Transfer of Knowledge Through Ontological Relationships.ipynb

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   "source": [
    "\n",
    "# Transfer of Knowledge Through Ontological Relationships\n",
    "\n",
    "Author: [Charles Tapley Hoyt](/~https://github.com/cthoyt)\n",
    "\n",
    "Estimated Run Time: 5 seconds\n",
    "\n",
    "This notebook shows how ontological relationships, such as chemical families and enzyme classes, can be used to make inferences in knowledge assemblies using the [infer_child_relations](http://pybel.readthedocs.io/en/latest/mutation.html#pybel.struct.mutation.infer_child_relations) mutations function."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import time\n",
    "import sys\n",
    "import random\n",
    "\n",
    "from pybel.utils import get_version\n",
    "from pybel.struct.mutation import infer_child_relations\n",
    "from pybel_tools.visualization import *\n",
    "from pybel.examples.statin_example import statin_graph, hmgcr_inhibitor, hmgcr, ec_11134"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Environment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sat Feb 10 14:42:36 2018\n"
     ]
    }
   ],
   "source": [
    "print(time.asctime())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3.6.4 (default, Jan  6 2018, 11:51:59) \n",
      "[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.39.2)]\n"
     ]
    }
   ],
   "source": [
    "print(sys.version)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set seed for visualization\n",
    "random.seed(127)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Dependencies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.11.1-dev\n"
     ]
    }
   ],
   "source": [
    "print(get_version())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example Graph\n",
    "\n",
    "This notebook uses a small example related to [statins](http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A87631) and their target, [HMG-CoA_reductase](https://en.wikipedia.org/wiki/HMG-CoA_reductase). While it is not exhaustively importing relationships using [Bio2BEL ExPASy](http://bio2bel-expasy.readthedocs.io) and [Bio2BEL ChEBI](http://bio2bel-chebi.readthedocs.io), it still provides an atomic example on how in- and out-edges can be inferred through hierarchies."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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\"CHEBI\"}, {\"cname\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \"], \"identifier\": \"35664\", \"name\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"namespace\": \"CHEBI\"}, {\"cname\": \"mevinolinic acid\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"mevinolinic acid\"], \"identifier\": \"82985\", \"name\": \"mevinolinic acid\", \"namespace\": \"CHEBI\"}, {\"cname\": \"HMGCR\", \"function\": \"Protein\", \"id\": [\"Protein\", \"HGNC\", \"HMGCR\"], \"identifier\": \"5006\", \"name\": \"HMGCR\", \"namespace\": \"HGNC\"}, {\"cname\": \"1.1.1.34\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.34\"], \"name\": \"1.1.1.34\", \"namespace\": \"EC\"}, {\"cname\": \"1.1.1.88\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.88\"], \"name\": \"1.1.1.88\", \"namespace\": \"EC\"}]}, \"#bqvxdaujygremoqt\", 1000, 650, {'Protein': '#1F77B4', 'Pathology': '#FF7F0E', 'BiologicalProcess': '#2CA02C', 'miRNA': '#D62728', 'Complex': '#9467bd', 'Composite': '#9467bd', 'Reaction': '#8c564b', 'Gene': '#e377c2', 'Abundance': '#bcbd22', 'RNA': '#17becf'});\n",
       "});"
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       "<IPython.core.display.Javascript object>"
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     },
     "execution_count": 6,
     "metadata": {},
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    }
   ],
   "source": [
    "to_jupyter(statin_graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Propogation on Chemical Hierarchy\n",
    "\n",
    "The first transformation made is to assert that all things true for EC 1.1.1.34/EC 1.1.88 inhibitors are also true for their descendants. There are two relationships showing decrease in the activities of the corresponding enzyme nodes that will be asserted for its two children, statin and mevinolinic acid, as well as recursively for their descendants."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
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       "    var focus_node = null;\n",
       "    var highlight_node = null;\n",
       "\n",
       "    // Highlight color variables\n",
       "\n",
       "    // Highlight color of the node boundering\n",
       "    const highlight_node_boundering = \"#4EB2D4\";\n",
       "\n",
       "    // Highlight color of the edge\n",
       "    const highlighted_link_color = \"#4EB2D4\";\n",
       "\n",
       "    // Text highlight color\n",
       "    const highlight_text = \"#4EB2D4\";\n",
       "\n",
       "    // Size when zooming scale\n",
       "    var size = d3.scalePow().exponent(1)\n",
       "        .domain([1, 100])\n",
       "        .range([8, 24]);\n",
       "\n",
       "    // Simulation parameters\n",
       "    const linkDistance = 100;\n",
       "    const fCharge = -1000;\n",
       "    const linkStrength = 0.7;\n",
       "    const collideStrength = 1;\n",
       "\n",
       "    // Simulation defined with variables\n",
       "    var simulation = d3.forceSimulation()\n",
       "        .force(\"link\", d3.forceLink()\n",
       "            .distance(linkDistance)\n",
       "            .strength(linkStrength)\n",
       "        )\n",
       "        .force(\"collide\", d3.forceCollide()\n",
       "            .radius(function (d) {\n",
       "                return d.r + 10\n",
       "            })\n",
       "            .strength(collideStrength)\n",
       "        )\n",
       "        .force(\"charge\", d3.forceManyBody()\n",
       "            .strength(fCharge)\n",
       "        )\n",
       "        .force(\"center\", d3.forceCenter(width / 2, height / 2))\n",
       "        .force(\"y\", d3.forceY(0))\n",
       "        .force(\"x\", d3.forceX(0));\n",
       "\n",
       "    // Pin down functionality\n",
       "    var node_drag = d3.drag()\n",
       "        .on(\"start\", dragstarted)\n",
       "        .on(\"drag\", dragged)\n",
       "        .on(\"end\", dragended);\n",
       "\n",
       "    function dragstarted(d) {\n",
       "        if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n",
       "        d.fx = d.x;\n",
       "        d.fy = d.y;\n",
       "    }\n",
       "\n",
       "    function dragged(d) {\n",
       "        d.fx = d3.event.x;\n",
       "        d.fy = d3.event.y;\n",
       "    }\n",
       "\n",
       "    function dragended(d) {\n",
       "        if (!d3.event.active) simulation.alphaTarget(0);\n",
       "    }\n",
       "\n",
       "    function releasenode(d) {\n",
       "        d.fx = null;\n",
       "        d.fy = null;\n",
       "    }\n",
       "\n",
       "    //END Pin down functionality\n",
       "\n",
       "    const color_circunferencia = \"black\";\n",
       "    const default_link_color = \"#AAAAAA\";\n",
       "    const nominal_base_node_size = 8;\n",
       "\n",
       "    // Normal and highlighted stroke of the links (double the width of the link when highlighted)\n",
       "    const nominal_stroke = 1.5;\n",
       "\n",
       "    // Zoom variables\n",
       "    const min_zoom = 0.1;\n",
       "    const max_zoom = 10;\n",
       "    const border = 1;\n",
       "    const bordercolor = 'black';\n",
       "\n",
       "    var svg = d3.select(chart).append(\"svg\")\n",
       "        .attr(\"width\", width)\n",
       "        .attr(\"height\", height);\n",
       "\n",
       "    // // Create definition for arrowhead.\n",
       "    svg.append(\"defs\").append(\"marker\")\n",
       "        .attr(\"id\", \"arrowhead\")\n",
       "        .attr(\"viewBox\", \"0 -5 10 10\")\n",
       "        .attr(\"refX\", 20)\n",
       "        .attr(\"refY\", 0)\n",
       "        .attr(\"markerUnits\", \"strokeWidth\")\n",
       "        .attr(\"markerWidth\", 6)\n",
       "        .attr(\"markerHeight\", 6)\n",
       "        .attr(\"orient\", \"auto\")\n",
       "        .append(\"path\")\n",
       "        .attr(\"d\", \"M0,-5L10,0L0,5\");\n",
       "\n",
       "    // // Create definition for stub.\n",
       "    svg.append(\"defs\").append(\"marker\")\n",
       "        .attr(\"id\", \"stub\")\n",
       "        .attr(\"viewBox\", \"-1 -5 2 10\")\n",
       "        .attr(\"refX\", 15)\n",
       "        .attr(\"refY\", 0)\n",
       "        .attr(\"markerUnits\", \"strokeWidth\")\n",
       "        .attr(\"markerWidth\", 6)\n",
       "        .attr(\"markerHeight\", 6)\n",
       "        .attr(\"orient\", \"auto\")\n",
       "        .append(\"path\")\n",
       "        .attr(\"d\", \"M 0,0 m -1,-5 L 1,-5 L 1,5 L -1,5 Z\");\n",
       "\n",
       "    // Background\n",
       "    svg.append(\"rect\")\n",
       "        .attr(\"width\", \"100%\")\n",
       "        .attr(\"height\", \"100%\")\n",
       "        .attr(\"fill\", \"#ffffff\")\n",
       "        .style(\"pointer-events\", \"all\")\n",
       "        // Zoom + panning functionality\n",
       "        .call(d3.zoom()\n",
       "            .scaleExtent([min_zoom, max_zoom])\n",
       "            .on(\"zoom\", zoomed))\n",
       "        .on(\"dblclick.zoom\", null);\n",
       "\n",
       "\n",
       "    function zoomed() {\n",
       "        g.attr(\"transform\", d3.event.transform);\n",
       "    }\n",
       "\n",
       "    // g = svg object where the graph will be appended\n",
       "    var g = svg.append(\"g\");\n",
       "\n",
       "    var linkedByIndex = {};\n",
       "    graph.links.forEach(function (d) {\n",
       "        linkedByIndex[d.source + \",\" + d.target] = true;\n",
       "    });\n",
       "\n",
       "    function isConnected(a, b) {\n",
       "        return linkedByIndex[a.index + \",\" + b.index] || linkedByIndex[b.index + \",\" + a.index] || a.index == b.index;\n",
       "    }\n",
       "\n",
       "    function ticked() {\n",
       "        link.attr(\"x1\", function (d) {\n",
       "            return d.source.x;\n",
       "        })\n",
       "            .attr(\"y1\", function (d) {\n",
       "                return d.source.y;\n",
       "            })\n",
       "            .attr(\"x2\", function (d) {\n",
       "                return d.target.x;\n",
       "            })\n",
       "            .attr(\"y2\", function (d) {\n",
       "                return d.target.y;\n",
       "            });\n",
       "\n",
       "        node\n",
       "            .attr(\"transform\", function (d) {\n",
       "                return \"translate(\" + d.x + \", \" + d.y + \")\";\n",
       "            });\n",
       "    }\n",
       "\n",
       "\n",
       "    simulation\n",
       "        .nodes(graph.nodes)\n",
       "        .on(\"tick\", ticked);\n",
       "\n",
       "    simulation.force(\"link\")\n",
       "        .links(graph.links);\n",
       "\n",
       "    // Definition of links nodes text...\n",
       "\n",
       "    var link = g.selectAll(\".link\")\n",
       "        .data(graph.links)\n",
       "        .enter().append(\"line\")\n",
       "        .style(\"stroke-width\", nominal_stroke)\n",
       "        .style(\"stroke\", default_link_color)\n",
       "        .style(\"stroke-dasharray\", function (d) {\n",
       "            if (['decreases', 'directlyDecreases', 'increases', 'directlyIncreases', 'negativeCorrelation',\n",
       "                    'positiveCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"none\"\n",
       "            } else {\n",
       "                return \"4, 4\"\n",
       "            }\n",
       "        })\n",
       "        .attr(\"marker-start\", function (d) {\n",
       "            if ('positiveCorrelation' == d.relation) {\n",
       "                return \"url(#arrowhead)\"\n",
       "            }\n",
       "            else if ('negativeCorrelation' == d.relation) {\n",
       "                return \"url(#stub)\"\n",
       "            }\n",
       "            else {\n",
       "                return \"\"\n",
       "            }\n",
       "        })\n",
       "        .attr(\"marker-end\", function (d) {\n",
       "            if (['increases', 'directlyIncreases', 'positiveCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"url(#arrowhead)\"\n",
       "            } else if (['decreases', 'directlyDecreases', 'negativeCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"url(#stub)\"\n",
       "            } else {\n",
       "                return \"\"\n",
       "            }\n",
       "        });\n",
       "\n",
       "    var node = g.selectAll(\".nodes\")\n",
       "        .data(graph.nodes)\n",
       "        .enter().append(\"g\")\n",
       "        .attr(\"class\", \"node\")\n",
       "        // Next two lines -> Pin down functionality\n",
       "        .on('dblclick', releasenode)\n",
       "        .call(node_drag);\n",
       "\n",
       "    var circle = node.append(\"path\")\n",
       "        .attr(\"d\", d3.symbol()\n",
       "            .size(function (d) {\n",
       "                return Math.PI * Math.pow(size(d.size) || nominal_base_node_size, 2);\n",
       "            })\n",
       "        )\n",
       "        .attr(\"class\", function (d) {\n",
       "            return d.function\n",
       "        })\n",
       "        .style('fill', function (d) {\n",
       "            return function_colors[d.function]\n",
       "        })\n",
       "        .style(\"stroke-width\", nominal_stroke)\n",
       "        .style(\"stroke\", color_circunferencia);\n",
       "\n",
       "    var text = node.append(\"text\")\n",
       "        .attr(\"class\", \"node-name\")\n",
       "        // .attr(\"id\", nodehashes[d])\n",
       "        .attr(\"fill\", \"black\")\n",
       "        .attr(\"dx\", 12)\n",
       "        .attr(\"dy\", \".35em\")\n",
       "        .text(function (d) {\n",
       "            return d.cname\n",
       "        });\n",
       "\n",
       "    // Highlight on mouseenter and back to normal on mouseout\n",
       "    node.on(\"mouseenter\", function (d) {\n",
       "        set_highlight(d);\n",
       "    })\n",
       "        .on(\"mousedown\", function () {\n",
       "            d3.event.stopPropagation();\n",
       "        }).on(\"mouseout\", function () {\n",
       "        exit_highlight();\n",
       "    });\n",
       "\n",
       "    function exit_highlight() {\n",
       "        highlight_node = null;\n",
       "        if (focus_node === null) {\n",
       "            if (highlight_node_boundering != color_circunferencia) {\n",
       "                circle.style(\"stroke\", color_circunferencia);\n",
       "                text.style(\"fill\", \"black\");\n",
       "                link.style(\"stroke\", default_link_color);\n",
       "            }\n",
       "        }\n",
       "    }\n",
       "\n",
       "    function set_highlight(d) {\n",
       "        if (focus_node !== null) d = focus_node;\n",
       "        highlight_node = d;\n",
       "\n",
       "        if (highlight_node_boundering != color_circunferencia) {\n",
       "            circle.style(\"stroke\", function (o) {\n",
       "                return isConnected(d, o) ? highlight_node_boundering : color_circunferencia;\n",
       "            });\n",
       "            text.style(\"fill\", function (o) {\n",
       "                return isConnected(d, o) ? highlight_text : \"black\";\n",
       "            });\n",
       "            link.style(\"stroke\", function (o) {\n",
       "                return o.source.index == d.index || o.target.index == d.index ? highlighted_link_color : default_link_color;\n",
       "            });\n",
       "        }\n",
       "    }\n",
       "\n",
       "\n",
       "    // Freeze the graph when space is pressed\n",
       "    function freezeGraph() {\n",
       "        // Space button Triggers STOP\n",
       "        if (d3.event.keyCode == 32) {\n",
       "            simulation.stop();\n",
       "        }\n",
       "    }\n",
       "\n",
       "    // Call freezeGraph when a key is pressed, freezeGraph checks whether this key is \"Space\" that triggers the freeze\n",
       "    d3.select(window).on(\"keydown\", freezeGraph);\n",
       "}\n",
       "\n",
       "require.config({\n",
       "    paths: {\n",
       "        d3: '//cdnjs.cloudflare.com/ajax/libs/d3/4.5.0/d3.min'\n",
       "    }\n",
       "});\n",
       "\n",
       "var elementInnerHTML = \"<div id='mkudpqcofahtyrge'></div>\";\n",
       "\n",
       "element.append(elementInnerHTML);\n",
       "\n",
       "require(['d3'], function (d3) {\n",
       "    return init_d3_force(d3, {\"directed\": true, \"graph\": {\"annotation_list\": {}, \"annotation_owl\": {}, \"annotation_pattern\": {}, \"annotation_url\": {\"Confidence\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/confidence/confidence-1.0.0.belanno\"}, \"document_metadata\": {\"authors\": \"Charles Tapley Hoyt\", \"contact\": \"charles.hoyt@scai.fraunhofer.de\", \"description\": \"The effects of statins from ChEBI\", \"name\": \"Statin Graph\", \"version\": \"1.0.0\"}, \"namespace_owl\": {}, \"namespace_pattern\": {}, \"namespace_url\": {\"CHEBI\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20170725.belns\", \"EC\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/enzyme-class/enzyme-class-20170508.belns\", \"HGNC\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc-human-genes/hgnc-human-genes-20170725.belns\"}, \"namespaces_uncached\": [], \"pybel_version\": \"0.11.1-dev\"}, \"links\": [{\"hash\": \"14dd626553df1ae125c978de313a11afa707e2e5a527accaf3ea1b7d7242fb3ce2818b2900fd92defa2262a1aec542de9778652150aad706a42323bafac31fb6\", \"key\": -8, \"relation\": \"isA\", \"source\": 0, \"target\": 1}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"14b72cdba1c29511b19d074bfdfc2d04aaab725dd053a7fba9e24cf46f8a437dae3b1cda2460f5f1af737af04685fd14b040fbf108c920eb3348ba2969648110\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 0, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"8b9b6a3556ef7d51255eae4a593ed01fd9d059d0305fb5cc5049288b72ae0cbfd6890451feded38dc579bc198485868aa738a2931e8ccd681ebd34885b42f795\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 0, \"target\": 8}, {\"hash\": \"4200d91ec97c937fa35e8d5c988c4f086d17251ad8e5b3ba00be062c7ec860f606ea28ee46d15c201806fede16130210bbc62bfa031ec2bc95bac762b50554dd\", \"key\": -8, \"relation\": \"isA\", \"source\": 1, \"target\": 3}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"af0a2208d2feacf5af404739e17505efcc0615c42a978c8c0186951c1dd84292a86bad43709fed88231c98b993de3b7e89de84823cf3401cb27b7abf2054cdff\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 1, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"53da25a8069b924bd2fd8c2022fa9859c9060d86cc667cc39e356fbd503d150b80aed6af822c6fa7acf8f8443d7d38ea621222406cb63ee1a0dbb392955b3cad\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 1, \"target\": 8}, {\"hash\": \"19e39dd153291f9dbe829ab777c3f563e53316f1a28b1a9b95bdb600dc0ac0dea97db607509f7069d7096318fe8ced0d91e2b691f69c52b3a3a0b81ccf4a6dfc\", \"key\": -8, \"relation\": \"isA\", \"source\": 2, \"target\": 1}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"53a82dad88fd27a2f35b6cb4949cf5f4eefd66524173d1a341bb1824bef15f30842196fcb232366a801dd3ee8c610ae320042ca0a2fbe93570fc511b14ad9065\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 2, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"4911e8448f43c2fc825ce4eff18ab79cc013bc0d3e9bc87ddd1e4e82aa1d70e3c90f43c1a6773b30c923bead4681feea28c47e90b3721e439db8e0e15f8397c4\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 2, \"target\": 8}, {\"hash\": \"0e0f72e221a4985d49f204478497d875b8cd2c4c2e53e66c19065d5173947451e8ef9e58970aa9c7476fdd1f51805c6f56964496cd4690c855bb8965c1bcb74e\", \"key\": -8, \"relation\": \"isA\", \"source\": 3, \"target\": 4}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"4a1867872cd2e344709c62018fade0fc46005a76f49afe75f8fa70e31486233f5bc069c73b4093ad0d35394fbaaca435a2ee8222a235646a0ad59b7a4455602a\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 3, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"aa5d5eb91050d0cb83ffd89a29d025fae1b074cc38f76493ac1720322301c64cc1852ea224760d4c4c2f5d05b0631da4f43da8b565f7943366ff57c4d6058b8d\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 3, \"target\": 8}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"ab40c0717f5b5d6f1f0f52e8afbd7ce7f250cd3280bb83ca5b0bac484a35516d3375ffe95da57639a1c63c0277ae033198cd11fab5e86c96790f54a02546c7e5\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 4, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"2d807eb1b224e95cead87d156590f793a3578fae47d9c94df1afc831b61d0e8a97163231286b60f77048dfc5e79e1ffec8d5a9e6f36da2e7f14ea0bc4fc94ba8\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 4, \"target\": 8}, {\"hash\": \"a15a054e36b7e206027e6f0a47a537dcf3c435e80a336ca6177a3ee7ec3d463b6f717206918845d178d18bc63891dd73dec48c8cb4c3ddbd17358a36fac3eaf2\", \"key\": -8, \"relation\": \"isA\", \"source\": 5, \"target\": 4}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"34cf3ed904ef6fba70f2a279e3b9e6c2dc2f02f1ff8de23008274a7d45b3a72b39841d3d2789c15ac081551f2e98ee5d75d1c30ca20ffcd45ba3c1f8706b4852\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"a7e4a8ae586acf60679d212c0acfd9215f921cd2092577e251b0593a15350b01c1036eda6046c650079cf2a3bb03b3e3cfaddbf71d5707e1f84c84bc82693c48\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 8}, {\"hash\": \"cb78df4a181cb1befb2890acd475cb9a55acb93293dd41ee4cd46059c3a5362f6a16a1a338bd1ee8ba442bc50fc01518382bdd696bc7d967b4c41846b4133460\", \"key\": -8, \"relation\": \"isA\", \"source\": 6, \"target\": 7}], \"multigraph\": true, \"nodes\": [{\"cname\": \"atorvastatin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"atorvastatin\"], \"identifier\": \"39548\", \"name\": \"atorvastatin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"statin (synthetic)\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"statin (synthetic)\"], \"identifier\": \"87635\", \"name\": \"statin (synthetic)\", \"namespace\": \"CHEBI\"}, {\"cname\": \"fluvastatin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"fluvastatin\"], \"identifier\": \"38561\", \"name\": \"fluvastatin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"statin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"statin\"], \"identifier\": \"87631\", \"name\": \"statin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \"], \"identifier\": \"35664\", \"name\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"namespace\": \"CHEBI\"}, {\"cname\": \"mevinolinic acid\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"mevinolinic acid\"], \"identifier\": \"82985\", \"name\": \"mevinolinic acid\", \"namespace\": \"CHEBI\"}, {\"cname\": \"HMGCR\", \"function\": \"Protein\", \"id\": [\"Protein\", \"HGNC\", \"HMGCR\"], \"identifier\": \"5006\", \"name\": \"HMGCR\", \"namespace\": \"HGNC\"}, {\"cname\": \"1.1.1.34\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.34\"], \"name\": \"1.1.1.34\", \"namespace\": \"EC\"}, {\"cname\": \"1.1.1.88\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.88\"], \"name\": \"1.1.1.88\", \"namespace\": \"EC\"}]}, \"#mkudpqcofahtyrge\", 1000, 650, {'Protein': '#1F77B4', 'Pathology': '#FF7F0E', 'BiologicalProcess': '#2CA02C', 'miRNA': '#D62728', 'Complex': '#9467bd', 'Composite': '#9467bd', 'Reaction': '#8c564b', 'Gene': '#e377c2', 'Abundance': '#bcbd22', 'RNA': '#17becf'});\n",
       "});"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "infer_child_relations(statin_graph, hmgcr_inhibitor)\n",
    "to_jupyter(statin_graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Propogation on Protein Hierarchy\n",
    "\n",
    "While EC 1.1.1.34 has several proteins across many species annotated in [ExPASy](https://enzyme.expasy.org/EC/1.1.1.34), [HMGCR](https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:5006) is normalized to its HGNC nomenclature and used as the only example in this graph. Since HMGCR is an EC 1.1.1.34, all of the relationships with this enzyme node are transferred below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "function init_d3_force(d3, graph, chart, width, height, function_colors) {\n",
       "    var focus_node = null;\n",
       "    var highlight_node = null;\n",
       "\n",
       "    // Highlight color variables\n",
       "\n",
       "    // Highlight color of the node boundering\n",
       "    const highlight_node_boundering = \"#4EB2D4\";\n",
       "\n",
       "    // Highlight color of the edge\n",
       "    const highlighted_link_color = \"#4EB2D4\";\n",
       "\n",
       "    // Text highlight color\n",
       "    const highlight_text = \"#4EB2D4\";\n",
       "\n",
       "    // Size when zooming scale\n",
       "    var size = d3.scalePow().exponent(1)\n",
       "        .domain([1, 100])\n",
       "        .range([8, 24]);\n",
       "\n",
       "    // Simulation parameters\n",
       "    const linkDistance = 100;\n",
       "    const fCharge = -1000;\n",
       "    const linkStrength = 0.7;\n",
       "    const collideStrength = 1;\n",
       "\n",
       "    // Simulation defined with variables\n",
       "    var simulation = d3.forceSimulation()\n",
       "        .force(\"link\", d3.forceLink()\n",
       "            .distance(linkDistance)\n",
       "            .strength(linkStrength)\n",
       "        )\n",
       "        .force(\"collide\", d3.forceCollide()\n",
       "            .radius(function (d) {\n",
       "                return d.r + 10\n",
       "            })\n",
       "            .strength(collideStrength)\n",
       "        )\n",
       "        .force(\"charge\", d3.forceManyBody()\n",
       "            .strength(fCharge)\n",
       "        )\n",
       "        .force(\"center\", d3.forceCenter(width / 2, height / 2))\n",
       "        .force(\"y\", d3.forceY(0))\n",
       "        .force(\"x\", d3.forceX(0));\n",
       "\n",
       "    // Pin down functionality\n",
       "    var node_drag = d3.drag()\n",
       "        .on(\"start\", dragstarted)\n",
       "        .on(\"drag\", dragged)\n",
       "        .on(\"end\", dragended);\n",
       "\n",
       "    function dragstarted(d) {\n",
       "        if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n",
       "        d.fx = d.x;\n",
       "        d.fy = d.y;\n",
       "    }\n",
       "\n",
       "    function dragged(d) {\n",
       "        d.fx = d3.event.x;\n",
       "        d.fy = d3.event.y;\n",
       "    }\n",
       "\n",
       "    function dragended(d) {\n",
       "        if (!d3.event.active) simulation.alphaTarget(0);\n",
       "    }\n",
       "\n",
       "    function releasenode(d) {\n",
       "        d.fx = null;\n",
       "        d.fy = null;\n",
       "    }\n",
       "\n",
       "    //END Pin down functionality\n",
       "\n",
       "    const color_circunferencia = \"black\";\n",
       "    const default_link_color = \"#AAAAAA\";\n",
       "    const nominal_base_node_size = 8;\n",
       "\n",
       "    // Normal and highlighted stroke of the links (double the width of the link when highlighted)\n",
       "    const nominal_stroke = 1.5;\n",
       "\n",
       "    // Zoom variables\n",
       "    const min_zoom = 0.1;\n",
       "    const max_zoom = 10;\n",
       "    const border = 1;\n",
       "    const bordercolor = 'black';\n",
       "\n",
       "    var svg = d3.select(chart).append(\"svg\")\n",
       "        .attr(\"width\", width)\n",
       "        .attr(\"height\", height);\n",
       "\n",
       "    // // Create definition for arrowhead.\n",
       "    svg.append(\"defs\").append(\"marker\")\n",
       "        .attr(\"id\", \"arrowhead\")\n",
       "        .attr(\"viewBox\", \"0 -5 10 10\")\n",
       "        .attr(\"refX\", 20)\n",
       "        .attr(\"refY\", 0)\n",
       "        .attr(\"markerUnits\", \"strokeWidth\")\n",
       "        .attr(\"markerWidth\", 6)\n",
       "        .attr(\"markerHeight\", 6)\n",
       "        .attr(\"orient\", \"auto\")\n",
       "        .append(\"path\")\n",
       "        .attr(\"d\", \"M0,-5L10,0L0,5\");\n",
       "\n",
       "    // // Create definition for stub.\n",
       "    svg.append(\"defs\").append(\"marker\")\n",
       "        .attr(\"id\", \"stub\")\n",
       "        .attr(\"viewBox\", \"-1 -5 2 10\")\n",
       "        .attr(\"refX\", 15)\n",
       "        .attr(\"refY\", 0)\n",
       "        .attr(\"markerUnits\", \"strokeWidth\")\n",
       "        .attr(\"markerWidth\", 6)\n",
       "        .attr(\"markerHeight\", 6)\n",
       "        .attr(\"orient\", \"auto\")\n",
       "        .append(\"path\")\n",
       "        .attr(\"d\", \"M 0,0 m -1,-5 L 1,-5 L 1,5 L -1,5 Z\");\n",
       "\n",
       "    // Background\n",
       "    svg.append(\"rect\")\n",
       "        .attr(\"width\", \"100%\")\n",
       "        .attr(\"height\", \"100%\")\n",
       "        .attr(\"fill\", \"#ffffff\")\n",
       "        .style(\"pointer-events\", \"all\")\n",
       "        // Zoom + panning functionality\n",
       "        .call(d3.zoom()\n",
       "            .scaleExtent([min_zoom, max_zoom])\n",
       "            .on(\"zoom\", zoomed))\n",
       "        .on(\"dblclick.zoom\", null);\n",
       "\n",
       "\n",
       "    function zoomed() {\n",
       "        g.attr(\"transform\", d3.event.transform);\n",
       "    }\n",
       "\n",
       "    // g = svg object where the graph will be appended\n",
       "    var g = svg.append(\"g\");\n",
       "\n",
       "    var linkedByIndex = {};\n",
       "    graph.links.forEach(function (d) {\n",
       "        linkedByIndex[d.source + \",\" + d.target] = true;\n",
       "    });\n",
       "\n",
       "    function isConnected(a, b) {\n",
       "        return linkedByIndex[a.index + \",\" + b.index] || linkedByIndex[b.index + \",\" + a.index] || a.index == b.index;\n",
       "    }\n",
       "\n",
       "    function ticked() {\n",
       "        link.attr(\"x1\", function (d) {\n",
       "            return d.source.x;\n",
       "        })\n",
       "            .attr(\"y1\", function (d) {\n",
       "                return d.source.y;\n",
       "            })\n",
       "            .attr(\"x2\", function (d) {\n",
       "                return d.target.x;\n",
       "            })\n",
       "            .attr(\"y2\", function (d) {\n",
       "                return d.target.y;\n",
       "            });\n",
       "\n",
       "        node\n",
       "            .attr(\"transform\", function (d) {\n",
       "                return \"translate(\" + d.x + \", \" + d.y + \")\";\n",
       "            });\n",
       "    }\n",
       "\n",
       "\n",
       "    simulation\n",
       "        .nodes(graph.nodes)\n",
       "        .on(\"tick\", ticked);\n",
       "\n",
       "    simulation.force(\"link\")\n",
       "        .links(graph.links);\n",
       "\n",
       "    // Definition of links nodes text...\n",
       "\n",
       "    var link = g.selectAll(\".link\")\n",
       "        .data(graph.links)\n",
       "        .enter().append(\"line\")\n",
       "        .style(\"stroke-width\", nominal_stroke)\n",
       "        .style(\"stroke\", default_link_color)\n",
       "        .style(\"stroke-dasharray\", function (d) {\n",
       "            if (['decreases', 'directlyDecreases', 'increases', 'directlyIncreases', 'negativeCorrelation',\n",
       "                    'positiveCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"none\"\n",
       "            } else {\n",
       "                return \"4, 4\"\n",
       "            }\n",
       "        })\n",
       "        .attr(\"marker-start\", function (d) {\n",
       "            if ('positiveCorrelation' == d.relation) {\n",
       "                return \"url(#arrowhead)\"\n",
       "            }\n",
       "            else if ('negativeCorrelation' == d.relation) {\n",
       "                return \"url(#stub)\"\n",
       "            }\n",
       "            else {\n",
       "                return \"\"\n",
       "            }\n",
       "        })\n",
       "        .attr(\"marker-end\", function (d) {\n",
       "            if (['increases', 'directlyIncreases', 'positiveCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"url(#arrowhead)\"\n",
       "            } else if (['decreases', 'directlyDecreases', 'negativeCorrelation'].indexOf(d.relation) >= 0) {\n",
       "                return \"url(#stub)\"\n",
       "            } else {\n",
       "                return \"\"\n",
       "            }\n",
       "        });\n",
       "\n",
       "    var node = g.selectAll(\".nodes\")\n",
       "        .data(graph.nodes)\n",
       "        .enter().append(\"g\")\n",
       "        .attr(\"class\", \"node\")\n",
       "        // Next two lines -> Pin down functionality\n",
       "        .on('dblclick', releasenode)\n",
       "        .call(node_drag);\n",
       "\n",
       "    var circle = node.append(\"path\")\n",
       "        .attr(\"d\", d3.symbol()\n",
       "            .size(function (d) {\n",
       "                return Math.PI * Math.pow(size(d.size) || nominal_base_node_size, 2);\n",
       "            })\n",
       "        )\n",
       "        .attr(\"class\", function (d) {\n",
       "            return d.function\n",
       "        })\n",
       "        .style('fill', function (d) {\n",
       "            return function_colors[d.function]\n",
       "        })\n",
       "        .style(\"stroke-width\", nominal_stroke)\n",
       "        .style(\"stroke\", color_circunferencia);\n",
       "\n",
       "    var text = node.append(\"text\")\n",
       "        .attr(\"class\", \"node-name\")\n",
       "        // .attr(\"id\", nodehashes[d])\n",
       "        .attr(\"fill\", \"black\")\n",
       "        .attr(\"dx\", 12)\n",
       "        .attr(\"dy\", \".35em\")\n",
       "        .text(function (d) {\n",
       "            return d.cname\n",
       "        });\n",
       "\n",
       "    // Highlight on mouseenter and back to normal on mouseout\n",
       "    node.on(\"mouseenter\", function (d) {\n",
       "        set_highlight(d);\n",
       "    })\n",
       "        .on(\"mousedown\", function () {\n",
       "            d3.event.stopPropagation();\n",
       "        }).on(\"mouseout\", function () {\n",
       "        exit_highlight();\n",
       "    });\n",
       "\n",
       "    function exit_highlight() {\n",
       "        highlight_node = null;\n",
       "        if (focus_node === null) {\n",
       "            if (highlight_node_boundering != color_circunferencia) {\n",
       "                circle.style(\"stroke\", color_circunferencia);\n",
       "                text.style(\"fill\", \"black\");\n",
       "                link.style(\"stroke\", default_link_color);\n",
       "            }\n",
       "        }\n",
       "    }\n",
       "\n",
       "    function set_highlight(d) {\n",
       "        if (focus_node !== null) d = focus_node;\n",
       "        highlight_node = d;\n",
       "\n",
       "        if (highlight_node_boundering != color_circunferencia) {\n",
       "            circle.style(\"stroke\", function (o) {\n",
       "                return isConnected(d, o) ? highlight_node_boundering : color_circunferencia;\n",
       "            });\n",
       "            text.style(\"fill\", function (o) {\n",
       "                return isConnected(d, o) ? highlight_text : \"black\";\n",
       "            });\n",
       "            link.style(\"stroke\", function (o) {\n",
       "                return o.source.index == d.index || o.target.index == d.index ? highlighted_link_color : default_link_color;\n",
       "            });\n",
       "        }\n",
       "    }\n",
       "\n",
       "\n",
       "    // Freeze the graph when space is pressed\n",
       "    function freezeGraph() {\n",
       "        // Space button Triggers STOP\n",
       "        if (d3.event.keyCode == 32) {\n",
       "            simulation.stop();\n",
       "        }\n",
       "    }\n",
       "\n",
       "    // Call freezeGraph when a key is pressed, freezeGraph checks whether this key is \"Space\" that triggers the freeze\n",
       "    d3.select(window).on(\"keydown\", freezeGraph);\n",
       "}\n",
       "\n",
       "require.config({\n",
       "    paths: {\n",
       "        d3: '//cdnjs.cloudflare.com/ajax/libs/d3/4.5.0/d3.min'\n",
       "    }\n",
       "});\n",
       "\n",
       "var elementInnerHTML = \"<div id='dtzjxqobeyqvgrmp'></div>\";\n",
       "\n",
       "element.append(elementInnerHTML);\n",
       "\n",
       "require(['d3'], function (d3) {\n",
       "    return init_d3_force(d3, {\"directed\": true, \"graph\": {\"annotation_list\": {}, \"annotation_owl\": {}, \"annotation_pattern\": {}, \"annotation_url\": {\"Confidence\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/confidence/confidence-1.0.0.belanno\"}, \"document_metadata\": {\"authors\": \"Charles Tapley Hoyt\", \"contact\": \"charles.hoyt@scai.fraunhofer.de\", \"description\": \"The effects of statins from ChEBI\", \"name\": \"Statin Graph\", \"version\": \"1.0.0\"}, \"namespace_owl\": {}, \"namespace_pattern\": {}, \"namespace_url\": {\"CHEBI\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20170725.belns\", \"EC\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/enzyme-class/enzyme-class-20170508.belns\", \"HGNC\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc-human-genes/hgnc-human-genes-20170725.belns\"}, \"namespaces_uncached\": [], \"pybel_version\": \"0.11.1-dev\"}, \"links\": [{\"hash\": 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\"source\": 0, \"target\": 8}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"acbfff05732cf55f4c7815009f60454cc90fb970e624cfaffe2599c794f45a849fbfea3a454e07d67d8efb1f0be61b0252034f21c7a88dc5a3ae9f2577a64a97\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 0, \"target\": 6}, {\"hash\": \"4200d91ec97c937fa35e8d5c988c4f086d17251ad8e5b3ba00be062c7ec860f606ea28ee46d15c201806fede16130210bbc62bfa031ec2bc95bac762b50554dd\", \"key\": -8, \"relation\": \"isA\", \"source\": 1, \"target\": 3}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"af0a2208d2feacf5af404739e17505efcc0615c42a978c8c0186951c1dd84292a86bad43709fed88231c98b993de3b7e89de84823cf3401cb27b7abf2054cdff\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 1, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"53da25a8069b924bd2fd8c2022fa9859c9060d86cc667cc39e356fbd503d150b80aed6af822c6fa7acf8f8443d7d38ea621222406cb63ee1a0dbb392955b3cad\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 1, \"target\": 8}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"69a93e4914e0ea728b19427a1a676c1fdc12a278b84d8e2762163d842a24be276604c08c91f89b3921d0fbcef9757a5de6a0923cacf6271acca776ac454e661f\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 1, \"target\": 6}, {\"hash\": 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\"source\": 2, \"target\": 8}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"553200a065978db1e1d36aed7b6c733f72cc688b0af1133f8d680c3496cac3780fdab03c81f23f28b3b08eb05403a8484b238d0d398574e7d293cfe9f19c5e52\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 2, \"target\": 6}, {\"hash\": \"0e0f72e221a4985d49f204478497d875b8cd2c4c2e53e66c19065d5173947451e8ef9e58970aa9c7476fdd1f51805c6f56964496cd4690c855bb8965c1bcb74e\", \"key\": -8, \"relation\": \"isA\", \"source\": 3, \"target\": 4}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"4a1867872cd2e344709c62018fade0fc46005a76f49afe75f8fa70e31486233f5bc069c73b4093ad0d35394fbaaca435a2ee8222a235646a0ad59b7a4455602a\", \"key\": 0, \"object\": {\"modifier\": 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\"f3fc1eaf22bc8c34eff5898fced506e2ca45ef12e1bd386ae90ea960cbfa877070921f0ac1200052f9bc83fee4d4d0c585f9c45bda9227a1416226bde334110f\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 4, \"target\": 6}, {\"hash\": \"a15a054e36b7e206027e6f0a47a537dcf3c435e80a336ca6177a3ee7ec3d463b6f717206918845d178d18bc63891dd73dec48c8cb4c3ddbd17358a36fac3eaf2\", \"key\": -8, \"relation\": \"isA\", \"source\": 5, \"target\": 4}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"34cf3ed904ef6fba70f2a279e3b9e6c2dc2f02f1ff8de23008274a7d45b3a72b39841d3d2789c15ac081551f2e98ee5d75d1c30ca20ffcd45ba3c1f8706b4852\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 7}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"a7e4a8ae586acf60679d212c0acfd9215f921cd2092577e251b0593a15350b01c1036eda6046c650079cf2a3bb03b3e3cfaddbf71d5707e1f84c84bc82693c48\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 8}, {\"annotations\": {\"Confidence\": {\"Axiomatic\": true}}, \"citation\": {\"reference\": \"23180789\", \"type\": \"PubMed\"}, \"evidence\": \"From ChEBI\", \"hash\": \"a5d9772f465a45bb224253e23e4b131e32e35096da61cdf8c29d6d44e5a7d5a130cda4720b8eef05a9a77133bff90833b2600be3f75d275c30edf10293da8efc\", \"key\": 0, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 6}, {\"hash\": \"cb78df4a181cb1befb2890acd475cb9a55acb93293dd41ee4cd46059c3a5362f6a16a1a338bd1ee8ba442bc50fc01518382bdd696bc7d967b4c41846b4133460\", \"key\": -8, \"relation\": \"isA\", \"source\": 6, \"target\": 7}], \"multigraph\": true, \"nodes\": [{\"cname\": \"atorvastatin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"atorvastatin\"], \"identifier\": \"39548\", \"name\": \"atorvastatin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"statin (synthetic)\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"statin (synthetic)\"], \"identifier\": \"87635\", \"name\": \"statin (synthetic)\", \"namespace\": \"CHEBI\"}, {\"cname\": \"fluvastatin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"fluvastatin\"], \"identifier\": \"38561\", \"name\": \"fluvastatin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"statin\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"statin\"], \"identifier\": \"87631\", \"name\": \"statin\", \"namespace\": \"CHEBI\"}, {\"cname\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \"], \"identifier\": \"35664\", \"name\": \"EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor \", \"namespace\": \"CHEBI\"}, {\"cname\": \"mevinolinic acid\", \"function\": \"Abundance\", \"id\": [\"Abundance\", \"CHEBI\", \"mevinolinic acid\"], \"identifier\": \"82985\", \"name\": \"mevinolinic acid\", \"namespace\": \"CHEBI\"}, {\"cname\": \"HMGCR\", \"function\": \"Protein\", \"id\": [\"Protein\", \"HGNC\", \"HMGCR\"], \"identifier\": \"5006\", \"name\": \"HMGCR\", \"namespace\": \"HGNC\"}, {\"cname\": \"1.1.1.34\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.34\"], \"name\": \"1.1.1.34\", \"namespace\": \"EC\"}, {\"cname\": \"1.1.1.88\", \"function\": \"Protein\", \"id\": [\"Protein\", \"EC\", \"1.1.1.88\"], \"name\": \"1.1.1.88\", \"namespace\": \"EC\"}]}, \"#dtzjxqobeyqvgrmp\", 1000, 650, {'Protein': '#1F77B4', 'Pathology': '#FF7F0E', 'BiologicalProcess': '#2CA02C', 'miRNA': '#D62728', 'Complex': '#9467bd', 'Composite': '#9467bd', 'Reaction': '#8c564b', 'Gene': '#e377c2', 'Abundance': '#bcbd22', 'RNA': '#17becf'});\n",
       "});"
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     },
     "execution_count": 8,
     "metadata": {},
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   ],
   "source": [
    "infer_child_relations(statin_graph, ec_11134)\n",
    "to_jupyter(statin_graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Discussion\n",
    "\n",
    "The simple interface provided by the [`infer_child_relations`](infer_child_relations) function allows for graphs to be completed.\n",
    "\n",
    "Another possibility is to propogate relationships the other direction through hierarchies. Sometimes, it might be reasonable to guess that a property of an invididual might be true for its parent as well, and then even also true for its siblings."
   ]
  }
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