notebooks/parent_go_terms.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How to extract information from parent GO terms\n",
    "\n",
    "* **1) Load the GO DAG**\n",
    "* **2) Pick a GO term and visualize**\n",
    "  * **2a) Print GO information**\n",
    "  * **2b) Plot GO term**\n",
    "* **3. Find GO parents for numerous GO IDs**\n",
    "  * **3a. Find GO parents up all relationships**\n",
    "  * **3b. Find GO parents up *is_a* relationships only**\n",
    "* **4. Find GO parents by traversing explicit relationships**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section1'></a>\n",
    "## 1. Load the GO DAG\n",
    "Required relationship between GO terms, *is_a*, is always loaded.\n",
    "\n",
    "Load optional relationships, like *part_of*, so we have the option of finding GO parents with or without relationships."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  EXISTS: go-basic.obo\n",
      "go-basic.obo: fmt(1.2) rel(2019-10-07) 47,285 GO Terms; optional_attrs(relationship)\n"
     ]
    }
   ],
   "source": [
    "from goatools.base import get_godag\n",
    "godag = get_godag('go-basic.obo', optional_attrs='relationship')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section2'></a>\n",
    "## 2. Pick a GO term and visualize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "goid = 'GO:0050807'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section2a'></a>\n",
    "### 2a. Print GO information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def prt_flds(gosubdag):\n",
    "    \"\"\"Print the available printing fields\"\"\"\n",
    "    print('Print fields:')\n",
    "    for fld in sorted(gosubdag.prt_attr['flds']):\n",
    "        print('    {F}'.format(F=fld))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "BP GO:0050807 D05 regulation of synapse organization\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "\n",
    "# Create a subset of the GO DAG which contains:\n",
    "#   * The selected GO term and\n",
    "#   * All the GO terms above it\n",
    "gosubdag = GoSubDag(goid, godag, relationships=True, prt=False)\n",
    "\n",
    "# Get additional information for chosen GO\n",
    "ntgo = gosubdag.go2nt[goid]\n",
    "\n",
    "# Choose fields and custom printing format\n",
    "# prt_flds(gosubdag)  # Uncomment to see the available print fields\n",
    "prtfmt = '{NS} {GO} D{depth:02} {GO_name}'\n",
    "\n",
    "# Print detailed information for GO\n",
    "print(prtfmt.format(**ntgo._asdict()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section2b'></a>\n",
    "### 2b. Plot GO term"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    1 usr  12 GOs  WROTE: reg_synapse_org.png\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.plot.gosubdag_plot import GoSubDagPlot\n",
    "GoSubDagPlot(gosubdag).plt_dag('reg_synapse_org.png')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![regulation of synapse organization](images/reg_synapse_org.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section3'></a>\n",
    "## 3. Find GO parents for numerous GO IDs\n",
    "### 3a. Find GO parents up all relationships"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "BP GO:0051128 D04 regulation of cellular component organization\n",
      "BP GO:0050803 D03 regulation of synapse structure or activity\n",
      "BP GO:0050808 D03 synapse organization\n"
     ]
    }
   ],
   "source": [
    "from goatools.godag.go_tasks import get_go2parents\n",
    "\n",
    "go2parents = get_go2parents(gosubdag.go2obj, gosubdag.relationships)\n",
    "for goid_parent in go2parents[goid]:\n",
    "    print(prtfmt.format(**gosubdag.go2nt[goid_parent]._asdict()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section3b'></a>\n",
    "### 3b. Find GO parents up *is_a* relationships only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "BP GO:0051128 D04 regulation of cellular component organization\n"
     ]
    }
   ],
   "source": [
    "from goatools.godag.go_tasks import get_go2parents_isa\n",
    "\n",
    "go2parents = get_go2parents_isa(gosubdag.go2obj)\n",
    "for goid_parent in go2parents[goid]:\n",
    "    print(prtfmt.format(**gosubdag.go2nt[goid_parent]._asdict()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id='section4'></a>\n",
    "## 4. Find GO parents by traversing explicit relationships"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Parents up \"is_a\": required relationship\n",
      "BP GO:0051128 D04 regulation of cellular component organization\n",
      "\n",
      "Parents up \"part_of\" optional relationship:\n",
      "BP GO:0050803 D03 regulation of synapse structure or activity\n",
      "\n",
      "Parents up \"regulates\" optional relationship:\n",
      "BP GO:0050808 D03 synapse organization\n",
      "\n",
      "Ancestors up all loaded relationships:\n",
      "BP GO:0050789 D02 regulation of biological process\n",
      "BP GO:0050794 D03 regulation of cellular process\n",
      "BP GO:0050803 D03 regulation of synapse structure or activity\n",
      "BP GO:0016043 D02 cellular component organization\n",
      "BP GO:0065008 D02 regulation of biological quality\n",
      "BP GO:0050808 D03 synapse organization\n",
      "BP GO:0008150 D00 biological_process\n",
      "BP GO:0009987 D01 cellular process\n",
      "BP GO:0065007 D01 biological regulation\n",
      "BP GO:0051128 D04 regulation of cellular component organization\n",
      "BP GO:0071840 D01 cellular component organization or biogenesis\n"
     ]
    }
   ],
   "source": [
    "goterm = godag[goid]\n",
    "\n",
    "print('Parents up \"is_a\": required relationship')\n",
    "for p_term in goterm.parents:\n",
    "    print(prtfmt.format(**gosubdag.go2nt[p_term.item_id]._asdict()))\n",
    "    \n",
    "if 'part_of' in goterm.relationship:\n",
    "    print('\\nParents up \"part_of\" optional relationship:')\n",
    "    for p_go in goterm.relationship['part_of']:\n",
    "        print(prtfmt.format(**gosubdag.go2nt[p_go.item_id]._asdict()))\n",
    "        \n",
    "if 'regulates' in goterm.relationship:\n",
    "    print('\\nParents up \"regulates\" optional relationship:')\n",
    "    for p_go in goterm.relationship['regulates']:\n",
    "        print(prtfmt.format(**gosubdag.go2nt[p_go.item_id]._asdict()))\n",
    "\n",
    "# godag must be loaded with: optional_attrs='relationship'\n",
    "# gosubdag must be loaded with: relationships=True\n",
    "print('\\nAncestors up all loaded relationships:')\n",
    "for p_go in gosubdag.rcntobj.go2ancestors[goid]:\n",
    "    print(prtfmt.format(**gosubdag.go2nt[p_go]._asdict()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Copyright (C) 2019-present, DV Klopfenstein, H Tang. All rights reserved."
   ]
  }
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