ITMP_COVID_KG.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "04f60936",
   "metadata": {},
   "outputs": [],
   "source": [
    "#pip install httplib2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ee5b920",
   "metadata": {},
   "outputs": [],
   "source": [
    "import httplib2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "faa7efb5",
   "metadata": {},
   "outputs": [],
   "source": [
    "import re\n",
    "import pybel\n",
    "from pybel.io.jupyter import to_jupyter\n",
    "from utils import *\n",
    "import seaborn as sns\n",
    "from kg_gen_3 import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6b327410",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_chem = pd.read_csv('C:\\\\Users\\\\reagon.karki\\\\Documents\\\\ITMP\\\\EOSC Future\\\\ITMP ChEMBL data\\\\CHEMBL4303805.csv',sep=';',usecols=['ChEMBL ID'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cfc7793f",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_chem = list(itmp_chem['ChEMBL ID'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "de9ca28f",
   "metadata": {},
   "outputs": [],
   "source": [
    "len(itmp_chem)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6b0c3d74",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_dis = RetDrugInd(itmp_chem)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8fdab82a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/itmp_drugInd.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(itmp_dis,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9f113052",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_mech = RetMech(itmp_chem)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "448f3551",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/itmp_mech.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(itmp_mech,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e3677996",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_act = RetAct_pchem_5(itmp_chem)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "22838552",
   "metadata": {},
   "outputs": [],
   "source": [
    "len(itmp_act)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11f4b7f1",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/itmp_act.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(itmp_act,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4835429b",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/itmp_mech.pkl','rb')\n",
    "itmp_mech = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "24c359dd",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/itmp_drugInd.pkl','rb')\n",
    "itmp_dis = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e1efd720",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/itmp_act.pkl','rb')\n",
    "itmp_act = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4a12ad1f",
   "metadata": {},
   "outputs": [],
   "source": [
    "prot_actMech = Ret_chembl_protein(itmp_act) + Ret_chembl_protein(itmp_mech)\n",
    "prot_actMech = set(prot_actMech)\n",
    "prot_actMech = list(prot_actMech)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b1117409",
   "metadata": {},
   "outputs": [],
   "source": [
    "actMech2uprot = chembl2uniprot(prot_actMech)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "58ab1a12",
   "metadata": {},
   "outputs": [],
   "source": [
    "uprot = Ret_uprotid(actMech2uprot)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "47c8a207",
   "metadata": {},
   "outputs": [],
   "source": [
    "uprot_ext = ExtractFromUniProt(uprot)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4234aa92",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/uprot.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(uprot_ext,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bc2ec5ed",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/uprot.pkl','rb')\n",
    "uprot_ext = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7e70a959",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_act"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "946b4744",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_act = chembl2gene2path(actMech2uprot,itmp_act)\n",
    "itmp_mech = chembl2gene2path(actMech2uprot,itmp_mech)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2b9cb155",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_graph = pybel.BELGraph(name='ITMP Graph 2024', version=\"0.0.1\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f78da6ea",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_graph = chem2moa_rel(itmp_mech,'HGNC',itmp_graph)\n",
    "itmp_graph = chem2dis_rel(itmp_dis,itmp_graph)\n",
    "itmp_graph = chem2act_rel(itmp_act,'HGNC',itmp_graph)\n",
    "itmp_graph = gene2path_rel(actMech2uprot,'HGNC',itmp_graph)\n",
    "itmp_graph = uniprot_rel(uprot_ext,'HGNC',itmp_graph)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "247a26e0",
   "metadata": {},
   "outputs": [],
   "source": [
    "advEvent = GetAdverseEvents(itmp_chem)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a40fe569",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/sideEffects.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(advEvent,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "292bdc7b",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_graph = chembl2adverseEffect_rel(advEvent,itmp_graph)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cfd91368",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/itmpGraph.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(itmp_graph,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "68452cce",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/covid19_kg_2024.pkl','rb')\n",
    "covidkg = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a1dddfb2",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/itmpGraph.pkl','rb')\n",
    "itmp_graph = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b444a4e9",
   "metadata": {},
   "outputs": [],
   "source": [
    "covidkg.summarize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "48bc6025",
   "metadata": {},
   "outputs": [],
   "source": [
    "itmp_graph.summarize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "62e5599c",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi = pd.read_csv('data/kgs/viral_diseases/covid19_kg_2024/covid_ppi.txt',sep='\\t')\n",
    "len(cvd_ppi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "42ec5b68",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "71e6bbc6",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "cvd_ppi.head(50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ef6c8916",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi = cvd_ppi[cvd_ppi['# ID(s) interactor A'].str.contains(\"uniprotkb\")]\n",
    "cvd_ppi = cvd_ppi[cvd_ppi['ID(s) interactor B'].str.contains(\"uniprotkb\")]\n",
    "cvd_ppi = cvd_ppi[cvd_ppi['Taxid interactor A'].str.contains(\"9606|2697049\")]\n",
    "cvd_ppi = cvd_ppi[cvd_ppi['Taxid interactor B'].str.contains(\"9606|2697049\")]\n",
    "\n",
    "int_a = cvd_ppi['# ID(s) interactor A']\n",
    "temp = []\n",
    "for item in int_a:\n",
    "    prot = item.split(':')[1]\n",
    "    #print(prot)\n",
    "    temp.append(prot)\n",
    "    #break\n",
    "    \n",
    "int_b = cvd_ppi['ID(s) interactor B']\n",
    "temp_2 = []\n",
    "for item in int_b:\n",
    "    prot = item.split(':')[1]\n",
    "    #print(prot)\n",
    "    temp_2.append(prot)\n",
    "    \n",
    "cvd_ppi['Int_A'] = temp\n",
    "cvd_ppi['Int_B'] = temp_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a876d17d",
   "metadata": {},
   "outputs": [],
   "source": [
    "int_a = cvd_ppi['# ID(s) interactor A']\n",
    "temp = []\n",
    "for item in int_a:\n",
    "    prot = item.split(':')[1]\n",
    "    #print(prot)\n",
    "    temp.append(prot)\n",
    "    #break\n",
    "    \n",
    "int_b = cvd_ppi['ID(s) interactor B']\n",
    "temp_2 = []\n",
    "for item in int_b:\n",
    "    prot = item.split(':')[1]\n",
    "    #print(prot)\n",
    "    temp_2.append(prot)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "24b244d1",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi['Int_A'] = temp\n",
    "cvd_ppi['Int_B'] = temp_2\n",
    "len(cvd_ppi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bb0a05c7",
   "metadata": {},
   "outputs": [],
   "source": [
    "temp = []\n",
    "for tax in cvd_ppi['Taxid interactor A']:\n",
    "    if '9606' in tax:\n",
    "        temp.append('HGNC')\n",
    "    else:\n",
    "        temp.append('VP')\n",
    "        \n",
    "temp_2 = []\n",
    "for tax in cvd_ppi['Taxid interactor B']:\n",
    "    if '9606' in tax:\n",
    "        temp_2.append('HGNC')\n",
    "    else:\n",
    "        temp_2.append('VP')\n",
    "        \n",
    "cvd_ppi['Species_A'] = temp\n",
    "cvd_ppi['Species_B'] = temp_2\n",
    "\n",
    "cvd_ppi = cvd_ppi.reset_index(drop=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "463fe8cf",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "len(cvd_ppi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "533a7d43",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fa9a8f78",
   "metadata": {},
   "outputs": [],
   "source": [
    "xx = ExtractFromUniProt(list(set(cvd_ppi['Int_A'])))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c9abe93c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/Ext_uprot_Int_A.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(xx,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "be48c800",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/Ext_uprot_Int_A.pkl','rb')\n",
    "xx = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2768fdc8",
   "metadata": {},
   "outputs": [],
   "source": [
    "xx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d6505053",
   "metadata": {},
   "outputs": [],
   "source": [
    "xx['Q53F19']['Gene']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "45857580",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi['Int_A']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "74785f1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "temp = []\n",
    "for uprot in cvd_ppi['Int_A']:\n",
    "    \n",
    "    getProt = ExtractFromUniProt([uprot])\n",
    "    if getProt[uprot]['Gene']:\n",
    "        temp.append(getProt[uprot]['Gene'])\n",
    "    else:\n",
    "        temp.append(uprot)    \n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cb45333e",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi['Gene_A'] = temp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "116b9102",
   "metadata": {},
   "outputs": [],
   "source": [
    "temp = []\n",
    "for uprot in cvd_ppi['Int_B']:\n",
    "    \n",
    "    getProt = ExtractFromUniProt([uprot])\n",
    "    if getProt[uprot]['Gene']:\n",
    "        temp.append(getProt[uprot]['Gene'])\n",
    "    else:\n",
    "        temp.append(uprot)    \n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "81c96792",
   "metadata": {},
   "outputs": [],
   "source": [
    "len(temp)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "695c9ca7",
   "metadata": {},
   "outputs": [],
   "source": [
    "cvd_ppi['Gene_B'] = temp\n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1a296b00",
   "metadata": {},
   "outputs": [],
   "source": [
    "def check_response(response):\n",
    "    try:\n",
    "        #print(response.raise_for_status())\n",
    "        response.raise_for_status()\n",
    "    except requests.HTTPError:\n",
    "        print(response.json())\n",
    "        raise\n",
    "        \n",
    "POLLING_INTERVAL = 5\n",
    "def check_id_mapping_results_ready(job_id):\n",
    "    while True:\n",
    "        \n",
    "        API_URL = \"https://rest.uniprot.org\"\n",
    "        session = requests.Session()\n",
    "        request = session.get(f\"{API_URL}/idmapping/status/{job_id}\")\n",
    "        check_response(request)\n",
    "        j = request.json()\n",
    "        if \"jobStatus\" in j:\n",
    "            if j[\"jobStatus\"] == \"RUNNING\":\n",
    "                print(f\"Retrying in {POLLING_INTERVAL}s\")\n",
    "                time.sleep(POLLING_INTERVAL)\n",
    "            else:\n",
    "                raise Exception(j[\"jobStatus\"])\n",
    "        else:\n",
    "            return bool(j[\"results\"] or j[\"failedIds\"])\n",
    "        \n",
    "def get_id_mapping_results_link(job_id):\n",
    "    API_URL = \"https://rest.uniprot.org\"\n",
    "    session = requests.Session()\n",
    "    url = f\"{API_URL}/idmapping/details/{job_id}\"\n",
    "    request = session.get(url)\n",
    "    return(request)\n",
    "    check_response(request)\n",
    "    return request.json()[\"redirectURL\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f3747c93",
   "metadata": {},
   "outputs": [],
   "source": [
    "def prot2crossRefDB(prot_list):\n",
    "    \n",
    "    import requests\n",
    "    \n",
    "    final_list = []\n",
    "    \n",
    "    for prot in tqdm(prot_list,desc='Fetching Cross-referenced DB ids'):\n",
    "        \n",
    "        #print(prot)\n",
    "        temp_list = []\n",
    "        \n",
    "        temp_list.append(prot)\n",
    "        \n",
    "        files = {\n",
    "        'from': (None, 'Gene_Name'),\n",
    "        'to': (None, 'UniProtKB-Swiss-Prot'),\n",
    "        'ids': (None, prot),\n",
    "        'taxId': (None, '9606'),\n",
    "        }\n",
    "    \n",
    "        response = requests.post('https://rest.uniprot.org/idmapping/run', files=files)\n",
    "        \n",
    "        response = response.json()\n",
    "        \n",
    "        job_id = response['jobId']\n",
    "        \n",
    "        #print(job_id)\n",
    "        \n",
    "#         try:\n",
    "#             output = get_id_mapping_results_link(job_id)\n",
    "            \n",
    "#         except: \n",
    "#             output = get_id_mapping_results_link(job_id)\n",
    "        \n",
    "        API_URL = \"https://rest.uniprot.org\"\n",
    "        session = requests.Session()\n",
    "        url = f\"{API_URL}/idmapping/details/{job_id}\"\n",
    "        \n",
    "        check_job = check_id_mapping_results_ready(job_id)\n",
    "        #print(check_job)\n",
    "        \n",
    "        \n",
    "        request = session.get(url)\n",
    "        \n",
    "        #time.sleep(3)\n",
    "        check_response(request)\n",
    "        #print(check_response)\n",
    "        #print(request.json())\n",
    "\n",
    "        output= request.json()[\"redirectURL\"]\n",
    "        \n",
    "\n",
    "        response = requests.get(output)\n",
    "        \n",
    "        response = response.json()\n",
    "        \n",
    "        if response['results']: \n",
    "        \n",
    "        #print(response)\n",
    "        \n",
    "            uprot = response['results'][0]['to']['primaryAccession']\n",
    "\n",
    "            temp_list.append(uprot)\n",
    "\n",
    "            uniProtkbId = response['results'][0]['to']['uniProtkbId'] \n",
    "            organism = response['results'][0]['to']['organism']['scientificName']\n",
    "\n",
    "            #get all crossRef DBs\n",
    "            crossRefs = response['results'][0]['to']['uniProtKBCrossReferences']\n",
    "\n",
    "            db_list = []\n",
    "            for item in crossRefs:\n",
    "\n",
    "                db_list.append(item['database'])\n",
    "\n",
    "\n",
    "            if 'OpenTargets' in db_list:\n",
    "                getIndex = db_list.index('OpenTargets')\n",
    "                temp_list.append(crossRefs[getIndex]['id'])\n",
    "\n",
    "            else:\n",
    "                temp_list.append('None')\n",
    "\n",
    "\n",
    "            if 'ChEMBL' in db_list:\n",
    "                getIndex = db_list.index('ChEMBL')\n",
    "                temp_list.append(crossRefs[getIndex]['id'])\n",
    "\n",
    "            else:\n",
    "                temp_list.append('None')\n",
    "\n",
    "\n",
    "            if 'HGNC' in db_list:\n",
    "                getIndex = db_list.index('HGNC')\n",
    "                temp_list.append(crossRefs[getIndex]['id'])\n",
    "\n",
    "            else:\n",
    "                temp_list.append('None')\n",
    "\n",
    "            temp_list.append(uniProtkbId)\n",
    "            temp_list.append(organism)\n",
    "\n",
    "            #print(temp_list)\n",
    "\n",
    "            final_list.append(temp_list)\n",
    "        \n",
    "        #print(final_list)\n",
    "        \n",
    "    cols = ['Protein','UniProt','ENSG','ChEMBL','HGNC','uniProtkbId','Organism']\n",
    "    \n",
    "    df= pd.DataFrame(final_list,columns=cols)             \n",
    "        \n",
    "    return(df)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a6e86127",
   "metadata": {},
   "outputs": [],
   "source": [
    "aa = get_id_mapping_results_link('59be157c25c1815efedf04e3561e0b6335de7add')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1659eeff",
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_9606 = pd.read_excel('data/misc/uniprotkb_taxonomy_id_9606_AND_reviewed_2024_06_20.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2bbcd133",
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_9606.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "56967aa3",
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_list = ['IGFBP3',\n",
    " 'IL13RA2',\n",
    " 'MAGEA4',\n",
    " 'LGALS1',\n",
    " 'CA9',\n",
    " 'CD74',\n",
    " 'S100A6',\n",
    " 'CD44',\n",
    " 'LINC01029',\n",
    " 'FN1',\n",
    " 'TGFBI',\n",
    " 'PAGE5',\n",
    " 'ANXA1',\n",
    " 'SLC14A1',\n",
    " 'GPRC5A',\n",
    " 'S100A16',\n",
    " 'ITGB4',\n",
    " 'TM4SF1',\n",
    " 'LAMB1',\n",
    " 'PRAME',\n",
    " 'PRRX1',\n",
    " 'TGFA',\n",
    " 'ERBB3',\n",
    " 'LTBR',\n",
    " 'CAVIN1',\n",
    " 'MAGEC2',\n",
    " 'CSPG4',\n",
    " 'LINC01419',\n",
    " 'FOSL1']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "77945a35",
   "metadata": {},
   "outputs": [],
   "source": [
    "genes = list(gene_9606['Gene Names'])\n",
    "genes = [x for x in genes if str(x) != 'nan']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "126e1b84",
   "metadata": {},
   "outputs": [],
   "source": [
    "#xx = prot2crossRefDB(list(cvd_ppi['Int_A']))\n",
    "#xx = prot2crossRefDB(['TNF','SNCA'])\n",
    "xx = prot2crossRefDB(genes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c88d52e7",
   "metadata": {},
   "outputs": [],
   "source": [
    "xx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fb29ad26",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "cvd_ppi.to_csv('data/kgs/viral_diseases/covid19_kg_2024/cvd_ppi.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "355faf8b",
   "metadata": {},
   "outputs": [],
   "source": [
    "merged_kg = nx.compose(itmp_graph,covidkg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d029103e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# filename = ('data/kgs/viral_diseases/covid19_kg_2024/covidKG_itmpChem_Graph.pkl')\n",
    "# outfile = open(filename,'wb')\n",
    "# pickle.dump(merged_kg,outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "56452f70",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile = open('data/kgs/viral_diseases/covid19_kg_2024/covidKG_itmpChem_Graph.pkl','rb')\n",
    "merged_kg = pickle.load(infile)\n",
    "infile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "53d73311",
   "metadata": {},
   "outputs": [],
   "source": [
    "def getProtfromKG(mainGraph):\n",
    "\n",
    "    prot_list = []\n",
    "    for u, v, data in tqdm(mainGraph.edges(data=True),desc='Filtering Proteins/Genes'):\n",
    "        \n",
    "        if 'VP' in u.namespace:\n",
    "            if u.name not in prot_list:\n",
    "                prot_list.append(u.name)\n",
    "\n",
    "        if 'VP' in v.namespace:\n",
    "            if v.name not in prot_list:\n",
    "                prot_list.append(v.name)\n",
    "                \n",
    "    return(prot_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "816aebc1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "1204b9ae832f45c0a60c2cfa41e20753",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Filtering Proteins/Genes:   0%|          | 0/438112 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "vp = getProtfromKG(merged_kg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "80430177",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['rep',\n",
       " 'N',\n",
       " 'P0DTC1',\n",
       " 'S',\n",
       " 'P0DTC3',\n",
       " 'E',\n",
       " 'P0DTC5',\n",
       " 'P0DTC8',\n",
       " 'P0DTD2',\n",
       " 'P0DTC6',\n",
       " 'P0DTC7',\n",
       " 'P0DTF1']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "648c27d4",
   "metadata": {},
   "outputs": [],
   "source": [
    "ppi_final = pd.read_csv('data/kgs/viral_diseases/covid19_kg_2024/ppi_final.csv',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "5d5823aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "score = ppi_final['Confidence value(s)']\n",
    "temp = []\n",
    "# for item in score:\n",
    "    \n",
    "#     x = float(item.split(':')[1])\n",
    "    \n",
    "temp = [float(x.split(':')[1]) for x in score ]    \n",
    "\n",
    "ppi_final['score'] = temp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "4a3cddf1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th># ID(s) interactor A</th>\n",
       "      <th>ID(s) interactor B</th>\n",
       "      <th>Alt. ID(s) interactor A</th>\n",
       "      <th>Alt. ID(s) interactor B</th>\n",
       "      <th>Alias(es) interactor A</th>\n",
       "      <th>Alias(es) interactor B</th>\n",
       "      <th>Interaction detection method(s)</th>\n",
       "      <th>Publication 1st author(s)</th>\n",
       "      <th>Publication Identifier(s)</th>\n",
       "      <th>Taxid interactor A</th>\n",
       "      <th>...</th>\n",
       "      <th>Source database(s)</th>\n",
       "      <th>Interaction identifier(s)</th>\n",
       "      <th>Confidence value(s)</th>\n",
       "      <th>Int_A</th>\n",
       "      <th>Int_B</th>\n",
       "      <th>Species_A</th>\n",
       "      <th>Species_B</th>\n",
       "      <th>Int_A_Gene</th>\n",
       "      <th>Int_B_Gene</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>uniprotkb:Q53F19</td>\n",
       "      <td>uniprotkb:P50395</td>\n",
       "      <td>uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...</td>\n",
       "      <td>uniprotkb:Q5SX88|uniprotkb:O43928|uniprotkb:Q9...</td>\n",
       "      <td>psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:gdib_human(display_short)|psi-mi:Rab GD...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623276|imex:IM-26480-1</td>\n",
       "      <td>intact-miscore:0.35</td>\n",
       "      <td>Q53F19</td>\n",
       "      <td>P50395</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP3</td>\n",
       "      <td>GDI2</td>\n",
       "      <td>0.35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>uniprotkb:Q53F19</td>\n",
       "      <td>uniprotkb:P51148</td>\n",
       "      <td>uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...</td>\n",
       "      <td>intact:EBI-21355794|intact:EBI-2798296|uniprot...</td>\n",
       "      <td>psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:rab5c_human(display_short)|psi-mi:Ras-r...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623276|imex:IM-26480-1</td>\n",
       "      <td>intact-miscore:0.35</td>\n",
       "      <td>Q53F19</td>\n",
       "      <td>P51148</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP3</td>\n",
       "      <td>RAB5C</td>\n",
       "      <td>0.35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>uniprotkb:Q53F19</td>\n",
       "      <td>uniprotkb:Q6I9Y2</td>\n",
       "      <td>uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...</td>\n",
       "      <td>uniprotkb:Q6P1L3|uniprotkb:Q8WUF2|uniprotkb:Q9...</td>\n",
       "      <td>psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:thoc7_human(display_short)|psi-mi:THO c...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623276|imex:IM-26480-1</td>\n",
       "      <td>intact-miscore:0.64</td>\n",
       "      <td>Q53F19</td>\n",
       "      <td>Q6I9Y2</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP3</td>\n",
       "      <td>THOC7</td>\n",
       "      <td>0.64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>uniprotkb:Q53F19</td>\n",
       "      <td>uniprotkb:P38919</td>\n",
       "      <td>uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...</td>\n",
       "      <td>intact:EBI-21354615|uniprotkb:Q15033|uniprotkb...</td>\n",
       "      <td>psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:if4a3_human(display_short)|psi-mi:Eukar...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623276|imex:IM-26480-1</td>\n",
       "      <td>intact-miscore:0.53</td>\n",
       "      <td>Q53F19</td>\n",
       "      <td>P38919</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP3</td>\n",
       "      <td>EIF4A3</td>\n",
       "      <td>0.53</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>uniprotkb:Q53F19</td>\n",
       "      <td>uniprotkb:Q96FV9</td>\n",
       "      <td>uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...</td>\n",
       "      <td>intact:EBI-28984554|uniprotkb:B2RBP6|uniprotkb...</td>\n",
       "      <td>psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:thoc1_human(display_short)|psi-mi:THO c...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623276|imex:IM-26480-1</td>\n",
       "      <td>intact-miscore:0.64</td>\n",
       "      <td>Q53F19</td>\n",
       "      <td>Q96FV9</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP3</td>\n",
       "      <td>THOC1</td>\n",
       "      <td>0.64</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 22 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  # ID(s) interactor A ID(s) interactor B  \\\n",
       "0     uniprotkb:Q53F19   uniprotkb:P50395   \n",
       "1     uniprotkb:Q53F19   uniprotkb:P51148   \n",
       "2     uniprotkb:Q53F19   uniprotkb:Q6I9Y2   \n",
       "3     uniprotkb:Q53F19   uniprotkb:P38919   \n",
       "4     uniprotkb:Q53F19   uniprotkb:Q96FV9   \n",
       "\n",
       "                             Alt. ID(s) interactor A  \\\n",
       "0  uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...   \n",
       "1  uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...   \n",
       "2  uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...   \n",
       "3  uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...   \n",
       "4  uniprotkb:Q9NXZ4|uniprotkb:B3KWG7|uniprotkb:Q9...   \n",
       "\n",
       "                             Alt. ID(s) interactor B  \\\n",
       "0  uniprotkb:Q5SX88|uniprotkb:O43928|uniprotkb:Q9...   \n",
       "1  intact:EBI-21355794|intact:EBI-2798296|uniprot...   \n",
       "2  uniprotkb:Q6P1L3|uniprotkb:Q8WUF2|uniprotkb:Q9...   \n",
       "3  intact:EBI-21354615|uniprotkb:Q15033|uniprotkb...   \n",
       "4  intact:EBI-28984554|uniprotkb:B2RBP6|uniprotkb...   \n",
       "\n",
       "                              Alias(es) interactor A  \\\n",
       "0  psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...   \n",
       "1  psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...   \n",
       "2  psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...   \n",
       "3  psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...   \n",
       "4  psi-mi:ncbp3_human(display_short)|psi-mi:Nucle...   \n",
       "\n",
       "                              Alias(es) interactor B  \\\n",
       "0  psi-mi:gdib_human(display_short)|psi-mi:Rab GD...   \n",
       "1  psi-mi:rab5c_human(display_short)|psi-mi:Ras-r...   \n",
       "2  psi-mi:thoc7_human(display_short)|psi-mi:THO c...   \n",
       "3  psi-mi:if4a3_human(display_short)|psi-mi:Eukar...   \n",
       "4  psi-mi:thoc1_human(display_short)|psi-mi:THO c...   \n",
       "\n",
       "  Interaction detection method(s) Publication 1st author(s)  \\\n",
       "0     psi-mi:\"MI:0096\"(pull down)  Gebhardt A. et al.(2015)   \n",
       "1     psi-mi:\"MI:0096\"(pull down)  Gebhardt A. et al.(2015)   \n",
       "2     psi-mi:\"MI:0096\"(pull down)  Gebhardt A. et al.(2015)   \n",
       "3     psi-mi:\"MI:0096\"(pull down)  Gebhardt A. et al.(2015)   \n",
       "4     psi-mi:\"MI:0096\"(pull down)  Gebhardt A. et al.(2015)   \n",
       "\n",
       "                           Publication Identifier(s)  \\\n",
       "0  intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "1  intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "2  intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "3  intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "4  intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "\n",
       "                           Taxid interactor A  ...  \\\n",
       "0  taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "1  taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "2  taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "3  taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "4  taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "\n",
       "                                  Source database(s)  \\\n",
       "0  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "1  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "2  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "3  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "4  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "\n",
       "             Interaction identifier(s)  Confidence value(s)   Int_A   Int_B  \\\n",
       "0  intact:EBI-20623276|imex:IM-26480-1  intact-miscore:0.35  Q53F19  P50395   \n",
       "1  intact:EBI-20623276|imex:IM-26480-1  intact-miscore:0.35  Q53F19  P51148   \n",
       "2  intact:EBI-20623276|imex:IM-26480-1  intact-miscore:0.64  Q53F19  Q6I9Y2   \n",
       "3  intact:EBI-20623276|imex:IM-26480-1  intact-miscore:0.53  Q53F19  P38919   \n",
       "4  intact:EBI-20623276|imex:IM-26480-1  intact-miscore:0.64  Q53F19  Q96FV9   \n",
       "\n",
       "  Species_A Species_B Int_A_Gene Int_B_Gene score  \n",
       "0      HGNC      HGNC      NCBP3       GDI2  0.35  \n",
       "1      HGNC      HGNC      NCBP3      RAB5C  0.35  \n",
       "2      HGNC      HGNC      NCBP3      THOC7  0.64  \n",
       "3      HGNC      HGNC      NCBP3     EIF4A3  0.53  \n",
       "4      HGNC      HGNC      NCBP3      THOC1  0.64  \n",
       "\n",
       "[5 rows x 22 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ppi_final.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "fb5e7256",
   "metadata": {},
   "outputs": [],
   "source": [
    "ppi_final = ppi_final[ppi_final['score'] >= 0.8]\n",
    "ppi_final = ppi_final.reset_index(drop=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "b000b8ff",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th># ID(s) interactor A</th>\n",
       "      <th>ID(s) interactor B</th>\n",
       "      <th>Alt. ID(s) interactor A</th>\n",
       "      <th>Alt. ID(s) interactor B</th>\n",
       "      <th>Alias(es) interactor A</th>\n",
       "      <th>Alias(es) interactor B</th>\n",
       "      <th>Interaction detection method(s)</th>\n",
       "      <th>Publication 1st author(s)</th>\n",
       "      <th>Publication Identifier(s)</th>\n",
       "      <th>Taxid interactor A</th>\n",
       "      <th>...</th>\n",
       "      <th>Source database(s)</th>\n",
       "      <th>Interaction identifier(s)</th>\n",
       "      <th>Confidence value(s)</th>\n",
       "      <th>Int_A</th>\n",
       "      <th>Int_B</th>\n",
       "      <th>Species_A</th>\n",
       "      <th>Species_B</th>\n",
       "      <th>Int_A_Gene</th>\n",
       "      <th>Int_B_Gene</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>uniprotkb:P52298</td>\n",
       "      <td>uniprotkb:Q09161</td>\n",
       "      <td>uniprotkb:E9PAR5|uniprotkb:Q14924|uniprotkb:Q2...</td>\n",
       "      <td>uniprotkb:Q59G76|uniprotkb:Q5T1V0|uniprotkb:B2...</td>\n",
       "      <td>psi-mi:ncbp2_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:ncbp1_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623424|imex:IM-26480-7</td>\n",
       "      <td>intact-miscore:0.96</td>\n",
       "      <td>P52298</td>\n",
       "      <td>Q09161</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP2</td>\n",
       "      <td>NCBP1</td>\n",
       "      <td>0.96</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>uniprotkb:P52298</td>\n",
       "      <td>uniprotkb:Q09161</td>\n",
       "      <td>uniprotkb:E9PAR5|uniprotkb:Q14924|uniprotkb:Q2...</td>\n",
       "      <td>uniprotkb:Q59G76|uniprotkb:Q5T1V0|uniprotkb:B2...</td>\n",
       "      <td>psi-mi:ncbp2_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:ncbp1_human(display_short)|psi-mi:Nucle...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Gebhardt A. et al.(2015)</td>\n",
       "      <td>intact:EBI-20623177|pubmed:26382858|imex:IM-26480</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-20623690|imex:IM-26480-3</td>\n",
       "      <td>intact-miscore:0.96</td>\n",
       "      <td>P52298</td>\n",
       "      <td>Q09161</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>NCBP2</td>\n",
       "      <td>NCBP1</td>\n",
       "      <td>0.96</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>uniprotkb:Q14155</td>\n",
       "      <td>uniprotkb:Q14160</td>\n",
       "      <td>intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...</td>\n",
       "      <td>uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...</td>\n",
       "      <td>psi-mi:arhg7_human(display_short)|psi-mi:Rho g...</td>\n",
       "      <td>psi-mi:scrib_human(display_short)|psi-mi:Prote...</td>\n",
       "      <td>psi-mi:\"MI:0084\"(phage display)</td>\n",
       "      <td>Ivarsson Y. et al.(2014)</td>\n",
       "      <td>intact:EBI-11668009|pubmed:24550280|imex:IM-25074</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...</td>\n",
       "      <td>intact:EBI-11791066|imex:IM-25074-2</td>\n",
       "      <td>intact-miscore:0.94</td>\n",
       "      <td>Q14155</td>\n",
       "      <td>Q14160</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>ARHGEF7</td>\n",
       "      <td>SCRIB</td>\n",
       "      <td>0.94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>uniprotkb:Q14160</td>\n",
       "      <td>uniprotkb:Q14155</td>\n",
       "      <td>uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...</td>\n",
       "      <td>intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...</td>\n",
       "      <td>psi-mi:scrib_human(display_short)|psi-mi:Prote...</td>\n",
       "      <td>psi-mi:arhg7_human(display_short)|psi-mi:Rho g...</td>\n",
       "      <td>psi-mi:\"MI:0084\"(phage display)</td>\n",
       "      <td>Ivarsson Y. et al.(2014)</td>\n",
       "      <td>intact:EBI-11668009|pubmed:24550280|imex:IM-25074</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...</td>\n",
       "      <td>intact:EBI-11791897|imex:IM-25074-150</td>\n",
       "      <td>intact-miscore:0.94</td>\n",
       "      <td>Q14160</td>\n",
       "      <td>Q14155</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>SCRIB</td>\n",
       "      <td>ARHGEF7</td>\n",
       "      <td>0.94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>uniprotkb:Q14160</td>\n",
       "      <td>uniprotkb:Q14155</td>\n",
       "      <td>uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...</td>\n",
       "      <td>intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...</td>\n",
       "      <td>psi-mi:scrib_human(display_short)|psi-mi:Prote...</td>\n",
       "      <td>psi-mi:arhg7_human(display_short)|psi-mi:Rho g...</td>\n",
       "      <td>psi-mi:\"MI:0084\"(phage display)</td>\n",
       "      <td>Ivarsson Y. et al.(2014)</td>\n",
       "      <td>intact:EBI-11668009|pubmed:24550280|imex:IM-25074</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...</td>\n",
       "      <td>intact:EBI-11791933|imex:IM-25074-90</td>\n",
       "      <td>intact-miscore:0.94</td>\n",
       "      <td>Q14160</td>\n",
       "      <td>Q14155</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>SCRIB</td>\n",
       "      <td>ARHGEF7</td>\n",
       "      <td>0.94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>650</th>\n",
       "      <td>uniprotkb:O94826</td>\n",
       "      <td>uniprotkb:P0DTD2</td>\n",
       "      <td>uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...</td>\n",
       "      <td>intact:EBI-25475909|uniprotkb:P0DTD2</td>\n",
       "      <td>psi-mi:tom70_human(display_short)|psi-mi:Mitoc...</td>\n",
       "      <td>psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Brandherm L. et al.(2021)</td>\n",
       "      <td>intact:EBI-27088033|pubmed:34502139|imex:IM-29236</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-27091279|imex:IM-29236-1</td>\n",
       "      <td>intact-miscore:0.98</td>\n",
       "      <td>O94826</td>\n",
       "      <td>P0DTD2</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>VP</td>\n",
       "      <td>TOMM70</td>\n",
       "      <td>9b</td>\n",
       "      <td>0.98</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>651</th>\n",
       "      <td>uniprotkb:O94826</td>\n",
       "      <td>uniprotkb:P0DTD2</td>\n",
       "      <td>uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...</td>\n",
       "      <td>intact:EBI-25475909|uniprotkb:P0DTD2</td>\n",
       "      <td>psi-mi:tom70_human(display_short)|psi-mi:Mitoc...</td>\n",
       "      <td>psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...</td>\n",
       "      <td>psi-mi:\"MI:0096\"(pull down)</td>\n",
       "      <td>Brandherm L. et al.(2021)</td>\n",
       "      <td>intact:EBI-27088033|pubmed:34502139|imex:IM-29236</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-27091375|imex:IM-29236-9</td>\n",
       "      <td>intact-miscore:0.98</td>\n",
       "      <td>O94826</td>\n",
       "      <td>P0DTD2</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>VP</td>\n",
       "      <td>TOMM70</td>\n",
       "      <td>9b</td>\n",
       "      <td>0.98</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>652</th>\n",
       "      <td>uniprotkb:O94826</td>\n",
       "      <td>uniprotkb:P0DTD2</td>\n",
       "      <td>uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...</td>\n",
       "      <td>intact:EBI-25475909|uniprotkb:P0DTD2</td>\n",
       "      <td>psi-mi:tom70_human(display_short)|psi-mi:Mitoc...</td>\n",
       "      <td>psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...</td>\n",
       "      <td>psi-mi:\"MI:0605\"(enzymatic footprinting)</td>\n",
       "      <td>Brandherm L. et al.(2021)</td>\n",
       "      <td>intact:EBI-27088033|pubmed:34502139|imex:IM-29236</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-27091406|imex:IM-29236-11</td>\n",
       "      <td>intact-miscore:0.98</td>\n",
       "      <td>O94826</td>\n",
       "      <td>P0DTD2</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>VP</td>\n",
       "      <td>TOMM70</td>\n",
       "      <td>9b</td>\n",
       "      <td>0.98</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>653</th>\n",
       "      <td>uniprotkb:Q9BYF1</td>\n",
       "      <td>uniprotkb:P0DTC2</td>\n",
       "      <td>intact:EBI-25767352|intact:MINT-4538816|intact...</td>\n",
       "      <td>intact:EBI-25474821|uniprotkb:P0DTC2</td>\n",
       "      <td>psi-mi:ace2_human(display_short)|psi-mi:Angiot...</td>\n",
       "      <td>psi-mi:spike_sars2(display_short)|psi-mi:Spike...</td>\n",
       "      <td>psi-mi:\"MI:0107\"(surface plasmon resonance)</td>\n",
       "      <td>Raghu D. et al.(2021)</td>\n",
       "      <td>intact:EBI-27091493|pubmed:34545316|imex:IM-29240</td>\n",
       "      <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0469\"(European Bioinformatics Insti...</td>\n",
       "      <td>intact:EBI-27092998|imex:IM-29240-1</td>\n",
       "      <td>intact-miscore:1.0</td>\n",
       "      <td>Q9BYF1</td>\n",
       "      <td>P0DTC2</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>VP</td>\n",
       "      <td>ACE2</td>\n",
       "      <td>S</td>\n",
       "      <td>1.00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>654</th>\n",
       "      <td>uniprotkb:P0DTC9</td>\n",
       "      <td>uniprotkb:Q13283</td>\n",
       "      <td>intact:EBI-25475856|uniprotkb:P0DTC9</td>\n",
       "      <td>intact:EBI-1384154|uniprotkb:Q5HYE9|ensembl:EN...</td>\n",
       "      <td>psi-mi:ncap_sars2(display_short)|psi-mi:Nucleo...</td>\n",
       "      <td>psi-mi:g3bp1_human(display_short)|psi-mi:Ras G...</td>\n",
       "      <td>psi-mi:\"MI:0397\"(two hybrid array)</td>\n",
       "      <td>Zhou Y. et al.(2022)</td>\n",
       "      <td>intact:EBI-36481508|doi:10.1038/s41587-022-014...</td>\n",
       "      <td>taxid:2697049(SARS-CoV-2)|taxid:2697049(SARS-C...</td>\n",
       "      <td>...</td>\n",
       "      <td>psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...</td>\n",
       "      <td>intact:EBI-40234275|imex:IM-29592-596</td>\n",
       "      <td>intact-miscore:0.98</td>\n",
       "      <td>P0DTC9</td>\n",
       "      <td>Q13283</td>\n",
       "      <td>VP</td>\n",
       "      <td>HGNC</td>\n",
       "      <td>N</td>\n",
       "      <td>G3BP1</td>\n",
       "      <td>0.98</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>655 rows × 22 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    # ID(s) interactor A ID(s) interactor B  \\\n",
       "0       uniprotkb:P52298   uniprotkb:Q09161   \n",
       "1       uniprotkb:P52298   uniprotkb:Q09161   \n",
       "2       uniprotkb:Q14155   uniprotkb:Q14160   \n",
       "3       uniprotkb:Q14160   uniprotkb:Q14155   \n",
       "4       uniprotkb:Q14160   uniprotkb:Q14155   \n",
       "..                   ...                ...   \n",
       "650     uniprotkb:O94826   uniprotkb:P0DTD2   \n",
       "651     uniprotkb:O94826   uniprotkb:P0DTD2   \n",
       "652     uniprotkb:O94826   uniprotkb:P0DTD2   \n",
       "653     uniprotkb:Q9BYF1   uniprotkb:P0DTC2   \n",
       "654     uniprotkb:P0DTC9   uniprotkb:Q13283   \n",
       "\n",
       "                               Alt. ID(s) interactor A  \\\n",
       "0    uniprotkb:E9PAR5|uniprotkb:Q14924|uniprotkb:Q2...   \n",
       "1    uniprotkb:E9PAR5|uniprotkb:Q14924|uniprotkb:Q2...   \n",
       "2    intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...   \n",
       "3    uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...   \n",
       "4    uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...   \n",
       "..                                                 ...   \n",
       "650  uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...   \n",
       "651  uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...   \n",
       "652  uniprotkb:D3DN48|ensembl:ENSP00000284320.5|int...   \n",
       "653  intact:EBI-25767352|intact:MINT-4538816|intact...   \n",
       "654               intact:EBI-25475856|uniprotkb:P0DTC9   \n",
       "\n",
       "                               Alt. ID(s) interactor B  \\\n",
       "0    uniprotkb:Q59G76|uniprotkb:Q5T1V0|uniprotkb:B2...   \n",
       "1    uniprotkb:Q59G76|uniprotkb:Q5T1V0|uniprotkb:B2...   \n",
       "2    uniprotkb:Q6P496|uniprotkb:Q7Z5D1|uniprotkb:Q8...   \n",
       "3    intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...   \n",
       "4    intact:EBI-25643109|uniprotkb:B1ALK6|uniprotkb...   \n",
       "..                                                 ...   \n",
       "650               intact:EBI-25475909|uniprotkb:P0DTD2   \n",
       "651               intact:EBI-25475909|uniprotkb:P0DTD2   \n",
       "652               intact:EBI-25475909|uniprotkb:P0DTD2   \n",
       "653               intact:EBI-25474821|uniprotkb:P0DTC2   \n",
       "654  intact:EBI-1384154|uniprotkb:Q5HYE9|ensembl:EN...   \n",
       "\n",
       "                                Alias(es) interactor A  \\\n",
       "0    psi-mi:ncbp2_human(display_short)|psi-mi:Nucle...   \n",
       "1    psi-mi:ncbp2_human(display_short)|psi-mi:Nucle...   \n",
       "2    psi-mi:arhg7_human(display_short)|psi-mi:Rho g...   \n",
       "3    psi-mi:scrib_human(display_short)|psi-mi:Prote...   \n",
       "4    psi-mi:scrib_human(display_short)|psi-mi:Prote...   \n",
       "..                                                 ...   \n",
       "650  psi-mi:tom70_human(display_short)|psi-mi:Mitoc...   \n",
       "651  psi-mi:tom70_human(display_short)|psi-mi:Mitoc...   \n",
       "652  psi-mi:tom70_human(display_short)|psi-mi:Mitoc...   \n",
       "653  psi-mi:ace2_human(display_short)|psi-mi:Angiot...   \n",
       "654  psi-mi:ncap_sars2(display_short)|psi-mi:Nucleo...   \n",
       "\n",
       "                                Alias(es) interactor B  \\\n",
       "0    psi-mi:ncbp1_human(display_short)|psi-mi:Nucle...   \n",
       "1    psi-mi:ncbp1_human(display_short)|psi-mi:Nucle...   \n",
       "2    psi-mi:scrib_human(display_short)|psi-mi:Prote...   \n",
       "3    psi-mi:arhg7_human(display_short)|psi-mi:Rho g...   \n",
       "4    psi-mi:arhg7_human(display_short)|psi-mi:Rho g...   \n",
       "..                                                 ...   \n",
       "650  psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...   \n",
       "651  psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...   \n",
       "652  psi-mi:orf9b_sars2(display_short)|psi-mi:ORF9b...   \n",
       "653  psi-mi:spike_sars2(display_short)|psi-mi:Spike...   \n",
       "654  psi-mi:g3bp1_human(display_short)|psi-mi:Ras G...   \n",
       "\n",
       "                 Interaction detection method(s)  Publication 1st author(s)  \\\n",
       "0                    psi-mi:\"MI:0096\"(pull down)   Gebhardt A. et al.(2015)   \n",
       "1                    psi-mi:\"MI:0096\"(pull down)   Gebhardt A. et al.(2015)   \n",
       "2                psi-mi:\"MI:0084\"(phage display)   Ivarsson Y. et al.(2014)   \n",
       "3                psi-mi:\"MI:0084\"(phage display)   Ivarsson Y. et al.(2014)   \n",
       "4                psi-mi:\"MI:0084\"(phage display)   Ivarsson Y. et al.(2014)   \n",
       "..                                           ...                        ...   \n",
       "650                  psi-mi:\"MI:0096\"(pull down)  Brandherm L. et al.(2021)   \n",
       "651                  psi-mi:\"MI:0096\"(pull down)  Brandherm L. et al.(2021)   \n",
       "652     psi-mi:\"MI:0605\"(enzymatic footprinting)  Brandherm L. et al.(2021)   \n",
       "653  psi-mi:\"MI:0107\"(surface plasmon resonance)      Raghu D. et al.(2021)   \n",
       "654           psi-mi:\"MI:0397\"(two hybrid array)       Zhou Y. et al.(2022)   \n",
       "\n",
       "                             Publication Identifier(s)  \\\n",
       "0    intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "1    intact:EBI-20623177|pubmed:26382858|imex:IM-26480   \n",
       "2    intact:EBI-11668009|pubmed:24550280|imex:IM-25074   \n",
       "3    intact:EBI-11668009|pubmed:24550280|imex:IM-25074   \n",
       "4    intact:EBI-11668009|pubmed:24550280|imex:IM-25074   \n",
       "..                                                 ...   \n",
       "650  intact:EBI-27088033|pubmed:34502139|imex:IM-29236   \n",
       "651  intact:EBI-27088033|pubmed:34502139|imex:IM-29236   \n",
       "652  intact:EBI-27088033|pubmed:34502139|imex:IM-29236   \n",
       "653  intact:EBI-27091493|pubmed:34545316|imex:IM-29240   \n",
       "654  intact:EBI-36481508|doi:10.1038/s41587-022-014...   \n",
       "\n",
       "                                    Taxid interactor A  ...  \\\n",
       "0           taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "1           taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "2           taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "3           taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "4           taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "..                                                 ...  ...   \n",
       "650         taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "651         taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "652         taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "653         taxid:9606(human)|taxid:9606(Homo sapiens)  ...   \n",
       "654  taxid:2697049(SARS-CoV-2)|taxid:2697049(SARS-C...  ...   \n",
       "\n",
       "                                    Source database(s)  \\\n",
       "0    psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "1    psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "2    psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...   \n",
       "3    psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...   \n",
       "4    psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...   \n",
       "..                                                 ...   \n",
       "650  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "651  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "652  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "653  psi-mi:\"MI:0469\"(European Bioinformatics Insti...   \n",
       "654  psi-mi:\"MI:0471\"(MINT, Dpt of Biology, Univers...   \n",
       "\n",
       "                 Interaction identifier(s)  Confidence value(s)   Int_A  \\\n",
       "0      intact:EBI-20623424|imex:IM-26480-7  intact-miscore:0.96  P52298   \n",
       "1      intact:EBI-20623690|imex:IM-26480-3  intact-miscore:0.96  P52298   \n",
       "2      intact:EBI-11791066|imex:IM-25074-2  intact-miscore:0.94  Q14155   \n",
       "3    intact:EBI-11791897|imex:IM-25074-150  intact-miscore:0.94  Q14160   \n",
       "4     intact:EBI-11791933|imex:IM-25074-90  intact-miscore:0.94  Q14160   \n",
       "..                                     ...                  ...     ...   \n",
       "650    intact:EBI-27091279|imex:IM-29236-1  intact-miscore:0.98  O94826   \n",
       "651    intact:EBI-27091375|imex:IM-29236-9  intact-miscore:0.98  O94826   \n",
       "652   intact:EBI-27091406|imex:IM-29236-11  intact-miscore:0.98  O94826   \n",
       "653    intact:EBI-27092998|imex:IM-29240-1   intact-miscore:1.0  Q9BYF1   \n",
       "654  intact:EBI-40234275|imex:IM-29592-596  intact-miscore:0.98  P0DTC9   \n",
       "\n",
       "      Int_B Species_A Species_B Int_A_Gene Int_B_Gene score  \n",
       "0    Q09161      HGNC      HGNC      NCBP2      NCBP1  0.96  \n",
       "1    Q09161      HGNC      HGNC      NCBP2      NCBP1  0.96  \n",
       "2    Q14160      HGNC      HGNC    ARHGEF7      SCRIB  0.94  \n",
       "3    Q14155      HGNC      HGNC      SCRIB    ARHGEF7  0.94  \n",
       "4    Q14155      HGNC      HGNC      SCRIB    ARHGEF7  0.94  \n",
       "..      ...       ...       ...        ...        ...   ...  \n",
       "650  P0DTD2      HGNC        VP     TOMM70         9b  0.98  \n",
       "651  P0DTD2      HGNC        VP     TOMM70         9b  0.98  \n",
       "652  P0DTD2      HGNC        VP     TOMM70         9b  0.98  \n",
       "653  P0DTC2      HGNC        VP       ACE2          S  1.00  \n",
       "654  Q13283        VP      HGNC          N      G3BP1  0.98  \n",
       "\n",
       "[655 rows x 22 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ppi_final"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "ab88850a",
   "metadata": {},
   "outputs": [],
   "source": [
    "ppi_kg = pybel.BELGraph(name='COVID19 PPIs', version=\"0.0.1\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0119c097",
   "metadata": {},
   "outputs": [],
   "source": [
    "bb = 'intact:EBI-20623177|pubmed:26382858|imex:IM-26480'\n",
    "\n",
    "import re\n",
    "\n",
    "#Check if the string starts with \"The\" and ends with \"Spain\":\n",
    "\n",
    "evidence = re.search(\"pubmed:[0-9]+\", bb)\n",
    "x = x.group()\n",
    "x\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "a13d3729",
   "metadata": {},
   "outputs": [],
   "source": [
    "def ppi_rel(ppi_df,\n",
    "    proteinList,\n",
    "    graph: BELGraph\n",
    ") -> BELGraph:\n",
    "    \"\"\"Method to add PPI relations to the KG\n",
    "\n",
    "    :param PPIs with 2 columns as proteins and 2 columns as organism abbreviation i.e. HGNC \n",
    "    :param Protein list from KG\n",
    "    :param graph:\n",
    "    :return:\n",
    "    \"\"\"\n",
    "    \n",
    "    \n",
    "    for prot_a, prot_b, uprot_a, uprot_b, sp_a, sp_b, pubmed in zip(ppi_df['Int_A_Gene'],ppi_df['Int_B_Gene'],ppi_df['Int_A'],\n",
    "                             ppi_df['Int_B'],ppi_df['Species_A'],ppi_df['Species_B'],ppi_df['Publication Identifier(s)']):\n",
    "        \n",
    "        \n",
    "        #regex to extract pubmedid \n",
    "    \n",
    "        evidence = re.search(\"pubmed:[0-9]*\", pubmed)\n",
    "        evidence = evidence.group()\n",
    "        #print(evidence)\n",
    "        \n",
    "        #condition 1\n",
    "        if sp_a == 'HGNC' and sp_b == 'HGNC':\n",
    "    \n",
    "            graph.add_association(\n",
    "            Protein(namespace=sp_a, name=prot_a),\n",
    "            Protein(namespace=sp_b, name=prot_b),\n",
    "            citation = 'IntAct',\n",
    "            evidence = evidence\n",
    "            )\n",
    "        \n",
    "        #condition 2\n",
    "        if sp_a == 'HGNC' and sp_b == 'VP':\n",
    "            \n",
    "            if prot_b in proteinList:\n",
    "    \n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=prot_a),\n",
    "                Protein(namespace=sp_b, name=prot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "            if prot_b not in proteinList:\n",
    "                \n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=prot_a),\n",
    "                Protein(namespace=sp_b, name=uprot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "          \n",
    "        #condition 3\n",
    "        if sp_a == 'VP' and sp_b == 'HGNC':\n",
    "            \n",
    "            if prot_a in proteinList:\n",
    "    \n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=prot_a),\n",
    "                Protein(namespace=sp_b, name=prot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "            if prot_a not in proteinList:\n",
    "                \n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=uprot_a),\n",
    "                Protein(namespace=sp_b, name=prot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "    \n",
    "        #condition 4\n",
    "        if sp_a == 'VP' and sp_b == 'VP':\n",
    "            \n",
    "            if prot_a in proteinList and prot_b in proteinList:\n",
    "\n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=prot_a),\n",
    "                Protein(namespace=sp_b, name=prot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "            if prot_a not in proteinList and prot_b not in proteinList:\n",
    "\n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=uprot_a),\n",
    "                Protein(namespace=sp_b, name=uprot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "                        \n",
    "            if prot_a in proteinList and prot_b not in proteinList:\n",
    "\n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=prot_a),\n",
    "                Protein(namespace=sp_b, name=uprot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "            if prot_a not in proteinList and prot_b  in proteinList:\n",
    "\n",
    "                graph.add_association(\n",
    "                Protein(namespace=sp_a, name=uprot_a),\n",
    "                Protein(namespace=sp_b, name=prot_b),\n",
    "                citation = 'IntAct',\n",
    "                evidence = evidence\n",
    "                )\n",
    "            \n",
    "    return graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "2d5f275e",
   "metadata": {},
   "outputs": [],
   "source": [
    "xx = ppi_rel(ppi_final,vp,ppi_kg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "86ae689e",
   "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",
       "\n",
       "    /**\n",
       "     * Gets the best name for a node object\n",
       "     * @param {object} d object\n",
       "     * @returns {str} canonical name of the node\n",
       "     */\n",
       "    function getCanonicalName(d) {\n",
       "        if (d.concept && d.concept.name && !(d.variants || d.reactants || d.products || d.members)) {\n",
       "            return d.concept.name\n",
       "        } else if (d.bel) {\n",
       "            return d.bel\n",
       "        } else {\n",
       "            console.log('Undefined node: ' + d);\n",
       "            return 'UNDEFINED'\n",
       "        }\n",
       "    }\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",
       "\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', 'isA', 'partOf'].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 getCanonicalName(d)\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='csebygozqhfqpkdt'></div>\";\n",
       "\n",
       "element.append(elementInnerHTML);\n",
       "\n",
       "require(['d3'], function (d3) {\n",
       "    return init_d3_force(d3, {\"directed\": true, \"multigraph\": true, \"graph\": {\"pybel_version\": \"0.15.5\", \"document_metadata\": {\"name\": \"COVID19 PPIs\", \"version\": \"0.0.1\"}, \"namespace_url\": {}, \"namespace_pattern\": {}, \"annotation_url\": {}, \"annotation_pattern\": {}, \"annotation_list\": {}, \"annotation_curie\": [], \"annotation_miriam\": []}, \"nodes\": [{\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"ACE2\"}, \"id\": \"bb9a231a2c68ff8f3bad2adad9ed6a94\", \"bel\": \"p(HGNC:ACE2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"ARHGEF7\"}, \"id\": \"3737ee590d6a1097b4aab771ec65b865\", \"bel\": \"p(HGNC:ARHGEF7)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"ATG13\"}, \"id\": \"5b108208ebc78d13d2050f5b01b19da0\", \"bel\": \"p(HGNC:ATG13)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"ATG14\"}, \"id\": \"7a3e2e034a908dc3c60cf186fbdba972\", \"bel\": \"p(HGNC:ATG14)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"BECN1\"}, \"id\": \"041a53ee1e7ac18234901ba9412c345a\", \"bel\": \"p(HGNC:BECN1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CCNA2\"}, \"id\": \"1fad7e9e1c43bac1ac107fb3c11e5b2a\", \"bel\": \"p(HGNC:CCNA2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CCNB1\"}, \"id\": \"55f1369d23de944064085b235c0d99d6\", \"bel\": \"p(HGNC:CCNB1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CCND1\"}, \"id\": \"af65521e8dc8a9417952f6aebb7725c6\", \"bel\": \"p(HGNC:CCND1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CCNE1\"}, \"id\": \"f813b52087d975e5654859cee633f74b\", \"bel\": \"p(HGNC:CCNE1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CDK1\"}, \"id\": \"dd8065837c4f267f62011d07d870f0a3\", \"bel\": \"p(HGNC:CDK1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CDK2\"}, \"id\": \"10f419c217b25dc1a0363b7341b8e0b8\", \"bel\": \"p(HGNC:CDK2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CDK4\"}, \"id\": \"72b88c249aeb10a8bbc2e43bc3e428f9\", \"bel\": \"p(HGNC:CDK4)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CDKN1B\"}, \"id\": \"6f4266e862549985ed5e681ce2e95639\", \"bel\": \"p(HGNC:CDKN1B)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"CREBBP\"}, \"id\": \"46148e81658994544d74b5db695e5cd8\", \"bel\": \"p(HGNC:CREBBP)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"G3BP1\"}, \"id\": \"393c18dd6afc93f9ceeca99a12444f80\", \"bel\": \"p(HGNC:G3BP1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"G3BP2\"}, \"id\": \"a9688a423c6c2793021ae7f33ce2bc97\", \"bel\": \"p(HGNC:G3BP2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"GABARAP\"}, \"id\": \"e412796548aa4b3c24ca0303c73e605f\", \"bel\": \"p(HGNC:GABARAP)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"GABARAPL2\"}, \"id\": \"78c4a4b770bb341f0f8a220fc138a25e\", \"bel\": \"p(HGNC:GABARAPL2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"IRF3\"}, \"id\": \"897eff5dfdc1e9477decd386f7648733\", \"bel\": \"p(HGNC:IRF3)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"KDM1A\"}, \"id\": \"d8f27b8ac5adaffef019391a37bec171\", \"bel\": \"p(HGNC:KDM1A)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"KPNA2\"}, \"id\": \"8b0251f6a9c9b5674bc426569e119922\", \"bel\": \"p(HGNC:KPNA2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"KPNB1\"}, \"id\": \"4fd7c82b679bf433d0c7bcadfca31720\", \"bel\": \"p(HGNC:KPNB1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MAP1LC3A\"}, \"id\": \"89badabd301b21ede7de4f845c3e918f\", \"bel\": \"p(HGNC:MAP1LC3A)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MAP1LC3B\"}, \"id\": \"f53a5ff9c9ef1b792d53708c559ac158\", \"bel\": \"p(HGNC:MAP1LC3B)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MAP1LC3C\"}, \"id\": \"bc1839de4cd0a8aa323f3900afd650f4\", \"bel\": \"p(HGNC:MAP1LC3C)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MAVS\"}, \"id\": \"057d75ee2f4b94b1ce2309b0965b0f2a\", \"bel\": \"p(HGNC:MAVS)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MDM2\"}, \"id\": \"6e3726349615c0706bf0d671ba20a453\", \"bel\": \"p(HGNC:MDM2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"MOV10\"}, \"id\": \"a3d996061c2c42d397f0143485631b39\", \"bel\": \"p(HGNC:MOV10)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"NCBP1\"}, \"id\": \"3c2cc7de254f8dc662351eb3a8186008\", \"bel\": \"p(HGNC:NCBP1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"NCBP2\"}, \"id\": \"cde1aa1c3c5c8066c15e2b1426946e86\", \"bel\": \"p(HGNC:NCBP2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"NLRP3\"}, \"id\": \"cce21ae03f3747819d71e4388a5f97c7\", \"bel\": \"p(HGNC:NLRP3)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"NUP98\"}, \"id\": \"38f36ad9e1d12ad0c543710427e93c7f\", \"bel\": \"p(HGNC:NUP98)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"PABPC1\"}, \"id\": \"310e799d1381e4759d74992a3e1dd5b3\", \"bel\": \"p(HGNC:PABPC1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"PAIP1\"}, \"id\": \"56cc5091d5400e1a1a0a42dd9adec57a\", \"bel\": \"p(HGNC:PAIP1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"PIK3C3\"}, \"id\": \"7d9c82cdfcb083d6ae8b0145df41ebbc\", \"bel\": \"p(HGNC:PIK3C3)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"PYCARD\"}, \"id\": \"10d690033122074e66a04216e823a542\", \"bel\": \"p(HGNC:PYCARD)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"RAE1\"}, \"id\": \"e92793b68c4db691f4f62c55f780be22\", \"bel\": \"p(HGNC:RAE1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"RB1CC1\"}, \"id\": \"d8247e6d6ea2d9b7fea2e8659c5a63ee\", \"bel\": \"p(HGNC:RB1CC1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"RCOR1\"}, \"id\": \"ee6d27af902fc6b0efbc628c26df5379\", \"bel\": \"p(HGNC:RCOR1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"RIGI\"}, \"id\": \"11fda3fc838a621d091cf4be3273c85e\", \"bel\": \"p(HGNC:RIGI)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"SCRIB\"}, \"id\": \"b2bf549efb76f105d622a733e15b0c7a\", \"bel\": \"p(HGNC:SCRIB)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"SNCA\"}, \"id\": \"8cd39bc202ad944395c27f63d95f6908\", \"bel\": \"p(HGNC:SNCA)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"SQSTM1\"}, \"id\": \"456f3e69523903bca01eb839840a4054\", \"bel\": \"p(HGNC:SQSTM1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"STING1\"}, \"id\": \"622295abd1a479d90d2e434c8d7d9f0e\", \"bel\": \"p(HGNC:STING1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"TBK1\"}, \"id\": \"23fc9956fab807934042c65b055af556\", \"bel\": \"p(HGNC:TBK1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"TOMM70\"}, \"id\": \"e21ac92eba3ff7f727040df13f4b0ead\", \"bel\": \"p(HGNC:TOMM70)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"ULK1\"}, \"id\": \"26534d61ef0ff460d702bcedd67fa492\", \"bel\": \"p(HGNC:ULK1)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"USP10\"}, \"id\": \"72dc2c1c14a7f4775467171b4467fc6f\", \"bel\": \"p(HGNC:USP10)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"USP7\"}, \"id\": \"d6d6ca34a6db13894d16b2041f1070d7\", \"bel\": \"p(HGNC:USP7)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"UVRAG\"}, \"id\": \"210b30f5adaace11860a256d1ec4f0b6\", \"bel\": \"p(HGNC:UVRAG)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"VPS16\"}, \"id\": \"1d647c9442ae3ff6d1c1ae8abc72349d\", \"bel\": \"p(HGNC:VPS16)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"VPS33A\"}, \"id\": \"199a3dc31084edc7179a6e6032ba2732\", \"bel\": \"p(HGNC:VPS33A)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"HGNC\", \"name\": \"VPS39\"}, \"id\": \"2476a09a362f42bf77848517d893ee86\", \"bel\": \"p(HGNC:VPS39)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"VP\", \"name\": \"N\"}, \"id\": \"532b3ed9d4b946a726fbde463ee7100b\", \"bel\": \"p(VP:N)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"VP\", \"name\": \"P0DTC3\"}, \"id\": \"98682264f532d292c58c2353e651ff75\", \"bel\": \"p(VP:P0DTC3)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"VP\", \"name\": \"P0DTC6\"}, \"id\": \"b5d56a91a54c0cab72be0a9511273cda\", \"bel\": \"p(VP:P0DTC6)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"VP\", \"name\": \"P0DTD2\"}, \"id\": \"905bb604c5c2397d9e2fac85e9641575\", \"bel\": \"p(VP:P0DTD2)\"}, {\"function\": \"Protein\", \"concept\": {\"namespace\": \"VP\", \"name\": \"S\"}, \"id\": \"e28d905f4fe35fcc118942061c153f78\", \"bel\": \"p(VP:S)\"}], \"links\": [{\"relation\": \"association\", \"evidence\": \"pubmed:26382858\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 28, \"target\": 29, \"key\": \"6d9ddf8e031e61a21961315054b570c8\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:26382858\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 29, \"target\": 28, \"key\": \"5b5003a777d425a77e98e09977d3a1fc\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:24550280\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 40, \"target\": 1, \"key\": \"3aead078926b5a5e0c4141f66e8a75c5\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:24550280\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 1, \"target\": 40, \"key\": \"603b25dd81acbc29149ab127b52044f1\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:32353859\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 14, \"target\": 53, \"key\": \"395d197087798e219f466a0296e271a2\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:33845483\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 14, \"target\": 53, \"key\": \"688008fe67d31cbc300cfc3476735785\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:32838362\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 14, \"target\": 53, \"key\": \"f893914002b0c671558bbe0d299ce574\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:34400613\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 14, \"target\": 53, \"key\": \"beecc30e979fb179cf1f91ba37c9c633\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:33060197\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 14, \"target\": 53, \"key\": 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{\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 41, \"target\": 41, \"key\": \"68da310de559b68f474acd8d29f567b8\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:34799561\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 26, \"target\": 48, \"key\": \"bfc0f29baa04d314e156868b4f09eb50\"}, {\"relation\": \"association\", \"evidence\": \"pubmed:34799561\", \"citation\": {\"namespace\": \"pubmed\", \"identifier\": \"IntAct\"}, \"source\": 48, \"target\": 26, \"key\": \"7c39236faaa4e3c8c3c9c7fc5b157294\"}]}, \"#csebygozqhfqpkdt\", 1000, 650, {'Protein': '#1F77B4', 'Pathology': '#FF7F0E', 'BiologicalProcess': '#2CA02C', 'miRNA': '#D62728', 'Complex': '#98DF8A', 'Composite': '#9467BD', 'Reaction': '#000000', 'Gene': '#FFBB78', 'Abundance': '#AEC7E8', 'RNA': '#FF9896'});\n",
       "});"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "to_jupyter(xx)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "02b348a1",
   "metadata": {},
   "outputs": [],
   "source": [
    "#to cytoscape compatible graphml \n",
    "pybel.to_graphml(merged_kg,'data/kgs/viral_diseases/covid19_kg_2024/covidKG_itmpChem_Graph.graphml')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "68ae19ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "merged_kg.summarize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "04ffd9c3",
   "metadata": {},
   "outputs": [],
   "source": [
    "node_data = {'Node':['Pathology','BiologicalProcess','Abundance','Protein'],\n",
    "       'Number':[9005,5669,19931,1347]}\n",
    "node = pd.DataFrame(node_data)\n",
    "a = sns.barplot(x=\"Node\", y=\"Number\", data=node)\n",
    "a.set(xlabel='Node',ylabel='Number',title= 'KG nodes in numbers (Total=35952)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3b0b95f3",
   "metadata": {},
   "outputs": [],
   "source": [
    "nspace_data = {'Namespace':['ChEMBLAssay','ChEMBL','GOBP','GOMF','HGNC','Disease','SideEffect','Reactome','MOA'],\n",
    "       'Number':[15835,4096,2085,1332,1347,1585,7420,1513,739]}\n",
    "nspace = pd.DataFrame(nspace_data)\n",
    "a = sns.barplot(x=\"Number\", y=\"Namespace\", data=nspace_data)\n",
    "a.set(xlabel='Number',ylabel='Namespace',title= 'KG Namespace in numbers')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "db746c14",
   "metadata": {},
   "outputs": [],
   "source": [
    "#to cytoscape compatible graphml \n",
    "pybel.to_graphml(itmp_graph,'data/export//bycovidgraph_2ndSep.graphml')\n",
    "\n",
    "#to regular BEL format\n",
    "pybel.dump(itmp_graph,'data/export//bycovidgraph_2ndSep.bel')\n",
    "\n",
    "#to neo4j\n",
    "pybel.to_csv(itmp_graph,'data/export//bycovidgraph_2ndSep.csv')\n",
    "\n",
    "#to sif\n",
    "pybel.to_sif(itmp_graph,'data/export//bycovidgraph_2ndSep.sif')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ad23d0a",
   "metadata": {},
   "outputs": [],
   "source": [
    "chemblprot = pd.read_csv('data/misc/chembl_uniprot_mapping.txt',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1b3b9ac1",
   "metadata": {},
   "outputs": [],
   "source": [
    "chemblprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49e14c8f",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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