TEXT - GRAKN - TEXT MINING - Inserting Data In Grakn using Spacy.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Reading medical data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# importing library for pubmed article \n",
    "from lxml import etree"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Parsing the xml file\n",
    "doc = etree.parse('../pubmed_result.xml')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "root = doc.getroot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'PubmedArticleSet'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Tag name of the root node\n",
    "root.tag"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "27246822\n"
     ]
    }
   ],
   "source": [
    "# Fetching PMID value \n",
    "for child in root.iter('PMID'):\n",
    "    print( child.text)\n",
    "    pmid = child.text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dabrafenib plus Trametinib: a Review in Advanced Melanoma with a BRAF (V600) Mutation.\n"
     ]
    }
   ],
   "source": [
    "# Fetching Article Title\n",
    "for child in root.iter('ArticleTitle'):\n",
    "    print( child.text)\n",
    "    title = child.text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The BRAF inhibitor dabrafenib (Tafinlar(®)) and the MEK inhibitor trametinib (Mekinist(®)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation. This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data. Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-naïve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation. Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of ≤ 15 % and stable disease in ≤ 50 % of patients in small phase I and II studies. Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable. Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway. Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.\n"
     ]
    }
   ],
   "source": [
    "# Fetching Abstract Text\n",
    "for child in root.iter('AbstractText'):\n",
    "    print( child.text)\n",
    "    annotatedAbstract = child.text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Abstract Data\n",
    "\n",
    "annotatedAbstract = annotatedAbstract.encode(encoding='UTF-8',errors='strict')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Connecting to Grakn\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "from grakn.client import GraknClient "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Inserted pmid into the text_mining keyspace with ID: V4200\n"
     ]
    }
   ],
   "source": [
    "# Inserting \n",
    "\n",
    "## Connecting and creating a client\n",
    "with GraknClient(uri=\"localhost:48555\") as client:\n",
    "    \n",
    "    ## Creating a session\n",
    "    with client.session(keyspace=\"text\") as session:\n",
    "        ## creating a write transaction\n",
    "        with session.transaction().write() as write_transaction:\n",
    "            \n",
    "            ## write transaction is open\n",
    "            insert_iterator = write_transaction.query('insert $x isa pubmed-article, has pmid \"{}\",has title \"{}\" ,has annotated-abstract \"{}\" ;'.format(pmid,title,annotatedAbstract))           \n",
    "    \n",
    "            insert_list = insert_iterator.collect_concepts()\n",
    "            print(\"Inserted pmid into the text_mining keyspace with ID: {0}\".format(insert_list[0].id))\n",
    "             \n",
    "                     \n",
    "            ## write transaction must always be committed (closed)\n",
    "            write_transaction.commit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Reading data form Grakn for text mining\n",
    "client= GraknClient(uri = 'localhost:48555')\n",
    "session = client.session(keyspace= 'text')\n",
    "transaction = session.transaction().read()\n",
    "query_iterator = transaction.query('match $a isa annotated-abstract;get;')\n",
    "#(query='match $p isa pubmed-article;get;')\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "query_concepts = query_iterator.collect_concepts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "V4240 -- b'The BRAF inhibitor dabrafenib (Tafinlar(\\xc2\\xae)) and the MEK inhibitor trametinib (Mekinist(\\xc2\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation. This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data. Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-na\\xc3\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation. Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\xe2\\x89\\xa4 15\\xc2\\xa0% and stable disease in \\xe2\\x89\\xa4 50\\xc2\\xa0% of patients in small phase I and II studies. Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable. Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway. Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'\n"
     ]
    }
   ],
   "source": [
    "for q in query_concepts:\n",
    "    print(q.id,\"--\",q.value())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# abstract id\n",
    "\n",
    "abstract_id = query_concepts[0].id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'V4240'"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "abstract_id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# abstract value\n",
    "\n",
    "abstract_value = query_concepts[0].value()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"b'The BRAF inhibitor dabrafenib (Tafinlar(\\\\xc2\\\\xae)) and the MEK inhibitor trametinib (Mekinist(\\\\xc2\\\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation. This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data. Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-na\\\\xc3\\\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation. Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\\\xe2\\\\x89\\\\xa4 15\\\\xc2\\\\xa0% and stable disease in \\\\xe2\\\\x89\\\\xa4 50\\\\xc2\\\\xa0% of patients in small phase I and II studies. Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable. Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway. Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'\""
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "abstract_value"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Spacy -- Work"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# import spacy \n",
    "import spacy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load custom trained model\n",
    "\n",
    "nlp = spacy.load(\"/home/ubuntu//Grakn/Spacy Play/spacy_en_core_web_lg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Store pubmed-article fetched from grakn\n",
    "# annotated_abstract"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "doc = nlp(abstract_value)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "b'The BRAF inhibitor dabrafenib (Tafinlar(\\xc2\\xae)) and the MEK inhibitor trametinib (Mekinist(\\xc2\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation. 0.0 \n",
      " ------\n",
      "This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data. 0.0 \n",
      " ------\n",
      "Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment- 0.0 \n",
      " ------\n",
      "na\\xc3\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation. 0.0 \n",
      " ------\n",
      "Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\xe2\\x89\\xa4 15\\xc2\\xa0% and stable disease in \\xe2\\x89\\xa4 50\\xc2\\xa0% of patients in small phase I and II studies. 0.0 \n",
      " ------\n",
      "Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable. 0.0 \n",
      " ------\n",
      "Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway. 0.0 \n",
      " ------\n",
      "Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.' 0.0 \n",
      " ------\n"
     ]
    }
   ],
   "source": [
    "# Migrate Sentences\n",
    "\n",
    "for sentence in doc.sents:\n",
    "    print(sentence.text, sentence.sentiment,\"\\n\",\"------\" )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Inserted sentence into the text keyspace with ID: V40964136\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V40968232\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V8336\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V12392\n",
      "Inserted sentence attribute into the text keyspace with ID: V12392\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V40968312\n",
      "Inserted sentence attribute into the text keyspace with ID: V40968312\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V40980520\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V40992808\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n",
      "Inserted sentence into the text keyspace with ID: V12400\n",
      "Inserted sentence attribute into the text keyspace with ID: V4240\n",
      "Insertion Done\n"
     ]
    }
   ],
   "source": [
    "# Inserting \n",
    "\n",
    "\n",
    "for sentence in doc.sents:\n",
    "    ## Connecting and creating a client\n",
    "    with GraknClient(uri=\"localhost:48555\") as client:\n",
    "\n",
    "        ## Creating a session\n",
    "        with client.session(keyspace=\"text\") as session:\n",
    "            ## creating a write transaction\n",
    "            with session.transaction().write() as write_transaction:\n",
    "\n",
    "                ## write transaction is open\n",
    "                insert_iterator = write_transaction.query('insert $x isa sentence, has text \"{}\",has sentiment \"{}\" ;'.format(sentence.text,sentence.sentiment))           \n",
    "\n",
    "                insert_list = insert_iterator.collect_concepts()\n",
    "                print(\"Inserted sentence into the text keyspace with ID: {0}\".format(insert_list[0].id))\n",
    "\n",
    "\n",
    "                # Another insert for relation with abstract and its id\n",
    "                insert_query = \"match $s id {};$a id {};\\\n",
    "                insert $acs(contained-sentence: $s, abstract-container: $a) isa abstract-containing-sentence;\".format(insert_list[0].id,abstract_id)\n",
    "                \n",
    "                insert_query_iterator = write_transaction.query(insert_query)\n",
    "                \n",
    "                insert_query_list = insert_query_iterator.collect_concepts()\n",
    "                print(\"Inserted sentence attribute into the text keyspace with ID: {0}\".format(insert_query_list[0].id))\n",
    "\n",
    "\n",
    "\n",
    "                ## write transaction must always be committed (closed)\n",
    "                write_transaction.commit()\n",
    "    print(\"Insertion Done\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "# # Check the insertion id and value\n",
    "# for i in insert_query_list:\n",
    "#     print(i.id,i.value())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "# # Quering ? reading all sentences\n",
    "\n",
    "# with GraknClient(uri='localhost:48555') as client:\n",
    "#     with client.session(keyspace=\"text_mining\") as session:\n",
    "#         # creating a query transaction\n",
    "#         with session.transaction().read() as read_transaction:\n",
    "            \n",
    "#             read_iterator = read_transaction.query('match $s isa sentence;get;')\n",
    "#             read_list = read_iterator.collect_concepts()\n",
    "            \n",
    "# #             for q in read_list:\n",
    "# #                 print(q.id, q.is_type())\n",
    "                \n",
    "#         with session.transaction().write() as write_transaction:\n",
    "            \n",
    "#             for q in read_list:\n",
    "#                 insert_query = \"match $s id {};$a id {};\\\n",
    "#                 insert $acs(contained-sentence: $s, abstract-container: $a) isa abstract-containing-sentence;\".format(q.id,abstract_id)\n",
    "\n",
    "\n",
    "#              ## write transaction is open\n",
    "#                 insert_iterator = write_transaction.query(insert_query)           \n",
    "\n",
    "#                 insert_list = insert_iterator.collect_concepts()\n",
    "#                 print(\"Inserted sentence attribute into the text_mining keyspace with ID: {0}\".format(insert_list[0].id))\n",
    "                \n",
    "#                 ## write transaction must always be committed (closed)\n",
    "#             write_transaction.commit()\n",
    "\n",
    "            \n",
    "            \n",
    "            \n",
    "        "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tokens Insertion"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Token Extraction - Spacy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "b'The BRAF inhibitor dabrafenib (Tafinlar(\\xc2\\xae)) and the MEK inhibitor trametinib (Mekinist(\\xc2\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation. This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data. Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-na\\xc3\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation. Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\xe2\\x89\\xa4 15\\xc2\\xa0% and stable disease in \\xe2\\x89\\xa4 50\\xc2\\xa0% of patients in small phase I and II studies. Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable. Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway. Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# spacy output of document \n",
    "doc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "b'The b'the ADJ JJ compound x'Xxx False False \n",
      "BRAF BRAF PROPN NNP compound XXXX True False gene\n",
      "inhibitor inhibitor NOUN NN compound xxxx True False \n",
      "dabrafenib dabrafenib NOUN NN nsubjpass xxxx True False drug\n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "Tafinlar(\\xc2\\xae tafinlar(\\xc2\\xae ADV RB appos Xxxxx(\\xxd\\xxx False False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "and and CCONJ CC cc xxx True True \n",
      "the the DET DT det xxx True True \n",
      "MEK MEK PROPN NNP compound XXX True False protien\n",
      "inhibitor inhibitor NOUN NN compound xxxx True False \n",
      "trametinib trametinib NOUN NN conj xxxx True False drug\n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "Mekinist(\\xc2\\xae mekinist(\\xc2\\xae NOUN NN advmod Xxxxx(\\xxd\\xxx False False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "are be VERB VBP auxpass xxx True True \n",
      "indicated indicate VERB VBN ROOT xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "as as ADP IN advmod xx True True \n",
      "monotherapy monotherapy ADV RB advmod xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "in in ADP IN advcl xx True True \n",
      "combination combination NOUN NN pobj xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "each each DET DT det xxxx True True \n",
      "other other ADJ JJ pobj xxxx True True \n",
      ", , PUNCT , punct , False False \n",
      "for for ADP IN conj xxx True True \n",
      "the the DET DT det xxx True True \n",
      "treatment treatment NOUN NN pobj xxxx True False \n",
      "of of ADP IN prep xx True True \n",
      "patients patient NOUN NNS pobj xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "unresectable unresectable ADJ JJ amod xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "metastatic metastatic ADJ JJ conj xxxx True False \n",
      "melanoma melanoma NOUN NN pobj xxxx True False diesease\n",
      "with with ADP IN prep xxxx True True \n",
      "a a DET DT det x True True \n",
      "BRAF BRAF PROPN NNP nmod XXXX True False gene\n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "V600 V600 PROPN NNP subtok Xddd False False varient\n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "mutation mutation NOUN NN pobj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "This this DET DT det Xxxx True True \n",
      "article article NOUN NN nsubj xxxx True False \n",
      "reviews review VERB VBZ ROOT xxxx True False \n",
      "the the DET DT det xxx True True \n",
      "therapeutic therapeutic ADJ JJ amod xxxx True False \n",
      "efficacy efficacy NOUN NN dobj xxxx True False \n",
      "and and CCONJ CC cc xxx True True \n",
      "tolerability tolerability NOUN NN conj xxxx True False \n",
      "of of ADP IN prep xx True True \n",
      "combination combination NOUN NN compound xxxx True False \n",
      "treatment treatment NOUN NN pobj xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "dabrafenib dabrafenib NOUN NN pobj xxxx True False \n",
      "and and CCONJ CC cc xxx True True \n",
      "trametinib trametinib NOUN NN conj xxxx True False drug\n",
      "in in ADP IN prep xx True True \n",
      "this this DET DT det xxxx True True \n",
      "indication indication NOUN NN pobj xxxx True False \n",
      "and and CCONJ CC cc xxx True True \n",
      "summarizes summarize VERB VBZ conj xxxx True False \n",
      "relevant relevant ADJ JJ amod xxxx True False \n",
      "pharmacological pharmacological ADJ JJ amod xxxx True False \n",
      "data datum NOUN NNS dobj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "Dabrafenib Dabrafenib PROPN NNP nsubj Xxxxx True False drug\n",
      "plus plus CCONJ CC cc xxxx True False \n",
      "trametinib trametinib NOUN NN conj xxxx True False drug\n",
      "significantly significantly ADV RB advmod xxxx True False \n",
      "prolonged prolong VERB VBD amod xxxx True False \n",
      "progression progression NOUN NN npadvmod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "free free ADJ JJ amod xxxx True False \n",
      "survival survival NOUN NN conj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "PFS PFS PROPN NNP appos XXX True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "and and CCONJ CC cc xxx True True \n",
      "overall overall ADJ JJ amod xxxx True False \n",
      "survival survival NOUN NN conj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "OS OS PROPN NNP appos XX True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      ", , PUNCT , punct , False False \n",
      "improved improve VERB VBN ROOT xxxx True False \n",
      "objective objective ADJ JJ amod xxxx True False \n",
      "response response NOUN NN compound xxxx True False \n",
      "rates rate NOUN NNS dobj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "ORRs orr NOUN NNS appos XXXx True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "and and CCONJ CC cc xxx True True \n",
      "preserved preserve VERB VBN amod xxxx True False \n",
      "health health NOUN NN npadvmod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "related relate VERB VBN amod xxxx True False \n",
      "quality quality NOUN NN conj xxxx True False \n",
      "of of ADP IN prep xx True True \n",
      "life life NOUN NN pobj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "HR HR PROPN NNP compound XX True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "QOL QOL PROPN NNP appos XXX True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "to to ADP IN prep xx True True \n",
      "a a DET DT det x True True \n",
      "greater great ADJ JJR amod xxxx True False \n",
      "extent extent NOUN NN pobj xxxx True False \n",
      "than than ADP IN prep xxxx True True \n",
      "dabrafenib dabrafenib NOUN NN pobj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "in in ADP IN prep xx True True \n",
      "the the DET DT det xxx True True \n",
      "double double ADJ JJ amod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "blind blind ADJ JJ amod xxxx True False \n",
      "COMBI combi NOUN NN compound XXXX True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "d d ADJ JJ compound x True False \n",
      "study study NOUN NN pobj xxxx True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "and and CCONJ CC cc xxx True True \n",
      "vemurafenib vemurafenib NOUN NN conj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "in in ADP IN prep xx True True \n",
      "the the DET DT det xxx True True \n",
      "open open ADJ JJ amod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "label label NOUN NN compound xxxx True False \n",
      "COMBI COMBI PROPN NNP compound XXXX True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "v v PROPN NNP compound x True False \n",
      "study study NOUN NN pobj xxxx True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "in in ADP IN prep xx True True \n",
      "two two NUM CD nummod xxx True True \n",
      "large large ADJ JJ amod xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "randomized randomize VERB VBN conj xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "phase phase NOUN NN compound xxxx True False \n",
      "III iii NUM CD compound XXX True False \n",
      "studies study NOUN NNS pobj xxxx True False \n",
      "in in ADP IN prep xx True True \n",
      "treatment treatment NOUN NN pobj xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "na\\xc3\\xafve na\\xc3\\xafve X XX nummod xx\\xxd\\xxxx False False \n",
      "patients patient NOUN NNS ROOT xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "unresectable unresectable ADJ JJ amod xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "metastatic metastatic ADJ JJ conj xxxx True False \n",
      "melanoma melanoma NOUN NN pobj xxxx True False diesease\n",
      "with with ADP IN prep xxxx True True \n",
      "BRAF BRAF PROPN NNP nmod XXXX True False gene\n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "V600E V600E PROPN NNP nmod XdddX False False varient\n",
      "/ / SYM SYM punct / False False varient\n",
      "K K PROPN NNP nmod X True False varient\n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "mutation mutation NOUN NN pobj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "Limited limited ADJ JJ amod Xxxxx True False \n",
      "treatment treatment NOUN NN compound xxxx True False \n",
      "benefit benefit NOUN NN nsubjpass xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "the the DET DT det xxx True True \n",
      "combination combination NOUN NN pobj xxxx True False \n",
      "was be VERB VBD auxpass xxx True True \n",
      "also also ADV RB advmod xxxx True True \n",
      "seen see VERB VBN ROOT xxxx True False \n",
      "in in ADP IN prep xx True True \n",
      "patients patient NOUN NNS pobj xxxx True False \n",
      "who who PRON WP nsubj xxx True True \n",
      "had have VERB VBD aux xxx True True \n",
      "progressed progress VERB VBN relcl xxxx True False \n",
      "on on ADP IN prep xx True True \n",
      "prior prior ADJ JJ amod xxxx True False \n",
      "BRAF BRAF PROPN NNP compound XXXX True False \n",
      "inhibitor inhibitor NOUN NN compound xxxx True False \n",
      "therapy therapy NOUN NN pobj xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "as as ADP IN mark xx True True \n",
      "indicated indicate VERB VBN advcl xxxx True False \n",
      "by by ADP IN agent xx True True \n",
      "ORRs orr NOUN NNS pobj XXXx True False \n",
      "of of ADP IN prep xx True True \n",
      "\\xe2\\x89\\xa4 \\xe2\\x89\\xa4 PROPN NNP pobj \\xxd\\xdd\\xxd False False \n",
      "15\\xc2\\xa0 15\\xc2\\xa0 NUM CD nummod dd\\xxd\\xxd False False \n",
      "% % NOUN NN npadvmod % False False \n",
      "and and CCONJ CC cc xxx True True \n",
      "stable stable ADJ JJ amod xxxx True False \n",
      "disease disease NOUN NN conj xxxx True False \n",
      "in in ADP IN prep xx True True \n",
      "\\xe2\\x89\\xa4 \\xe2\\x89\\xa4 PROPN NNP pobj \\xxd\\xdd\\xxd False False \n",
      "50\\xc2\\xa0 50\\xc2\\xa0 NUM CD nummod dd\\xxd\\xxd False False \n",
      "% % NOUN NN dobj % False False \n",
      "of of ADP IN prep xx True True \n",
      "patients patient NOUN NNS pobj xxxx True False \n",
      "in in ADP IN prep xx True True \n",
      "small small ADJ JJ amod xxxx True False \n",
      "phase phase NOUN NN nmod xxxx True False \n",
      "I -PRON- PRON PRP nmod X True True \n",
      "and and CCONJ CC cc xxx True True \n",
      "II II PROPN NNP conj XX True False \n",
      "studies study NOUN NNS pobj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "Combination combination NOUN NN compound Xxxxx True False \n",
      "therapy therapy NOUN NN nsubj xxxx True False \n",
      "did do VERB VBD aux xxx True True \n",
      "not not ADV RB neg xxx True True \n",
      "increase increase VERB VB ROOT xxxx True False \n",
      "overall overall ADJ JJ amod xxxx True False \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "toxicity toxicity NOUN NN dobj xxxx True False \n",
      "relative relative ADJ JJ amod xxxx True False \n",
      "to to ADP IN prep xx True True \n",
      "dabrafenib dabrafenib NOUN NN pobj xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "vemurafenib vemurafenib NOUN NN conj xxxx True False drug\n",
      "monotherapy monotherapy NOUN NN advmod xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "with with ADP IN prep xxxx True True \n",
      "most most ADJ JJS amod xxxx True True \n",
      "adverse adverse ADJ JJ amod xxxx True False \n",
      "events event NOUN NNS pobj xxxx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "AEs AEs PROPN NNP appos XXx True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "mild mild ADJ JJ amod xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "moderate moderate ADJ JJ conj xxxx True False \n",
      "in in ADP IN prep xx True True \n",
      "severity severity NOUN NN pobj xxxx True False \n",
      "and and CCONJ CC cc xxx True True \n",
      "generally generally ADV RB advmod xxxx True False \n",
      "manageable manageable ADJ JJ conj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "Fewer few ADJ JJR amod Xxxxx True False \n",
      "skin skin NOUN NN npadvmod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "related relate VERB VBN amod xxxx True False \n",
      "AEs ae NOUN NNS nsubjpass XXx True False \n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "e.g. e.g. X FW amod x.x. False False \n",
      "cutaneous cutaneous ADJ JJ amod xxxx True False \n",
      "malignancies malignancy NOUN NNS appos xxxx True False \n",
      ", , PUNCT , punct , False False \n",
      "hyperkeratinosis hyperkeratinosis NOUN NN conj xxxx True False \n",
      "and and CCONJ CC cc xxx True True \n",
      "hand hand NOUN NN compound xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "foot foot NOUN NN compound xxxx True False \n",
      "syndrome syndrome NOUN NN conj xxxx True False \n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "were be VERB VBD auxpass xxxx True True \n",
      "reported report VERB VBN ROOT xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "combination combination NOUN NN compound xxxx True False \n",
      "therapy therapy NOUN NN pobj xxxx True False \n",
      "than than ADP IN prep xxxx True True \n",
      "with with ADP IN prep xxxx True True \n",
      "dabrafenib dabrafenib NOUN NN pobj xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "vemurafenib vemurafenib NOUN NN conj xxxx True False drug\n",
      ", , PUNCT , punct , False False \n",
      "probably probably ADV RB advmod xxxx True False \n",
      "because because ADP IN prep xxxx True True \n",
      "of of ADP IN pcomp xx True True \n",
      "reduced reduced ADJ JJ amod xxxx True False \n",
      "paradoxical paradoxical ADJ JJ amod xxxx True False \n",
      "activation activation NOUN NN pobj xxxx True False \n",
      "of of ADP IN prep xx True True \n",
      "the the DET DT det xxx True True \n",
      "MAPK MAPK PROPN NNP compound XXXX True False \n",
      "pathway pathway NOUN NN pobj xxxx True False \n",
      ". . PUNCT . punct . False False \n",
      "Thus thus ADV RB advmod Xxxx True True \n",
      ", , PUNCT , punct , False False \n",
      "dabrafenib dabrafenib NOUN NN nsubj xxxx True False \n",
      "plus plus CCONJ CC cc xxxx True False \n",
      "trametinib trametinib NOUN NN conj xxxx True False drug\n",
      "provides provide VERB VBZ ROOT xxxx True False \n",
      "an an DET DT det xx True True \n",
      "important important ADJ JJ amod xxxx True False \n",
      "treatment treatment NOUN NN compound xxxx True False \n",
      "option option NOUN NN dobj xxxx True False \n",
      "for for ADP IN prep xxx True True \n",
      "patients patient NOUN NNS pobj xxxx True False \n",
      "with with ADP IN prep xxxx True True \n",
      "BRAF BRAF PROPN NNP pobj XXXX True False gene\n",
      "( ( PUNCT -LRB- punct ( False False \n",
      "V600 V600 PROPN NNP subtok Xddd False False varient\n",
      ") ) PUNCT -RRB- punct ) False False \n",
      "mutation mutation NOUN NN npadvmod xxxx True False \n",
      "- - PUNCT HYPH punct - False False \n",
      "positive positive ADJ JJ amod xxxx True False \n",
      "unresectable unresectable ADJ JJ amod xxxx True False \n",
      "or or CCONJ CC cc xx True True \n",
      "metastatic metastatic ADJ JJ conj xxxx True False \n",
      "melanoma melanoma NOUN NN appos xxxx True False diesease\n",
      ". . PUNCT . punct . False False \n",
      "' ' PUNCT '' punct ' False False \n"
     ]
    }
   ],
   "source": [
    "for token in doc:\n",
    "    print(token.text,\\\n",
    "          token.lemma_,\\\n",
    "          token.pos_,\\\n",
    "          token.tag_,\\\n",
    "          token.dep_,\\\n",
    "          token.shape_,\\\n",
    "          token.is_alpha,\\\n",
    "          token.is_stop,\n",
    "         token.ent_type_)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Quering Grakn DB for sentences\n",
    "\n",
    "### Inserting token form queried sentences "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<grakn.service.Session.util.ResponseReader.ResponseIterator object at 0x7f5acbd57eb8>\n",
      "V8336\n",
      "Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V20584\n",
      "Inserted token attribute into the text keyspace with ID: V20568\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V32856\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V57488\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V41001000\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V32984\n",
      "Inserted token attribute into the text keyspace with ID: V69776\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V40996984\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V82032\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V90256\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V57432\n",
      "Inserted token attribute into the text keyspace with ID: V41176\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V57448\n",
      "Inserted token attribute into the text keyspace with ID: V110736\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V41056\n",
      "Inserted token attribute into the text keyspace with ID: V127120\n",
      "Inserted token attribute into the text keyspace with ID: V61656\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V110704\n",
      "Inserted token attribute into the text keyspace with ID: V61544\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V53344\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V77928\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V61536\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V159856\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V168080\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V180368\n",
      "Inserted token attribute into the text keyspace with ID: V94296\n",
      "Inserted token attribute into the text keyspace with ID: V184464\n",
      "Inserted token attribute into the text keyspace with ID: V82016\n",
      "Inserted token attribute into the text keyspace with ID: V188560\n",
      "Inserted token attribute into the text keyspace with ID: V86112\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V200848\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V106712\n",
      "Inserted token attribute into the text keyspace with ID: V118888\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "Inserted token attribute into the text keyspace with ID: V8336\n",
      "V12392\n",
      "na\\xc3\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation.\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V217200\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V233616\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V41091112\n",
      "Inserted token attribute into the text keyspace with ID: V233584\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V135272\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "Inserted token attribute into the text keyspace with ID: V254096\n",
      "Inserted token attribute into the text keyspace with ID: V12392\n",
      "V12400\n",
      "Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V41087096\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V41107496\n",
      "Inserted token attribute into the text keyspace with ID: V274576\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V155752\n",
      "Inserted token attribute into the text keyspace with ID: V139352\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V41091192\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V295024\n",
      "Inserted token attribute into the text keyspace with ID: V163944\n",
      "Inserted token attribute into the text keyspace with ID: V299120\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V12400\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Inserted token attribute into the text keyspace with ID: V12400\n",
      "Inserted token attribute into the text keyspace with ID: V323696\n",
      "V40964136\n",
      "b'The BRAF inhibitor dabrafenib (Tafinlar(\\xc2\\xae)) and the MEK inhibitor trametinib (Mekinist(\\xc2\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation.\n",
      "Inserted token attribute into the text keyspace with ID: V164056\n",
      "Inserted token attribute into the text keyspace with ID: V327792\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V335984\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V176344\n",
      "Inserted token attribute into the text keyspace with ID: V135264\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V331920\n",
      "Inserted token attribute into the text keyspace with ID: V340080\n",
      "Inserted token attribute into the text keyspace with ID: V344176\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V155744\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V360592\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V41148536\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V41152552\n",
      "Inserted token attribute into the text keyspace with ID: V184408\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V393328\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V205016\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "Inserted token attribute into the text keyspace with ID: V213208\n",
      "Inserted token attribute into the text keyspace with ID: V40964136\n",
      "V40968232\n",
      "This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data.\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V426096\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V192608\n",
      "Inserted token attribute into the text keyspace with ID: V209000\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V438384\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V41193592\n",
      "Inserted token attribute into the text keyspace with ID: V217192\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V454768\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V40968232\n",
      "Inserted token attribute into the text keyspace with ID: V233688\n",
      "Inserted token attribute into the text keyspace with ID: V422032\n",
      "V40968312\n",
      "Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\xe2\\x89\\xa4 15\\xc2\\xa0% and stable disease in \\xe2\\x89\\xa4 50\\xc2\\xa0% of patients in small phase I and II studies.\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V426128\n",
      "Inserted token attribute into the text keyspace with ID: V241880\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V442512\n",
      "Inserted token attribute into the text keyspace with ID: V41209976\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V450704\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V503920\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V225368\n",
      "Inserted token attribute into the text keyspace with ID: V458896\n",
      "Inserted token attribute into the text keyspace with ID: V254168\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V237656\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V262360\n",
      "Inserted token attribute into the text keyspace with ID: V471184\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V258152\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V274648\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V286824\n",
      "Inserted token attribute into the text keyspace with ID: V290920\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V295016\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V245848\n",
      "Inserted token attribute into the text keyspace with ID: V40968312\n",
      "Inserted token attribute into the text keyspace with ID: V557168\n",
      "Inserted token attribute into the text keyspace with ID: V307304\n",
      "V40980520\n",
      "Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable.\n",
      "Inserted token attribute into the text keyspace with ID: V41213992\n",
      "Inserted token attribute into the text keyspace with ID: V41218088\n",
      "Inserted token attribute into the text keyspace with ID: V41222184\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V319592\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V241760\n",
      "Inserted token attribute into the text keyspace with ID: V41259128\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V581744\n",
      "Inserted token attribute into the text keyspace with ID: V331880\n",
      "Inserted token attribute into the text keyspace with ID: V41271416\n",
      "Inserted token attribute into the text keyspace with ID: V41238568\n",
      "Inserted token attribute into the text keyspace with ID: V557200\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V589936\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V40980520\n",
      "Inserted token attribute into the text keyspace with ID: V348264\n",
      "Inserted token attribute into the text keyspace with ID: V577680\n",
      "Inserted token attribute into the text keyspace with ID: V606320\n",
      "Inserted token attribute into the text keyspace with ID: V581776\n",
      "V40992808\n",
      "Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway.\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V41259048\n",
      "Inserted token attribute into the text keyspace with ID: V622704\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V634992\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V602256\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V41267240\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V41308280\n",
      "Inserted token attribute into the text keyspace with ID: V254048\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V262240\n",
      "Inserted token attribute into the text keyspace with ID: V659568\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V381032\n",
      "Inserted token attribute into the text keyspace with ID: V295000\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V41328760\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V626832\n",
      "Inserted token attribute into the text keyspace with ID: V630928\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V385128\n",
      "Inserted token attribute into the text keyspace with ID: V635024\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V647312\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "Inserted token attribute into the text keyspace with ID: V315480\n",
      "Inserted token attribute into the text keyspace with ID: V40992808\n",
      "write completed\n"
     ]
    }
   ],
   "source": [
    "# Transaction query on doc\n",
    "\n",
    "client = GraknClient(uri='localhost:48555')\n",
    "session = client.session(keyspace=\"text\")\n",
    "\n",
    "# creating a query transaction\n",
    "query_transaction = session.transaction() \n",
    "\n",
    "query_iterator = query_transaction.read().query('match $s isa sentence,has text $t;get $s;')\n",
    "\n",
    "query_list = query_iterator.collect_concepts()\n",
    "\n",
    "print(query_iterator)\n",
    "\n",
    "\n",
    "# Write transaction\n",
    "\n",
    "for q in query_list:\n",
    "    print(q.id)\n",
    "    \n",
    "    \n",
    "    for text in q.attributes():\n",
    "        #esult.append(text.value())\n",
    "        if text.type().label() == 'text':\n",
    "            print(text.value())\n",
    "    \n",
    "            sent_id = q.id\n",
    "            # Tokenizing extracted sentence\n",
    "            doc = nlp(text.value())\n",
    "            for token in doc:\n",
    "                token_text = token.text\n",
    "                token_lemma = token.lemma_\n",
    "                token_pos = token.pos_\n",
    "                token_tag = token.tag_\n",
    "                token_ner = token.ent_type_\n",
    "\n",
    "\n",
    "                ## Creating a session\n",
    "                with client.session(keyspace=\"text\") as session:\n",
    "                    ## creating a write transaction\n",
    "                    with session.transaction().write() as write_transaction:\n",
    "                        # Grakn Insert Query\n",
    "                        insert_query = 'match $s id {};\\\n",
    "                        insert $t isa token,\\\n",
    "                        has tag \"{}\",\\\n",
    "                        has lemma \"{}\",\\\n",
    "                        has ner \"{}\";\\\n",
    "                        $sct(sentence-container: $s,contained-token : $t) isa sentence-containing-token;'.format(sent_id,token_tag,token_lemma,token_ner)\n",
    "\n",
    "                        #print(insert_query,\"\\n\")\n",
    "\n",
    "                        insert_query_iterator = write_transaction.query(insert_query)\n",
    "\n",
    "                        insert_query_list = insert_query_iterator.collect_concepts()\n",
    "                        print(\"Inserted token attribute into the text keyspace with ID: {0}\".format(insert_query_list[0].id))\n",
    "\n",
    "                        ## write transaction must always be committed (closed)\n",
    "                        write_transaction.commit()\n",
    "\n",
    "        \n",
    "print('write completed')\n",
    "# query_transaction.read().close()\n",
    "# session.close()\n",
    "# client.close()\n",
    "                \n",
    "             "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Migrate Mined relation "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "# new_query = \"match $s isa sentence, has text 'Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.''; \\\n",
    "# $subjectToken isa token, has lemma 'melanoma';\\\n",
    "# $objectToken1 isa token, has lemma 'trametinib';\\\n",
    "# $objectToken2 isa token, has lemma 'dabrafenib';\\\n",
    "# insert $r (mentioning-sentence: $s, subject: $subjectToken, object: $objectToken1, object: $objectToken2) isa mined-relation, has confidence 1.0, has relation-type 'treatment';\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "new_query = \"match $s id V12400;\\\n",
    "            $subjectToken id V315504;\\\n",
    "            $objectToken1 id V131160;\\\n",
    "            $objectToken2 id V258192;\\\n",
    "            insert $r (mentioning-sentence: $s, subject: $subjectToken, object: $objectToken1, object: $objectToken2) isa mined-relation, has confidence 1.0, has relation-type 'treatment';\"\n",
    "            \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"match $s id V12400;            $subjectToken id V315504;            $objectToken1 id V131160;            $objectToken2 id V258192;            insert $r (mentioning-sentence: $s, subject: $subjectToken, object: $objectToken1, object: $objectToken2) isa mined-relation, has confidence 1.0, has relation-type 'treatment';\""
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_query"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[<grakn.service.Session.Concept.Concept.Entity object at 0x7f5acbd695c0>, <grakn.service.Session.Concept.Concept.Relation object at 0x7f5acbd696d8>, <grakn.service.Session.Concept.Concept.Entity object at 0x7f5acbd6ce80>, <grakn.service.Session.Concept.Concept.Entity object at 0x7f5acbd6c9b0>, <grakn.service.Session.Concept.Concept.Entity object at 0x7f5acbd6cda0>]\n",
      "Inserted mined-relations\n"
     ]
    }
   ],
   "source": [
    "# # Migrating Mined Relation inot Grakn\n",
    "# # Using Dummy Relationship\n",
    "\n",
    "with GraknClient(uri='localhost:48555') as client:\n",
    "\n",
    "    with client.session(keyspace=\"text\") as session:\n",
    "            \n",
    "        with session.transaction().write() as write_transaction:\n",
    "\n",
    "             ## write transaction is open\n",
    "                   \n",
    "                insert_query = \"match $s isa sentence, has text 'Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'; \" +\\\n",
    "                \"$subjectToken isa token, has lemma 'melanoma', has start-position 1720.0, has end-position 1728.0; \" +\\\n",
    "                \"$objectToken1 isa token, has lemma 'trametinib', has start-position 1595.0, has end-position 1605.0; \" +\\\n",
    "                \"$objectToken2 isa token, has lemma 'dabrafenib', has start-position 1579.0, has end-position 1589.0; \" +\\\n",
    "                \"insert $r (mentioning-sentence: $s, subject: $subjectToken, object: $objectToken1, object: $objectToken2) isa mined-relation, has confidence 1.0, has relation-type 'treatment';\"\n",
    "                \n",
    "                \n",
    "                #print(insert_query,\"\\n\")\n",
    "\n",
    "                insert_query_iterator = write_transaction.query(new_query)#(insert_query)\n",
    "\n",
    "                insert_query_list = insert_query_iterator.collect_concepts()\n",
    "                print(insert_query_list)\n",
    "                #(\"Inserted relationship attribute into the text keyspace with ID: {0}\".format(insert_query_list[0].id))\n",
    "\n",
    "                ## write transaction must always be committed (closed)\n",
    "                write_transaction.commit()\n",
    "                \n",
    "                \n",
    "                print(\"Inserted mined-relations\")\n",
    "\n",
    "\n",
    "            \n",
    "            \n",
    "            \n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<grakn.service.Session.Concept.Concept.Entity at 0x7f5acbd695c0>,\n",
       " <grakn.service.Session.Concept.Concept.Relation at 0x7f5acbd696d8>,\n",
       " <grakn.service.Session.Concept.Concept.Entity at 0x7f5acbd6ce80>,\n",
       " <grakn.service.Session.Concept.Concept.Entity at 0x7f5acbd6c9b0>,\n",
       " <grakn.service.Session.Concept.Concept.Entity at 0x7f5acbd6cda0>]"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "insert_query_list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Migrate Entity Mention and Mention "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fewer --> \n",
      "skin --> \n",
      "- --> \n",
      "related --> \n",
      "AEs --> \n",
      "( --> \n",
      "e.g. --> \n",
      "cutaneous --> \n",
      "malignancies --> \n",
      ", --> \n",
      "hyperkeratinosis --> \n",
      "and --> \n",
      "hand --> \n",
      "- --> \n",
      "foot --> \n",
      "syndrome --> \n",
      ") --> \n",
      "were --> \n",
      "reported --> \n",
      "with --> \n",
      "combination --> \n",
      "therapy --> \n",
      "than --> \n",
      "with --> \n",
      "dabrafenib --> \n",
      "or --> \n",
      "vemurafenib --> drug\n",
      ", --> \n",
      "probably --> \n",
      "because --> \n",
      "of --> \n",
      "reduced --> \n",
      "paradoxical --> \n",
      "activation --> \n",
      "of --> \n",
      "the --> \n",
      "MAPK --> \n",
      "pathway --> \n",
      ". --> \n"
     ]
    }
   ],
   "source": [
    "for token in doc:\n",
    "    print(token.text,\"-->\",\n",
    "         token.ent_type_\n",
    "        )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<grakn.service.Session.util.ResponseReader.ResponseIterator object at 0x7f5acbd57eb8>\n",
      "V8336\n",
      "Dabrafenib plus trametinib significantly prolonged progression-free survival (PFS) and overall survival (OS), improved objective response rates (ORRs) and preserved health-related quality of life (HR-QOL) to a greater extent than dabrafenib (in the double-blind COMBI-d study) and vemurafenib (in the open-label COMBI-v study) in two large, randomized, phase III studies in treatment-\n",
      "Dabrafenib --> drug\n",
      "trametinib --> drug\n",
      "Entity Mention Insertion completed\n",
      "V12392\n",
      "na\\xc3\\xafve patients with unresectable or metastatic melanoma with BRAF (V600E/K) mutation.\n",
      "BRAF --> gene\n",
      "V600E --> varient\n",
      "/ --> varient\n",
      "K --> varient\n",
      "Entity Mention Insertion completed\n",
      "V12400\n",
      "Thus, dabrafenib plus trametinib provides an important treatment option for patients with BRAF (V600) mutation-positive unresectable or metastatic melanoma.'\n",
      "trametinib --> drug\n",
      "BRAF --> gene\n",
      "V600 --> varient\n",
      "melanoma --> diesease\n",
      "Entity Mention Insertion completed\n",
      "V40964136\n",
      "b'The BRAF inhibitor dabrafenib (Tafinlar(\\xc2\\xae)) and the MEK inhibitor trametinib (Mekinist(\\xc2\\xae)) are indicated, as monotherapy or in combination with each other, for the treatment of patients with unresectable or metastatic melanoma with a BRAF (V600) mutation.\n",
      "BRAF --> gene\n",
      "dabrafenib --> drug\n",
      "MEK --> protien\n",
      "trametinib --> drug\n",
      "melanoma --> diesease\n",
      "BRAF --> gene\n",
      "V600 --> varient\n",
      "Entity Mention Insertion completed\n",
      "V40968232\n",
      "This article reviews the therapeutic efficacy and tolerability of combination treatment with dabrafenib and trametinib in this indication and summarizes relevant pharmacological data.\n",
      "trametinib --> drug\n",
      "Entity Mention Insertion completed\n",
      "V40968312\n",
      "Limited treatment benefit with the combination was also seen in patients who had progressed on prior BRAF inhibitor therapy, as indicated by ORRs of \\xe2\\x89\\xa4 15\\xc2\\xa0% and stable disease in \\xe2\\x89\\xa4 50\\xc2\\xa0% of patients in small phase I and II studies.\n",
      "BRAF --> gene\n",
      "Entity Mention Insertion completed\n",
      "V40980520\n",
      "Combination therapy did not increase overall toxicity relative to dabrafenib or vemurafenib monotherapy, with most adverse events (AEs) mild or moderate in severity and generally manageable.\n",
      "vemurafenib --> drug\n",
      "Entity Mention Insertion completed\n",
      "V40992808\n",
      "Fewer skin-related AEs (e.g. cutaneous malignancies, hyperkeratinosis and hand-foot syndrome) were reported with combination therapy than with dabrafenib or vemurafenib, probably because of reduced paradoxical activation of the MAPK pathway.\n",
      "vemurafenib --> drug\n",
      "Entity Mention Insertion completed\n"
     ]
    }
   ],
   "source": [
    "# Transaction query on doc\n",
    "\n",
    "with GraknClient(uri='localhost:48555') as client:\n",
    "\n",
    "    with client.session(keyspace=\"text\") as session:\n",
    "            \n",
    "        with session.transaction().read() as read_transaction:\n",
    "            read_query_iterator = read_transaction.query('match $s isa sentence,has text $t;get $s;')\n",
    "            read_query_list = read_query_iterator.collect_concepts()\n",
    "            \n",
    "            print(query_iterator)\n",
    "\n",
    "\n",
    "            # Write transaction\n",
    "\n",
    "            for q in read_query_list:\n",
    "                print(q.id)\n",
    "    \n",
    "                # Inner For loop for reading the text from the retrieved sentence concpet\n",
    "                for text in q.attributes():\n",
    "                    #esult.append(text.value())\n",
    "                    if text.type().label() == 'text':\n",
    "                        print(text.value())\n",
    "    \n",
    "                        sent_id = q.id\n",
    "                        # Tokenizing extracted sentence\n",
    "                        doc = nlp(text.value())\n",
    "                        for token in doc:\n",
    "                            if token.ent_type_:\n",
    "                                entity_value = token.text\n",
    "                            \n",
    "                                entity_type = token.ent_type_\n",
    "                                print(entity_value, \"-->\",entity_type)\n",
    "\n",
    "\n",
    "                            ## Creating a session\n",
    "                            with client.session(keyspace=\"text\") as session:\n",
    "                                ## creating a write transaction\n",
    "                                with session.transaction().write() as write_transaction:\n",
    "                                    # Grakn Insert Query\n",
    "                                    insert_query = 'match $s id {};\\\n",
    "                                    insert $e isa entity-mention,\\\n",
    "                                    has value \"{}\",\\\n",
    "                                    has entity-type \"{}\";\\\n",
    "                                    $m(mentioned-entity: $e,mentioning-sentence : $s) isa mention;'.format(sent_id,entity_value,entity_type)\n",
    "\n",
    "                                    #print(insert_query,\"\\n\")\n",
    "\n",
    "                                    insert_query_iterator = write_transaction.query(insert_query)\n",
    "\n",
    "                                    insert_query_list = insert_query_iterator.collect_concepts()\n",
    "                                    #print(\"Inserted token attribute into the text keyspace with ID: {0}\".format(insert_query_list[0].id))\n",
    "\n",
    "                                    ## write transaction must always be committed (closed)\n",
    "                                    write_transaction.commit()\n",
    "                        print('Entity Mention Insertion completed')\n",
    "\n",
    "                \n",
    "             "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Migrate entity-containing-token "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "V303240\n",
      "vemurafenib --> vemurafenib\n",
      "V307336\n",
      "vemurafenib --> vemurafenib\n",
      "V311432\n",
      "vemurafenib --> vemurafenib\n",
      "V336008\n",
      "dabrafenib --> dabrafenib\n",
      "V340104\n",
      "dabrafenib --> dabrafenib\n",
      "V344312\n",
      "vemurafenib --> vemurafenib\n",
      "V348296\n",
      "trametinib --> trametinib\n",
      "V348408\n",
      "vemurafenib --> vemurafenib\n",
      "V352392\n",
      "trametinib --> trametinib\n",
      "V360584\n",
      "trametinib --> trametinib\n",
      "V360696\n",
      "BRAF --> BRAF\n",
      "V364792\n",
      "MEK --> MEK\n",
      "V372984\n",
      "trametinib --> trametinib\n",
      "V376968\n",
      "V600 --> v600\n",
      "V377080\n",
      "trametinib --> trametinib\n",
      "V381064\n",
      "V600 --> v600\n",
      "V381072\n",
      "vemurafenib --> vemurafenib\n",
      "V385160\n",
      "V600 --> v600\n",
      "V385272\n",
      "melanoma --> melanoma\n",
      "V389264\n",
      "vemurafenib --> vemurafenib\n",
      "V397448\n",
      "vemurafenib --> vemurafenib\n",
      "V401656\n",
      "V600 --> v600\n",
      "V405632\n",
      "vemurafenib --> vemurafenib\n",
      "V405648\n",
      "trametinib --> trametinib\n",
      "V405752\n",
      "vemurafenib --> vemurafenib\n",
      "V409728\n",
      "trametinib --> trametinib\n",
      "V409736\n",
      "vemurafenib --> vemurafenib\n",
      "V409744\n",
      "trametinib --> trametinib\n",
      "V409848\n",
      "vemurafenib --> vemurafenib\n",
      "V413824\n",
      "trametinib --> trametinib\n",
      "V413832\n",
      "vemurafenib --> vemurafenib\n",
      "V413944\n",
      "vemurafenib --> vemurafenib\n",
      "V417920\n",
      "BRAF --> BRAF\n",
      "V417936\n",
      "trametinib --> trametinib\n",
      "V422136\n",
      "vemurafenib --> vemurafenib\n",
      "V426120\n",
      "vemurafenib --> vemurafenib\n",
      "V426128\n",
      "trametinib --> trametinib\n",
      "V426232\n",
      "vemurafenib --> vemurafenib\n",
      "V430208\n",
      "trametinib --> trametinib\n",
      "V430328\n",
      "vemurafenib --> vemurafenib\n",
      "V434304\n",
      "trametinib --> trametinib\n",
      "V434320\n",
      "trametinib --> trametinib\n",
      "V434424\n",
      "vemurafenib --> vemurafenib\n",
      "V438400\n",
      "trametinib --> trametinib\n",
      "V438408\n",
      "vemurafenib --> vemurafenib\n",
      "V438416\n",
      "trametinib --> trametinib\n",
      "V446592\n",
      "trametinib --> trametinib\n",
      "V446600\n",
      "vemurafenib --> vemurafenib\n",
      "V446608\n",
      "trametinib --> trametinib\n",
      "V450696\n",
      "trametinib --> trametinib\n",
      "V450808\n",
      "trametinib --> trametinib\n",
      "V454784\n",
      "trametinib --> trametinib\n",
      "V454792\n",
      "trametinib --> trametinib\n",
      "V454800\n",
      "BRAF --> BRAF\n",
      "V459000\n",
      "trametinib --> trametinib\n",
      "V463096\n",
      "trametinib --> trametinib\n",
      "V471176\n",
      "trametinib --> trametinib\n",
      "V471184\n",
      "vemurafenib --> vemurafenib\n",
      "V475280\n",
      "vemurafenib --> vemurafenib\n",
      "V475384\n",
      "trametinib --> trametinib\n",
      "V479360\n",
      "V600 --> v600\n",
      "V479376\n",
      "vemurafenib --> vemurafenib\n",
      "V483456\n",
      "V600 --> v600\n",
      "V483464\n",
      "trametinib --> trametinib\n",
      "V487552\n",
      "V600 --> v600\n",
      "V487672\n",
      "trametinib --> trametinib\n",
      "V491664\n",
      "vemurafenib --> vemurafenib\n",
      "V491768\n",
      "trametinib --> trametinib\n",
      "V495744\n",
      "vemurafenib --> vemurafenib\n",
      "V495760\n",
      "vemurafenib --> vemurafenib\n",
      "V495864\n",
      "trametinib --> trametinib\n",
      "V499840\n",
      "vemurafenib --> vemurafenib\n",
      "V499960\n",
      "trametinib --> trametinib\n",
      "V503936\n",
      "vemurafenib --> vemurafenib\n",
      "V503944\n",
      "trametinib --> trametinib\n",
      "V504056\n",
      "trametinib --> trametinib\n",
      "V512128\n",
      "vemurafenib --> vemurafenib\n",
      "V516232\n",
      "trametinib --> trametinib\n",
      "V516240\n",
      "trametinib --> trametinib\n",
      "V520336\n",
      "trametinib --> trametinib\n",
      "V524416\n",
      "vemurafenib --> vemurafenib\n",
      "V524432\n",
      "trametinib --> trametinib\n",
      "V524536\n",
      "BRAF --> BRAF\n",
      "V528520\n",
      "trametinib --> trametinib\n",
      "V528528\n",
      "trametinib --> trametinib\n",
      "V532624\n",
      "trametinib --> trametinib\n",
      "V536704\n",
      "vemurafenib --> vemurafenib\n",
      "V536712\n",
      "BRAF --> BRAF\n",
      "V536720\n",
      "trametinib --> trametinib\n",
      "V540920\n",
      "melanoma --> melanoma\n",
      "V544904\n",
      "BRAF --> BRAF\n",
      "V544912\n",
      "trametinib --> trametinib\n",
      "V545016\n",
      "BRAF --> BRAF\n",
      "V549008\n",
      "trametinib --> trametinib\n",
      "V553096\n",
      "BRAF --> BRAF\n",
      "V553104\n",
      "trametinib --> trametinib\n",
      "V553208\n",
      "K --> k\n",
      "V561280\n",
      "trametinib --> trametinib\n",
      "V561296\n",
      "trametinib --> trametinib\n",
      "V569488\n",
      "trametinib --> trametinib\n",
      "V573568\n",
      "trametinib --> trametinib\n",
      "V573576\n",
      "trametinib --> trametinib\n",
      "V577672\n",
      "BRAF --> BRAF\n",
      "V577680\n",
      "trametinib --> trametinib\n",
      "V581760\n",
      "trametinib --> trametinib\n",
      "V581768\n",
      "V600 --> v600\n",
      "V581776\n",
      "trametinib --> trametinib\n",
      "V585856\n",
      "trametinib --> trametinib\n",
      "V585864\n",
      "V600 --> v600\n",
      "V589968\n",
      "BRAF --> BRAF\n",
      "V594048\n",
      "trametinib --> trametinib\n",
      "V598160\n",
      "BRAF --> BRAF\n",
      "V602240\n",
      "trametinib --> trametinib\n",
      "V606336\n",
      "trametinib --> trametinib\n",
      "V606352\n",
      "BRAF --> BRAF\n",
      "V614528\n",
      "trametinib --> trametinib\n",
      "V614544\n",
      "BRAF --> BRAF\n",
      "V618624\n",
      "trametinib --> trametinib\n",
      "V618640\n",
      "BRAF --> BRAF\n",
      "V622720\n",
      "trametinib --> trametinib\n",
      "V626816\n",
      "trametinib --> trametinib\n",
      "V626832\n",
      "BRAF --> BRAF\n",
      "V630912\n",
      "trametinib --> trametinib\n",
      "V630928\n",
      "BRAF --> BRAF\n",
      "V643216\n",
      "BRAF --> BRAF\n",
      "V647296\n",
      "BRAF --> BRAF\n",
      "V651392\n",
      "BRAF --> BRAF\n",
      "V651408\n",
      "trametinib --> trametinib\n",
      "V655504\n",
      "trametinib --> trametinib\n",
      "V659584\n",
      "BRAF --> BRAF\n",
      "V659600\n",
      "V600 --> v600\n",
      "V663696\n",
      "melanoma --> melanoma\n",
      "V667792\n",
      "melanoma --> melanoma\n",
      "V667816\n",
      "vemurafenib --> vemurafenib\n",
      "V671888\n",
      "melanoma --> melanoma\n",
      "V671912\n",
      "vemurafenib --> vemurafenib\n",
      "V680080\n",
      "melanoma --> melanoma\n",
      "V680104\n",
      "vemurafenib --> vemurafenib\n",
      "V688256\n",
      "BRAF --> BRAF\n",
      "V692352\n",
      "K --> k\n",
      "V696464\n",
      "/ --> /\n",
      "V696488\n",
      "trametinib --> trametinib\n",
      "V700584\n",
      "trametinib --> trametinib\n",
      "V704632\n",
      "vemurafenib --> vemurafenib\n",
      "V704680\n",
      "trametinib --> trametinib\n",
      "V708776\n",
      "trametinib --> trametinib\n",
      "V716968\n",
      "dabrafenib --> dabrafenib\n",
      "V725112\n",
      "trametinib --> trametinib\n",
      "V729256\n",
      "MEK --> MEK\n",
      "V733304\n",
      "trametinib --> trametinib\n",
      "V745592\n",
      "dabrafenib --> dabrafenib\n",
      "V749736\n",
      "trametinib --> trametinib\n",
      "V753784\n",
      "dabrafenib --> dabrafenib\n",
      "V753832\n",
      "trametinib --> trametinib\n",
      "V761976\n",
      "dabrafenib --> dabrafenib\n",
      "V762024\n",
      "melanoma --> melanoma\n",
      "V766120\n",
      "BRAF --> BRAF\n",
      "V770216\n",
      "V600 --> v600\n",
      "V778360\n",
      "trametinib --> trametinib\n",
      "V782504\n",
      "vemurafenib --> vemurafenib\n",
      "V786552\n",
      "trametinib --> trametinib\n",
      "V790696\n",
      "vemurafenib --> vemurafenib\n",
      "V794744\n",
      "trametinib --> trametinib\n",
      "V794792\n",
      "vemurafenib --> vemurafenib\n",
      "V798888\n",
      "vemurafenib --> vemurafenib\n",
      "V802936\n",
      "V600 --> v600\n",
      "V802984\n",
      "vemurafenib --> vemurafenib\n",
      "V807032\n",
      "V600 --> v600\n",
      "V807080\n",
      "vemurafenib --> vemurafenib\n",
      "V811128\n",
      "V600 --> v600\n",
      "V827512\n",
      "V600 --> v600\n",
      "V827560\n",
      "vemurafenib --> vemurafenib\n",
      "V835704\n",
      "vemurafenib --> vemurafenib\n",
      "V839800\n",
      "vemurafenib --> vemurafenib\n",
      "V839848\n",
      "vemurafenib --> vemurafenib\n",
      "V843896\n",
      "vemurafenib --> vemurafenib\n",
      "V843944\n",
      "vemurafenib --> vemurafenib\n",
      "V847992\n",
      "vemurafenib --> vemurafenib\n",
      "V852088\n",
      "vemurafenib --> vemurafenib\n",
      "V856232\n",
      "vemurafenib --> vemurafenib\n",
      "V860280\n",
      "vemurafenib --> vemurafenib\n",
      "V864424\n",
      "vemurafenib --> vemurafenib\n",
      "V868472\n",
      "vemurafenib --> vemurafenib\n",
      "V872568\n",
      "vemurafenib --> vemurafenib\n",
      "V876712\n",
      "vemurafenib --> vemurafenib\n",
      "V880808\n",
      "vemurafenib --> vemurafenib\n",
      "V884856\n",
      "vemurafenib --> vemurafenib\n",
      "V884904\n",
      "vemurafenib --> vemurafenib\n",
      "V888952\n",
      "vemurafenib --> vemurafenib\n",
      "V893048\n",
      "vemurafenib --> vemurafenib\n",
      "V893096\n",
      "trametinib --> trametinib\n",
      "V897144\n",
      "vemurafenib --> vemurafenib\n",
      "V905336\n",
      "vemurafenib --> vemurafenib\n",
      "V909432\n",
      "Dabrafenib --> Dabrafenib\n",
      "V909480\n",
      "trametinib --> trametinib\n",
      "V913528\n",
      "Dabrafenib --> Dabrafenib\n",
      "V917672\n",
      "trametinib --> trametinib\n",
      "V925816\n",
      "trametinib --> trametinib\n",
      "V929960\n",
      "trametinib --> trametinib\n",
      "V934056\n",
      "trametinib --> trametinib\n",
      "V938104\n",
      "trametinib --> trametinib\n",
      "V942200\n",
      "trametinib --> trametinib\n",
      "V946296\n",
      "trametinib --> trametinib\n",
      "V954488\n",
      "trametinib --> trametinib\n",
      "V958584\n",
      "trametinib --> trametinib\n",
      "V958632\n",
      "trametinib --> trametinib\n",
      "V962728\n",
      "trametinib --> trametinib\n",
      "V966776\n",
      "trametinib --> trametinib\n",
      "V970872\n",
      "trametinib --> trametinib\n",
      "V974968\n",
      "trametinib --> trametinib\n",
      "V983160\n",
      "trametinib --> trametinib\n",
      "V983208\n",
      "trametinib --> trametinib\n",
      "V987304\n",
      "trametinib --> trametinib\n",
      "V991352\n",
      "trametinib --> trametinib\n",
      "V995496\n",
      "trametinib --> trametinib\n",
      "V1003640\n",
      "trametinib --> trametinib\n",
      "V1007784\n",
      "trametinib --> trametinib\n",
      "V1011832\n",
      "trametinib --> trametinib\n",
      "V1011880\n",
      "trametinib --> trametinib\n",
      "V1015928\n",
      "trametinib --> trametinib\n",
      "V1028216\n",
      "trametinib --> trametinib\n",
      "V1032312\n",
      "trametinib --> trametinib\n",
      "V1036456\n",
      "trametinib --> trametinib\n",
      "V1040504\n",
      "trametinib --> trametinib\n",
      "V1040552\n",
      "trametinib --> trametinib\n",
      "V1044648\n",
      "BRAF --> BRAF\n",
      "V1052792\n",
      "trametinib --> trametinib\n",
      "V1052840\n",
      "BRAF --> BRAF\n",
      "V1056888\n",
      "trametinib --> trametinib\n",
      "V1060984\n",
      "trametinib --> trametinib\n",
      "V1061032\n",
      "BRAF --> BRAF\n",
      "V1065128\n",
      "BRAF --> BRAF\n",
      "V1069176\n",
      "trametinib --> trametinib\n",
      "V1073320\n",
      "BRAF --> BRAF\n",
      "V1077368\n",
      "trametinib --> trametinib\n",
      "V1081464\n",
      "trametinib --> trametinib\n",
      "V1085560\n",
      "trametinib --> trametinib\n",
      "V1085608\n",
      "trametinib --> trametinib\n",
      "V1089704\n",
      "trametinib --> trametinib\n",
      "V1093752\n",
      "BRAF --> BRAF\n",
      "V1097896\n",
      "BRAF --> BRAF\n",
      "V1101944\n",
      "BRAF --> BRAF\n",
      "V1106040\n",
      "BRAF --> BRAF\n",
      "V1110136\n",
      "BRAF --> BRAF\n",
      "V1118376\n",
      "V600 --> v600\n",
      "V1122424\n",
      "BRAF --> BRAF\n",
      "V1126520\n",
      "BRAF --> BRAF\n",
      "V1130616\n",
      "BRAF --> BRAF\n",
      "V1130664\n",
      "melanoma --> melanoma\n",
      "V1134712\n",
      "BRAF --> BRAF\n",
      "V1134760\n",
      "melanoma --> melanoma\n",
      "V1138808\n",
      "BRAF --> BRAF\n",
      "V1151096\n",
      "trametinib --> trametinib\n",
      "V1155192\n",
      "trametinib --> trametinib\n",
      "V1159288\n",
      "trametinib --> trametinib\n",
      "V1171576\n",
      "trametinib --> trametinib\n",
      "V1179768\n",
      "V600 --> v600\n",
      "V1183864\n",
      "melanoma --> melanoma\n",
      "V1192056\n",
      "melanoma --> melanoma\n",
      "V1200248\n",
      "V600E --> v600e\n",
      "V1204344\n",
      "K --> k\n",
      "V41238560\n",
      "vemurafenib --> vemurafenib\n",
      "V41259040\n",
      "vemurafenib --> vemurafenib\n",
      "V41263136\n",
      "trametinib --> trametinib\n",
      "V41275424\n",
      "dabrafenib --> dabrafenib\n",
      "V41295904\n",
      "trametinib --> trametinib\n",
      "V41300000\n",
      "melanoma --> melanoma\n",
      "V41308192\n",
      "V600 --> v600\n",
      "V41312280\n",
      "trametinib --> trametinib\n",
      "V41316384\n",
      "V600 --> v600\n",
      "V41324568\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "trametinib --> trametinib\n",
      "V41324576\n",
      "V600 --> v600\n",
      "V41328664\n",
      "trametinib --> trametinib\n",
      "V41336856\n",
      "trametinib --> trametinib\n",
      "V41345048\n",
      "trametinib --> trametinib\n",
      "V41345056\n",
      "vemurafenib --> vemurafenib\n",
      "V41361440\n",
      "vemurafenib --> vemurafenib\n",
      "V41377824\n",
      "trametinib --> trametinib\n",
      "V41381912\n",
      "vemurafenib --> vemurafenib\n",
      "V41381920\n",
      "trametinib --> trametinib\n",
      "V41394200\n",
      "vemurafenib --> vemurafenib\n",
      "V41394208\n",
      "trametinib --> trametinib\n",
      "V41398296\n",
      "vemurafenib --> vemurafenib\n",
      "V41398304\n",
      "trametinib --> trametinib\n",
      "V41402392\n",
      "vemurafenib --> vemurafenib\n",
      "V41402400\n",
      "trametinib --> trametinib\n",
      "V41406496\n",
      "trametinib --> trametinib\n",
      "V41410584\n",
      "vemurafenib --> vemurafenib\n",
      "V41418776\n",
      "trametinib --> trametinib\n",
      "V41422880\n",
      "trametinib --> trametinib\n",
      "V41426968\n",
      "trametinib --> trametinib\n",
      "V41435160\n",
      "trametinib --> trametinib\n",
      "V41439256\n",
      "trametinib --> trametinib\n",
      "V41439264\n",
      "trametinib --> trametinib\n",
      "V41443352\n",
      "trametinib --> trametinib\n",
      "V41443360\n",
      "BRAF --> BRAF\n",
      "V41447448\n",
      "trametinib --> trametinib\n",
      "V41451544\n",
      "trametinib --> trametinib\n",
      "V41451552\n",
      "BRAF --> BRAF\n",
      "V41463840\n",
      "V600 --> v600\n",
      "V41472032\n",
      "melanoma --> melanoma\n",
      "V41476128\n",
      "melanoma --> melanoma\n",
      "V41480216\n",
      "BRAF --> BRAF\n",
      "V41484312\n",
      "BRAF --> BRAF\n",
      "V41492504\n",
      "V600 --> v600\n",
      "V41500696\n",
      "V600 --> v600\n",
      "V41508888\n",
      "K --> k\n"
     ]
    }
   ],
   "source": [
    "# Transaction query on doc\n",
    "\n",
    "with GraknClient(uri='localhost:48555') as client:\n",
    "\n",
    "    with client.session(keyspace=\"text\") as session:\n",
    "            \n",
    "        with session.transaction().read() as read_transaction:\n",
    "            read_query_iterator = read_transaction.query('match $e isa entity-mention;get $e;')\n",
    "            read_query_list = read_query_iterator.collect_concepts()\n",
    "            \n",
    "            for q in read_query_list:\n",
    "                print(q.id)\n",
    "                for value in q.attributes():\n",
    "                    if value.type().label() == 'value':\n",
    "                        #print(value.value())\n",
    "                        \n",
    "                        spacy_entity_doc = nlp(value.value())\n",
    "                        for token in spacy_entity_doc:\n",
    "                            print(token.text, \"-->\", token.lemma_)\n",
    "                            \n",
    "#                             with client.session(keyspace=\"text_mining\") as session:\n",
    "#                                 ## creating a write transaction\n",
    "#                                 with session.transaction().write() as write_transaction:\n",
    "#                                     # Grakn Insert Query\n",
    "#                                     insert_query = 'match $e isa entity-mention,\\\n",
    "#                                     has value \"{}\";\\\n",
    "#                                     $t isa token,\\\n",
    "#                                     has lemma \"{}\";\\\n",
    "#                                     insert $ect(containing-entity: $e,contained-token : $t) isa entity-containing-token;'\\\n",
    "#                                     .format(token.text,token.lemma_)\n",
    "\n",
    "#                                     #print(insert_query,\"\\n\")\n",
    "\n",
    "#                                     insert_query_iterator = write_transaction.query(insert_query)\n",
    "\n",
    "#                                     insert_query_list = insert_query_iterator.collect_concepts()\n",
    "#                                     #print(\"Inserted token attribute into the text_mining keyspace with ID: {0}\".format(insert_query_list[0].id))\n",
    "\n",
    "#                                     ## write transaction must always be committed (closed)\n",
    "#                                     write_transaction.commit()\n",
    "#                         print('Entity Containing Token Mention Insertion completed')\n",
    "            \n",
    "\n",
    "                \n",
    "             "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Close Grakn Connection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "client.close()"
   ]
  }
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