clinical_ie_multi_agents.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Multi Agents: Clinical Metadata Extraction\n",
    "\n",
    "This project provides a powerful system for extracting and structuring clinical metadata from a given set of text chunks, such as those found in medical case studies.\n",
    "\n",
    "The system is composed of two main components:\n",
    "\n",
    "## 1. RetrieverAgent\n",
    "\n",
    "The `RetrieverAgent` is responsible for iteratively querying a vector database to retrieve the relevant text chunks for a given metadata category. It takes the following inputs:\n",
    "\n",
    "- A language model (LLM) for generating the queries\n",
    "- A `RetrieverManager`: contain tools for querying the vector database and ranking the retrieved chunks\n",
    "- A `ChunkManager`: contain tools for managing the storage of retrieved text chunks\n",
    "\n",
    "The `RetrieverAgent` follows an iterative process to extract the relevant text chunks:\n",
    "\n",
    "1. The agent uses initial query and the `RetrieverManager` to retrieve and rank the relevant chunks.\n",
    "2. The agent then analyze if retrieved chunks are relevant and then stores them using the `ChunkManager` for later use by the `MetadataExtractionAgent`.\n",
    "3. If retrieved chunks are not relevant then the agent refine the initial query and retrieve the chunks again.\n",
    "4. The process continues until the agent is confident that it has extracted all relevant chunks.\n",
    "\n",
    "## 2. MetadataExtractionAgent\n",
    "\n",
    "The `MetadataExtractionAgent` is responsible for the overall process of extracting and structuring the clinical metadata. It takes the following inputs:\n",
    "\n",
    "- A language model (LLM) for generating the metadata\n",
    "- A `ChunkManager`: contain tools for managing the storage of retrieved text chunks\n",
    "- A `MetadataManager`: contain tools for managing the stored sentence snippets from each chunks\n",
    "- An `OutputValidator`: Tool for validating the final structured metadata output\n",
    "\n",
    "The `MetadataExtractionAgent` follows a multi-step process to produce the final metadata:\n",
    "\n",
    "1. It generates a detailed prompt that instructs the LLM to analyze the text chunks and extract relevant information for the specified metadata categories.\n",
    "2. The agent analyze each chunks and extract sentence snippets which are relevant for a speicific metadata categories. \n",
    "3. It uses `MetadataManager` tool for maintain all extracted sentence snippets and later generates the final structured output.\n",
    "3. The agent validates the generated output using the `OutputValidator` tool, and if errors or missing fields are detected, the agent will retry the process until the valid output is generated.\n",
    "4. The final, validated metadata is returned as a structured dictionary.\n",
    "\n",
    "## How the System Works\n",
    "\n",
    "The complete system works as follows:\n",
    "\n",
    "1. The `RetrieverAgent` is used to extract relevant text chunks for a subset of the metadata categories.\n",
    "2. The `MetadataExtractionAgent` is then used to generate the final structured metadata, leveraging the text chunks retrieved by the `RetrieverAgent`.\n",
    "3. The `OutputValidator` is used to ensure the generated metadata conforms to the expected data model.\n",
    "\n",
    "This two-step approach, with the `RetrieverAgent` handling the chunk extraction and the `MetadataExtractionAgent` handling the final metadata generation, allows the system to efficiently and accurately extract clinical metadata from the given text data.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Sample predicted output:\n",
    "\n",
    "```json\n",
    "{\n",
    "  \"Life_Style\": [],\n",
    "  \"Family_History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"],\n",
    "  \"Social_History\": [],\n",
    "  \"Medical_Surgical_History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"],\n",
    "  \"Signs_and_Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"],\n",
    "  \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"],\n",
    "  \"Diagnostic_Techniques_and_Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"],\n",
    "  \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"],\n",
    "  \"Laboratory_Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"],\n",
    "  \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"],\n",
    "  \"Pharmacological_Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"],\n",
    "  \"Interventional_Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"],\n",
    "  \"Patient_Outcome_Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"],\n",
    "  \"Age\": 73,\n",
    "  \"Gender\": \"\"\n",
    "}\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import json\n",
    "\n",
    "from typing import Dict\n",
    "from dotenv import load_dotenv\n",
    "\n",
    "from llama_index.llms.openai import OpenAI\n",
    "from llama_index.core.tools import FunctionTool\n",
    "from llama_index.core.agent import ReActAgent \n",
    "\n",
    "from clinical_ie.tools import ChunkManager, RetrieverManager, MetadataManager, OutputValidator, ClinicalMetadata\n",
    "from clinical_ie.simple_rag_pipeline.rag_utils import get_retriever, get_embedding_model, load_reranker_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "load_dotenv()\n",
    "\n",
    "base_path = \"clinical_ie/MACCR/\"\n",
    "\n",
    "pdf_fn = \"Tsuchiya et al. - 2017 - A case of concomitant colitic cancer and intrahepa.pdf\"\n",
    "pdf_file = base_path+pdf_fn\n",
    "\n",
    "top_k = 3 # for ranking\n",
    "node_parsing_method = \"semantic\"\n",
    "\n",
    "OPEN_AI_MODEL_NAME = \"gpt-4o-2024-08-06\" # \"gpt-4o-mini-2024-07-18\" # \n",
    "KEY = os.environ.get(\"OPENAI_API_KEY\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Model Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "============================== Embedding mixedbread-ai/mxbai-embed-large-v1 is loaded successfully using the provider huggingface\n",
      "Found 6 total number of pages from the document clinical_ie/MACCR/Tsuchiya et al. - 2017 - A case of concomitant colitic cancer and intrahepa.pdf, after cleaning 5 left\n"
     ]
    }
   ],
   "source": [
    "llm = OpenAI(model=OPEN_AI_MODEL_NAME,api_key=KEY)\n",
    "\n",
    "embed_model = get_embedding_model()\n",
    "\n",
    "retriever = get_retriever(pdf_file, embed_model, node_parsing_method,top_k=10)\n",
    "\n",
    "reranker_model = load_reranker_model()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Retriever Agent: Extract all relevant piece of chunk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "class RetrieverAgent(ReActAgent):\n",
    "    def __init__(self, retriever_manager : RetrieverManager, llm, chunk_manager : ChunkManager):\n",
    "        self.llm = llm\n",
    "        self.chunk_manager = chunk_manager\n",
    "        self.retriever_manager = retriever_manager\n",
    "        \n",
    "        tools = [\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.chunk_manager.save_chunks\n",
    "            ),\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.chunk_manager.get_chunks\n",
    "            ),\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.retriever_manager.retrieve_chunks\n",
    "            ),\n",
    "            \n",
    "        ]\n",
    "        super().__init__(tools=tools, llm=self.llm, memory=None, max_iterations=20, verbose=True)\n",
    "\n",
    "    def extract_metadata_chunks(self, metadata_category: str, initial_query) -> None:\n",
    "        prompt = f\"\"\"You are an advanced clinical information retrieval system with expertise in analyzing medical case studies. Your task is to iteratively generate queries to extract relevant chunks of information for specific metadata categories from a clinical case study. You will later use these chunks to compile comprehensive metadata for each category.\n",
    "\n",
    "        Metadata Category:\n",
    "        {metadata_category}\n",
    "\n",
    "        Initial Query:\n",
    "        {initial_query}\n",
    "\n",
    "        Instructions:\n",
    "        1. Start with a initial query for the metadata category {metadata_category}. Use the vector_db_query tool to search for relevant chunks.\n",
    "\n",
    "        2. Retrieved chunk:\n",
    "        a. Analyze its relevance to the current metadata category.\n",
    "        b. If relevant, use the save_chunks tool to store it.\n",
    "        c. If not relevant, briefly explain why and use this information to refine your next query.\n",
    "\n",
    "        4. Iterative Query Refinement Process:\n",
    "        a. If initial queries don't yield sufficient relevant information:\n",
    "            - Use synonyms or related medical terms.\n",
    "            - Consider indirect references or contextual clues.\n",
    "            - Broaden the search to include related concepts.\n",
    "        b. If queries yield too much irrelevant information:\n",
    "            - Make your queries more specific.\n",
    "        c. If you find partial information:\n",
    "            - Generate follow-up queries to find missing details.\n",
    "\n",
    "        5. Consider these aspects when searching:\n",
    "        - Direct mentions of the category or related terms.\n",
    "        - Contextual information that implies relevant data.\n",
    "\n",
    "        6. Continue this process until:\n",
    "        a. You are confident you have extracted all relevant information.\n",
    "        b. Multiple consecutive refined queries yield no new unique chunks.\n",
    "\n",
    "        Remember:\n",
    "        - Accuracy and comprehensiveness are crucial.\n",
    "        \"\"\"\n",
    "        _ = self.chat(prompt)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Metadata Extraction Agent: Extract important metadata from retrieved chunks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "class MetadataExtractionAgent(ReActAgent):\n",
    "    def __init__(self, llm, chunk_manager:ChunkManager, metadata_manager:MetadataManager, output_validator:OutputValidator):\n",
    "        self.llm = llm\n",
    "        self.chunk_manager = chunk_manager\n",
    "        self.metadata_manager = metadata_manager\n",
    "        self.output_validator = output_validator\n",
    "        tools = [\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.chunk_manager.get_chunk\n",
    "            ),\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.metadata_manager.add_metadatas\n",
    "            ),\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.metadata_manager.get_all_metadata\n",
    "            ),\n",
    "            FunctionTool.from_defaults(\n",
    "                fn=self.output_validator.validate_generated_metadata\n",
    "            )\n",
    "\n",
    "        ]\n",
    "        super().__init__(tools=tools, llm=self.llm, memory=None, max_iterations=25, verbose=True)\n",
    "\n",
    "    def extract_metadata(self, categories: str, chunk_ids: str) -> Dict[str, str]:\n",
    "        prompt = f\"\"\"You are an expert clinical information specialist with extensive experience in analyzing medical case studies and extracting precise metadata.\n",
    "        \n",
    "        Your task is to analyze clinical case study chunks and extract sentence snippets relevant to {categories}. Follow these steps:\n",
    "        \n",
    "        1. Use the `get_chunk` tool to get relevant chunks using the chunk id.\n",
    "\n",
    "        2. Analyze each chunk sequentially, focusing on extractive rather than generative approaches:\n",
    "        - Extract sentence snippet or piece of text that fit into the following clinical metadata categories: {categories}.\n",
    "        - Use the sentence saving tool `add_metadatas` to store relevant snippets all categories.\n",
    "\n",
    "        3. After analyzing all chunks:\n",
    "        - Get all sentence snippets saved in previous step using the tool `get_all_metadata`.\n",
    "        - Now combine sentence snippets which makes sense and refine others with minimal paraphrasing if they don't make sense.\n",
    "        - Discard any information that doesn't make sense in the context of the category.\n",
    "\n",
    "        4. Final output should be in json format containing category as a key and list of metadata as a value.\n",
    "        Use the `generate_clinical_metadata`, a parser tool to structure your final output.\n",
    "\n",
    "        5. If the parser indicates errors or missing fields:\n",
    "        - Review the extracted information.\n",
    "        - Make necessary adjustments.\n",
    "        - Try the parser again.\n",
    "        - Repeat this process up to 3 times if needed.\n",
    "\n",
    "        ## Important Notes:\n",
    "\n",
    "        - Prioritize extraction over generation. Only paraphrase when necessary for clarity.\n",
    "        - Ensure all extracted information is relevant to its assigned category.\n",
    "        - Be thorough in your analysis, but avoid redundancy in the final output.\n",
    "        - The final output must conform to the `generate_clinical_metadata` model structure.\n",
    "\n",
    "        Remember, your goal is to produce accurate, structured clinical metadata from the given case study chunks.\n",
    "\n",
    "\n",
    "        Chunks ids to analyze:\n",
    "        {chunk_ids}\n",
    "        \"\"\"\n",
    "        \n",
    "        response = self.chat(prompt)\n",
    "        return response.response"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> Running step af244fed-8745-47b2-870d-a8054b67297c. Step input: You are an advanced clinical information retrieval system with expertise in analyzing medical case studies. Your task is to iteratively generate queries to extract relevant chunks of information for specific metadata categories from a clinical case study. You will later use these chunks to compile comprehensive metadata for each category.\n",
      "\n",
      "        Metadata Category:\n",
      "        Diagnostic Techniques and Procedures\n",
      "\n",
      "        Initial Query:\n",
      "        Describe the diagnostic techniques and procedures used to evaluate the patient.\n",
      "\n",
      "        Instructions:\n",
      "        1. Start with a initial query for the metadata category Diagnostic Techniques and Procedures. Use the vector_db_query tool to search for relevant chunks.\n",
      "\n",
      "        2. Retrieved chunk:\n",
      "        a. Analyze its relevance to the current metadata category.\n",
      "        b. If relevant, use the save_chunks tool to store it.\n",
      "        c. If not relevant, briefly explain why and use this information to refine your next query.\n",
      "\n",
      "        4. Iterative Query Refinement Process:\n",
      "        a. If initial queries don't yield sufficient relevant information:\n",
      "            - Use synonyms or related medical terms.\n",
      "            - Consider indirect references or contextual clues.\n",
      "            - Broaden the search to include related concepts.\n",
      "        b. If queries yield too much irrelevant information:\n",
      "            - Make your queries more specific.\n",
      "        c. If you find partial information:\n",
      "            - Generate follow-up queries to find missing details.\n",
      "\n",
      "        5. Consider these aspects when searching:\n",
      "        - Direct mentions of the category or related terms.\n",
      "        - Contextual information that implies relevant data.\n",
      "\n",
      "        6. Continue this process until:\n",
      "        a. You are confident you have extracted all relevant information.\n",
      "        b. Multiple consecutive refined queries yield no new unique chunks.\n",
      "\n",
      "        Remember:\n",
      "        - Accuracy and comprehensiveness are crucial.\n",
      "        \n",
      "\u001b[1;3;38;5;200mThought: The current language of the user is English. I need to use a tool to help me answer the question by retrieving relevant chunks for the metadata category \"Diagnostic Techniques and Procedures\" using the initial query provided.\n",
      "Action: retrieve_chunks\n",
      "Action Input: {'query': 'Describe the diagnostic techniques and procedures used to evaluate the patient.'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Relevant Chunks:\n",
      "23e45bdb-9030-4eca-bb09-18d4c95df110 --> important. In the present case, annual colonoscopy was able to detect colitic cancer at the early stage. The European guidelines recommend surveillance involving highquality visual inspection of the mucosa, using chromoen-doscopy and target biopsy with endoscopic recognition of colorectal dysplasia in patients with inammatory bowel disease (IBD) [ 12]. In our case, chromoendoscopic examination revealed an elevated lesion surrounded by erosion with unclear margins, indicating a dysplasia-associated lesion or mass for which we performed surgery. Eventually, the surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia asindicated by p53 staining. In colitic cancer, p53 immunoreactivity is useful to conne the basal half of the glands associated with early neoplastic lesions [ 13]. With these detailed ndings, we nally diagnosed our patient as having colitic cancer, not sporadic cancer. \n",
      "bdf20b87-9e30-4855-a9c9-d238c688bb8c --> 1b). Considering that this patient with UC and CARC was elderly, laparoscopic total proctocolectomy combined with abdominoperineal resec-tion and ileostomy was performed to avoid the risk of residual cancer and fecal incontinence. The resulting resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma (Fig. 2a, b), and dysplastic epithelium was observed in the area surrounding the cancer lesion. Fur-thermore, abnormal p53 accumulation was found by immunohistochemical examination (Fig. 2ce), which was compatible with CARC. The cancer invaded the muscularlayer without node metastasis, and therefore was eventually diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition [ 6]. At the same time of admission for surgery for CARC, the patients laboratory data revealed elevated c-glutamyltransferase and alkaline phosphatase levels of 133and 371 IU/L, respectively. The aspartate transaminase and alanine transaminase levels were normal, and the carbohydrate antigen 19-9 (CA19-9) level was 32.3 U/mL.Abdominal enhanced CT revealed partial intrahepatic bileduct dilation in the left lateral section of the liver (Fig. 3a), and endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct in the left lateral sector (Fig. 3b). At the same time, cholangiography demonstrated a pruned-tree appearance in the bile duct of the right lobe which led to a suspicious diagnosis of primary sclerotic cholangitis. However, brush cytology of the stenotic siterevealed no malignancy. At 6 months after the total proctocolectomy, the patients laboratory data revealed elevation of his CA19-9 level to 56.4 U/mL. Although a malignant tumor of the bile duct could still not be observed, the possibility of ICC at the stenosis in thehepatic duct was suspected because biliary stenosis with atrophy of the left lateral section had not changed. Therefore, we decided to perform a left hepatectomy and toattempt intraoperative pathological diagnosis in the cut edge of the bile duct to determine whether to add extrahepatic bile duct resection. After the left hepatectomy, an intraoperative diagnosis of adenocarcinoma in the liver was made, and abnormal cells were observed in the left bile duct at the rst resectedsite. An additional resected specimen of the left bile duct and caudate branch revealed no malignant tumor. The resected specimen showed a bile duct carcinoma of 2 cm indiameter and stenosis of the hepatic duct wall, which represented an ICC of the periductal inltration invading the left branch of the portal vein (Fig. 4a). The primary well-differentiated tubular adenocarcinoma inltrating the liver parenchyma was diagnosed histologically (Fig. 4b). In addition, an onion-skin appearance indicating PSC wasfound in the non-cancerous region of the liver (Fig. 4c). Finally, the periductal inltration type was classied as T4, and was diagnosed as pT4 and pN0, Stage IVa according tothe UICC classication 7th edition [ 6]. Fig. \n",
      "380cb6e6-75ee-45e0-a883-56d0c45530ea --> 3 Findings of computed tomography and endoscopic retrograde cholangiography (ERC). aComputed tomography revealed limited dilation of the intrahepatic bile duct in the lateral segment of the liver(arrowheads ), although no tumor was detected. bERC demonstrateda pruned-tree appearance in the bile duct of the right lobe, which was compatible with primary sclerosing cholangitis. A band-like strictureof 5 mm in length in the left lateral sector ( arrowhead ) and dilation of the bile duct suggested a malignancyClin J Gastroenterol (2017) 10:157162 159\n",
      "\u001b[0m> Running step eba7af44-e954-4a7a-8491-166376afbb80. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved three chunks related to the initial query about diagnostic techniques and procedures. I need to analyze their relevance to the metadata category \"Diagnostic Techniques and Procedures.\"\n",
      "\n",
      "1. Chunk 23e45bdb-9030-4eca-bb09-18d4c95df110 discusses the use of colonoscopy, chromoendoscopy, and p53 staining in diagnosing colitic cancer, which is relevant to the category.\n",
      "2. Chunk bdf20b87-9e30-4855-a9c9-d238c688bb8c describes laparoscopic surgery, CT scans, endoscopic retrograde cholangiography, and intraoperative pathological diagnosis, which are relevant diagnostic techniques.\n",
      "3. Chunk 380cb6e6-75ee-45e0-a883-56d0c45530ea provides details on CT findings and endoscopic retrograde cholangiography, which are relevant diagnostic procedures.\n",
      "\n",
      "All chunks are relevant to the category, so I will save them.\n",
      "Action: save_chunks\n",
      "Action Input: {'chunks_dict': [['23e45bdb-9030-4eca-bb09-18d4c95df110', 'important. In the present case, annual colonoscopy was able to detect colitic cancer at the early stage. The European guidelines recommend surveillance involving highquality visual inspection of the mucosa, using chromoen-doscopy and target biopsy with endoscopic recognition of colorectal dysplasia in patients with inammatory bowel disease (IBD) [ 12]. In our case, chromoendoscopic examination revealed an elevated lesion surrounded by erosion with unclear margins, indicating a dysplasia-associated lesion or mass for which we performed surgery. Eventually, the surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia asindicated by p53 staining. In colitic cancer, p53 immunoreactivity is useful to conne the basal half of the glands associated with early neoplastic lesions [ 13]. With these detailed ndings, we nally diagnosed our patient as having colitic cancer, not sporadic cancer.'], ['bdf20b87-9e30-4855-a9c9-d238c688bb8c', '1b). Considering that this patient with UC and CARC was elderly, laparoscopic total proctocolectomy combined with abdominoperineal resec-tion and ileostomy was performed to avoid the risk of residual cancer and fecal incontinence. The resulting resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma (Fig. 2a, b), and dysplastic epithelium was observed in the area surrounding the cancer lesion. Fur-thermore, abnormal p53 accumulation was found by immunohistochemical examination (Fig. 2ce), which was compatible with CARC. The cancer invaded the muscularlayer without node metastasis, and therefore was eventually diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition [ 6]. At the same time of admission for surgery for CARC, the patients laboratory data revealed elevated c-glutamyltransferase and alkaline phosphatase levels of 133and 371 IU/L, respectively. The aspartate transaminase and alanine transaminase levels were normal, and the carbohydrate antigen 19-9 (CA19-9) level was 32.3 U/mL.Abdominal enhanced CT revealed partial intrahepatic bileduct dilation in the left lateral section of the liver (Fig. 3a), and endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct in the left lateral sector (Fig. 3b). At the same time, cholangiography demonstrated a pruned-tree appearance in the bile duct of the right lobe which led to a suspicious diagnosis of primary sclerotic cholangitis. However, brush cytology of the stenotic siterevealed no malignancy. At 6 months after the total proctocolectomy, the patients laboratory data revealed elevation of his CA19-9 level to 56.4 U/mL. Although a malignant tumor of the bile duct could still not be observed, the possibility of ICC at the stenosis in thehepatic duct was suspected because biliary stenosis with atrophy of the left lateral section had not changed. Therefore, we decided to perform a left hepatectomy and toattempt intraoperative pathological diagnosis in the cut edge of the bile duct to determine whether to add extrahepatic bile duct resection. After the left hepatectomy, an intraoperative diagnosis of adenocarcinoma in the liver was made, and abnormal cells were observed in the left bile duct at the rst resectedsite. An additional resected specimen of the left bile duct and caudate branch revealed no malignant tumor. The resected specimen showed a bile duct carcinoma of 2 cm indiameter and stenosis of the hepatic duct wall, which represented an ICC of the periductal inltration invading the left branch of the portal vein (Fig. 4a). The primary well-differentiated tubular adenocarcinoma inltrating the liver parenchyma was diagnosed histologically (Fig. 4b). In addition, an onion-skin appearance indicating PSC wasfound in the non-cancerous region of the liver (Fig. 4c). Finally, the periductal inltration type was classied as T4, and was diagnosed as pT4 and pN0, Stage IVa according tothe UICC classication 7th edition [ 6]. Fig.'], ['380cb6e6-75ee-45e0-a883-56d0c45530ea', '3 Findings of computed tomography and endoscopic retrograde cholangiography (ERC). aComputed tomography revealed limited dilation of the intrahepatic bile duct in the lateral segment of the liver(arrowheads ), although no tumor was detected. bERC demonstrateda pruned-tree appearance in the bile duct of the right lobe, which was compatible with primary sclerosing cholangitis. A band-like strictureof 5 mm in length in the left lateral sector ( arrowhead ) and dilation of the bile duct suggested a malignancyClin J Gastroenterol (2017) 10:157162 159']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: All chunks saved.\n",
      "\u001b[0m> Running step 2443dfc6-2903-4d50-bc93-c68b80309977. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully saved all relevant chunks for the metadata category \"Diagnostic Techniques and Procedures.\" Since I have extracted comprehensive information from the initial query, there is no need for further refinement or additional queries.\n",
      "Answer: I have extracted and saved all relevant information regarding the diagnostic techniques and procedures used in the case study. The techniques include colonoscopy, chromoendoscopy, p53 staining, laparoscopic surgery, CT scans, endoscopic retrograde cholangiography, and intraoperative pathological diagnosis.\n",
      "\u001b[0m> Running step c42716fc-2b99-44f1-a1d8-56cc9717c238. Step input: You are an advanced clinical information retrieval system with expertise in analyzing medical case studies. Your task is to iteratively generate queries to extract relevant chunks of information for specific metadata categories from a clinical case study. You will later use these chunks to compile comprehensive metadata for each category.\n",
      "\n",
      "        Metadata Category:\n",
      "        Medical/Surgical History\n",
      "\n",
      "        Initial Query:\n",
      "        Outline the patient's past medical and surgical history, including previous diagnoses, treatments, and surgeries.\n",
      "\n",
      "        Instructions:\n",
      "        1. Start with a initial query for the metadata category Medical/Surgical History. Use the vector_db_query tool to search for relevant chunks.\n",
      "\n",
      "        2. Retrieved chunk:\n",
      "        a. Analyze its relevance to the current metadata category.\n",
      "        b. If relevant, use the save_chunks tool to store it.\n",
      "        c. If not relevant, briefly explain why and use this information to refine your next query.\n",
      "\n",
      "        4. Iterative Query Refinement Process:\n",
      "        a. If initial queries don't yield sufficient relevant information:\n",
      "            - Use synonyms or related medical terms.\n",
      "            - Consider indirect references or contextual clues.\n",
      "            - Broaden the search to include related concepts.\n",
      "        b. If queries yield too much irrelevant information:\n",
      "            - Make your queries more specific.\n",
      "        c. If you find partial information:\n",
      "            - Generate follow-up queries to find missing details.\n",
      "\n",
      "        5. Consider these aspects when searching:\n",
      "        - Direct mentions of the category or related terms.\n",
      "        - Contextual information that implies relevant data.\n",
      "\n",
      "        6. Continue this process until:\n",
      "        a. You are confident you have extracted all relevant information.\n",
      "        b. Multiple consecutive refined queries yield no new unique chunks.\n",
      "\n",
      "        Remember:\n",
      "        - Accuracy and comprehensiveness are crucial.\n",
      "        \n",
      "\u001b[1;3;38;5;200mThought: The current language of the user is English. I need to use a tool to help me answer the question by retrieving relevant chunks for the metadata category \"Medical/Surgical History.\"\n",
      "Action: retrieve_chunks\n",
      "Action Input: {'query': \"Outline the patient's past medical and surgical history, including previous diagnoses, treatments, and surgeries.\"}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Relevant Chunks:\n",
      "bdf20b87-9e30-4855-a9c9-d238c688bb8c --> 1b). Considering that this patient with UC and CARC was elderly, laparoscopic total proctocolectomy combined with abdominoperineal resec-tion and ileostomy was performed to avoid the risk of residual cancer and fecal incontinence. The resulting resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma (Fig. 2a, b), and dysplastic epithelium was observed in the area surrounding the cancer lesion. Fur-thermore, abnormal p53 accumulation was found by immunohistochemical examination (Fig. 2ce), which was compatible with CARC. The cancer invaded the muscularlayer without node metastasis, and therefore was eventually diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition [ 6]. At the same time of admission for surgery for CARC, the patients laboratory data revealed elevated c-glutamyltransferase and alkaline phosphatase levels of 133and 371 IU/L, respectively. The aspartate transaminase and alanine transaminase levels were normal, and the carbohydrate antigen 19-9 (CA19-9) level was 32.3 U/mL.Abdominal enhanced CT revealed partial intrahepatic bileduct dilation in the left lateral section of the liver (Fig. 3a), and endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct in the left lateral sector (Fig. 3b). At the same time, cholangiography demonstrated a pruned-tree appearance in the bile duct of the right lobe which led to a suspicious diagnosis of primary sclerotic cholangitis. However, brush cytology of the stenotic siterevealed no malignancy. At 6 months after the total proctocolectomy, the patients laboratory data revealed elevation of his CA19-9 level to 56.4 U/mL. Although a malignant tumor of the bile duct could still not be observed, the possibility of ICC at the stenosis in thehepatic duct was suspected because biliary stenosis with atrophy of the left lateral section had not changed. Therefore, we decided to perform a left hepatectomy and toattempt intraoperative pathological diagnosis in the cut edge of the bile duct to determine whether to add extrahepatic bile duct resection. After the left hepatectomy, an intraoperative diagnosis of adenocarcinoma in the liver was made, and abnormal cells were observed in the left bile duct at the rst resectedsite. An additional resected specimen of the left bile duct and caudate branch revealed no malignant tumor. The resected specimen showed a bile duct carcinoma of 2 cm indiameter and stenosis of the hepatic duct wall, which represented an ICC of the periductal inltration invading the left branch of the portal vein (Fig. 4a). The primary well-differentiated tubular adenocarcinoma inltrating the liver parenchyma was diagnosed histologically (Fig. 4b). In addition, an onion-skin appearance indicating PSC wasfound in the non-cancerous region of the liver (Fig. 4c). Finally, the periductal inltration type was classied as T4, and was diagnosed as pT4 and pN0, Stage IVa according tothe UICC classication 7th edition [ 6]. Fig. \n",
      "00bfb919-8b79-443a-8750-afe44a72bf46 --> The patient was discharged after an uneventful postoperative period. A month after the hepatectomy the patients CA19-9 level returned to normal (14.1 U/mL). Adjuvant therapy for ICC consisting of combination therapy ofgemcitabine and S-1 was administered for 6 months. The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC orcolitic cancer observed. Discussion In this report, we presented a case of CARC and ICC thatdeveloped after a 19-year follow-up of UC associated with PSC. A search of the Japanese literature found only oneprevious case report of CARC and ICC complicating UC, indicating the rarity of the present case [ 7]. A PubMed search revealed no other reports like our case diagnosed denitely as CARC-complicated cholangiocarcinoma inUC and PSC. Colitic cancer was rst reported by Crohn and Rosenberg in 1925 as colitis-associated cancer [ 8]. Following this, Morson and Pang reported that surveillance for dysplasia would lead to the identication of colitic cancer [ 9]. In recent years, colonoscopic surveillance for long-stand-ing UC patients is generally accepted to avoid unnecessary prophylactic colectomy and to reduce mortality due to colitic cancer [ 10]. As the prognosis of Stage III colitic cancer is worse than that of sporadic cancer in Japan [ 11], the early detection of cancer by careful surveillance is Fig. \n",
      "23e45bdb-9030-4eca-bb09-18d4c95df110 --> important. In the present case, annual colonoscopy was able to detect colitic cancer at the early stage. The European guidelines recommend surveillance involving highquality visual inspection of the mucosa, using chromoen-doscopy and target biopsy with endoscopic recognition of colorectal dysplasia in patients with inammatory bowel disease (IBD) [ 12]. In our case, chromoendoscopic examination revealed an elevated lesion surrounded by erosion with unclear margins, indicating a dysplasia-associated lesion or mass for which we performed surgery. Eventually, the surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia asindicated by p53 staining. In colitic cancer, p53 immunoreactivity is useful to conne the basal half of the glands associated with early neoplastic lesions [ 13]. With these detailed ndings, we nally diagnosed our patient as having colitic cancer, not sporadic cancer. \n",
      "\u001b[0m> Running step 11281248-6c7f-4f88-a278-01f6a5abc155. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The retrieved chunks contain relevant information about the patient's medical and surgical history, including previous diagnoses, treatments, and surgeries. I will analyze each chunk for relevance to the metadata category \"Medical/Surgical History.\"\n",
      "\n",
      "1. Chunk bdf20b87-9e30-4855-a9c9-d238c688bb8c: This chunk provides detailed information about the patient's surgical history, including a laparoscopic total proctocolectomy and left hepatectomy, as well as the diagnoses of ulcerative colitis (UC), colitis-associated cancer (CARC), and intrahepatic cholangiocarcinoma (ICC). It also mentions the patient's laboratory data and imaging findings. This is highly relevant to the category.\n",
      "\n",
      "2. Chunk 00bfb919-8b79-443a-8750-afe44a72bf46: This chunk discusses the patient's postoperative course, adjuvant therapy, and follow-up, which are relevant to the patient's medical history.\n",
      "\n",
      "3. Chunk 23e45bdb-9030-4eca-bb09-18d4c95df110: This chunk provides information about the detection and diagnosis of colitic cancer, which is part of the patient's medical history.\n",
      "\n",
      "All chunks are relevant to the metadata category. I will save these chunks.\n",
      "Action: save_chunks\n",
      "Action Input: {'chunks_dict': [['bdf20b87-9e30-4855-a9c9-d238c688bb8c', '1b). Considering that this patient with UC and CARC was elderly, laparoscopic total proctocolectomy combined with abdominoperineal resec-tion and ileostomy was performed to avoid the risk of residual cancer and fecal incontinence. The resulting resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma (Fig. 2a, b), and dysplastic epithelium was observed in the area surrounding the cancer lesion. Fur-thermore, abnormal p53 accumulation was found by immunohistochemical examination (Fig. 2ce), which was compatible with CARC. The cancer invaded the muscularlayer without node metastasis, and therefore was eventually diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition [ 6]. At the same time of admission for surgery for CARC, the patients laboratory data revealed elevated c-glutamyltransferase and alkaline phosphatase levels of 133and 371 IU/L, respectively. The aspartate transaminase and alanine transaminase levels were normal, and the carbohydrate antigen 19-9 (CA19-9) level was 32.3 U/mL.Abdominal enhanced CT revealed partial intrahepatic bileduct dilation in the left lateral section of the liver (Fig. 3a), and endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct in the left lateral sector (Fig. 3b). At the same time, cholangiography demonstrated a pruned-tree appearance in the bile duct of the right lobe which led to a suspicious diagnosis of primary sclerotic cholangitis. However, brush cytology of the stenotic siterevealed no malignancy. At 6 months after the total proctocolectomy, the patients laboratory data revealed elevation of his CA19-9 level to 56.4 U/mL. Although a malignant tumor of the bile duct could still not be observed, the possibility of ICC at the stenosis in thehepatic duct was suspected because biliary stenosis with atrophy of the left lateral section had not changed. Therefore, we decided to perform a left hepatectomy and toattempt intraoperative pathological diagnosis in the cut edge of the bile duct to determine whether to add extrahepatic bile duct resection. After the left hepatectomy, an intraoperative diagnosis of adenocarcinoma in the liver was made, and abnormal cells were observed in the left bile duct at the rst resectedsite. An additional resected specimen of the left bile duct and caudate branch revealed no malignant tumor. The resected specimen showed a bile duct carcinoma of 2 cm indiameter and stenosis of the hepatic duct wall, which represented an ICC of the periductal inltration invading the left branch of the portal vein (Fig. 4a). The primary well-differentiated tubular adenocarcinoma inltrating the liver parenchyma was diagnosed histologically (Fig. 4b). In addition, an onion-skin appearance indicating PSC wasfound in the non-cancerous region of the liver (Fig. 4c). Finally, the periductal inltration type was classied as T4, and was diagnosed as pT4 and pN0, Stage IVa according tothe UICC classication 7th edition [ 6]. Fig.'], ['00bfb919-8b79-443a-8750-afe44a72bf46', 'The patient was discharged after an uneventful postoperative period. A month after the hepatectomy the patients CA19-9 level returned to normal (14.1 U/mL). Adjuvant therapy for ICC consisting of combination therapy ofgemcitabine and S-1 was administered for 6 months. The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC orcolitic cancer observed. Discussion In this report, we presented a case of CARC and ICC thatdeveloped after a 19-year follow-up of UC associated with PSC. A search of the Japanese literature found only oneprevious case report of CARC and ICC complicating UC, indicating the rarity of the present case [ 7]. A PubMed search revealed no other reports like our case diagnosed denitely as CARC-complicated cholangiocarcinoma inUC and PSC. Colitic cancer was rst reported by Crohn and Rosenberg in 1925 as colitis-associated cancer [ 8]. Following this, Morson and Pang reported that surveillance for dysplasia would lead to the identication of colitic cancer [ 9]. In recent years, colonoscopic surveillance for long-stand-ing UC patients is generally accepted to avoid unnecessary prophylactic colectomy and to reduce mortality due to colitic cancer [ 10]. As the prognosis of Stage III colitic cancer is worse than that of sporadic cancer in Japan [ 11], the early detection of cancer by careful surveillance is Fig.'], ['23e45bdb-9030-4eca-bb09-18d4c95df110', 'important. In the present case, annual colonoscopy was able to detect colitic cancer at the early stage. The European guidelines recommend surveillance involving highquality visual inspection of the mucosa, using chromoen-doscopy and target biopsy with endoscopic recognition of colorectal dysplasia in patients with inammatory bowel disease (IBD) [ 12]. In our case, chromoendoscopic examination revealed an elevated lesion surrounded by erosion with unclear margins, indicating a dysplasia-associated lesion or mass for which we performed surgery. Eventually, the surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia asindicated by p53 staining. In colitic cancer, p53 immunoreactivity is useful to conne the basal half of the glands associated with early neoplastic lesions [ 13]. With these detailed ndings, we nally diagnosed our patient as having colitic cancer, not sporadic cancer.']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: chunk ids ['bdf20b87-9e30-4855-a9c9-d238c688bb8c', '23e45bdb-9030-4eca-bb09-18d4c95df110'] already exists.\n",
      "\u001b[0m> Running step c7fa8a81-58c5-42ce-99b8-880d3ac3be2f. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: Two of the chunks were already saved, indicating they were previously identified as relevant. I will proceed with refining the query to ensure all relevant information is captured, especially focusing on any missing details or indirect references related to the patient's medical and surgical history.\n",
      "Action: retrieve_chunks\n",
      "Action Input: {'query': \"Patient's previous diagnoses, treatments, and surgeries related to ulcerative colitis, CARC, and ICC.\"}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Relevant Chunks:\n",
      "c89d11e5-88a3-44bc-9745-60e09d37adc9 --> CASE REPORT A case of concomitant colitic cancer and intrahepatic cholangiocarcinoma during follow-up for ulcerative colitis Kazuyo Tsuchiya1Atsushi Nanashima2Takuto Ikeda1Shiro Minami3 Motoaki Nagano4Takeomi Hamada2Koichi Yano2Yoshiro Fujii2 Received: 8 November 2016 / Accepted: 17 January 2017 / Published online: 30 January 2017 /C211Japanese Society of Gastroenterology 2017 Abstract Colitis-associated colorectal cancer (CAC) is known to occur in long-standing and extensive ulcerative colitis (UC). Furthermore, UC is known to complicate primary sclerosing cholangitis (PSC), which subsequently results in an increased risk of developing cholangiocarcinoma. We report a case of colitis-associated rectal cancer (CARC) accompanied by intrahepatic cholangiocarcinoma (ICC) based on UC and PSC. A 73-year-old man had suffered from UC for 19 years. During surveillance colonoscopy, a tumor was found in the rectum that was pathologically diagnosed as CARC from the resected specimen. Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct, and endoscopic retrograde cholangiography revealed a bandlike stricture. This remarkable tumor lesion was not observed in the hepatic duct. Left hepatectomy was performed because of the suspicion of possible ICC at the stenosis of the hepatic duct. The presence of ICC was conrmed at the lesion causing the stricture. \n",
      "493cb455-3d34-4d6d-8c47-a5c6323a281f --> The pathological diagnosis from the resected specimen was ICC based on PSC. Adjuvant chemotherapy for ICC was performed for 6 months. Neither cancer has recurred for 2.5 years after hepatectomy. Patients with PSCconcomitant with UC should be considered a high-risk group for CAC and ICC. Keywords Colitic cancer /C1Cholangiocarcinoma /C1UC /C1 PSC Introduction Colitic cancer is appreciated as a colitis-associated colorectal cancer that develops in long-standing and extensive ulcerative colitis (UC). The number of patients with colitic cancer has increased recently along with increased morbidity from UC in Japan [ 1]. The risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer, and additionally, the complication of primary sclerosing cholangitis (PSC) [2,3]. Patients with PSC are also at increased risk of developing cholangiocarcinoma [ 4], which is known as a disease with poor prognosis in terms of the difculty in making an imaging diagnosis and the involvement of lymph nodes [ 4,5]. We report a patient with concomitant UC and PSC who developed colitis-associated rectal cancer (CARC) and intrahepatic cholangiocarcinoma (ICC), which we successfully cured by surgery. This is a rare case of CARC and ICC complicating these diseases in Japan. Case report A 73-year-old man with a 19-year history of UC was referred to our hospital. He had undergone colonoscopy every year at a previous outpatient clinic. The patient had extensive colitis and had been treated with aminosalicylate&Atsushi Nanashima a_nanashima@med.miyazaki-u.ac.jp 1Division of Gastrointestinal, Endocrine and Pediatric Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, Miyazaki, Japan 2Division of Hepato-Biliary-Pancreas Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan 3Ikime Coloproctological Clinic, Miyazaki, Japan 4Miyazaki Medical Center Hospital, Miyazaki, Japan 123Clin J Gastroenterol (2017) 10:157162 DOI 10.1007/s12328-017-0715-6\n",
      "00bfb919-8b79-443a-8750-afe44a72bf46 --> The patient was discharged after an uneventful postoperative period. A month after the hepatectomy the patients CA19-9 level returned to normal (14.1 U/mL). Adjuvant therapy for ICC consisting of combination therapy ofgemcitabine and S-1 was administered for 6 months. The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC orcolitic cancer observed. Discussion In this report, we presented a case of CARC and ICC thatdeveloped after a 19-year follow-up of UC associated with PSC. A search of the Japanese literature found only oneprevious case report of CARC and ICC complicating UC, indicating the rarity of the present case [ 7]. A PubMed search revealed no other reports like our case diagnosed denitely as CARC-complicated cholangiocarcinoma inUC and PSC. Colitic cancer was rst reported by Crohn and Rosenberg in 1925 as colitis-associated cancer [ 8]. Following this, Morson and Pang reported that surveillance for dysplasia would lead to the identication of colitic cancer [ 9]. In recent years, colonoscopic surveillance for long-stand-ing UC patients is generally accepted to avoid unnecessary prophylactic colectomy and to reduce mortality due to colitic cancer [ 10]. As the prognosis of Stage III colitic cancer is worse than that of sporadic cancer in Japan [ 11], the early detection of cancer by careful surveillance is Fig. \n",
      "\u001b[0m> Running step 4f83aa6c-8bca-4e57-8b95-d9aa160504d6. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The newly retrieved chunks provide additional relevant information about the patient's medical and surgical history, particularly focusing on the diagnoses and treatments related to ulcerative colitis (UC), colitis-associated rectal cancer (CARC), and intrahepatic cholangiocarcinoma (ICC).\n",
      "\n",
      "1. Chunk c89d11e5-88a3-44bc-9745-60e09d37adc9: This chunk provides a comprehensive overview of the patient's medical history, including the diagnosis of CARC and ICC, the patient's long-standing history of UC, and the treatments received. It also mentions the patient's surgical history, including left hepatectomy. This is highly relevant to the category.\n",
      "\n",
      "2. Chunk 493cb455-3d34-4d6d-8c47-a5c6323a281f: This chunk discusses the pathological diagnosis and adjuvant chemotherapy for ICC, which are relevant to the patient's medical history.\n",
      "\n",
      "I will save these relevant chunks.\n",
      "Action: save_chunks\n",
      "Action Input: {'chunks_dict': [['c89d11e5-88a3-44bc-9745-60e09d37adc9', 'CASE REPORT A case of concomitant colitic cancer and intrahepatic cholangiocarcinoma during follow-up for ulcerative colitis Kazuyo Tsuchiya1Atsushi Nanashima2Takuto Ikeda1Shiro Minami3 Motoaki Nagano4Takeomi Hamada2Koichi Yano2Yoshiro Fujii2 Received: 8 November 2016 / Accepted: 17 January 2017 / Published online: 30 January 2017 /C211Japanese Society of Gastroenterology 2017 Abstract Colitis-associated colorectal cancer (CAC) is known to occur in long-standing and extensive ulcerative colitis (UC). Furthermore, UC is known to complicate primary sclerosing cholangitis (PSC), which subsequently results in an increased risk of developing cholangiocarcinoma. We report a case of colitis-associated rectal cancer (CARC) accompanied by intrahepatic cholangiocarcinoma (ICC) based on UC and PSC. A 73-year-old man had suffered from UC for 19 years. During surveillance colonoscopy, a tumor was found in the rectum that was pathologically diagnosed as CARC from the resected specimen. Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct, and endoscopic retrograde cholangiography revealed a bandlike stricture. This remarkable tumor lesion was not observed in the hepatic duct. Left hepatectomy was performed because of the suspicion of possible ICC at the stenosis of the hepatic duct. The presence of ICC was conrmed at the lesion causing the stricture.'], ['493cb455-3d34-4d6d-8c47-a5c6323a281f', 'The pathological diagnosis from the resected specimen was ICC based on PSC. Adjuvant chemotherapy for ICC was performed for 6 months. Neither cancer has recurred for 2.5 years after hepatectomy. Patients with PSCconcomitant with UC should be considered a high-risk group for CAC and ICC. Keywords Colitic cancer /C1Cholangiocarcinoma /C1UC /C1 PSC Introduction Colitic cancer is appreciated as a colitis-associated colorectal cancer that develops in long-standing and extensive ulcerative colitis (UC). The number of patients with colitic cancer has increased recently along with increased morbidity from UC in Japan [ 1]. The risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer, and additionally, the complication of primary sclerosing cholangitis (PSC) [2,3]. Patients with PSC are also at increased risk of developing cholangiocarcinoma [ 4], which is known as a disease with poor prognosis in terms of the difculty in making an imaging diagnosis and the involvement of lymph nodes [ 4,5]. We report a patient with concomitant UC and PSC who developed colitis-associated rectal cancer (CARC) and intrahepatic cholangiocarcinoma (ICC), which we successfully cured by surgery. This is a rare case of CARC and ICC complicating these diseases in Japan. Case report A 73-year-old man with a 19-year history of UC was referred to our hospital. He had undergone colonoscopy every year at a previous outpatient clinic. The patient had extensive colitis and had been treated with aminosalicylate&Atsushi Nanashima a_nanashima@med.miyazaki-u.ac.jp 1Division of Gastrointestinal, Endocrine and Pediatric Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, Miyazaki, Japan 2Division of Hepato-Biliary-Pancreas Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan 3Ikime Coloproctological Clinic, Miyazaki, Japan 4Miyazaki Medical Center Hospital, Miyazaki, Japan 123Clin J Gastroenterol (2017) 10:157162 DOI 10.1007/s12328-017-0715-6']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: All chunks saved.\n",
      "\u001b[0m> Running step 817f332d-96bf-4315-856d-96ba3ea31af0. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully saved all relevant chunks related to the patient's medical and surgical history, including previous diagnoses, treatments, and surgeries. This information will be used to compile comprehensive metadata for the category \"Medical/Surgical History.\"\n",
      "Answer: I have extracted and saved all relevant information regarding the patient's medical and surgical history, including details about ulcerative colitis, colitis-associated rectal cancer, intrahepatic cholangiocarcinoma, and the treatments and surgeries the patient underwent. This information is now ready for compiling comprehensive metadata for the specified category.\n",
      "\u001b[0m"
     ]
    }
   ],
   "source": [
    "# Describtion of metadata\n",
    " \n",
    "metadata_categories = {\n",
    "    'Life Style': 'Describe the patient\\'s lifestyle, including smoking, alcohol consumption, diet, and exercise habits.',\n",
    "    'Family History': 'Provide the patient\\'s family medical history, including any hereditary conditions or diseases.',\n",
    "    'Social History': 'Detail the patient\\'s social history, including occupation, living situation, and social support systems.',\n",
    "    'Medical/Surgical History': 'Outline the patient\\'s past medical and surgical history, including previous diagnoses, treatments, and surgeries.',\n",
    "    'Signs and Symptoms': 'List the signs and symptoms the patient presented with.',\n",
    "    'Comorbidities': 'List any comorbid conditions the patient has.',\n",
    "    'Diagnostic Techniques and Procedures': 'Describe the diagnostic techniques and procedures used to evaluate the patient.',\n",
    "    'Diagnosis': 'What was the final diagnosis given to the patient?',\n",
    "    'Laboratory Values': 'List the laboratory values obtained from tests conducted on the patient.',\n",
    "    'Pathology': 'Provide details about any pathology findings from the patient\\'s case.',\n",
    "    'Pharmacological Therapy': 'Detail the prescribed pharmacological therapy, including medications and dosages.',\n",
    "    'Interventional Therapy': 'Describe any interventional therapies administered to the patient.',\n",
    "    'Patient Outcome Assessment': 'Describe the outcomes following the patient\\'s treatment.',\n",
    "    'Age': 'What is the patient\\'s age?',\n",
    "    'Gender': 'What is the patient\\'s gender?'\n",
    "}\n",
    "\n",
    "\n",
    "categories_subset = [\"Diagnostic Techniques and Procedures\",\"Medical/Surgical History\"]\n",
    "chunk_manager = ChunkManager()\n",
    "retriever_manager = RetrieverManager(retriever,reranker_model,top_k=top_k)\n",
    "\n",
    "for category in categories_subset:\n",
    "    query_agent = RetrieverAgent(retriever_manager,llm,chunk_manager)\n",
    "    query_agent.extract_metadata_chunks(category,metadata_categories[category])\n",
    "\n",
    "with open('clinical_ie/chunks.json','w') as f:\n",
    "    json.dump(chunk_manager.chunks,f)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'All chunks saved.'"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with open('clinical_ie/chunks.json','r') as f:\n",
    "    chunks_dict = json.load(f)\n",
    "\n",
    "\n",
    "chunk_manager = ChunkManager()\n",
    "chunk_manager.save_chunks(chunks_dict=[(k,v) for k,v in chunks_dict.items()])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> Running step f10026b6-fe17-42e9-aeea-23a6ebfedb87. Step input: You are an expert clinical information specialist with extensive experience in analyzing medical case studies and extracting precise metadata.\n",
      "        \n",
      "        Your task is to analyze clinical case study chunks and extract sentence snippets relevant to ['Life Style', 'Family History', 'Social History', 'Medical/Surgical History', 'Signs and Symptoms', 'Comorbidities', 'Diagnostic Techniques and Procedures', 'Diagnosis', 'Laboratory Values', 'Pathology', 'Pharmacological Therapy', 'Interventional Therapy', 'Patient Outcome Assessment', 'Age', 'Gender']. Follow these steps:\n",
      "        \n",
      "        1. Use the `get_chunk` tool to get relevant chunks using the chunk id.\n",
      "\n",
      "        2. Analyze each chunk sequentially, focusing on extractive rather than generative approaches:\n",
      "        - Extract sentence snippet or piece of text that fit into the following clinical metadata categories: ['Life Style', 'Family History', 'Social History', 'Medical/Surgical History', 'Signs and Symptoms', 'Comorbidities', 'Diagnostic Techniques and Procedures', 'Diagnosis', 'Laboratory Values', 'Pathology', 'Pharmacological Therapy', 'Interventional Therapy', 'Patient Outcome Assessment', 'Age', 'Gender'].\n",
      "        - Use the sentence saving tool `add_metadatas` to store relevant snippets all categories.\n",
      "\n",
      "        3. After analyzing all chunks:\n",
      "        - Get all sentence snippets saved in previous step using the tool `get_all_metadata`.\n",
      "        - Now combine sentence snippets which makes sense and refine others with minimal paraphrasing if they don't make sense.\n",
      "        - Discard any information that doesn't make sense in the context of the category.\n",
      "\n",
      "        4. Final output should be in json format containing category as a key and list of metadata as a value.\n",
      "        Use the `generate_clinical_metadata`, a parser tool to structure your final output.\n",
      "\n",
      "        5. If the parser indicates errors or missing fields:\n",
      "        - Review the extracted information.\n",
      "        - Make necessary adjustments.\n",
      "        - Try the parser again.\n",
      "        - Repeat this process up to 3 times if needed.\n",
      "\n",
      "        ## Important Notes:\n",
      "\n",
      "        - Prioritize extraction over generation. Only paraphrase when necessary for clarity.\n",
      "        - Ensure all extracted information is relevant to its assigned category.\n",
      "        - Be thorough in your analysis, but avoid redundancy in the final output.\n",
      "        - The final output must conform to the `generate_clinical_metadata` model structure.\n",
      "\n",
      "        Remember, your goal is to produce accurate, structured clinical metadata from the given case study chunks.\n",
      "\n",
      "\n",
      "        Chunks ids to analyze:\n",
      "        id: 23e45bdb-9030-4eca-bb09-18d4c95df110\n",
      "id: bdf20b87-9e30-4855-a9c9-d238c688bb8c\n",
      "id: 380cb6e6-75ee-45e0-a883-56d0c45530ea\n",
      "id: 00bfb919-8b79-443a-8750-afe44a72bf46\n",
      "id: c89d11e5-88a3-44bc-9745-60e09d37adc9\n",
      "id: 493cb455-3d34-4d6d-8c47-a5c6323a281f\n",
      "        \n",
      "\u001b[1;3;38;5;200mThought: The current language of the user is English. I need to use the `get_chunk` tool to retrieve the content of each chunk using the provided chunk IDs.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': '23e45bdb-9030-4eca-bb09-18d4c95df110'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: important. In the present case, annual colonoscopy was able to detect colitic cancer at the early stage. The European guidelines recommend surveillance involving highquality visual inspection of the mucosa, using chromoen-doscopy and target biopsy with endoscopic recognition of colorectal dysplasia in patients with inammatory bowel disease (IBD) [ 12]. In our case, chromoendoscopic examination revealed an elevated lesion surrounded by erosion with unclear margins, indicating a dysplasia-associated lesion or mass for which we performed surgery. Eventually, the surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia asindicated by p53 staining. In colitic cancer, p53 immunoreactivity is useful to conne the basal half of the glands associated with early neoplastic lesions [ 13]. With these detailed ndings, we nally diagnosed our patient as having colitic cancer, not sporadic cancer.\n",
      "\u001b[0m> Running step bdfaadca-d8df-4fc6-88f9-041d89421154. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the first chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk. After that, I will proceed to retrieve the next chunk.\n",
      "Action: add_metadatas\n",
      "Action Input: {}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Error: MetadataManager.add_metadatas() missing 1 required positional argument: 'metadata'\n",
      "\u001b[0m> Running step 6eb03672-b209-479c-82cf-93f5578924e3. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I need to extract relevant sentence snippets from the chunk and categorize them before using the `add_metadatas` tool. Let's extract and categorize the information from the current chunk.\n",
      "\n",
      "1. **Diagnostic Techniques and Procedures**: \"annual colonoscopy was able to detect colitic cancer at the early stage\", \"chromoendoscopic examination revealed an elevated lesion\", \"p53 staining\"\n",
      "2. **Diagnosis**: \"diagnosed our patient as having colitic cancer, not sporadic cancer\"\n",
      "3. **Pathology**: \"surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia\"\n",
      "4. **Signs and Symptoms**: \"elevated lesion surrounded by erosion with unclear margins\"\n",
      "5. **Interventional Therapy**: \"we performed surgery\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Diagnostic Techniques and Procedures', 'annual colonoscopy was able to detect colitic cancer at the early stage; chromoendoscopic examination revealed an elevated lesion; p53 staining'], ['Diagnosis', 'diagnosed our patient as having colitic cancer, not sporadic cancer'], ['Pathology', 'surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia'], ['Signs and Symptoms', 'elevated lesion surrounded by erosion with unclear margins'], ['Interventional Therapy', 'we performed surgery']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step c63f49c1-ab35-411f-b5b7-4d49590a5f43. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from the first chunk. Now, I will proceed to retrieve the content of the next chunk using its ID.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': 'bdf20b87-9e30-4855-a9c9-d238c688bb8c'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: 1b). Considering that this patient with UC and CARC was elderly, laparoscopic total proctocolectomy combined with abdominoperineal resec-tion and ileostomy was performed to avoid the risk of residual cancer and fecal incontinence. The resulting resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma (Fig. 2a, b), and dysplastic epithelium was observed in the area surrounding the cancer lesion. Fur-thermore, abnormal p53 accumulation was found by immunohistochemical examination (Fig. 2ce), which was compatible with CARC. The cancer invaded the muscularlayer without node metastasis, and therefore was eventually diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition [ 6]. At the same time of admission for surgery for CARC, the patients laboratory data revealed elevated c-glutamyltransferase and alkaline phosphatase levels of 133and 371 IU/L, respectively. The aspartate transaminase and alanine transaminase levels were normal, and the carbohydrate antigen 19-9 (CA19-9) level was 32.3 U/mL.Abdominal enhanced CT revealed partial intrahepatic bileduct dilation in the left lateral section of the liver (Fig. 3a), and endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct in the left lateral sector (Fig. 3b). At the same time, cholangiography demonstrated a pruned-tree appearance in the bile duct of the right lobe which led to a suspicious diagnosis of primary sclerotic cholangitis. However, brush cytology of the stenotic siterevealed no malignancy. At 6 months after the total proctocolectomy, the patients laboratory data revealed elevation of his CA19-9 level to 56.4 U/mL. Although a malignant tumor of the bile duct could still not be observed, the possibility of ICC at the stenosis in thehepatic duct was suspected because biliary stenosis with atrophy of the left lateral section had not changed. Therefore, we decided to perform a left hepatectomy and toattempt intraoperative pathological diagnosis in the cut edge of the bile duct to determine whether to add extrahepatic bile duct resection. After the left hepatectomy, an intraoperative diagnosis of adenocarcinoma in the liver was made, and abnormal cells were observed in the left bile duct at the rst resectedsite. An additional resected specimen of the left bile duct and caudate branch revealed no malignant tumor. The resected specimen showed a bile duct carcinoma of 2 cm indiameter and stenosis of the hepatic duct wall, which represented an ICC of the periductal inltration invading the left branch of the portal vein (Fig. 4a). The primary well-differentiated tubular adenocarcinoma inltrating the liver parenchyma was diagnosed histologically (Fig. 4b). In addition, an onion-skin appearance indicating PSC wasfound in the non-cancerous region of the liver (Fig. 4c). Finally, the periductal inltration type was classied as T4, and was diagnosed as pT4 and pN0, Stage IVa according tothe UICC classication 7th edition [ 6]. Fig.\n",
      "\u001b[0m> Running step 2561ff38-23b1-4dcf-8ec8-34d29f5d245c. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the second chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk and store them using the `add_metadatas` tool.\n",
      "\n",
      "1. **Medical/Surgical History**: \"laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed\"\n",
      "2. **Pathology**: \"resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma\", \"abnormal p53 accumulation was found\", \"cancer invaded the muscular layer without node metastasis\"\n",
      "3. **Diagnosis**: \"diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition\", \"suspicious diagnosis of primary sclerotic cholangitis\", \"intraoperative diagnosis of adenocarcinoma in the liver\", \"diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition\"\n",
      "4. **Laboratory Values**: \"elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L\", \"CA19-9 level was 32.3 U/mL\", \"CA19-9 level to 56.4 U/mL\"\n",
      "5. **Diagnostic Techniques and Procedures**: \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation\", \"endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct\", \"brush cytology of the stenotic site revealed no malignancy\"\n",
      "6. **Interventional Therapy**: \"decided to perform a left hepatectomy\", \"additional resected specimen of the left bile duct and caudate branch\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Medical/Surgical History', 'laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed'], ['Pathology', 'resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma; abnormal p53 accumulation was found; cancer invaded the muscular layer without node metastasis'], ['Diagnosis', 'diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition; suspicious diagnosis of primary sclerotic cholangitis; intraoperative diagnosis of adenocarcinoma in the liver; diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition'], ['Laboratory Values', 'elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L; CA19-9 level was 32.3 U/mL; CA19-9 level to 56.4 U/mL'], ['Diagnostic Techniques and Procedures', 'Abdominal enhanced CT revealed partial intrahepatic bile duct dilation; endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct; brush cytology of the stenotic site revealed no malignancy'], ['Interventional Therapy', 'decided to perform a left hepatectomy; additional resected specimen of the left bile duct and caudate branch']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step 552f13e1-a197-4877-bc26-fb5e50461e29. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from the second chunk. Now, I will proceed to retrieve the content of the next chunk using its ID.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': '380cb6e6-75ee-45e0-a883-56d0c45530ea'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: 3 Findings of computed tomography and endoscopic retrograde cholangiography (ERC). aComputed tomography revealed limited dilation of the intrahepatic bile duct in the lateral segment of the liver(arrowheads ), although no tumor was detected. bERC demonstrateda pruned-tree appearance in the bile duct of the right lobe, which was compatible with primary sclerosing cholangitis. A band-like strictureof 5 mm in length in the left lateral sector ( arrowhead ) and dilation of the bile duct suggested a malignancyClin J Gastroenterol (2017) 10:157162 159\n",
      "\u001b[0m> Running step 55bba38c-0359-44d8-bffe-42508732e271. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the third chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk and store them using the `add_metadatas` tool.\n",
      "\n",
      "1. **Diagnostic Techniques and Procedures**: \"computed tomography revealed limited dilation of the intrahepatic bile duct\", \"ERC demonstrated a pruned-tree appearance in the bile duct\", \"band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy\"\n",
      "2. **Diagnosis**: \"compatible with primary sclerosing cholangitis\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Diagnostic Techniques and Procedures', 'computed tomography revealed limited dilation of the intrahepatic bile duct; ERC demonstrated a pruned-tree appearance in the bile duct; band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy'], ['Diagnosis', 'compatible with primary sclerosing cholangitis']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step 798a209d-612a-4d80-8143-d84916e7768c. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from the third chunk. Now, I will proceed to retrieve the content of the next chunk using its ID.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': '00bfb919-8b79-443a-8750-afe44a72bf46'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: The patient was discharged after an uneventful postoperative period. A month after the hepatectomy the patients CA19-9 level returned to normal (14.1 U/mL). Adjuvant therapy for ICC consisting of combination therapy ofgemcitabine and S-1 was administered for 6 months. The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC orcolitic cancer observed. Discussion In this report, we presented a case of CARC and ICC thatdeveloped after a 19-year follow-up of UC associated with PSC. A search of the Japanese literature found only oneprevious case report of CARC and ICC complicating UC, indicating the rarity of the present case [ 7]. A PubMed search revealed no other reports like our case diagnosed denitely as CARC-complicated cholangiocarcinoma inUC and PSC. Colitic cancer was rst reported by Crohn and Rosenberg in 1925 as colitis-associated cancer [ 8]. Following this, Morson and Pang reported that surveillance for dysplasia would lead to the identication of colitic cancer [ 9]. In recent years, colonoscopic surveillance for long-stand-ing UC patients is generally accepted to avoid unnecessary prophylactic colectomy and to reduce mortality due to colitic cancer [ 10]. As the prognosis of Stage III colitic cancer is worse than that of sporadic cancer in Japan [ 11], the early detection of cancer by careful surveillance is Fig.\n",
      "\u001b[0m> Running step 36791835-31b6-4e39-950e-454d2a1d4fe8. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the fourth chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk and store them using the `add_metadatas` tool.\n",
      "\n",
      "1. **Patient Outcome Assessment**: \"The patient was discharged after an uneventful postoperative period\", \"CA19-9 level returned to normal (14.1 U/mL)\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed\"\n",
      "2. **Pharmacological Therapy**: \"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months\"\n",
      "3. **Medical/Surgical History**: \"developed after a 19-year follow-up of UC associated with PSC\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Patient Outcome Assessment', 'The patient was discharged after an uneventful postoperative period; CA19-9 level returned to normal (14.1 U/mL); The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed'], ['Pharmacological Therapy', 'Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months'], ['Medical/Surgical History', 'developed after a 19-year follow-up of UC associated with PSC']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step 6558cdf9-a04a-4fda-9b74-f8340f4d39ae. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from the fourth chunk. Now, I will proceed to retrieve the content of the next chunk using its ID.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': 'c89d11e5-88a3-44bc-9745-60e09d37adc9'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: CASE REPORT A case of concomitant colitic cancer and intrahepatic cholangiocarcinoma during follow-up for ulcerative colitis Kazuyo Tsuchiya1Atsushi Nanashima2Takuto Ikeda1Shiro Minami3 Motoaki Nagano4Takeomi Hamada2Koichi Yano2Yoshiro Fujii2 Received: 8 November 2016 / Accepted: 17 January 2017 / Published online: 30 January 2017 /C211Japanese Society of Gastroenterology 2017 Abstract Colitis-associated colorectal cancer (CAC) is known to occur in long-standing and extensive ulcerative colitis (UC). Furthermore, UC is known to complicate primary sclerosing cholangitis (PSC), which subsequently results in an increased risk of developing cholangiocarcinoma. We report a case of colitis-associated rectal cancer (CARC) accompanied by intrahepatic cholangiocarcinoma (ICC) based on UC and PSC. A 73-year-old man had suffered from UC for 19 years. During surveillance colonoscopy, a tumor was found in the rectum that was pathologically diagnosed as CARC from the resected specimen. Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct, and endoscopic retrograde cholangiography revealed a bandlike stricture. This remarkable tumor lesion was not observed in the hepatic duct. Left hepatectomy was performed because of the suspicion of possible ICC at the stenosis of the hepatic duct. The presence of ICC was conrmed at the lesion causing the stricture.\n",
      "\u001b[0m> Running step aca70982-be42-481c-9880-8d42fca6d376. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the fifth chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk and store them using the `add_metadatas` tool.\n",
      "\n",
      "1. **Medical/Surgical History**: \"A 73-year-old man had suffered from UC for 19 years\"\n",
      "2. **Diagnosis**: \"pathologically diagnosed as CARC from the resected specimen\", \"presence of ICC was confirmed at the lesion causing the stricture\"\n",
      "3. **Age**: \"73-year-old man\"\n",
      "4. **Diagnostic Techniques and Procedures**: \"surveillance colonoscopy, a tumor was found in the rectum\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct\", \"endoscopic retrograde cholangiography revealed a bandlike stricture\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Medical/Surgical History', 'A 73-year-old man had suffered from UC for 19 years'], ['Diagnosis', 'pathologically diagnosed as CARC from the resected specimen; presence of ICC was confirmed at the lesion causing the stricture'], ['Age', '73-year-old man'], ['Diagnostic Techniques and Procedures', 'surveillance colonoscopy, a tumor was found in the rectum; Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct; endoscopic retrograde cholangiography revealed a bandlike stricture']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step 77677ed2-a6b2-4015-bda8-dc46ede1fabf. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from the fifth chunk. Now, I will proceed to retrieve the content of the final chunk using its ID.\n",
      "Action: get_chunk\n",
      "Action Input: {'id': '493cb455-3d34-4d6d-8c47-a5c6323a281f'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: The pathological diagnosis from the resected specimen was ICC based on PSC. Adjuvant chemotherapy for ICC was performed for 6 months. Neither cancer has recurred for 2.5 years after hepatectomy. Patients with PSCconcomitant with UC should be considered a high-risk group for CAC and ICC. Keywords Colitic cancer /C1Cholangiocarcinoma /C1UC /C1 PSC Introduction Colitic cancer is appreciated as a colitis-associated colorectal cancer that develops in long-standing and extensive ulcerative colitis (UC). The number of patients with colitic cancer has increased recently along with increased morbidity from UC in Japan [ 1]. The risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer, and additionally, the complication of primary sclerosing cholangitis (PSC) [2,3]. Patients with PSC are also at increased risk of developing cholangiocarcinoma [ 4], which is known as a disease with poor prognosis in terms of the difculty in making an imaging diagnosis and the involvement of lymph nodes [ 4,5]. We report a patient with concomitant UC and PSC who developed colitis-associated rectal cancer (CARC) and intrahepatic cholangiocarcinoma (ICC), which we successfully cured by surgery. This is a rare case of CARC and ICC complicating these diseases in Japan. Case report A 73-year-old man with a 19-year history of UC was referred to our hospital. He had undergone colonoscopy every year at a previous outpatient clinic. The patient had extensive colitis and had been treated with aminosalicylate&Atsushi Nanashima a_nanashima@med.miyazaki-u.ac.jp 1Division of Gastrointestinal, Endocrine and Pediatric Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, Miyazaki, Japan 2Division of Hepato-Biliary-Pancreas Surgery, Department of Surgery, University of Miyazaki Faculty of Medicine, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan 3Ikime Coloproctological Clinic, Miyazaki, Japan 4Miyazaki Medical Center Hospital, Miyazaki, Japan 123Clin J Gastroenterol (2017) 10:157162 DOI 10.1007/s12328-017-0715-6\n",
      "\u001b[0m> Running step 2f718dee-0f40-4899-a19a-cbcabc3bb65f. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved the content of the final chunk. I will now extract relevant sentence snippets for each clinical metadata category from this chunk and store them using the `add_metadatas` tool.\n",
      "\n",
      "1. **Diagnosis**: \"pathological diagnosis from the resected specimen was ICC based on PSC\"\n",
      "2. **Pharmacological Therapy**: \"Adjuvant chemotherapy for ICC was performed for 6 months\"\n",
      "3. **Patient Outcome Assessment**: \"Neither cancer has recurred for 2.5 years after hepatectomy\"\n",
      "4. **Family History**: \"risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer\"\n",
      "5. **Medical/Surgical History**: \"73-year-old man with a 19-year history of UC\", \"had undergone colonoscopy every year\"\n",
      "6. **Comorbidities**: \"Patients with PSC concomitant with UC should be considered a high-risk group for CAC and ICC\"\n",
      "\n",
      "Now, I will use the `add_metadatas` tool to store these snippets.\n",
      "Action: add_metadatas\n",
      "Action Input: {'metadata': [['Diagnosis', 'pathological diagnosis from the resected specimen was ICC based on PSC'], ['Pharmacological Therapy', 'Adjuvant chemotherapy for ICC was performed for 6 months'], ['Patient Outcome Assessment', 'Neither cancer has recurred for 2.5 years after hepatectomy'], ['Family History', 'risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer'], ['Medical/Surgical History', '73-year-old man with a 19-year history of UC; had undergone colonoscopy every year'], ['Comorbidities', 'Patients with PSC concomitant with UC should be considered a high-risk group for CAC and ICC']]}\n",
      "\u001b[0m\u001b[1;3;34mObservation: succesfully added metadata\n",
      "\u001b[0m> Running step d85e7b56-34a5-4311-b45a-fd35f7defb49. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully added the extracted metadata from all the chunks. Now, I will retrieve all the stored metadata using the `get_all_metadata` tool to review and refine them if necessary.\n",
      "Action: get_all_metadata\n",
      "Action Input: {}\n",
      "\u001b[0m\u001b[1;3;34mObservation: {'Life Style': [], 'Family History': ['risk factors for colitic cancer are considered to be long disease duration, extensive lesions, family history of colon cancer'], 'Social History': [], 'Medical/Surgical History': ['laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed', 'developed after a 19-year follow-up of UC associated with PSC', 'A 73-year-old man had suffered from UC for 19 years', '73-year-old man with a 19-year history of UC', ' had undergone colonoscopy every year'], 'Signs and Symptoms': ['elevated lesion surrounded by erosion with unclear margins'], 'Comorbidities': ['Patients with PSC concomitant with UC should be considered a high-risk group for CAC and ICC'], 'Diagnostic Techniques and Procedures': ['annual colonoscopy was able to detect colitic cancer at the early stage', ' chromoendoscopic examination revealed an elevated lesion', ' p53 staining', 'Abdominal enhanced CT revealed partial intrahepatic bile duct dilation', ' endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct', ' brush cytology of the stenotic site revealed no malignancy', 'computed tomography revealed limited dilation of the intrahepatic bile duct', ' ERC demonstrated a pruned-tree appearance in the bile duct', ' band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy', 'surveillance colonoscopy, a tumor was found in the rectum', ' Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct', ' endoscopic retrograde cholangiography revealed a bandlike stricture'], 'Diagnosis': ['diagnosed our patient as having colitic cancer, not sporadic cancer', 'diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition', ' suspicious diagnosis of primary sclerotic cholangitis', ' intraoperative diagnosis of adenocarcinoma in the liver', ' diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition', 'compatible with primary sclerosing cholangitis', 'pathologically diagnosed as CARC from the resected specimen', ' presence of ICC was confirmed at the lesion causing the stricture', 'pathological diagnosis from the resected specimen was ICC based on PSC'], 'Laboratory Values': ['elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L', ' CA19-9 level was 32.3 U/mL', ' CA19-9 level to 56.4 U/mL'], 'Pathology': ['surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia', 'resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma', ' abnormal p53 accumulation was found', ' cancer invaded the muscular layer without node metastasis'], 'Pharmacological Therapy': ['Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months', 'Adjuvant chemotherapy for ICC was performed for 6 months'], 'Interventional Therapy': ['we performed surgery', 'decided to perform a left hepatectomy', ' additional resected specimen of the left bile duct and caudate branch'], 'Patient Outcome Assessment': ['The patient was discharged after an uneventful postoperative period', ' CA19-9 level returned to normal (14.1 U/mL)', ' The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed', 'Neither cancer has recurred for 2.5 years after hepatectomy'], 'Age': ['73-year-old man'], 'Gender': []}\n",
      "\u001b[0m> Running step 48ebb88a-b959-4969-a8c0-78ac4db3de2b. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have retrieved all the stored metadata. Now, I will review and refine the extracted snippets to ensure clarity and relevance. I will then structure the final output in JSON format.\n",
      "\n",
      "1. **Family History**: \"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"\n",
      "2. **Medical/Surgical History**: \"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed. Developed after a 19-year follow-up of UC associated with PSC. A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"\n",
      "3. **Signs and Symptoms**: \"Elevated lesion surrounded by erosion with unclear margins.\"\n",
      "4. **Comorbidities**: \"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"\n",
      "5. **Diagnostic Techniques and Procedures**: \"Annual colonoscopy detected colitic cancer at an early stage. Chromoendoscopic examination revealed an elevated lesion. P53 staining was performed. Abdominal enhanced CT revealed partial intrahepatic bile duct dilation. Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct. Brush cytology of the stenotic site revealed no malignancy. Computed tomography revealed limited dilation of the intrahepatic bile duct. ERC demonstrated a pruned-tree appearance in the bile duct. A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy. Surveillance colonoscopy found a tumor in the rectum. Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct. Endoscopic retrograde cholangiography revealed a bandlike stricture.\"\n",
      "6. **Diagnosis**: \"Diagnosed with colitic cancer, not sporadic cancer. Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition. Suspicious diagnosis of primary sclerotic cholangitis. Intraoperative diagnosis of adenocarcinoma in the liver. Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition. Compatible with primary sclerosing cholangitis. Pathologically diagnosed as CARC from the resected specimen. Presence of ICC was confirmed at the lesion causing the stricture. Pathological diagnosis from the resected specimen was ICC based on PSC.\"\n",
      "7. **Laboratory Values**: \"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L. CA19-9 level was 32.3 U/mL. CA19-9 level increased to 56.4 U/mL.\"\n",
      "8. **Pathology**: \"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia. Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma. Abnormal p53 accumulation was found. Cancer invaded the muscular layer without node metastasis.\"\n",
      "9. **Pharmacological Therapy**: \"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months. Adjuvant chemotherapy for ICC was performed for 6 months.\"\n",
      "10. **Interventional Therapy**: \"Surgery was performed. Decided to perform a left hepatectomy. Additional resected specimen of the left bile duct and caudate branch.\"\n",
      "11. **Patient Outcome Assessment**: \"The patient was discharged after an uneventful postoperative period. CA19-9 level returned to normal (14.1 U/mL). The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed. Neither cancer has recurred for 2.5 years after hepatectomy.\"\n",
      "12. **Age**: \"73-year-old man.\"\n",
      "\n",
      "Now, I will structure this information in JSON format.\n",
      "Action: validate_generated_metadata\n",
      "Action Input: {'text': '{\"Family History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"], \"Medical/Surgical History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"], \"Signs and Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"], \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"], \"Diagnostic Techniques and Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"], \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"], \"Laboratory Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"], \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"], \"Pharmacological Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"], \"Interventional Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"], \"Patient Outcome Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"], \"Age\": [\"73-year-old man.\"]}'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Error during parsing the generated text: 12 validation errors for ClinicalMetadata\n",
      "Life_Style\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Family_History\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Social_History\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Medical_Surgical_History\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Signs_and_Symptoms\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Diagnostic_Techniques_and_Procedures\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Laboratory_Values\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Pharmacological_Therapy\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Interventional_Therapy\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Patient_Outcome_Assessment\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Age\n",
      "  Input should be a valid integer [type=int_type, input_value=['73-year-old man.'], input_type=list]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/int_type\n",
      "Gender\n",
      "  Field required [type=missing, input_value={'Family History': ['Risk...': ['73-year-old man.']}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "\u001b[0m> Running step 92b67d25-8be2-4c09-a12e-a239446905e8. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The parser indicates that there are missing fields and an issue with the \"Age\" field. I need to ensure that all required fields are present and correctly formatted. Specifically, I need to address the \"Age\" field to be an integer and ensure all categories are included, even if they are empty.\n",
      "\n",
      "Let's correct the \"Age\" field and ensure all required fields are present in the JSON structure.\n",
      "\n",
      "1. **Age**: Convert \"73-year-old man\" to 73.\n",
      "\n",
      "Now, I will structure the information again in JSON format, ensuring all required fields are present.\n",
      "Action: validate_generated_metadata\n",
      "Action Input: {'text': '{\"Life Style\": [], \"Family History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"], \"Social History\": [], \"Medical/Surgical History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"], \"Signs and Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"], \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"], \"Diagnostic Techniques and Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"], \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"], \"Laboratory Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"], \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"], \"Pharmacological Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"], \"Interventional Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"], \"Patient Outcome Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"], \"Age\": 73, \"Gender\": []}'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Error during parsing the generated text: 11 validation errors for ClinicalMetadata\n",
      "Life_Style\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Family_History\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Social_History\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Medical_Surgical_History\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Signs_and_Symptoms\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Diagnostic_Techniques_and_Procedures\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Laboratory_Values\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Pharmacological_Therapy\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Interventional_Therapy\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Patient_Outcome_Assessment\n",
      "  Field required [type=missing, input_value={'Life Style': [], 'Famil...'Age': 73, 'Gender': []}, input_type=dict]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/missing\n",
      "Gender\n",
      "  Input should be a valid string [type=string_type, input_value=[], input_type=list]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/string_type\n",
      "\u001b[0m> Running step 0c73b0a0-6379-4f6a-b7cf-165417a06923. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The parser indicates that the fields need to be present even if they are empty, and the \"Gender\" field should be a string. I will ensure all fields are included and correctly formatted, and set \"Gender\" to an empty string if no information is available.\n",
      "\n",
      "Let's correct the \"Gender\" field and ensure all required fields are present in the JSON structure.\n",
      "\n",
      "1. **Gender**: Set to an empty string if no information is available.\n",
      "\n",
      "Now, I will structure the information again in JSON format, ensuring all required fields are present.\n",
      "Action: validate_generated_metadata\n",
      "Action Input: {'text': '{\"Life_Style\": \"\", \"Family_History\": \"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\", \"Social_History\": \"\", \"Medical_Surgical_History\": \"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed. Developed after a 19-year follow-up of UC associated with PSC. A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\", \"Signs_and_Symptoms\": \"Elevated lesion surrounded by erosion with unclear margins.\", \"Comorbidities\": \"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\", \"Diagnostic_Techniques_and_Procedures\": \"Annual colonoscopy detected colitic cancer at an early stage. Chromoendoscopic examination revealed an elevated lesion. P53 staining was performed. Abdominal enhanced CT revealed partial intrahepatic bile duct dilation. Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct. Brush cytology of the stenotic site revealed no malignancy. Computed tomography revealed limited dilation of the intrahepatic bile duct. ERC demonstrated a pruned-tree appearance in the bile duct. A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy. Surveillance colonoscopy found a tumor in the rectum. Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct. Endoscopic retrograde cholangiography revealed a bandlike stricture.\", \"Diagnosis\": \"Diagnosed with colitic cancer, not sporadic cancer. Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition. Suspicious diagnosis of primary sclerotic cholangitis. Intraoperative diagnosis of adenocarcinoma in the liver. Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition. Compatible with primary sclerosing cholangitis. Pathologically diagnosed as CARC from the resected specimen. Presence of ICC was confirmed at the lesion causing the stricture. Pathological diagnosis from the resected specimen was ICC based on PSC.\", \"Laboratory_Values\": \"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L. CA19-9 level was 32.3 U/mL. CA19-9 level increased to 56.4 U/mL.\", \"Pathology\": \"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia. Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma. Abnormal p53 accumulation was found. Cancer invaded the muscular layer without node metastasis.\", \"Pharmacological_Therapy\": \"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months. Adjuvant chemotherapy for ICC was performed for 6 months.\", \"Interventional_Therapy\": \"Surgery was performed. Decided to perform a left hepatectomy. Additional resected specimen of the left bile duct and caudate branch.\", \"Patient_Outcome_Assessment\": \"The patient was discharged after an uneventful postoperative period. CA19-9 level returned to normal (14.1 U/mL). The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed. Neither cancer has recurred for 2.5 years after hepatectomy.\", \"Age\": 73, \"Gender\": \"\"}'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Error during parsing the generated text: 13 validation errors for ClinicalMetadata\n",
      "Life_Style\n",
      "  Input should be a valid array [type=list_type, input_value='', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Family_History\n",
      "  Input should be a valid array [type=list_type, input_value='Risk factors for colitic...istory of colon cancer.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Social_History\n",
      "  Input should be a valid array [type=list_type, input_value='', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Medical_Surgical_History\n",
      "  Input should be a valid array [type=list_type, input_value='Laparoscopic total proct...colonoscopy every year.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Signs_and_Symptoms\n",
      "  Input should be a valid array [type=list_type, input_value='Elevated lesion surround...n with unclear margins.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Comorbidities\n",
      "  Input should be a valid array [type=list_type, input_value='Patients with PSC concom... group for CAC and ICC.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Diagnostic_Techniques_and_Procedures\n",
      "  Input should be a valid array [type=list_type, input_value='Annual colonoscopy detec...d a bandlike stricture.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Diagnosis\n",
      "  Input should be a valid array [type=list_type, input_value='Diagnosed with colitic c...n was ICC based on PSC.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Laboratory_Values\n",
      "  Input should be a valid array [type=list_type, input_value='Elevated c-glutamyltrans...increased to 56.4 U/mL.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Pathology\n",
      "  Input should be a valid array [type=list_type, input_value='Surgically resected spec...ithout node metastasis.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Pharmacological_Therapy\n",
      "  Input should be a valid array [type=list_type, input_value='Adjuvant therapy for ICC...performed for 6 months.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Interventional_Therapy\n",
      "  Input should be a valid array [type=list_type, input_value='Surgery was performed. D...uct and caudate branch.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "Patient_Outcome_Assessment\n",
      "  Input should be a valid array [type=list_type, input_value='The patient was discharg...ears after hepatectomy.', input_type=str]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/list_type\n",
      "\u001b[0m> Running step e2b1b351-3b2b-4997-82ee-bf5dc6aab9d7. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The parser indicates that each field should be a list, even if it contains only one string or is empty. I will correct the format by ensuring each field is a list.\n",
      "\n",
      "Let's correct the format and ensure all fields are lists in the JSON structure.\n",
      "\n",
      "Now, I will structure the information again in JSON format, ensuring all required fields are lists.\n",
      "Action: validate_generated_metadata\n",
      "Action Input: {'text': '{\"Life_Style\": [], \"Family_History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"], \"Social_History\": [], \"Medical_Surgical_History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"], \"Signs_and_Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"], \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"], \"Diagnostic_Techniques_and_Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"], \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"], \"Laboratory_Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"], \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"], \"Pharmacological_Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"], \"Interventional_Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"], \"Patient_Outcome_Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"], \"Age\": [73], \"Gender\": [\"\"]}'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Error during parsing the generated text: 2 validation errors for ClinicalMetadata\n",
      "Age\n",
      "  Input should be a valid integer [type=int_type, input_value=[73], input_type=list]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/int_type\n",
      "Gender\n",
      "  Input should be a valid string [type=string_type, input_value=[''], input_type=list]\n",
      "    For further information visit https://errors.pydantic.dev/2.9/v/string_type\n",
      "\u001b[0m> Running step aafaba18-6ed0-415f-830c-e6a696b26de2. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: The parser indicates that the \"Age\" field should be a single integer, not a list, and the \"Gender\" field should be a single string, not a list. I will correct these fields accordingly.\n",
      "\n",
      "Let's correct the \"Age\" and \"Gender\" fields to ensure they are in the correct format.\n",
      "\n",
      "Now, I will structure the information again in JSON format, ensuring all fields are correctly formatted.\n",
      "Action: validate_generated_metadata\n",
      "Action Input: {'text': '{\"Life_Style\": [], \"Family_History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"], \"Social_History\": [], \"Medical_Surgical_History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"], \"Signs_and_Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"], \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"], \"Diagnostic_Techniques_and_Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"], \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"], \"Laboratory_Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"], \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"], \"Pharmacological_Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"], \"Interventional_Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"], \"Patient_Outcome_Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"], \"Age\": 73, \"Gender\": \"\"}'}\n",
      "\u001b[0m\u001b[1;3;34mObservation: Life_Style=[] Family_History=['Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.'] Social_History=[] Medical_Surgical_History=['Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.', 'Developed after a 19-year follow-up of UC associated with PSC.', 'A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.'] Signs_and_Symptoms=['Elevated lesion surrounded by erosion with unclear margins.'] Comorbidities=['Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.'] Diagnostic_Techniques_and_Procedures=['Annual colonoscopy detected colitic cancer at an early stage.', 'Chromoendoscopic examination revealed an elevated lesion.', 'P53 staining was performed.', 'Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.', 'Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.', 'Brush cytology of the stenotic site revealed no malignancy.', 'Computed tomography revealed limited dilation of the intrahepatic bile duct.', 'ERC demonstrated a pruned-tree appearance in the bile duct.', 'A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.', 'Surveillance colonoscopy found a tumor in the rectum.', 'Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.', 'Endoscopic retrograde cholangiography revealed a bandlike stricture.'] Diagnosis=['Diagnosed with colitic cancer, not sporadic cancer.', 'Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.', 'Suspicious diagnosis of primary sclerotic cholangitis.', 'Intraoperative diagnosis of adenocarcinoma in the liver.', 'Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.', 'Compatible with primary sclerosing cholangitis.', 'Pathologically diagnosed as CARC from the resected specimen.', 'Presence of ICC was confirmed at the lesion causing the stricture.', 'Pathological diagnosis from the resected specimen was ICC based on PSC.'] Laboratory_Values=['Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.', 'CA19-9 level was 32.3 U/mL.', 'CA19-9 level increased to 56.4 U/mL.'] Pathology=['Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.', 'Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.', 'Abnormal p53 accumulation was found.', 'Cancer invaded the muscular layer without node metastasis.'] Pharmacological_Therapy=['Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.', 'Adjuvant chemotherapy for ICC was performed for 6 months.'] Interventional_Therapy=['Surgery was performed.', 'Decided to perform a left hepatectomy.', 'Additional resected specimen of the left bile duct and caudate branch.'] Patient_Outcome_Assessment=['The patient was discharged after an uneventful postoperative period.', 'CA19-9 level returned to normal (14.1 U/mL).', 'The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.', 'Neither cancer has recurred for 2.5 years after hepatectomy.'] Age=73 Gender=''\n",
      "\u001b[0m> Running step 6dbe456f-281e-4046-9cb3-3bcfcf0e29fa. Step input: None\n",
      "\u001b[1;3;38;5;200mThought: I have successfully structured the clinical metadata into the required format. The final output is now ready and validated.\n",
      "Answer: The structured clinical metadata has been successfully extracted and validated. Here is the final output:\n",
      "\n",
      "```json\n",
      "{\n",
      "  \"Life_Style\": [],\n",
      "  \"Family_History\": [\"Risk factors for colitic cancer include long disease duration, extensive lesions, and a family history of colon cancer.\"],\n",
      "  \"Social_History\": [],\n",
      "  \"Medical_Surgical_History\": [\"Laparoscopic total proctocolectomy combined with abdominoperineal resection and ileostomy was performed.\", \"Developed after a 19-year follow-up of UC associated with PSC.\", \"A 73-year-old man had suffered from UC for 19 years and had undergone colonoscopy every year.\"],\n",
      "  \"Signs_and_Symptoms\": [\"Elevated lesion surrounded by erosion with unclear margins.\"],\n",
      "  \"Comorbidities\": [\"Patients with PSC concomitant with UC are considered a high-risk group for CAC and ICC.\"],\n",
      "  \"Diagnostic_Techniques_and_Procedures\": [\"Annual colonoscopy detected colitic cancer at an early stage.\", \"Chromoendoscopic examination revealed an elevated lesion.\", \"P53 staining was performed.\", \"Abdominal enhanced CT revealed partial intrahepatic bile duct dilation.\", \"Endoscopic retrograde cholangiography demonstrated stenosis and dilation of the bile duct.\", \"Brush cytology of the stenotic site revealed no malignancy.\", \"Computed tomography revealed limited dilation of the intrahepatic bile duct.\", \"ERC demonstrated a pruned-tree appearance in the bile duct.\", \"A band-like stricture of 5 mm in length in the left lateral sector and dilation of the bile duct suggested a malignancy.\", \"Surveillance colonoscopy found a tumor in the rectum.\", \"Abdominal computed tomography also revealed a localized dilation of the intrahepatic bile duct.\", \"Endoscopic retrograde cholangiography revealed a bandlike stricture.\"],\n",
      "  \"Diagnosis\": [\"Diagnosed with colitic cancer, not sporadic cancer.\", \"Diagnosed as pT2 and pN0, Stage I according to the Union for International Cancer Control (UICC) 7th edition.\", \"Suspicious diagnosis of primary sclerotic cholangitis.\", \"Intraoperative diagnosis of adenocarcinoma in the liver.\", \"Diagnosed as pT4 and pN0, Stage IVa according to the UICC classification 7th edition.\", \"Compatible with primary sclerosing cholangitis.\", \"Pathologically diagnosed as CARC from the resected specimen.\", \"Presence of ICC was confirmed at the lesion causing the stricture.\", \"Pathological diagnosis from the resected specimen was ICC based on PSC.\"],\n",
      "  \"Laboratory_Values\": [\"Elevated c-glutamyltransferase and alkaline phosphatase levels of 133 and 371 IU/L.\", \"CA19-9 level was 32.3 U/mL.\", \"CA19-9 level increased to 56.4 U/mL.\"],\n",
      "  \"Pathology\": [\"Surgically resected specimen showed invasive adenocarcinoma with the coexistence of dysplasia.\", \"Resected specimen showed well-differentiated tubular adenocarcinoma with a component of mucinous adenocarcinoma.\", \"Abnormal p53 accumulation was found.\", \"Cancer invaded the muscular layer without node metastasis.\"],\n",
      "  \"Pharmacological_Therapy\": [\"Adjuvant therapy for ICC consisting of combination therapy of gemcitabine and S-1 was administered for 6 months.\", \"Adjuvant chemotherapy for ICC was performed for 6 months.\"],\n",
      "  \"Interventional_Therapy\": [\"Surgery was performed.\", \"Decided to perform a left hepatectomy.\", \"Additional resected specimen of the left bile duct and caudate branch.\"],\n",
      "  \"Patient_Outcome_Assessment\": [\"The patient was discharged after an uneventful postoperative period.\", \"CA19-9 level returned to normal (14.1 U/mL).\", \"The patient remains alive and has been followed-up for 2.5 years after hepatectomy with no recurrence of ICC or colitic cancer observed.\", \"Neither cancer has recurred for 2.5 years after hepatectomy.\"],\n",
      "  \"Age\": 73,\n",
      "  \"Gender\": \"\"\n",
      "}\n",
      "```\n",
      "\u001b[0m"
     ]
    },
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<string>, line 1)",
     "output_type": "error",
     "traceback": [
      "Traceback \u001b[0;36m(most recent call last)\u001b[0m:\n",
      "\u001b[0m  File \u001b[1;32m~/miniforge3/envs/nl2sql/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3577\u001b[0m in \u001b[1;35mrun_code\u001b[0m\n    exec(code_obj, self.user_global_ns, self.user_ns)\u001b[0m\n",
      "\u001b[0m  Cell \u001b[1;32mIn[17], line 11\u001b[0m\n    metadata = extraction_agent.extract_metadata(all_categories, concated_chunks_ids)\u001b[0m\n",
      "\u001b[0;36m  Cell \u001b[0;32mIn[5], line 64\u001b[0;36m in \u001b[0;35mextract_metadata\u001b[0;36m\n\u001b[0;31m    metadata = eval(response.response)\u001b[0;36m\n",
      "\u001b[0;36m  File \u001b[0;32m<string>:1\u001b[0;36m\u001b[0m\n\u001b[0;31m    The structured clinical metadata has been successfully extracted and validated. Here is the final output:\u001b[0m\n\u001b[0m        ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "all_categories = ['Life Style', 'Family History', 'Social History', 'Medical/Surgical History', 'Signs and Symptoms',\n",
    "  'Comorbidities', 'Diagnostic Techniques and Procedures', 'Diagnosis', 'Laboratory Values', 'Pathology',\n",
    "    'Pharmacological Therapy', 'Interventional Therapy', 'Patient Outcome Assessment', 'Age', 'Gender']\n",
    "\n",
    "output_validator = OutputValidator(ClinicalMetadata)\n",
    "metadata_manager = MetadataManager(categories=all_categories)\n",
    "\n",
    "if len(chunk_manager.chunks) > 0:\n",
    "    extraction_agent = MetadataExtractionAgent(llm, chunk_manager, metadata_manager, output_validator)\n",
    "    concated_chunks_ids = \"\\n\".join([f\"id: {k}\" for k,_ in chunk_manager.chunks.items()])\n",
    "    metadata = extraction_agent.extract_metadata(all_categories, concated_chunks_ids)\n",
    "else:\n",
    "    print('No relevant chunks found')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "crs-rlhf-env",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.15"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}