Adding relationships in the gene ontology notebook.

notebooks/relatonships_in_the_go.ipynb

@@ -0,0 +1,356 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Relationships in the GO\n",
+ "_Alex Warwick Vesztrocy, March 2016_"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "For some analyses, it is possible to only use the <code>is_a</code> definitions given in the Gene Ontology. \n",
+ "\n",
+ "However, it is important to remember that this isn't always the case. As such, <code>GOATOOLS</code> includes the option to load the relationship definitions also."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Loading GO graph with the relationship tags\n",
+ "This is possible by using the <code>optional_attrs</code> argument, upon instantiating a <code>GODag</code>. This can be done with either the full or the basic version of the ontology. Here, the __full__ version shall be used. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "load obo file go.obo\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "go.obo: format-version(1.2) data-version(releases/2016-03-26)\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "46317 nodes imported\n"
+ ]
+ }
+ ],
+ "source": [
+ "from goatools.obo_parser import GODag\n",
+ "import wget\n",
+ "\n",
+ "go_fn = wget.download('https://geneontology.org/ontology/go.obo')\n",
+ "go = GODag(go_fn, optional_attrs=['relationship'])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Viewing relationships in the GO graph"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "So now, when looking at an individual term (which has relationships defined in the GO) these are listed in a nested manner. As an example, look at <code>GO:1901990</code> which has a single <code>has_part</code> relationship, as well as a <code>regulates</code> one."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "eg_term = go['GO:1901990']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "GOTerm('GO:1901990'):\n",
+ " name:regulation of mitotic cell cycle phase transition\n",
+ " children: 7 items\n",
+ " GO:0060564\tlevel-07\tdepth-13\tnegative regulation of APC-Cdc20 complex activity [biological_process] \n",
+ " GO:2000045\tlevel-07\tdepth-08\tregulation of G1/S transition of mitotic cell cycle [biological_process] \n",
+ " GO:1901992\tlevel-07\tdepth-08\tpositive regulation of mitotic cell cycle phase transition [biological_process] \n",
+ " GO:1901991\tlevel-07\tdepth-08\tnegative regulation of mitotic cell cycle phase transition [biological_process] \n",
+ " GO:0010389\tlevel-07\tdepth-08\tregulation of G2/M transition of mitotic cell cycle [biological_process] \n",
+ " GO:0030071\tlevel-07\tdepth-10\tregulation of mitotic metaphase/anaphase transition [biological_process] \n",
+ " GO:0007096\tlevel-07\tdepth-08\tregulation of exit from mitosis [biological_process] \n",
+ " parents: 2 items\n",
+ " GO:0007346\tlevel-05\tdepth-05\tregulation of mitotic cell cycle [biological_process] \n",
+ " GO:1901987\tlevel-06\tdepth-06\tregulation of cell cycle phase transition [biological_process] \n",
+ " level:6\n",
+ " depth:7\n",
+ " alt_ids: 0 items\n",
+ " _parents: 2 items\n",
+ " GO:0007346\n",
+ " GO:1901987\n",
+ " relationship: 2 items\n",
+ " has_part: 1 items\n",
+ " GO:0051437\tlevel-07\tdepth-12\tpositive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition [biological_process] \n",
+ " regulates: 1 items\n",
+ " GO:0044772\tlevel-05\tdepth-05\tmitotic cell cycle phase transition [biological_process] \n",
+ " id:GO:1901990\n",
+ " namespace:biological_process\n",
+ " is_obsolete:False"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "eg_term"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "These different relationship types are stored as a dictionary within the relationship attribute on a GO term."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "dict_keys(['has_part', 'regulates'])\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(eg_term.relationship.keys())"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{GOTerm('GO:0044772'):\n",
+ " name:mitotic cell cycle phase transition\n",
+ " children: 4 items\n",
+ " GO:0000086\tlevel-06\tdepth-06\tG2/M transition of mitotic cell cycle [biological_process] \n",
+ " GO:0007091\tlevel-06\tdepth-10\tmetaphase/anaphase transition of mitotic cell cycle [biological_process] \n",
+ " GO:0010458\tlevel-06\tdepth-06\texit from mitosis [biological_process] \n",
+ " GO:0000082\tlevel-06\tdepth-06\tG1/S transition of mitotic cell cycle [biological_process] \n",
+ " parents: 2 items\n",
+ " GO:0044770\tlevel-04\tdepth-04\tcell cycle phase transition [biological_process] \n",
+ " GO:1903047\tlevel-04\tdepth-04\tmitotic cell cycle process [biological_process] \n",
+ " level:5\n",
+ " depth:5\n",
+ " alt_ids: 0 items\n",
+ " _parents: 2 items\n",
+ " GO:0044770\n",
+ " GO:1903047\n",
+ " relationship: 1 items\n",
+ " part_of: 1 items\n",
+ " GO:0000278\tlevel-04\tdepth-04\tmitotic cell cycle [biological_process] \n",
+ " id:GO:0044772\n",
+ " namespace:biological_process\n",
+ " is_obsolete:False}\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(eg_term.relationship['regulates'])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Example use case\n",
+ "One example use case for the relationship terms, would be to look for all functions which regulate pseudohyphal growth (<code>GO:0007124</code>). That is:\n",
+ "\n",
+ "> A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate. \n",
+ ">\n",
+ "> _Source: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007124#term=info&info=1_"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "term_of_interest = go['GO:0007124']"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "First, find the relationship types which contain \"regulates\":"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "frozenset({'positively_regulates', 'negatively_regulates', 'regulates'})\n"
+ ]
+ }
+ ],
+ "source": [
+ "regulates = frozenset([typedef \n",
+ " for typedef in go.typedefs.keys() \n",
+ " if 'regulates' in typedef])\n",
+ "print(regulates)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now, search through the terms in the tree for those with a relationship in this list and add them to a dictionary dependent on the type of regulation."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from collections import defaultdict\n",
+ "\n",
+ "regulating_terms = defaultdict(list)\n",
+ "\n",
+ "for t in go.values():\n",
+ " if hasattr(t, 'relationship'):\n",
+ " for typedef in regulates.intersection(t.relationship.keys()):\n",
+ " if term_of_interest in t.relationship[typedef]:\n",
+ " regulating_terms['{:s}d_by'.format(typedef[:-1])].append(t)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now <code>regulating_terms</code> contains the GO terms which relate to regulating protein localisation to the nucleolus."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "pseudohyphal growth (GO:0007124) is:\n",
+ "\n",
+ " - negatively_regulated_by:\n",
+ " -- GO:1900462 negative regulation of pseudohyphal growth by negative regulation of transcription from RNA polymerase II promoter\n",
+ " -- GO:2000221 negative regulation of pseudohyphal growth\n",
+ " -- GO:0100042 negative regulation of pseudohyphal growth by transcription from RNA polymerase II promoter\n",
+ "\n",
+ " - positively_regulated_by:\n",
+ " -- GO:2000222 positive regulation of pseudohyphal growth\n",
+ " -- GO:0100041 positive regulation of pseudohyphal growth by transcription from RNA polymerase II promoter\n",
+ " -- GO:1900461 positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter\n",
+ "\n",
+ " - regulated_by:\n",
+ " -- GO:2000220 regulation of pseudohyphal growth\n"
+ ]
+ }
+ ],
+ "source": [
+ "print('{:s} ({:s}) is:'.format(term_of_interest.name, term_of_interest.id))\n",
+ "for (k, v) in regulating_terms.items():\n",
+ " print('\\n - {:s}:'.format(k))\n",
+ " for t in v:\n",
+ " print(' -- {:s} {:s}'.format(t.id, t.name))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.5.1"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}