\n",
      "    \"regulates_transitivity_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"CARO:0030000\\\",\\\"lbl\\\":\\\"biological entity\\\"},{\\\"id\\\":\\\"CL:0000000\\\",\\\"lbl\\\":\\\"cell\\\"},{\\\"id\\\":\\\"GO:1905754\\\",\\\"lbl\\\":\\\"ascospore-type prospore nucleus\\\"},{\\\"id\\\":\\\"GO:0005575\\\",\\\"lbl\\\":\\\"cellular_component\\\"},{\\\"id\\\":\\\"GO:0042763\\\",\\\"lbl\\\":\\\"intracellular immature spore\\\"},{\\\"id\\\":\\\"GO:0042764\\\",\\\"lbl\\\":\\\"ascospore-type prospore\\\"},{\\\"id\\\":\\\"UBERON:0001062\\\",\\\"lbl\\\":\\\"anatomical entity\\\"},{\\\"id\\\":\\\"UBERON:0000061\\\",\\\"lbl\\\":\\\"anatomical structure\\\"},{\\\"id\\\":\\\"GO:0043227\\\",\\\"lbl\\\":\\\"membrane-bounded organelle\\\"},{\\\"id\\\":\\\"GO:0043226\\\",\\\"lbl\\\":\\\"organelle\\\"},{\\\"id\\\":\\\"GO:0043229\\\",\\\"lbl\\\":\\\"intracellular organelle\\\"},{\\\"id\\\":\\\"GO:0005634\\\",\\\"lbl\\\":\\\"nucleus\\\"},{\\\"id\\\":\\\"http://www.w3.org/2002/07/owl#Thing\\\",\\\"lbl\\\":\\\"Thing\\\"},{\\\"id\\\":\\\"GO:0110165\\\",\\\"lbl\\\":\\\"cellular anatomical entity\\\"},{\\\"id\\\":\\\"GO:0005622\\\",\\\"lbl\\\":\\\"intracellular anatomical structure\\\"},{\\\"id\\\":\\\"CARO:0000006\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"UBERON:0000465\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"CARO:0000003\\\",\\\"lbl\\\":\\\"connected anatomical structure\\\"},{\\\"id\\\":\\\"GO:0043231\\\",\\\"lbl\\\":\\\"intracellular membrane-bounded organelle\\\"},{\\\"id\\\":\\\"CARO:0000000\\\",\\\"lbl\\\":\\\"anatomical entity\\\"}],\\\"edges\\\":[{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000003\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0030000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000465\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0030000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000006\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000465\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"http://www.w3.org/2002/07/owl#Thing\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043231\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042764\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042763\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0001062\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005575\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000003\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CL:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043227\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005634\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043229\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043226\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005622\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005575\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000006\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0001062\\\",\\\"pred\\\":\\\"is_a\\\"}],\\\"meta\\\":{}}\",\n",
      "    \"isa_partof_transitivity_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"CARO:0030000\\\",\\\"lbl\\\":\\\"biological entity\\\"},{\\\"id\\\":\\\"CL:0000000\\\",\\\"lbl\\\":\\\"cell\\\"},{\\\"id\\\":\\\"GO:1905754\\\",\\\"lbl\\\":\\\"ascospore-type prospore nucleus\\\"},{\\\"id\\\":\\\"GO:0005575\\\",\\\"lbl\\\":\\\"cellular_component\\\"},{\\\"id\\\":\\\"GO:0042763\\\",\\\"lbl\\\":\\\"intracellular immature spore\\\"},{\\\"id\\\":\\\"GO:0042764\\\",\\\"lbl\\\":\\\"ascospore-type prospore\\\"},{\\\"id\\\":\\\"UBERON:0001062\\\",\\\"lbl\\\":\\\"anatomical entity\\\"},{\\\"id\\\":\\\"UBERON:0000061\\\",\\\"lbl\\\":\\\"anatomical structure\\\"},{\\\"id\\\":\\\"GO:0043227\\\",\\\"lbl\\\":\\\"membrane-bounded organelle\\\"},{\\\"id\\\":\\\"GO:0043226\\\",\\\"lbl\\\":\\\"organelle\\\"},{\\\"id\\\":\\\"GO:0043229\\\",\\\"lbl\\\":\\\"intracellular organelle\\\"},{\\\"id\\\":\\\"GO:0005634\\\",\\\"lbl\\\":\\\"nucleus\\\"},{\\\"id\\\":\\\"http://www.w3.org/2002/07/owl#Thing\\\",\\\"lbl\\\":\\\"Thing\\\"},{\\\"id\\\":\\\"GO:0110165\\\",\\\"lbl\\\":\\\"cellular anatomical entity\\\"},{\\\"id\\\":\\\"GO:0005622\\\",\\\"lbl\\\":\\\"intracellular anatomical structure\\\"},{\\\"id\\\":\\\"CARO:0000006\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"UBERON:0000465\\\",\\\"lbl\\\":\\\"material anatomical entity\\\"},{\\\"id\\\":\\\"CARO:0000003\\\",\\\"lbl\\\":\\\"connected anatomical structure\\\"},{\\\"id\\\":\\\"GO:0043231\\\",\\\"lbl\\\":\\\"intracellular membrane-bounded organelle\\\"},{\\\"id\\\":\\\"CARO:0000000\\\",\\\"lbl\\\":\\\"anatomical entity\\\"}],\\\"edges\\\":[{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000003\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0030000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000465\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0110165\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0030000\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000006\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000465\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"http://www.w3.org/2002/07/owl#Thing\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043231\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042764\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042763\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0001062\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005575\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000003\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CL:0000000\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0000061\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043227\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005634\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043229\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0043226\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005622\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005575\\\",\\\"pred\\\":\\\"part of\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"CARO:0000006\\\",\\\"pred\\\":\\\"is_a\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"UBERON:0001062\\\",\\\"pred\\\":\\\"is_a\\\"}],\\\"meta\\\":{}}\",\n",
      "    \"neighborhood_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:1905754\\\",\\\"lbl\\\":\\\"ascospore-type prospore nucleus\\\"},{\\\"id\\\":\\\"GO:0042764\\\",\\\"lbl\\\":\\\"ascospore-type prospore\\\"},{\\\"id\\\":\\\"NCBITaxon:4890\\\",\\\"lbl\\\":\\\"Ascomycota\\\"},{\\\"id\\\":\\\"GO:0005634\\\",\\\"lbl\\\":\\\"nucleus\\\"}],\\\"edges\\\":[{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"NCBITaxon:4890\\\",\\\"pred\\\":\\\"RO:0002162\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042764\\\",\\\"pred\\\":\\\"BFO:0000050\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005634\\\",\\\"pred\\\":\\\"is_a\\\"}],\\\"meta\\\":{}}\",\n",
      "    \"neighborhood_limited_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:1905754\\\",\\\"lbl\\\":\\\"ascospore-type prospore nucleus\\\"},{\\\"id\\\":\\\"GO:0042764\\\",\\\"lbl\\\":\\\"ascospore-type prospore\\\"},{\\\"id\\\":\\\"NCBITaxon:4890\\\",\\\"lbl\\\":\\\"Ascomycota\\\"},{\\\"id\\\":\\\"GO:0005634\\\",\\\"lbl\\\":\\\"nucleus\\\"}],\\\"edges\\\":[{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"NCBITaxon:4890\\\",\\\"pred\\\":\\\"RO:0002162\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0042764\\\",\\\"pred\\\":\\\"BFO:0000050\\\"},{\\\"sub\\\":\\\"GO:1905754\\\",\\\"obj\\\":\\\"GO:0005634\\\",\\\"pred\\\":\\\"is_a\\\"}],\\\"meta\\\":{}}\",\n",
      "    \"isa_partof_closure_label\": [\n",
      "      \"intracellular organelle\",\n",
      "      \"cell\",\n",
      "      \"ascospore-type prospore nucleus\",\n",
      "      \"biological entity\",\n",
      "      \"cellular anatomical entity\",\n",
      "      \"intracellular immature spore\",\n",
      "      \"organelle\",\n",
      "      \"ascospore-type prospore\",\n",
      "      \"cellular_component\",\n",
      "      \"intracellular anatomical structure\",\n",
      "      \"anatomical entity\",\n",
      "      \"anatomical structure\",\n",
      "      \"membrane-bounded organelle\",\n",
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      "    \"id\": \"UBERON:0025930\",\n",
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      "  {\n",
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      "  },\n",
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      "    \"id\": \"GO:0035105\",\n",
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      "    \"annotation_class_label_searchable\": \"obsolete sterol regulatory element binding protein import into nucleus\",\n",
      "    \"description\": \"OBSOLETE. The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes.\",\n",
      "    \"description_searchable\": \"OBSOLETE. The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes.\",\n",
      "    \"source\": \"biological_process\",\n",
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      "    \"regulates_transitivity_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:0035105\\\",\\\"lbl\\\":\\\"obsolete sterol regulatory element binding protein import into nucleus\\\"}],\\\"edges\\\":[],\\\"meta\\\":{}}\",\n",
      "    \"isa_partof_transitivity_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:0035105\\\",\\\"lbl\\\":\\\"obsolete sterol regulatory element binding protein import into nucleus\\\"}],\\\"edges\\\":[],\\\"meta\\\":{}}\",\n",
      "    \"neighborhood_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:0035105\\\",\\\"lbl\\\":\\\"obsolete sterol regulatory element binding protein import into nucleus\\\"}],\\\"edges\\\":[],\\\"meta\\\":{}}\",\n",
      "    \"neighborhood_limited_graph_json\": \"{\\\"nodes\\\":[{\\\"id\\\":\\\"GO:0035105\\\",\\\"lbl\\\":\\\"obsolete sterol regulatory element binding protein import into nucleus\\\"}],\\\"edges\\\":[],\\\"meta\\\":{}}\",\n",
      "    \"isa_partof_closure_label\": [\n",
      "      \"obsolete sterol regulatory element binding protein import into nucleus\"\n",
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      "      \"sterol depletion response, sterol regulatory element binding protein import into nucleus\",\n",
      "      \"SREBP nuclear translocation\",\n",
      "      \"sterol depletion response, SREBP nuclear translocation\",\n",
      "      \"sterol depletion response, sterol regulatory element binding protein nuclear translocation\",\n",
      "      \"sterol regulatory element binding protein import into nucleus involved in sterol depletion response\",\n",
      "      \"sterol regulatory element binding protein nuclear translocation\",\n",
      "      \"sterol regulatory element binding protein nuclear translocation involved in sterol depletion response\"\n",
      "    ],\n",
      "    \"isa_partof_closure_label_searchable\": [\n",
      "      \"obsolete sterol regulatory element binding protein import into nucleus\"\n",
      "    ],\n",
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      "    ],\n",
      "    \"comment_searchable\": [\n",
      "      \"The reason for obsoletion is that all proteins are imported into the nucleus via the same mechanism, so the import of individual proteins should be captured with extensions or by GO-CAM models.\"\n",
      "    ],\n",
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      "      \"sterol depletion response, sterol regulatory element binding protein import into nucleus\",\n",
      "      \"SREBP nuclear translocation\",\n",
      "      \"sterol depletion response, SREBP nuclear translocation\",\n",
      "      \"sterol depletion response, sterol regulatory element binding protein nuclear translocation\",\n",
      "      \"sterol regulatory element binding protein import into nucleus involved in sterol depletion response\",\n",
      "      \"sterol regulatory element binding protein nuclear translocation\",\n",
      "      \"sterol regulatory element binding protein nuclear translocation involved in sterol depletion response\"\n",
      "    ],\n",
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      "    ],\n",
      "    \"regulates_closure_label\": [\n",
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      "    ],\n",
      "    \"comment\": [\n",
      "      \"The reason for obsoletion is that all proteins are imported into the nucleus via the same mechanism, so the import of individual proteins should be captured with extensions or by GO-CAM models.\"\n",
      "    ],\n",
      "    \"consider\": [\n",
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      "      \"NCBITaxon_Union:0000025\",\n",
      "      \"UBERON:0000955\",\n",
      "      \"NCBITaxon_Union:0000024\",\n",
      "      \"UBERON:0002616\",\n",
      "      \"UBERON:0000064\",\n",
      "      \"UBERON:0000062\",\n",
      "      \"UBERON:0000061\",\n",
      "      \"UBERON:0000468\",\n",
      "      \"UBERON:0000467\",\n",
      "      \"UBERON:0000465\",\n",
      "      \"NCBITaxon_Union:0000030\",\n",
      "      \"UBERON:0009663\",\n",
      "      \"UBERON:0011300\",\n",
      "      \"UBERON:0007245\",\n",
      "      \"UBERON:0001062\",\n",
      "      \"UBERON:0019264\",\n",
      "      \"CARO:0000006\",\n",
      "      \"UBERON:0003528\",\n",
      "      \"CARO:0000003\",\n",
      "      \"CARO:0000000\",\n",
      "      \"UBERON:0001869\",\n",
      "      \"OBI:0100026\",\n",
      "      \"UBERON:0010000\",\n",
      "      \"CARO:0030000\",\n",
      "      \"UBERON:0011216\",\n",
      "      \"UBERON:0011215\",\n",
      "      \"UBERON:0001890\",\n",
      "      \"NCBITaxon:6072\",\n",
      "      \"UBERON:0000481\",\n",
      "      \"UBERON:0004121\",\n",
      "      \"UBERON:0002020\",\n",
      "      \"UBERON:0000446\",\n",
      "      \"UBERON:0001017\",\n",
      "      \"NCBITaxon:131567\",\n",
      "      \"NCBITaxon:2759\",\n",
      "      \"UBERON:0001893\",\n",
      "      \"UBERON:0002743\",\n",
      "      \"UBERON:0002663\",\n",
      "      \"UBERON:0001016\",\n",
      "      \"UBERON:0000125\",\n",
      "      \"NCBITaxon:33208\",\n",
      "      \"UBERON:0015212\",\n",
      "      \"UBERON:0011176\",\n",
      "      \"UBERON:0002308\",\n",
      "      \"UBERON:0011173\"\n",
      "    ],\n",
      "    \"isa_closure\": [\n",
      "      \"UBERON:0005162\",\n",
      "      \"UBERON:0009663\",\n",
      "      \"CARO:0030000\",\n",
      "      \"UBERON:0011215\",\n",
      "      \"UBERON:0004121\",\n",
      "      \"UBERON:0001062\",\n",
      "      \"UBERON:0000061\",\n",
      "      \"CARO:0000006\",\n",
      "      \"CARO:0000003\",\n",
      "      \"CARO:0000000\",\n",
      "      \"UBERON:0000125\",\n",
      "      \"UBERON:0000465\",\n",
      "      \"UBERON:0011176\",\n",
      "      \"UBERON:0002308\"\n",
      "    ],\n",
      "    \"isa_closure_label_searchable\": [\n",
      "      \"multi cell part structure\",\n",
      "      \"telencephalic nucleus\",\n",
      "      \"biological entity\",\n",
      "      \"central nervous system cell part cluster\",\n",
      "      \"ectoderm-derived structure\",\n",
      "      \"anatomical entity\",\n",
      "      \"anatomical structure\",\n",
      "      \"material anatomical entity\",\n",
      "      \"connected anatomical structure\",\n",
      "      \"anatomical entity\",\n",
      "      \"neural nucleus\",\n",
      "      \"material anatomical entity\",\n",
      "      \"oval nucleus of stria terminalis\",\n",
      "      \"nucleus of brain\"\n",
      "    ],\n",
      "    \"isa_closure_label\": [\n",
      "      \"multi cell part structure\",\n",
      "      \"telencephalic nucleus\",\n",
      "      \"biological entity\",\n",
      "      \"central nervous system cell part cluster\",\n",
      "      \"ectoderm-derived structure\",\n",
      "      \"anatomical entity\",\n",
      "      \"anatomical structure\",\n",
      "      \"material anatomical entity\",\n",
      "      \"connected anatomical structure\",\n",
      "      \"anatomical entity\",\n",
      "      \"neural nucleus\",\n",
      "      \"material anatomical entity\",\n",
      "      \"oval nucleus of stria terminalis\",\n",
      "      \"nucleus of brain\"\n",
      "    ]\n",
      "  }\n",
      "]\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "linkml-store -v --stacktrace -C input/golr.config.yaml -c ontology_class search 'nucleus*'"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-04-24T02:40:40.339793Z",
     "start_time": "2024-04-24T02:40:38.540369Z"
    }
   },
   "id": "38302b5fbb06e73d"
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "outputs": [],
   "source": [],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-04-24T02:17:51.413434Z",
     "start_time": "2024-04-24T02:17:51.404214Z"
    }
   },
   "id": "f949e8ecef6276f1"
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [],
   "metadata": {
    "collapsed": false
   },
   "id": "31d61b1c2f5c3e6c"
  }
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