notebooks/Optional_attribute_definition.ipynb

{
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   "cell_type": "markdown",
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   "source": [
    "# Loading the optional definition attribute\n",
    "\n",
    "1) Load the ontology file while also loading the optional definition attribute (\"def\" or \"defn\") for each GO term"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "go-basic.obo: fmt(1.2) rel(2021-02-01) 47,291 Terms; optional_attrs(def)\n"
     ]
    }
   ],
   "source": [
    "from os.path import exists\n",
    "from goatools.obo_parser import GODag\n",
    "\n",
    "if not exists('go-basic.obo'):\n",
    "    !wget http://geneontology.org/ontology/go-basic.obo\n",
    "dag = GODag('go-basic.obo', optional_attrs=['def'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get one GOTerm object\n",
    "\n",
    "The DAG is a dictionary where:\n",
    "  * a key is an ID field (Example: GO:NNNNNNN)\n",
    "  * a value is a GOTerm object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "term = next(iter(dag.values()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The optional 'def' obo field becomes a 'defn' data member in a GOTerm object\n",
    "Because \"def\" is a keyword in Python, the optional obo attribute \"def\" gets renamed as \"defn\", meaning \"definition\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_parents', 'alt_ids', 'children', 'defn', 'depth', 'get_all_child_edges', 'get_all_children', 'get_all_lower', 'get_all_parent_edges', 'get_all_parents', 'get_all_upper', 'get_goterms_lower', 'get_goterms_lower_rels', 'get_goterms_upper', 'get_goterms_upper_rels', 'has_child', 'has_parent', 'id', 'is_obsolete', 'item_id', 'level', 'name', 'namespace', 'parents']\n"
     ]
    }
   ],
   "source": [
    "print(dir(term))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Print one GO term and its optional definition (defn) data member value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0000001 mitochondrion inheritance\n",
      "\"The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton.\" [GOC:mcc, PMID:10873824, PMID:11389764]\n"
     ]
    }
   ],
   "source": [
    "pattern = '{ID} {NAME}\\n{DEF}'\n",
    "print(pattern.format(ID=term.item_id, NAME=term.name, DEF=term.defn))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Print the first term in biological process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0000001 mitochondrion inheritance\n",
      "\"The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton.\" [GOC:mcc, PMID:10873824, PMID:11389764]\n"
     ]
    }
   ],
   "source": [
    "term1 = dag['GO:0000001']\n",
    "print(pattern.format(ID=term1.item_id, NAME=term1.name, DEF=term1.defn))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Copyright (C) 2021-present, DV Klopfenstein and Haibao Tang. All rights reserved."
   ]
  }
 ],
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