{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# General Information"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook assembles some personal experiences in accessing the [Basic Formal Ontology](https://basic-formal-ontology.org/users.html)(BFO) with [Owlready2](https://owlready2.readthedocs.io/en/latest/index.html)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sun Feb  7 16:11:56 2021\n"
     ]
    }
   ],
   "source": [
    "import time\n",
    "print(time.ctime())\n",
    "%load_ext ipydex.displaytools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import owlready2 as owl2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "info(original_iris) := \"<class 'dict'> with length: 142\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "original_iris = dict(owl2.default_world.graph._abbreviate_d) ##:i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# bfo = owl2.get_ontology(\"external_data/bfo.owl\").load()\n",
    "\n",
    "bfo = owl2.get_ontology(\"http://purl.obolibrary.org/obo/bfo.owl\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "info(all_iris) := \"<class 'dict'> with length: 282\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "all_iris = dict(owl2.default_world.graph._abbreviate_d) ##:i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "info(new_iris) := \"<class 'list'> with length: 140\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "['http://basic-formal-ontology.org',\n",
       " 'http://creativecommons.org/licenses/by/4.0',\n",
       " 'http://groups.google.com/group/bfo-devel',\n",
       " 'http://groups.google.com/group/bfo-discuss',\n",
       " 'http://groups.google.com/group/bfo-owl-devel',\n",
       " 'http://ifomis.org/bfo',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000001',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000002',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000003',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000004',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000006',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000008',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000009',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000011',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000015',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000016',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000017',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000018',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000019',\n",
       " 'http://purl.obolibrary.org/obo/BFO_0000020']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_iris = [key for key in all_iris.keys() if key not in original_iris] ##:i\n",
    "\n",
    "new_iris[:20]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[obo.BFO_0000001,\n",
       " obo.BFO_0000002,\n",
       " obo.BFO_0000003,\n",
       " obo.BFO_0000004,\n",
       " obo.BFO_0000020,\n",
       " obo.BFO_0000031,\n",
       " obo.BFO_0000006,\n",
       " obo.BFO_0000141,\n",
       " obo.BFO_0000029,\n",
       " obo.BFO_0000140]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "classes = list(bfo.classes())\n",
    "\n",
    "c0 = classes[0]\n",
    "classes[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(c0.name) := 'BFO_0000001'"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "(c0.label) := ['entity']"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "(c0.iri) := 'http://purl.obolibrary.org/obo/BFO_0000001'"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "(bfo.base_iri) := 'http://purl.obolibrary.org/obo/bfo.owl#'"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "c0.name ##:\n",
    "c0.label ##:\n",
    "\n",
    "c0.iri ##:\n",
    "bfo.base_iri ##:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## How to access a class by its `name` (i.e. not by its `label`)?\n",
    "\n",
    "### Manually building the iri\n",
    "\n",
    "This requires to know the internal iri-prefix which is not the same as `bfo.base_iri`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "klass := obo.BFO_0000001"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "klass = bfo.world[\"http://purl.obolibrary.org/obo/BFO_0000001\"] ##:\n",
    "\n",
    "klass == c0"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###  Fixing (hacking) `.base_iri`\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Inherently, `bfo.BFO_0000001` cannot be resolved due to iri mismatch.\n",
    "bfo.BFO_0000001 is None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# changing the base_iri to the string wich is used as prefix in `bfo.world.graph._abbreviate_d`\n",
    "\n",
    "bfo.base_iri = 'http://purl.obolibrary.org/obo/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(bfo.BFO_0000001 is None) := False"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "obo.BFO_0000001"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# now this works as intended\n",
    "bfo.BFO_0000001 is None ##:\n",
    "\n",
    "bfo.BFO_0000001"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Access via `.search(...)`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[obo.BFO_0000001]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# this does not require to alter the base_iri\n",
    "bfo.search(iri=\"*BFO_0000001\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[obo.BFO_0000001]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bfo.search(label=\"entity\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'http://purl.obolibrary.org/obo/BFO_0000001'"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bfo.search(label=\"entity\").first().iri"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## General overview of the entities in BFO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "BFO_0000001 ['entity']\n",
      "BFO_0000002 ['continuant']\n",
      "BFO_0000003 ['occurrent']\n",
      "BFO_0000004 ['independent continuant']\n",
      "BFO_0000020 ['specifically dependent continuant']\n",
      "BFO_0000031 ['generically dependent continuant']\n",
      "BFO_0000006 ['spatial region']\n",
      "BFO_0000141 ['immaterial entity']\n",
      "BFO_0000029 ['site']\n",
      "BFO_0000140 ['continuant fiat boundary']\n",
      "BFO_0000008 ['temporal region']\n",
      "BFO_0000011 ['spatiotemporal region']\n",
      "BFO_0000015 ['process']\n",
      "BFO_0000035 ['process boundary']\n",
      "BFO_0000009 ['two-dimensional spatial region']\n",
      "BFO_0000028 ['three-dimensional spatial region']\n",
      "BFO_0000016 ['disposition']\n",
      "BFO_0000017 ['realizable entity']\n",
      "BFO_0000023 ['role']\n",
      "BFO_0000019 ['quality']\n",
      "BFO_0000018 ['zero-dimensional spatial region']\n",
      "BFO_0000024 ['fiat object part']\n",
      "BFO_0000040 ['material entity']\n",
      "BFO_0000026 ['one-dimensional spatial region']\n",
      "BFO_0000027 ['object aggregate']\n",
      "BFO_0000030 ['object']\n",
      "BFO_0000034 ['function']\n",
      "BFO_0000038 ['one-dimensional temporal region']\n",
      "BFO_0000148 ['zero-dimensional temporal region']\n",
      "BFO_0000142 ['one-dimensional continuant fiat boundary']\n",
      "BFO_0000146 ['two-dimensional continuant fiat boundary']\n",
      "BFO_0000147 ['zero-dimensional continuant fiat boundary']\n",
      "BFO_0000144 ['process profile']\n",
      "BFO_0000182 ['history']\n",
      "BFO_0000145 ['relational quality']\n"
     ]
    }
   ],
   "source": [
    "for e in classes:\n",
    "    print(e.name, e.label)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "info(annotation_properties) := \"<class 'list'> with length: 22\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "---"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "annotation_properties = list(bfo.annotation_properties()) ##:i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "tab = []\n",
    "\n",
    "for e in annotation_properties:\n",
    "    try:\n",
    "        label = e.label\n",
    "    except TypeError:\n",
    "        label = \"<TypeError>\"\n",
    "    tab.append((e.name, label))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "import tabulate"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-----------  --------------------------------\n",
      "isDefinedBy  <TypeError>\n",
      "seeAlso      <TypeError>\n",
      "IAO_0000116  ['editor note']\n",
      "contributor  []\n",
      "license      []\n",
      "homepage     []\n",
      "mbox         []\n",
      "BFO_0000179  ['BFO OWL specification label']\n",
      "IAO_0000115  ['definition']\n",
      "IAO_0000232  ['curator note']\n",
      "BFO_0000180  ['BFO CLIF specification label']\n",
      "IAO_0000119  ['definition source']\n",
      "IAO_0000111  ['editor preferred term']\n",
      "IAO_0000112  ['example of usage']\n",
      "IAO_0000117  ['term editor']\n",
      "IAO_0000118  ['alternative term']\n",
      "IAO_0000412  ['imported from']\n",
      "IAO_0000600  ['elucidation']\n",
      "IAO_0000601  ['has associated axiom(nl)']\n",
      "IAO_0000602  ['has associated axiom(fol)']\n",
      "IAO_0010000  ['has axiom label']\n",
      "member       []\n",
      "-----------  --------------------------------\n"
     ]
    }
   ],
   "source": [
    "print(tabulate.tabulate(tab))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['editor note']"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "annotation_properties[2].label"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "isolated problem reproduction (after kernel restart)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['editor note']\n",
      "[]\n"
     ]
    },
    {
     "ename": "TypeError",
     "evalue": "'NoneType' object is not subscriptable",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-bf2b883b90ca>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0;31m# works not -> TypeError:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mannotation_properties\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/media/workcard/workstickdir/RST/expertise_system/ontologie_experimente/owlready2_cvk_fork/owlready2/prop.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(Prop, attr)\u001b[0m\n\u001b[1;32m    258\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    259\u001b[0m   \u001b[0;32mdef\u001b[0m \u001b[0m__getattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mProp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 260\u001b[0;31m     \u001b[0;32mif\u001b[0m \u001b[0mProp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnamespace\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mworld\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mowl_world\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mAnnot\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCURRENT_NAMESPACES\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mworld\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_props\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    261\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m                                 \u001b[0mAnnot\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mProp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnamespace\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mworld\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_props\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    262\u001b[0m     \u001b[0;31m#l = CURRENT_NAMESPACES.get()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mTypeError\u001b[0m: 'NoneType' object is not subscriptable"
     ]
    }
   ],
   "source": [
    "import owlready2 as owl2\n",
    "bfo = owl2.get_ontology(\"http://purl.obolibrary.org/obo/bfo.owl\").load()\n",
    "\n",
    "annotation_properties = list(bfo.annotation_properties())\n",
    "\n",
    "# works -> List[str]\n",
    "print(annotation_properties[2].label)\n",
    "\n",
    "# works -> empty list\n",
    "print(annotation_properties[3].label)\n",
    "\n",
    "# works not -> TypeError:\n",
    "print(annotation_properties[0].label)"
   ]
  }
 ],
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