{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# CellCollective Knowledge Base\n",
    "\n",
    "Models from [CellCollective.org](https://cellcollective.org) can be directly imported by CoLoMoTo tools (such as `bioLQM` or `Pint`) by giving their URL as the argument of the ``.load`` function, for instance, ``lqm = biolqm.load(\"https://cellcollective.org/#2329/apoptosis-network\")``.\n",
    "\n",
    "In this notebook, we show how to use the API of the `cellcollective` python module to access metadata of network species, such as UnitProt and NCBI gene identifiers."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import cellcollective"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Model loading from cellcollective.org\n",
    "\n",
    "A CellCollective model can be imported using its URL on https://cellcollective.org.\n",
    "Alternatively, you can also use \"cellcollective://MODEL_ID\" syntax."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "Downloading http://api.cellcollective.org/model/export/2329?type=SBML"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sbml = cellcollective.load(\"https://cellcollective.org/#2329/apoptosis-network\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The cellcollective python module supports basic access to the SBML-qual file, including the list of defined qualitative species:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'A20',\n",
       " 'AKT',\n",
       " 'APC',\n",
       " 'Apaf1',\n",
       " 'Apoptosis',\n",
       " 'BAD',\n",
       " 'BID',\n",
       " 'BclX',\n",
       " 'Cas12',\n",
       " 'Cas3',\n",
       " 'Cas6',\n",
       " 'Cas7',\n",
       " 'Cas8',\n",
       " 'Cas9',\n",
       " 'DNADamageEvent',\n",
       " 'FADD',\n",
       " 'GF',\n",
       " 'GFR',\n",
       " 'IAP',\n",
       " 'IKK',\n",
       " 'IkB',\n",
       " 'JNK',\n",
       " 'JNKK',\n",
       " 'MEKK1',\n",
       " 'Mdm2',\n",
       " 'Mito',\n",
       " 'NFkB',\n",
       " 'NIK',\n",
       " 'PI3K',\n",
       " 'PIP2',\n",
       " 'PIP3',\n",
       " 'PTEN',\n",
       " 'RIP',\n",
       " 'TNF',\n",
       " 'TNFR1',\n",
       " 'TNFR2',\n",
       " 'TRADD',\n",
       " 'TRAF',\n",
       " 'TRAF2',\n",
       " 'cFLIP',\n",
       " 'p53'}"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sbml.species"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Access metadata\n",
    "\n",
    "In most models on CellCollective, authors attached to nodes several metadata, including identifiers of biological species:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'UniProtID': 'P42574', 'GeneName': 'CASP3', 'NCBIGeneID': '836'}"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sbml.species_metadata(\"Cas3\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The link to UnitProt knowledge or NCBI gene database can be obtained as follows:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "[https://www.uniprot.org/uniprot/P42574](https://www.uniprot.org/uniprot/P42574)"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sbml.species_uniprotkb(\"Cas3\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "[https://www.ncbi.nlm.nih.gov/gene/836](https://www.ncbi.nlm.nih.gov/gene/836)"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sbml.species_ncbi_gene(\"Cas3\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There exists several python interfaces to programmatically query information from these databases:\n",
    "- using NBCI Gene ID: https://github.com/biocommons/eutils\n",
    "- using UniProt ID: https://github.com/jdrudolph/uniprot"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Convert to bioLQM for model analysis\n",
    "\n",
    "Finally, a CellCollective model can be imported in the `bioLQM` tool, for further processing, such as dynamical analysis and simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "lqm = cellcollective.to_biolqm(sbml)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'A20',\n",
       " 'AKT',\n",
       " 'APC',\n",
       " 'Apaf1',\n",
       " 'Apoptosis',\n",
       " 'BAD',\n",
       " 'BID',\n",
       " 'BclX',\n",
       " 'Cas12',\n",
       " 'Cas3',\n",
       " 'Cas6',\n",
       " 'Cas7',\n",
       " 'Cas8',\n",
       " 'Cas9',\n",
       " 'DNADamageEvent',\n",
       " 'FADD',\n",
       " 'GF',\n",
       " 'GFR',\n",
       " 'IAP',\n",
       " 'IKK',\n",
       " 'IkB',\n",
       " 'JNK',\n",
       " 'JNKK',\n",
       " 'MEKK1',\n",
       " 'Mdm2',\n",
       " 'Mito',\n",
       " 'NFkB',\n",
       " 'NIK',\n",
       " 'PI3K',\n",
       " 'PIP2',\n",
       " 'PIP3',\n",
       " 'PTEN',\n",
       " 'RIP',\n",
       " 'TNF',\n",
       " 'TNFR1',\n",
       " 'TNFR2',\n",
       " 'TRADD',\n",
       " 'TRAF',\n",
       " 'TRAF2',\n",
       " 'cFLIP',\n",
       " 'p53'}"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "set([str(c) for c in lqm.getComponents()])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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