localm

.gitattributes

@@ -1,2 +1,35 @@
-output/biomedbert_vector_db/faiss.index filter=lfs diff=lfs merge=lfs -text
-output/biomedbert_vector_db/metadata.pkl filter=lfs diff=lfs merge=lfs -text
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -1,16 +0,0 @@
-FROM python:3.10-slim
-
-RUN apt-get update && apt-get install -y \
-    poppler-utils \
-    tesseract-ocr \
-    libgl1 \
-    && rm -rf /var/lib/apt/lists/*
-
-WORKDIR /app
-
-COPY requirements.txt .
-RUN pip install --no-cache-dir -r requirements.txt
-
-COPY . .
-
-CMD ["python", "app.py"]

README.md

@@ -1,15 +1,16 @@
 ---
-title: Pathology RAG System
-colorFrom: blue
+title: Automate Knowledge Extraction From Pathology Reports
+emoji: 💬
+colorFrom: yellow
 colorTo: purple
 sdk: gradio
-sdk_version: 6.3.0
+sdk_version: 5.42.0
 app_file: app.py
 pinned: false
+hf_oauth: true
+hf_oauth_scopes:
+- inference-api
+license: mit
 ---
 
-# 🔬 Pathology RAG System
-
-Pathology Report Search & Question Answering System
-
-Upload pathology PDFs and ask questions using natural language!
+An example chatbot using [Gradio](https://gradio.app), [`huggingface_hub`](https://huggingface.co/docs/huggingface_hub/v0.22.2/en/index), and the [Hugging Face Inference API](https://huggingface.co/docs/api-inference/index).

app.py

@@ -1,258 +1,70 @@
-#!/usr/bin/env python3
-"""
-Pathology RAG System - Hugging Face Deployment
-
-Features:
-- Global RAG across all reports
-- Report-specific RAG via dropdown selection
-- No PDF or OCR text stored
-- Fixed top_k = 5 (internal)
-"""
-
-import os
-import sys
-from pathlib import Path
-from datetime import datetime
 import gradio as gr
+from huggingface_hub import InferenceClient
 
-# --------------------------------------------------
-# Environment setup
-# --------------------------------------------------
-
-os.environ["CUDA_VISIBLE_DEVICES"] = ""
-
-sys.path.append("src")
-
-# --------------------------------------------------
-# Configuration
-# --------------------------------------------------
-
-FAISS_DB_PATH = "output/biomedbert_vector_db"
-EMBEDDING_MODEL = "microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext"
-
-# --------------------------------------------------
-# Sanity check
-# --------------------------------------------------
-
-if not Path(FAISS_DB_PATH).exists():
-    print("Error: FAISS database not found.")
-    sys.exit(1)
-
-# --------------------------------------------------
-# Imports
-# --------------------------------------------------
-
-try:
-    from retriever import CompleteRAGPipeline
-    from document_processor import DynamicRAGUpdater
-except ImportError as e:
-    print(f"Import Error: {e}")
-    sys.exit(1)
-
-
-# ==================================================
-# UI CLASS
-# ==================================================
-
-class PathologyRAGUI:
-    def __init__(self, faiss_db_path: str, embedding_model: str):
-        print("Initializing Pathology RAG System...")
-
-        self.faiss_db_path = faiss_db_path
-        self.embedding_model = embedding_model
-
-        self.pipeline = CompleteRAGPipeline(
-            faiss_db_path=faiss_db_path,
-            embedding_model=embedding_model,
-        )
-
-        self.updater = DynamicRAGUpdater(
-            vector_db_path=faiss_db_path,
-            embedding_model=embedding_model,
-        )
-
-        self.query_count = 0
-        self.upload_count = 0
-
-        print("System ready.")
-
-    # --------------------------------------------------
-    # Helpers
-    # --------------------------------------------------
-
-    def get_report_choices(self):
-        reports = self.pipeline.get_available_reports()
-        return ["All reports"] + reports
-
-    # --------------------------------------------------
-    # Upload PDF
-    # --------------------------------------------------
-
-    def upload_pdf(self, file):
-        if file is None:
-            return "No file uploaded.", "", gr.update()
-
-        try:
-            stats = self.updater.process_and_add_pdf(file.path)
-
-            self.pipeline = CompleteRAGPipeline(
-                faiss_db_path=self.faiss_db_path,
-                embedding_model=self.embedding_model,
-            )
-
-            self.upload_count += 1
-
-            status = (
-                f"Upload successful\n\n"
-                f"Chunks created: {stats['num_chunks']}\n"
-                f"Vectors added: {stats['vectors_added']}\n"
-                f"Processing time: {stats['processing_time_seconds']:.2f}s"
-            )
-
-            return (
-                status,
-                f"Total uploads: {self.upload_count}",
-                gr.update(choices=self.get_report_choices(), value="All reports"),
-            )
-
-        except Exception as e:
-            return f"Error: {str(e)}", "", gr.update()
 
-    # --------------------------------------------------
-    # Process Query
-    # --------------------------------------------------
+def respond(
+    message,
+    history: list[dict[str, str]],
+    system_message,
+    max_tokens,
+    temperature,
+    top_p,
+    hf_token: gr.OAuthToken,
+):
+    """
+    For more information on `huggingface_hub` Inference API support, please check the docs: https://huggingface.co/docs/huggingface_hub/v0.22.2/en/guides/inference
+    """
+    client = InferenceClient(token=hf_token.token, model="openai/gpt-oss-20b")
 
-    def process_query(self, question: str, selected_report: str):
-        if not question or not question.strip():
-            return "Please enter a question.", "", ""
+    messages = [{"role": "system", "content": system_message}]
 
-        self.query_count += 1
+    messages.extend(history)
 
-        report_name = None if selected_report == "All reports" else selected_report
+    messages.append({"role": "user", "content": message})
 
-        result = self.pipeline.ask(
-            question,
-            report_name=report_name,
-        )
+    response = ""
 
-        answer = result.get("answer", "No answer generated.")
-        sources = result.get("sources", [])
+    for message in client.chat_completion(
+        messages,
+        max_tokens=max_tokens,
+        stream=True,
+        temperature=temperature,
+        top_p=top_p,
+    ):
+        choices = message.choices
+        token = ""
+        if len(choices) and choices[0].delta.content:
+            token = choices[0].delta.content
 
-        sources_text = self.format_sources(sources)
+        response += token
+        yield response
 
-        metadata = (
-            f"Query number: {self.query_count}\n"
-            f"Time: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}\n"
-            f"Scope: {selected_report}"
-        )
 
-        return answer, sources_text, metadata
-
-    # --------------------------------------------------
-    # Format sources
-    # --------------------------------------------------
-
-    def format_sources(self, sources):
-        if not sources:
-            return "No sources available."
-
-        formatted = []
-        for i, src in enumerate(sources, 1):
-            chunk = src["chunk"]
-            score = src.get("ce_score", src.get("score", 0.0))
-
-            formatted.append(
-                f"Source {i}\n"
-                f"File: {chunk.get('filename', 'N/A')}\n"
-                f"Score: {score:.3f}\n"
-                f"{chunk.get('text', '')[:300]}...\n"
-            )
-
-        return "\n---\n".join(formatted)
-
-    # --------------------------------------------------
-    # UI
-    # --------------------------------------------------
-
-    def create_interface(self):
-        with gr.Blocks(title="Pathology RAG System") as demo:
-
-            gr.Markdown(
-                "# Pathology Report Analysis System\n"
-                "Search and question answering over pathology reports"
-            )
-
-            with gr.Tabs():
-
-                # Upload
-                with gr.Tab("Upload Report"):
-                    file_upload = gr.File(
-                        label="Select PDF",
-                        file_types=[".pdf"],
-                    )
-
-                    upload_btn = gr.Button("Process and Add", variant="primary")
-
-                    upload_status = gr.Markdown("")
-                    upload_stats = gr.Markdown("")
-
-                    report_dropdown = gr.Dropdown(
-                        choices=self.get_report_choices(),
-                        value="All reports",
-                        label="Select report",
-                    )
-
-                    upload_btn.click(
-                        fn=self.upload_pdf,
-                        inputs=[file_upload],
-                        outputs=[upload_status, upload_stats, report_dropdown],
-                    )
-
-                # Query
-                with gr.Tab("Search and Ask"):
-                    question_input = gr.Textbox(
-                        label="Ask a question",
-                        lines=3,
-                    )
-
-                    report_dropdown_query = gr.Dropdown(
-                        choices=self.get_report_choices(),
-                        value="All reports",
-                        label="Select report",
-                    )
-
-                    submit_btn = gr.Button("Search", variant="primary")
-
-                    answer_output = gr.Markdown("")
-                    sources_output = gr.Markdown("")
-                    metadata_output = gr.Markdown("")
-
-                    submit_btn.click(
-                        fn=self.process_query,
-                        inputs=[question_input, report_dropdown_query],
-                        outputs=[answer_output, sources_output, metadata_output],
-                    )
-
-            gr.Markdown(
-                "---\nFor research and educational purposes only."
-            )
-
-        return demo
-
-
-# ==================================================
-# MAIN
-# ==================================================
-
-def main():
-    ui = PathologyRAGUI(
-        faiss_db_path=FAISS_DB_PATH,
-        embedding_model=EMBEDDING_MODEL,
-    )
-
-    demo = ui.create_interface()
-    demo.launch()
+"""
+For information on how to customize the ChatInterface, peruse the gradio docs: https://www.gradio.app/docs/chatinterface
+"""
+chatbot = gr.ChatInterface(
+    respond,
+    type="messages",
+    additional_inputs=[
+        gr.Textbox(value="You are a friendly Chatbot.", label="System message"),
+        gr.Slider(minimum=1, maximum=2048, value=512, step=1, label="Max new tokens"),
+        gr.Slider(minimum=0.1, maximum=4.0, value=0.7, step=0.1, label="Temperature"),
+        gr.Slider(
+            minimum=0.1,
+            maximum=1.0,
+            value=0.95,
+            step=0.05,
+            label="Top-p (nucleus sampling)",
+        ),
+    ],
+)
+
+with gr.Blocks() as demo:
+    with gr.Sidebar():
+        gr.LoginButton()
+    chatbot.render()
 
 
 if __name__ == "__main__":
-    main()
+    demo.launch()

output/biomedbert_output/00103fa2-43e4-4c6a-babb-d8b46612399e_nlp.json

@@ -1,560 +0,0 @@
-{
-  "filename": "00103fa2-43e4-4c6a-babb-d8b46612399e",
-  "timestamp": "2026-01-05T14:42:18.277630",
-  "entities": [
-    {
-      "text": "C8BBFFAA-4A45-44D3",
-      "type": "ENTITY",
-      "start": 21,
-      "end": 39
-    },
-    {
-      "text": "TCGA-XS-A8T3-01A-PR",
-      "type": "ENTITY",
-      "start": 58,
-      "end": 77
-    },
-    {
-      "text": "QruyNbS C 53.oy Nature",
-      "type": "ENTITY",
-      "start": 102,
-      "end": 124
-    },
-    {
-      "text": "Cervix tJ",
-      "type": "ENTITY",
-      "start": 138,
-      "end": 147
-    },
-    {
-      "text": "MACROSCOPY",
-      "type": "ENTITY",
-      "start": 182,
-      "end": 192
-    },
-    {
-      "text": "Specimen",
-      "type": "ENTITY",
-      "start": 193,
-      "end": 201
-    },
-    {
-      "text": "uterus",
-      "type": "ENTITY",
-      "start": 218,
-      "end": 224
-    },
-    {
-      "text": "left fallopian tube",
-      "type": "ENTITY",
-      "start": 229,
-      "end": 248
-    },
-    {
-      "text": "tube measures",
-      "type": "ENTITY",
-      "start": 276,
-      "end": 289
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 300,
-      "end": 306
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 311,
-      "end": 319
-    },
-    {
-      "text": "ranges",
-      "type": "ENTITY",
-      "start": 320,
-      "end": 326
-    },
-    {
-      "text": "cuts",
-      "type": "ENTITY",
-      "start": 358,
-      "end": 362
-    },
-    {
-      "text": "wall",
-      "type": "ENTITY",
-      "start": 367,
-      "end": 371
-    },
-    {
-      "text": "thin",
-      "type": "ENTITY",
-      "start": 375,
-      "end": 379
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 381,
-      "end": 390
-    },
-    {
-      "text": "light",
-      "type": "ENTITY",
-      "start": 403,
-      "end": 408
-    },
-    {
-      "text": "dilated",
-      "type": "ENTITY",
-      "start": 412,
-      "end": 419
-    },
-    {
-      "text": "hemorrhagic",
-      "type": "ENTITY",
-      "start": 436,
-      "end": 447
-    },
-    {
-      "text": "content",
-      "type": "ENTITY",
-      "start": 448,
-      "end": 455
-    },
-    {
-      "text": "uterus",
-      "type": "ENTITY",
-      "start": 461,
-      "end": 467
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 468,
-      "end": 476
-    },
-    {
-      "text": "longitudinal axis",
-      "type": "ENTITY",
-      "start": 492,
-      "end": 509
-    },
-    {
-      "text": "anteroposterior",
-      "type": "ENTITY",
-      "start": 521,
-      "end": 536
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 537,
-      "end": 545
-    },
-    {
-      "text": "bicorneal",
-      "type": "ENTITY",
-      "start": 560,
-      "end": 569
-    },
-    {
-      "text": "distance",
-      "type": "ENTITY",
-      "start": 570,
-      "end": 578
-    },
-    {
-      "text": "cervix measures",
-      "type": "ENTITY",
-      "start": 584,
-      "end": 599
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 610,
-      "end": 618
-    },
-    {
-      "text": "surrounded",
-      "type": "ENTITY",
-      "start": 626,
-      "end": 636
-    },
-    {
-      "text": "vaginal dome",
-      "type": "ENTITY",
-      "start": 644,
-      "end": 656
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 658,
-      "end": 667
-    },
-    {
-      "text": "hard",
-      "type": "ENTITY",
-      "start": 707,
-      "end": 711
-    },
-    {
-      "text": "ulcerated lesion",
-      "type": "ENTITY",
-      "start": 716,
-      "end": 732
-    },
-    {
-      "text": "poorly",
-      "type": "ENTITY",
-      "start": 738,
-      "end": 744
-    },
-    {
-      "text": "edges",
-      "type": "ENTITY",
-      "start": 753,
-      "end": 758
-    },
-    {
-      "text": "granular",
-      "type": "ENTITY",
-      "start": 763,
-      "end": 771
-    },
-    {
-      "text": "background",
-      "type": "ENTITY",
-      "start": 772,
-      "end": 782
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 784,
-      "end": 793
-    },
-    {
-      "text": "quadrants",
-      "type": "ENTITY",
-      "start": 822,
-      "end": 831
-    },
-    {
-      "text": "cervix",
-      "type": "ENTITY",
-      "start": 839,
-      "end": 845
-    },
-    {
-      "text": "cuts",
-      "type": "ENTITY",
-      "start": 854,
-      "end": 858
-    },
-    {
-      "text": "myometrium",
-      "type": "ENTITY",
-      "start": 864,
-      "end": 874
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 875,
-      "end": 883
-    },
-    {
-      "text": "bottom",
-      "type": "ENTITY",
-      "start": 898,
-      "end": 904
-    },
-    {
-      "text": "thicker",
-      "type": "ENTITY",
-      "start": 915,
-      "end": 922
-    },
-    {
-      "text": "multiple round",
-      "type": "ENTITY",
-      "start": 935,
-      "end": 949
-    },
-    {
-      "text": "firm",
-      "type": "ENTITY",
-      "start": 951,
-      "end": 955
-    },
-    {
-      "text": "whitish",
-      "type": "ENTITY",
-      "start": 960,
-      "end": 967
-    },
-    {
-      "text": "lesions",
-      "type": "ENTITY",
-      "start": 968,
-      "end": 975
-    },
-    {
-      "text": "crisscrossing",
-      "type": "ENTITY",
-      "start": 982,
-      "end": 995
-    },
-    {
-      "text": "endometrium",
-      "type": "ENTITY",
-      "start": 1007,
-      "end": 1018
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 1019,
-      "end": 1027
-    },
-    {
-      "text": "description",
-      "type": "ENTITY",
-      "start": 1059,
-      "end": 1070
-    },
-    {
-      "text": "DIAGNOSTIC",
-      "type": "ENTITY",
-      "start": 1073,
-      "end": 1083
-    },
-    {
-      "text": "hysterectomy",
-      "type": "ENTITY",
-      "start": 1095,
-      "end": 1107
-    },
-    {
-      "text": "left salpingectomy",
-      "type": "ENTITY",
-      "start": 1112,
-      "end": 1130
-    },
-    {
-      "text": "squamous cell carcinoma",
-      "type": "ENTITY",
-      "start": 1142,
-      "end": 1165
-    },
-    {
-      "text": "non-keratinizing",
-      "type": "ENTITY",
-      "start": 1167,
-      "end": 1183
-    },
-    {
-      "text": "differentiated",
-      "type": "ENTITY",
-      "start": 1196,
-      "end": 1210
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 1211,
-      "end": 1220
-    },
-    {
-      "text": "axis",
-      "type": "ENTITY",
-      "start": 1243,
-      "end": 1247
-    },
-    {
-      "text": "infiltrating",
-      "type": "ENTITY",
-      "start": 1252,
-      "end": 1264
-    },
-    {
-      "text": "stroma",
-      "type": "ENTITY",
-      "start": 1269,
-      "end": 1275
-    },
-    {
-      "text": "depth",
-      "type": "ENTITY",
-      "start": 1293,
-      "end": 1298
-    },
-    {
-      "text": "horizontal",
-      "type": "ENTITY",
-      "start": 1313,
-      "end": 1323
-    },
-    {
-      "text": "extent",
-      "type": "ENTITY",
-      "start": 1324,
-      "end": 1330
-    },
-    {
-      "text": "compromising",
-      "type": "ENTITY",
-      "start": 1340,
-      "end": 1352
-    },
-    {
-      "text": "uterine isthmus",
-      "type": "ENTITY",
-      "start": 1353,
-      "end": 1368
-    },
-    {
-      "text": "circumferential",
-      "type": "ENTITY",
-      "start": 1372,
-      "end": 1387
-    },
-    {
-      "text": "vaginal resection margins",
-      "type": "ENTITY",
-      "start": 1392,
-      "end": 1417
-    },
-    {
-      "text": "Presence",
-      "type": "ENTITY",
-      "start": 1422,
-      "end": 1430
-    },
-    {
-      "text": "squamous cell carcinoma",
-      "type": "ENTITY",
-      "start": 1457,
-      "end": 1480
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 1481,
-      "end": 1488
-    },
-    {
-      "text": "Presence",
-      "type": "ENTITY",
-      "start": 1493,
-      "end": 1501
-    },
-    {
-      "text": "neoplastic",
-      "type": "ENTITY",
-      "start": 1505,
-      "end": 1515
-    },
-    {
-      "text": "Uterine leiomyomas",
-      "type": "ENTITY",
-      "start": 1542,
-      "end": 1560
-    },
-    {
-      "text": "Endometriosis",
-      "type": "ENTITY",
-      "start": 1564,
-      "end": 1577
-    },
-    {
-      "text": "parametrium",
-      "type": "ENTITY",
-      "start": 1581,
-      "end": 1592
-    },
-    {
-      "text": "bilaterally",
-      "type": "ENTITY",
-      "start": 1593,
-      "end": 1604
-    },
-    {
-      "text": "left fallopian tube",
-      "type": "ENTITY",
-      "start": 1616,
-      "end": 1635
-    },
-    {
-      "text": "Dysfunctional",
-      "type": "ENTITY",
-      "start": 1639,
-      "end": 1652
-    },
-    {
-      "text": "endometrium",
-      "type": "ENTITY",
-      "start": 1653,
-      "end": 1664
-    },
-    {
-      "text": "moderate",
-      "type": "ENTITY",
-      "start": 1670,
-      "end": 1678
-    },
-    {
-      "text": "stromal edema",
-      "type": "ENTITY",
-      "start": 1679,
-      "end": 1692
-    },
-    {
-      "text": "Pathological staging",
-      "type": "ENTITY",
-      "start": 1696,
-      "end": 1716
-    },
-    {
-      "text": "pT1b1",
-      "type": "ENTITY",
-      "start": 1718,
-      "end": 1723
-    },
-    {
-      "text": "pN1",
-      "type": "ENTITY",
-      "start": 1725,
-      "end": 1728
-    },
-    {
-      "text": "TNM",
-      "type": "ENTITY",
-      "start": 1730,
-      "end": 1733
-    },
-    {
-      "text": "lymph node biopsy",
-      "type": "ENTITY",
-      "start": 1746,
-      "end": 1763
-    },
-    {
-      "text": "biopsy number",
-      "type": "ENTITY",
-      "start": 1769,
-      "end": 1782
-    },
-    {
-      "text": "service",
-      "type": "ENTITY",
-      "start": 1792,
-      "end": 1799
-    }
-  ],
-  "entity_count": 92,
-  "has_embedding": true
-}

output/biomedbert_output/0010ce59-fd1e-4a45-8753-a224164fb818_nlp.json

@@ -1,596 +0,0 @@
-{
-  "filename": "0010ce59-fd1e-4a45-8753-a224164fb818",
-  "timestamp": "2026-01-05T14:44:03.910849",
-  "entities": [
-    {
-      "text": "2 Department of Cancer",
-      "type": "ENTITY",
-      "start": 25,
-      "end": 47
-    },
-    {
-      "text": "copy No. Date",
-      "type": "ENTITY",
-      "start": 58,
-      "end": 71
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 73,
-      "end": 84
-    },
-    {
-      "text": "Histopathological examination Examination No.",
-      "type": "ENTITY",
-      "start": 86,
-      "end": 131
-    },
-    {
-      "text": "Cost",
-      "type": "ENTITY",
-      "start": 133,
-      "end": 137
-    },
-    {
-      "text": "diagnostic procedure",
-      "type": "ENTITY",
-      "start": 141,
-      "end": 161
-    },
-    {
-      "text": "Internal invoice No. Age",
-      "type": "ENTITY",
-      "start": 162,
-      "end": 186
-    },
-    {
-      "text": "ender",
-      "type": "ENTITY",
-      "start": 188,
-      "end": 193
-    },
-    {
-      "text": "F",
-      "type": "ENTITY",
-      "start": 195,
-      "end": 196
-    },
-    {
-      "text": "pesel",
-      "type": "ENTITY",
-      "start": 197,
-      "end": 202
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 208,
-      "end": 215
-    },
-    {
-      "text": "XXX",
-      "type": "ENTITY",
-      "start": 217,
-      "end": 220
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 229,
-      "end": 237
-    },
-    {
-      "text": "Total organ",
-      "type": "ENTITY",
-      "start": 239,
-      "end": 250
-    },
-    {
-      "text": "left breast ad",
-      "type": "ENTITY",
-      "start": 264,
-      "end": 278
-    },
-    {
-      "text": "axillary tissues",
-      "type": "ENTITY",
-      "start": 279,
-      "end": 295
-    },
-    {
-      "text": "nf {tatv7 duct",
-      "type": "ENTITY",
-      "start": 306,
-      "end": 320
-    },
-    {
-      "text": "charge",
-      "type": "ENTITY",
-      "start": 392,
-      "end": 398
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 400,
-      "end": 408
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 424,
-      "end": 432
-    },
-    {
-      "text": "collected",
-      "type": "ENTITY",
-      "start": 433,
-      "end": 442
-    },
-    {
-      "text": "Expected time",
-      "type": "ENTITY",
-      "start": 447,
-      "end": 460
-    },
-    {
-      "text": "examination",
-      "type": "ENTITY",
-      "start": 464,
-      "end": 475
-    },
-    {
-      "text": "working days",
-      "type": "ENTITY",
-      "start": 485,
-      "end": 497
-    },
-    {
-      "text": "Clinical diagnosis",
-      "type": "ENTITY",
-      "start": 498,
-      "end": 516
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 518,
-      "end": 529
-    },
-    {
-      "text": "performed",
-      "type": "ENTITY",
-      "start": 530,
-      "end": 539
-    },
-    {
-      "text": "Macroscopic",
-      "type": "ENTITY",
-      "start": 544,
-      "end": 555
-    },
-    {
-      "text": "description",
-      "type": "ENTITY",
-      "start": 556,
-      "end": 567
-    },
-    {
-      "text": "Left breast'sized",
-      "type": "ENTITY",
-      "start": 569,
-      "end": 586
-    },
-    {
-      "text": "axillary tissues",
-      "type": "ENTITY",
-      "start": 617,
-      "end": 633
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 634,
-      "end": 639
-    },
-    {
-      "text": "skin flap",
-      "type": "ENTITY",
-      "start": 662,
-      "end": 671
-    },
-    {
-      "text": "Tumour",
-      "type": "ENTITY",
-      "start": 687,
-      "end": 693
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 694,
-      "end": 699
-    },
-    {
-      "text": "subaurolar part",
-      "type": "ENTITY",
-      "start": 729,
-      "end": 744
-    },
-    {
-      "text": "upper boundary",
-      "type": "ENTITY",
-      "start": 770,
-      "end": 784
-    },
-    {
-      "text": "base",
-      "type": "ENTITY",
-      "start": 802,
-      "end": 806
-    },
-    {
-      "text": "Metastatic lymph nodes 2",
-      "type": "ENTITY",
-      "start": 832,
-      "end": 856
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 863,
-      "end": 869
-    },
-    {
-      "text": "description",
-      "type": "ENTITY",
-      "start": 883,
-      "end": 894
-    },
-    {
-      "text": "Carcinoma",
-      "type": "ENTITY",
-      "start": 897,
-      "end": 906
-    },
-    {
-      "text": "ductale",
-      "type": "ENTITY",
-      "start": 907,
-      "end": 914
-    },
-    {
-      "text": "invasivum",
-      "type": "ENTITY",
-      "start": 915,
-      "end": 924
-    },
-    {
-      "text": "NHG2",
-      "type": "ENTITY",
-      "start": 927,
-      "end": 931
-    },
-    {
-      "text": "1",
-      "type": "ENTITY",
-      "start": 941,
-      "end": 942
-    },
-    {
-      "text": "HPF",
-      "type": "ENTITY",
-      "start": 958,
-      "end": 961
-    },
-    {
-      "text": "visual",
-      "type": "ENTITY",
-      "start": 964,
-      "end": 970
-    },
-    {
-      "text": "Foci",
-      "type": "ENTITY",
-      "start": 985,
-      "end": 989
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 993,
-      "end": 1002
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 1011,
-      "end": 1018
-    },
-    {
-      "text": "detected",
-      "type": "ENTITY",
-      "start": 1024,
-      "end": 1032
-    },
-    {
-      "text": "tumour",
-      "type": "ENTITY",
-      "start": 1044,
-      "end": 1050
-    },
-    {
-      "text": "cribrate",
-      "type": "ENTITY",
-      "start": 1052,
-      "end": 1060
-    },
-    {
-      "text": "solid type",
-      "type": "ENTITY",
-      "start": 1065,
-      "end": 1075
-    },
-    {
-      "text": "nuclear atypia",
-      "type": "ENTITY",
-      "start": 1086,
-      "end": 1100
-    },
-    {
-      "text": "comedo necrosis",
-      "type": "ENTITY",
-      "start": 1106,
-      "end": 1121
-    },
-    {
-      "text": "tumour",
-      "type": "ENTITY",
-      "start": 1133,
-      "end": 1139
-    },
-    {
-      "text": "Mamilla sine",
-      "type": "ENTITY",
-      "start": 1142,
-      "end": 1154
-    },
-    {
-      "text": "laesionibus",
-      "type": "ENTITY",
-      "start": 1155,
-      "end": 1166
-    },
-    {
-      "text": "Glandular tissue",
-      "type": "ENTITY",
-      "start": 1168,
-      "end": 1184
-    },
-    {
-      "text": "lesions",
-      "type": "ENTITY",
-      "start": 1193,
-      "end": 1200
-    },
-    {
-      "text": "type mastopathia fibrosa",
-      "type": "ENTITY",
-      "start": 1208,
-      "end": 1232
-    },
-    {
-      "text": "lymphonodis",
-      "type": "ENTITY",
-      "start": 1285,
-      "end": 1296
-    },
-    {
-      "text": "Infiltratio capsulae lymphonodis",
-      "type": "ENTITY",
-      "start": 1309,
-      "end": 1341
-    },
-    {
-      "text": "telae perinodalis",
-      "type": "ENTITY",
-      "start": 1345,
-      "end": 1362
-    },
-    {
-      "text": "Histopathological",
-      "type": "ENTITY",
-      "start": 1364,
-      "end": 1381
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 1382,
-      "end": 1391
-    },
-    {
-      "text": "Carcinoma",
-      "type": "ENTITY",
-      "start": 1393,
-      "end": 1402
-    },
-    {
-      "text": "ductale",
-      "type": "ENTITY",
-      "start": 1403,
-      "end": 1410
-    },
-    {
-      "text": "invasivum",
-      "type": "ENTITY",
-      "start": 1411,
-      "end": 1420
-    },
-    {
-      "text": "ductale",
-      "type": "ENTITY",
-      "start": 1424,
-      "end": 1431
-    },
-    {
-      "text": "in situ mammae sinistrae",
-      "type": "ENTITY",
-      "start": 1432,
-      "end": 1456
-    },
-    {
-      "text": "Invasive ductal",
-      "type": "ENTITY",
-      "start": 1458,
-      "end": 1473
-    },
-    {
-      "text": "in situ ductal carclrioma",
-      "type": "ENTITY",
-      "start": 1478,
-      "end": 1503
-    },
-    {
-      "text": "feft breast Metastases carcinomatosae",
-      "type": "ENTITY",
-      "start": 1511,
-      "end": 1548
-    },
-    {
-      "text": "lymphonodis axillae",
-      "type": "ENTITY",
-      "start": 1552,
-      "end": 1571
-    },
-    {
-      "text": "Cancer metastases",
-      "type": "ENTITY",
-      "start": 1584,
-      "end": 1601
-    },
-    {
-      "text": "axillary lymph nodes",
-      "type": "ENTITY",
-      "start": 1609,
-      "end": 1629
-    },
-    {
-      "text": "NHG2",
-      "type": "ENTITY",
-      "start": 1643,
-      "end": 1647
-    },
-    {
-      "text": "UUID:53ED4388-8CD2",
-      "type": "ENTITY",
-      "start": 1662,
-      "end": 1680
-    },
-    {
-      "text": "TCGA-D8-A1Y0-01A-PR",
-      "type": "ENTITY",
-      "start": 1704,
-      "end": 1723
-    },
-    {
-      "text": "Hef1",
-      "type": "ENTITY",
-      "start": 1733,
-      "end": 1737
-    },
-    {
-      "text": "2",
-      "type": "ENTITY",
-      "start": 1763,
-      "end": 1764
-    },
-    {
-      "text": "Compliance",
-      "type": "ENTITY",
-      "start": 1765,
-      "end": 1775
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 1790,
-      "end": 1801
-    },
-    {
-      "text": "performed",
-      "type": "ENTITY",
-      "start": 1802,
-      "end": 1811
-    },
-    {
-      "text": "Results",
-      "type": "ENTITY",
-      "start": 1816,
-      "end": 1823
-    },
-    {
-      "text": "immunohistochemical examination",
-      "type": "ENTITY",
-      "start": 1827,
-      "end": 1858
-    },
-    {
-      "text": "Estrogen receptors",
-      "type": "ENTITY",
-      "start": 1860,
-      "end": 1878
-    },
-    {
-      "text": "neoplastic cell",
-      "type": "ENTITY",
-      "start": 1900,
-      "end": 1915
-    },
-    {
-      "text": "Progesterone receptors",
-      "type": "ENTITY",
-      "start": 1924,
-      "end": 1946
-    },
-    {
-      "text": "neoplastic cell",
-      "type": "ENTITY",
-      "start": 1968,
-      "end": 1983
-    },
-    {
-      "text": "HER2 protein stained with",
-      "type": "ENTITY",
-      "start": 1992,
-      "end": 2017
-    },
-    {
-      "text": "HercepTestTM",
-      "type": "ENTITY",
-      "start": 2018,
-      "end": 2030
-    },
-    {
-      "text": "DAKO",
-      "type": "ENTITY",
-      "start": 2034,
-      "end": 2038
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 2062,
-      "end": 2070
-    },
-    {
-      "text": "Score",
-      "type": "ENTITY",
-      "start": 2089,
-      "end": 2094
-    }
-  ],
-  "entity_count": 98,
-  "has_embedding": true
-}

output/biomedbert_output/00157a93-7d77-41d8-ac9c-6317c9ae38fe_nlp.json

@@ -1,164 +0,0 @@
-{
-  "filename": "00157a93-7d77-41d8-ac9c-6317c9ae38fe",
-  "timestamp": "2026-01-05T14:43:39.940299",
-  "entities": [
-    {
-      "text": "Jcs-0",
-      "type": "ENTITY",
-      "start": 16,
-      "end": 21
-    },
-    {
-      "text": "3",
-      "type": "ENTITY",
-      "start": 24,
-      "end": 25
-    },
-    {
-      "text": "Curcinonn mf1tnaHnz",
-      "type": "ENTITY",
-      "start": 26,
-      "end": 45
-    },
-    {
-      "text": "ductul",
-      "type": "ENTITY",
-      "start": 46,
-      "end": 52
-    },
-    {
-      "text": "nsos",
-      "type": "ENTITY",
-      "start": 53,
-      "end": 57
-    },
-    {
-      "text": "BUsotj LbQ",
-      "type": "ENTITY",
-      "start": 70,
-      "end": 80
-    },
-    {
-      "text": "Pish",
-      "type": "ENTITY",
-      "start": 95,
-      "end": 99
-    },
-    {
-      "text": "Sit: Brst",
-      "type": "ENTITY",
-      "start": 100,
-      "end": 109
-    },
-    {
-      "text": "CqcF",
-      "type": "ENTITY",
-      "start": 121,
-      "end": 125
-    },
-    {
-      "text": "Diagnosis",
-      "type": "ENTITY",
-      "start": 126,
-      "end": 135
-    },
-    {
-      "text": "Right-sided breast excision material",
-      "type": "ENTITY",
-      "start": 137,
-      "end": 173
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 227,
-      "end": 236
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 237,
-      "end": 246
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 265,
-      "end": 273
-    },
-    {
-      "text": "lymph vessels",
-      "type": "ENTITY",
-      "start": 281,
-      "end": 294
-    },
-    {
-      "text": "minimum margin",
-      "type": "ENTITY",
-      "start": 301,
-      "end": 315
-    },
-    {
-      "text": "o'clock",
-      "type": "ENTITY",
-      "start": 330,
-      "end": 337
-    },
-    {
-      "text": "o'clock",
-      "type": "ENTITY",
-      "start": 354,
-      "end": 361
-    },
-    {
-      "text": "o'clock",
-      "type": "ENTITY",
-      "start": 392,
-      "end": 399
-    },
-    {
-      "text": "intraductal tumor component",
-      "type": "ENTITY",
-      "start": 404,
-      "end": 431
-    },
-    {
-      "text": "Tumor classification",
-      "type": "ENTITY",
-      "start": 433,
-      "end": 453
-    },
-    {
-      "text": "M-8500/3",
-      "type": "ENTITY",
-      "start": 455,
-      "end": 463
-    },
-    {
-      "text": "G 3",
-      "type": "ENTITY",
-      "start": 465,
-      "end": 468
-    },
-    {
-      "text": "pN 3a",
-      "type": "ENTITY",
-      "start": 476,
-      "end": 481
-    },
-    {
-      "text": "stage III c. R",
-      "type": "ENTITY",
-      "start": 496,
-      "end": 510
-    },
-    {
-      "text": "Redacted",
-      "type": "ENTITY",
-      "start": 537,
-      "end": 545
-    }
-  ],
-  "entity_count": 26,
-  "has_embedding": true
-}

output/biomedbert_output/001fee13-0e0d-464d-8b18-5641d51c86db_nlp.json

@@ -1,932 +0,0 @@
-{
-  "filename": "001fee13-0e0d-464d-8b18-5641d51c86db",
-  "timestamp": "2026-01-05T14:42:16.013256",
-  "entities": [
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 27,
-      "end": 35
-    },
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 53,
-      "end": 61
-    },
-    {
-      "text": "COLON",
-      "type": "ENTITY",
-      "start": 62,
-      "end": 67
-    },
-    {
-      "text": "RIGHT HEMICOLECTOMY",
-      "type": "ENTITY",
-      "start": 69,
-      "end": 88
-    },
-    {
-      "text": "EXOPHYTIC",
-      "type": "ENTITY",
-      "start": 92,
-      "end": 101
-    },
-    {
-      "text": "CIRCUMFERENTIAL",
-      "type": "ENTITY",
-      "start": 102,
-      "end": 117
-    },
-    {
-      "text": "INVASIVE",
-      "type": "ENTITY",
-      "start": 128,
-      "end": 136
-    },
-    {
-      "text": "DIFEERENTIATED",
-      "type": "ENTITY",
-      "start": 156,
-      "end": 170
-    },
-    {
-      "text": "CECUM",
-      "type": "ENTITY",
-      "start": 189,
-      "end": 194
-    },
-    {
-      "text": "ASCENDING",
-      "type": "ENTITY",
-      "start": 205,
-      "end": 214
-    },
-    {
-      "text": "EXTENSION TO SUB- SEROSAL",
-      "type": "ENTITY",
-      "start": 298,
-      "end": 323
-    },
-    {
-      "text": "PERICOLIC",
-      "type": "ENTITY",
-      "start": 369,
-      "end": 378
-    },
-    {
-      "text": "LYMPH NODES",
-      "type": "ENTITY",
-      "start": 379,
-      "end": 390
-    },
-    {
-      "text": "WITH PERINODAL",
-      "type": "ENTITY",
-      "start": 392,
-      "end": 406
-    },
-    {
-      "text": "EXTENSION",
-      "type": "ENTITY",
-      "start": 411,
-      "end": 420
-    },
-    {
-      "text": "SIZE",
-      "type": "ENTITY",
-      "start": 425,
-      "end": 429
-    },
-    {
-      "text": "TUMOR-",
-      "type": "ENTITY",
-      "start": 433,
-      "end": 439
-    },
-    {
-      "text": "CM",
-      "type": "ENTITY",
-      "start": 449,
-      "end": 451
-    },
-    {
-      "text": "TUBULOVILLOUS",
-      "type": "ENTITY",
-      "start": 455,
-      "end": 468
-    },
-    {
-      "text": "CM",
-      "type": "ENTITY",
-      "start": 488,
-      "end": 490
-    },
-    {
-      "text": "VERMIFORM",
-      "type": "ENTITY",
-      "start": 495,
-      "end": 504
-    },
-    {
-      "text": "APPENDIX",
-      "type": "ENTITY",
-      "start": 505,
-      "end": 513
-    },
-    {
-      "text": "NEGATIVE",
-      "type": "ENTITY",
-      "start": 516,
-      "end": 524
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 529,
-      "end": 534
-    },
-    {
-      "text": "PROXIMAL",
-      "type": "ENTITY",
-      "start": 537,
-      "end": 545
-    },
-    {
-      "text": "DISTAL",
-      "type": "ENTITY",
-      "start": 547,
-      "end": 553
-    },
-    {
-      "text": "RADIAL MARGINS",
-      "type": "ENTITY",
-      "start": 558,
-      "end": 572
-    },
-    {
-      "text": "RESECTION",
-      "type": "ENTITY",
-      "start": 576,
-      "end": 585
-    },
-    {
-      "text": "NEGATIVEE",
-      "type": "ENTITY",
-      "start": 588,
-      "end": 597
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 602,
-      "end": 607
-    },
-    {
-      "text": "COLORECTAL CANCER",
-      "type": "ENTITY",
-      "start": 609,
-      "end": 626
-    },
-    {
-      "text": "Specimen Type",
-      "type": "ENTITY",
-      "start": 636,
-      "end": 649
-    },
-    {
-      "text": "Right hemicolectomy Tumor Site",
-      "type": "ENTITY",
-      "start": 651,
-      "end": 681
-    },
-    {
-      "text": "Cecum",
-      "type": "ENTITY",
-      "start": 683,
-      "end": 688
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 689,
-      "end": 697
-    },
-    {
-      "text": "Tumor Configuration",
-      "type": "ENTITY",
-      "start": 714,
-      "end": 733
-    },
-    {
-      "text": "Exophytic (polypoid",
-      "type": "ENTITY",
-      "start": 735,
-      "end": 754
-    },
-    {
-      "text": "Infiltrative",
-      "type": "ENTITY",
-      "start": 757,
-      "end": 769
-    },
-    {
-      "text": "Ulcerating",
-      "type": "ENTITY",
-      "start": 771,
-      "end": 781
-    },
-    {
-      "text": "Tumor Size",
-      "type": "ENTITY",
-      "start": 782,
-      "end": 792
-    },
-    {
-      "text": "Histologic Type",
-      "type": "ENTITY",
-      "start": 813,
-      "end": 828
-    },
-    {
-      "text": "Adenocarcinoma",
-      "type": "ENTITY",
-      "start": 830,
-      "end": 844
-    },
-    {
-      "text": "Histologic Grade",
-      "type": "ENTITY",
-      "start": 845,
-      "end": 861
-    },
-    {
-      "text": "Extent",
-      "type": "ENTITY",
-      "start": 866,
-      "end": 872
-    },
-    {
-      "text": "Invasion",
-      "type": "ENTITY",
-      "start": 876,
-      "end": 884
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 929,
-      "end": 947
-    },
-    {
-      "text": "Venous/Lymphatic Invasion",
-      "type": "ENTITY",
-      "start": 949,
-      "end": 974
-    },
-    {
-      "text": "Perineural Invasion",
-      "type": "ENTITY",
-      "start": 984,
-      "end": 1003
-    },
-    {
-      "text": "Pathologic",
-      "type": "ENTITY",
-      "start": 1024,
-      "end": 1034
-    },
-    {
-      "text": "Findings",
-      "type": "ENTITY",
-      "start": 1035,
-      "end": 1043
-    },
-    {
-      "text": "Adenoma",
-      "type": "ENTITY",
-      "start": 1045,
-      "end": 1052
-    },
-    {
-      "text": "Extent",
-      "type": "ENTITY",
-      "start": 1053,
-      "end": 1059
-    },
-    {
-      "text": "Resection",
-      "type": "ENTITY",
-      "start": 1063,
-      "end": 1072
-    },
-    {
-      "text": "R0 Positive (6/36)",
-      "type": "ENTITY",
-      "start": 1074,
-      "end": 1092
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 1093,
-      "end": 1104
-    },
-    {
-      "text": "Absent EGFR",
-      "type": "ENTITY",
-      "start": 1117,
-      "end": 1128
-    },
-    {
-      "text": "Expression",
-      "type": "ENTITY",
-      "start": 1129,
-      "end": 1139
-    },
-    {
-      "text": "Pathologic Stage",
-      "type": "ENTITY",
-      "start": 1149,
-      "end": 1165
-    },
-    {
-      "text": "pT3 N2 MX ADDENDUM",
-      "type": "ENTITY",
-      "start": 1167,
-      "end": 1185
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 1198,
-      "end": 1204
-    },
-    {
-      "text": "Results",
-      "type": "ENTITY",
-      "start": 1206,
-      "end": 1213
-    },
-    {
-      "text": "immunostain",
-      "type": "ENTITY",
-      "start": 1217,
-      "end": 1228
-    },
-    {
-      "text": "EGFR",
-      "type": "ENTITY",
-      "start": 1230,
-      "end": 1234
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 1237,
-      "end": 1244
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 1263,
-      "end": 1271
-    },
-    {
-      "text": "immunoreactivity",
-      "type": "ENTITY",
-      "start": 1272,
-      "end": 1288
-    },
-    {
-      "text": "SPECIMEN(S",
-      "type": "ENTITY",
-      "start": 1290,
-      "end": 1300
-    },
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 1303,
-      "end": 1311
-    },
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 1337,
-      "end": 1345
-    },
-    {
-      "text": "COLON TERMINAL",
-      "type": "ENTITY",
-      "start": 1346,
-      "end": 1360
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 1377,
-      "end": 1382
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 1383,
-      "end": 1390
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 1400,
-      "end": 1409
-    },
-    {
-      "text": "unit number",
-      "type": "ENTITY",
-      "start": 1416,
-      "end": 1427
-    },
-    {
-      "text": "\"right colon terminal",
-      "type": "ENTITY",
-      "start": 1432,
-      "end": 1453
-    },
-    {
-      "text": "ileum'",
-      "type": "ENTITY",
-      "start": 1454,
-      "end": 1460
-    },
-    {
-      "text": "right hemicolectomy",
-      "type": "ENTITY",
-      "start": 1481,
-      "end": 1500
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1501,
-      "end": 1509
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 1515,
-      "end": 1520
-    },
-    {
-      "text": "circumference",
-      "type": "ENTITY",
-      "start": 1548,
-      "end": 1561
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 1567,
-      "end": 1572
-    },
-    {
-      "text": "circumference",
-      "type": "ENTITY",
-      "start": 1602,
-      "end": 1615
-    },
-    {
-      "text": "appendix",
-      "type": "ENTITY",
-      "start": 1633,
-      "end": 1641
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 1673,
-      "end": 1681
-    },
-    {
-      "text": "serosal surface",
-      "type": "ENTITY",
-      "start": 1687,
-      "end": 1702
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1710,
-      "end": 1718
-    },
-    {
-      "text": "smooth",
-      "type": "ENTITY",
-      "start": 1727,
-      "end": 1733
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1752,
-      "end": 1763
-    },
-    {
-      "text": "palpated",
-      "type": "ENTITY",
-      "start": 1768,
-      "end": 1776
-    },
-    {
-      "text": "adherent",
-      "type": "ENTITY",
-      "start": 1792,
-      "end": 1800
-    },
-    {
-      "text": "pericolonic fat",
-      "type": "ENTITY",
-      "start": 1801,
-      "end": 1816
-    },
-    {
-      "text": "cecum",
-      "type": "ENTITY",
-      "start": 1824,
-      "end": 1829
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1835,
-      "end": 1843
-    },
-    {
-      "text": "opened",
-      "type": "ENTITY",
-      "start": 1849,
-      "end": 1855
-    },
-    {
-      "text": "circumferential",
-      "type": "ENTITY",
-      "start": 1864,
-      "end": 1879
-    },
-    {
-      "text": "indurated",
-      "type": "ENTITY",
-      "start": 1928,
-      "end": 1937
-    },
-    {
-      "text": "peripheral borders",
-      "type": "ENTITY",
-      "start": 1938,
-      "end": 1956
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 1967,
-      "end": 1975
-    },
-    {
-      "text": "cecum",
-      "type": "ENTITY",
-      "start": 1992,
-      "end": 1997
-    },
-    {
-      "text": "iliocecal valve",
-      "type": "ENTITY",
-      "start": 2029,
-      "end": 2044
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2045,
-      "end": 2054
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 2102,
-      "end": 2108
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 2124,
-      "end": 2132
-    },
-    {
-      "text": "Cut sections",
-      "type": "ENTITY",
-      "start": 2140,
-      "end": 2152
-    },
-    {
-      "text": "tan white granular",
-      "type": "ENTITY",
-      "start": 2158,
-      "end": 2176
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2189,
-      "end": 2194
-    },
-    {
-      "text": "infiltrating muscle wall",
-      "type": "ENTITY",
-      "start": 2200,
-      "end": 2224
-    },
-    {
-      "text": "grossly",
-      "type": "ENTITY",
-      "start": 2229,
-      "end": 2236
-    },
-    {
-      "text": "subjacent",
-      "type": "ENTITY",
-      "start": 2258,
-      "end": 2267
-    },
-    {
-      "text": "subserosal fat",
-      "type": "ENTITY",
-      "start": 2268,
-      "end": 2282
-    },
-    {
-      "text": "colonic mucosa",
-      "type": "ENTITY",
-      "start": 2296,
-      "end": 2310
-    },
-    {
-      "text": "flattened",
-      "type": "ENTITY",
-      "start": 2319,
-      "end": 2328
-    },
-    {
-      "text": "appearance",
-      "type": "ENTITY",
-      "start": 2329,
-      "end": 2339
-    },
-    {
-      "text": "small polyp",
-      "type": "ENTITY",
-      "start": 2348,
-      "end": 2359
-    },
-    {
-      "text": "hepatic flexure",
-      "type": "ENTITY",
-      "start": 2366,
-      "end": 2381
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2382,
-      "end": 2391
-    },
-    {
-      "text": "1.2x1.1",
-      "type": "ENTITY",
-      "start": 2392,
-      "end": 2399
-    },
-    {
-      "text": "Dissection",
-      "type": "ENTITY",
-      "start": 2404,
-      "end": 2414
-    },
-    {
-      "text": "adherent",
-      "type": "ENTITY",
-      "start": 2422,
-      "end": 2430
-    },
-    {
-      "text": "pericolonic fat",
-      "type": "ENTITY",
-      "start": 2431,
-      "end": 2446
-    },
-    {
-      "text": "multiple lymph nodes",
-      "type": "ENTITY",
-      "start": 2453,
-      "end": 2473
-    },
-    {
-      "text": "Iargest",
-      "type": "ENTITY",
-      "start": 2478,
-      "end": 2485
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2486,
-      "end": 2495
-    },
-    {
-      "text": "Appendix",
-      "type": "ENTITY",
-      "start": 2510,
-      "end": 2518
-    },
-    {
-      "text": "Multiple sections",
-      "type": "ENTITY",
-      "start": 2545,
-      "end": 2562
-    },
-    {
-      "text": "cassettes",
-      "type": "ENTITY",
-      "start": 2590,
-      "end": 2599
-    },
-    {
-      "text": "A1-A17",
-      "type": "ENTITY",
-      "start": 2608,
-      "end": 2614
-    },
-    {
-      "text": "A1",
-      "type": "ENTITY",
-      "start": 2632,
-      "end": 2634
-    },
-    {
-      "text": "margin A2",
-      "type": "ENTITY",
-      "start": 2636,
-      "end": 2645
-    },
-    {
-      "text": "apex",
-      "type": "ENTITY",
-      "start": 2647,
-      "end": 2651
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2665,
-      "end": 2670
-    },
-    {
-      "text": "tandom section",
-      "type": "ENTITY",
-      "start": 2675,
-      "end": 2689
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 2695,
-      "end": 2700
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 2704,
-      "end": 2709
-    },
-    {
-      "text": "tumor A9-A11",
-      "type": "ENTITY",
-      "start": 2717,
-      "end": 2729
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2731,
-      "end": 2736
-    },
-    {
-      "text": "deep section",
-      "type": "ENTITY",
-      "start": 2737,
-      "end": 2749
-    },
-    {
-      "text": "A12",
-      "type": "ENTITY",
-      "start": 2750,
-      "end": 2753
-    },
-    {
-      "text": "polyp",
-      "type": "ENTITY",
-      "start": 2755,
-      "end": 2760
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2772,
-      "end": 2783
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 2784,
-      "end": 2789
-    },
-    {
-      "text": "A14",
-      "type": "ENTITY",
-      "start": 2791,
-      "end": 2794
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2802,
-      "end": 2813
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 2814,
-      "end": 2819
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2824,
-      "end": 2835
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2853,
-      "end": 2864
-    },
-    {
-      "text": "cecum colon A17",
-      "type": "ENTITY",
-      "start": 2865,
-      "end": 2880
-    },
-    {
-      "text": "lymph nodes distal colon A19-21",
-      "type": "ENTITY",
-      "start": 2886,
-      "end": 2917
-    },
-    {
-      "text": "lymph nodes distal colon A26-30",
-      "type": "ENTITY",
-      "start": 2919,
-      "end": 2950
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 2952,
-      "end": 2960
-    },
-    {
-      "text": "A29",
-      "type": "ENTITY",
-      "start": 2971,
-      "end": 2974
-    },
-    {
-      "text": "A30",
-      "type": "ENTITY",
-      "start": 2979,
-      "end": 2982
-    },
-    {
-      "text": "random",
-      "type": "ENTITY",
-      "start": 2987,
-      "end": 2993
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 2994,
-      "end": 3002
-    }
-  ],
-  "entity_count": 154,
-  "has_embedding": true
-}

output/biomedbert_output/004d2c0d-6209-43f1-900e-fc8d923dd9b5_nlp.json

@@ -1,1460 +0,0 @@
-{
-  "filename": "004d2c0d-6209-43f1-900e-fc8d923dd9b5",
-  "timestamp": "2026-01-05T14:43:03.049082",
-  "entities": [
-    {
-      "text": "DOC",
-      "type": "ENTITY",
-      "start": 121,
-      "end": 124
-    },
-    {
-      "text": "COLL",
-      "type": "ENTITY",
-      "start": 134,
-      "end": 138
-    },
-    {
-      "text": "ISTOPATHOLOGY",
-      "type": "ENTITY",
-      "start": 175,
-      "end": 188
-    },
-    {
-      "text": "A. Right frontal tumour",
-      "type": "ENTITY",
-      "start": 246,
-      "end": 269
-    },
-    {
-      "text": "B. Right",
-      "type": "ENTITY",
-      "start": 271,
-      "end": 279
-    },
-    {
-      "text": "tissue sections",
-      "type": "ENTITY",
-      "start": 314,
-      "end": 329
-    },
-    {
-      "text": "glioma",
-      "type": "ENTITY",
-      "start": 337,
-      "end": 343
-    },
-    {
-      "text": "immunohistochemical studies",
-      "type": "ENTITY",
-      "start": 376,
-      "end": 403
-    },
-    {
-      "text": "Fish",
-      "type": "ENTITY",
-      "start": 419,
-      "end": 423
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 424,
-      "end": 431
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 443,
-      "end": 454
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 474,
-      "end": 482
-    },
-    {
-      "text": "glioma",
-      "type": "ENTITY",
-      "start": 490,
-      "end": 496
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 558,
-      "end": 569
-    },
-    {
-      "text": "appearances",
-      "type": "ENTITY",
-      "start": 570,
-      "end": 581
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 601,
-      "end": 607
-    },
-    {
-      "text": "Variable",
-      "type": "ENTITY",
-      "start": 610,
-      "end": 618
-    },
-    {
-      "text": "cytoarchitectural patterns",
-      "type": "ENTITY",
-      "start": 619,
-      "end": 645
-    },
-    {
-      "text": "cellular microcystic",
-      "type": "ENTITY",
-      "start": 681,
-      "end": 701
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 714,
-      "end": 725
-    },
-    {
-      "text": "neoplastic cells",
-      "type": "ENTITY",
-      "start": 750,
-      "end": 766
-    },
-    {
-      "text": "aggregate",
-      "type": "ENTITY",
-      "start": 767,
-      "end": 776
-    },
-    {
-      "text": "pleomorphic",
-      "type": "ENTITY",
-      "start": 806,
-      "end": 817
-    },
-    {
-      "text": "hyperchromatic nuclei",
-      "type": "ENTITY",
-      "start": 822,
-      "end": 843
-    },
-    {
-      "text": "minimal",
-      "type": "ENTITY",
-      "start": 845,
-      "end": 852
-    },
-    {
-      "text": "cytoplasm",
-      "type": "ENTITY",
-      "start": 853,
-      "end": 862
-    },
-    {
-      "text": "nuclear angulation",
-      "type": "ENTITY",
-      "start": 886,
-      "end": 904
-    },
-    {
-      "text": "irregularity",
-      "type": "ENTITY",
-      "start": 909,
-      "end": 921
-    },
-    {
-      "text": "No areas",
-      "type": "ENTITY",
-      "start": 923,
-      "end": 931
-    },
-    {
-      "text": "vascular endothelial proliferation",
-      "type": "ENTITY",
-      "start": 935,
-      "end": 969
-    },
-    {
-      "text": "palisading necrosis",
-      "type": "ENTITY",
-      "start": 973,
-      "end": 992
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 1003,
-      "end": 1013
-    },
-    {
-      "text": "Maximal",
-      "type": "ENTITY",
-      "start": 1015,
-      "end": 1022
-    },
-    {
-      "text": "mitotie",
-      "type": "ENTITY",
-      "start": 1023,
-      "end": 1030
-    },
-    {
-      "text": "counts",
-      "type": "ENTITY",
-      "start": 1031,
-      "end": 1037
-    },
-    {
-      "text": "hypercellular areas",
-      "type": "ENTITY",
-      "start": 1049,
-      "end": 1068
-    },
-    {
-      "text": "mitotic figures",
-      "type": "ENTITY",
-      "start": 1076,
-      "end": 1091
-    },
-    {
-      "text": "field area",
-      "type": "ENTITY",
-      "start": 1118,
-      "end": 1128
-    },
-    {
-      "text": "proliferation index",
-      "type": "ENTITY",
-      "start": 1152,
-      "end": 1171
-    },
-    {
-      "text": "immunohistochemical staining",
-      "type": "ENTITY",
-      "start": 1186,
-      "end": 1214
-    },
-    {
-      "text": "proliferation marker",
-      "type": "ENTITY",
-      "start": 1223,
-      "end": 1243
-    },
-    {
-      "text": "Mrs I",
-      "type": "ENTITY",
-      "start": 1244,
-      "end": 1249
-    },
-    {
-      "text": "variable",
-      "type": "ENTITY",
-      "start": 1253,
-      "end": 1261
-    },
-    {
-      "text": "Low-grade",
-      "type": "ENTITY",
-      "start": 1264,
-      "end": 1273
-    },
-    {
-      "text": "microcystic areas",
-      "type": "ENTITY",
-      "start": 1288,
-      "end": 1305
-    },
-    {
-      "text": "MIs",
-      "type": "ENTITY",
-      "start": 1325,
-      "end": 1328
-    },
-    {
-      "text": "indices",
-      "type": "ENTITY",
-      "start": 1331,
-      "end": 1338
-    },
-    {
-      "text": "nuclear labelling",
-      "type": "ENTITY",
-      "start": 1361,
-      "end": 1378
-    },
-    {
-      "text": "small hypercellular foci",
-      "type": "ENTITY",
-      "start": 1388,
-      "end": 1412
-    },
-    {
-      "text": "elevated",
-      "type": "ENTITY",
-      "start": 1425,
-      "end": 1433
-    },
-    {
-      "text": "labelling",
-      "type": "ENTITY",
-      "start": 1434,
-      "end": 1443
-    },
-    {
-      "text": "Immunohistochemical staining",
-      "type": "ENTITY",
-      "start": 1445,
-      "end": 1473
-    },
-    {
-      "text": "p53 protein",
-      "type": "ENTITY",
-      "start": 1478,
-      "end": 1489
-    },
-    {
-      "text": "nuclear positivity",
-      "type": "ENTITY",
-      "start": 1517,
-      "end": 1535
-    },
-    {
-      "text": "Synaptophysin",
-      "type": "ENTITY",
-      "start": 1538,
-      "end": 1551
-    },
-    {
-      "text": "neoplastic cells",
-      "type": "ENTITY",
-      "start": 1587,
-      "end": 1603
-    },
-    {
-      "text": "hypercellular",
-      "type": "ENTITY",
-      "start": 1621,
-      "end": 1634
-    },
-    {
-      "text": "foci",
-      "type": "ENTITY",
-      "start": 1635,
-      "end": 1639
-    },
-    {
-      "text": "granular",
-      "type": "ENTITY",
-      "start": 1663,
-      "end": 1671
-    },
-    {
-      "text": "cytoplasmic",
-      "type": "ENTITY",
-      "start": 1672,
-      "end": 1683
-    },
-    {
-      "text": "positivity",
-      "type": "ENTITY",
-      "start": 1686,
-      "end": 1696
-    },
-    {
-      "text": "perinuclear dot",
-      "type": "ENTITY",
-      "start": 1713,
-      "end": 1728
-    },
-    {
-      "text": "exenteration",
-      "type": "ENTITY",
-      "start": 1734,
-      "end": 1746
-    },
-    {
-      "text": "positivity",
-      "type": "ENTITY",
-      "start": 1771,
-      "end": 1781
-    },
-    {
-      "text": "NeuN",
-      "type": "ENTITY",
-      "start": 1786,
-      "end": 1790
-    },
-    {
-      "text": "mononuclear",
-      "type": "ENTITY",
-      "start": 1819,
-      "end": 1830
-    },
-    {
-      "text": "abnormal",
-      "type": "ENTITY",
-      "start": 1872,
-      "end": 1880
-    },
-    {
-      "text": "clustering",
-      "type": "ENTITY",
-      "start": 1881,
-      "end": 1891
-    },
-    {
-      "text": "cytologic features",
-      "type": "ENTITY",
-      "start": 1895,
-      "end": 1913
-    },
-    {
-      "text": "binucleation",
-      "type": "ENTITY",
-      "start": 1922,
-      "end": 1934
-    },
-    {
-      "text": "Neurofilament",
-      "type": "ENTITY",
-      "start": 1936,
-      "end": 1949
-    },
-    {
-      "text": "non-neoplastic population",
-      "type": "ENTITY",
-      "start": 1966,
-      "end": 1991
-    },
-    {
-      "text": "entrapped",
-      "type": "ENTITY",
-      "start": 2010,
-      "end": 2019
-    },
-    {
-      "text": "network",
-      "type": "ENTITY",
-      "start": 2020,
-      "end": 2027
-    },
-    {
-      "text": "processes",
-      "type": "ENTITY",
-      "start": 2031,
-      "end": 2040
-    },
-    {
-      "text": "background",
-      "type": "ENTITY",
-      "start": 2044,
-      "end": 2054
-    },
-    {
-      "text": "neuropii",
-      "type": "ENTITY",
-      "start": 2055,
-      "end": 2063
-    },
-    {
-      "text": "Representative formalin fixed paraffin",
-      "type": "ENTITY",
-      "start": 2065,
-      "end": 2103
-    },
-    {
-      "text": "FIsh",
-      "type": "ENTITY",
-      "start": 2155,
-      "end": 2159
-    },
-    {
-      "text": "fluorescence in situ",
-      "type": "ENTITY",
-      "start": 2161,
-      "end": 2181
-    },
-    {
-      "text": "studies",
-      "type": "ENTITY",
-      "start": 2198,
-      "end": 2205
-    },
-    {
-      "text": "lp",
-      "type": "ENTITY",
-      "start": 2216,
-      "end": 2218
-    },
-    {
-      "text": "19q",
-      "type": "ENTITY",
-      "start": 2220,
-      "end": 2223
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 2232,
-      "end": 2239
-    },
-    {
-      "text": "studies",
-      "type": "ENTITY",
-      "start": 2247,
-      "end": 2254
-    },
-    {
-      "text": "Ip",
-      "type": "ENTITY",
-      "start": 2317,
-      "end": 2319
-    },
-    {
-      "text": "Ecrr amplification",
-      "type": "ENTITY",
-      "start": 2344,
-      "end": 2362
-    },
-    {
-      "text": "detected",
-      "type": "ENTITY",
-      "start": 2371,
-      "end": 2379
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 2417,
-      "end": 2424
-    },
-    {
-      "text": "findings",
-      "type": "ENTITY",
-      "start": 2440,
-      "end": 2448
-    },
-    {
-      "text": "glioma",
-      "type": "ENTITY",
-      "start": 2463,
-      "end": 2469
-    },
-    {
-      "text": "Grade IIl mixed",
-      "type": "ENTITY",
-      "start": 2512,
-      "end": 2527
-    },
-    {
-      "text": "conctusion",
-      "type": "ENTITY",
-      "start": 2548,
-      "end": 2558
-    },
-    {
-      "text": "Right frontal tumor",
-      "type": "ENTITY",
-      "start": 2560,
-      "end": 2579
-    },
-    {
-      "text": "Grade IIl mixed oligo-astrocytoma",
-      "type": "ENTITY",
-      "start": 2585,
-      "end": 2618
-    },
-    {
-      "text": "ip",
-      "type": "ENTITY",
-      "start": 2628,
-      "end": 2630
-    },
-    {
-      "text": "deletions",
-      "type": "ENTITY",
-      "start": 2639,
-      "end": 2648
-    },
-    {
-      "text": "Egrr amplification",
-      "type": "ENTITY",
-      "start": 2680,
-      "end": 2698
-    },
-    {
-      "text": "Grading",
-      "type": "ENTITY",
-      "start": 2709,
-      "end": 2716
-    },
-    {
-      "text": "oligoastrocytomas",
-      "type": "ENTITY",
-      "start": 2720,
-      "end": 2737
-    },
-    {
-      "text": "problematic area",
-      "type": "ENTITY",
-      "start": 2743,
-      "end": 2759
-    },
-    {
-      "text": "surgical neuropathology",
-      "type": "ENTITY",
-      "start": 2763,
-      "end": 2786
-    },
-    {
-      "text": "grading",
-      "type": "ENTITY",
-      "start": 2809,
-      "end": 2816
-    },
-    {
-      "text": "oligoastrocytoma",
-      "type": "ENTITY",
-      "start": 2828,
-      "end": 2844
-    },
-    {
-      "text": "Classification",
-      "type": "ENTITY",
-      "start": 2868,
-      "end": 2882
-    },
-    {
-      "text": "Tumors",
-      "type": "ENTITY",
-      "start": 2886,
-      "end": 2892
-    },
-    {
-      "text": "CNs",
-      "type": "ENTITY",
-      "start": 2900,
-      "end": 2903
-    },
-    {
-      "text": "grading oligoastrocytoma",
-      "type": "ENTITY",
-      "start": 2908,
-      "end": 2932
-    },
-    {
-      "text": "authorities",
-      "type": "ENTITY",
-      "start": 2939,
-      "end": 2950
-    },
-    {
-      "text": "grading scheme",
-      "type": "ENTITY",
-      "start": 2970,
-      "end": 2984
-    },
-    {
-      "text": "oligodendroglioma",
-      "type": "ENTITY",
-      "start": 2997,
-      "end": 3014
-    },
-    {
-      "text": "criteria",
-      "type": "ENTITY",
-      "start": 3030,
-      "end": 3038
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 3045,
-      "end": 3054
-    },
-    {
-      "text": "Grade III anaplastic glioma",
-      "type": "ENTITY",
-      "start": 3062,
-      "end": 3089
-    },
-    {
-      "text": "authorities",
-      "type": "ENTITY",
-      "start": 3133,
-      "end": 3144
-    },
-    {
-      "text": "mitotic activity",
-      "type": "ENTITY",
-      "start": 3152,
-      "end": 3168
-    },
-    {
-      "text": "mitotic figures",
-      "type": "ENTITY",
-      "start": 3185,
-      "end": 3200
-    },
-    {
-      "text": "fields",
-      "type": "ENTITY",
-      "start": 3219,
-      "end": 3225
-    },
-    {
-      "text": "parameter",
-      "type": "ENTITY",
-      "start": 3257,
-      "end": 3266
-    },
-    {
-      "text": "anaplasia",
-      "type": "ENTITY",
-      "start": 3270,
-      "end": 3279
-    },
-    {
-      "text": "absence",
-      "type": "ENTITY",
-      "start": 3287,
-      "end": 3294
-    },
-    {
-      "text": "endothelial proliferation",
-      "type": "ENTITY",
-      "start": 3298,
-      "end": 3323
-    },
-    {
-      "text": "palisading necrosis",
-      "type": "ENTITY",
-      "start": 3325,
-      "end": 3344
-    },
-    {
-      "text": "frankly",
-      "type": "ENTITY",
-      "start": 3349,
-      "end": 3356
-    },
-    {
-      "text": "anaplastic cytology",
-      "type": "ENTITY",
-      "start": 3357,
-      "end": 3376
-    },
-    {
-      "text": "hypercellularity",
-      "type": "ENTITY",
-      "start": 3381,
-      "end": 3397
-    },
-    {
-      "text": "case",
-      "type": "ENTITY",
-      "start": 3407,
-      "end": 3411
-    },
-    {
-      "text": "overt",
-      "type": "ENTITY",
-      "start": 3413,
-      "end": 3418
-    },
-    {
-      "text": "features",
-      "type": "ENTITY",
-      "start": 3419,
-      "end": 3427
-    },
-    {
-      "text": "anaplasia",
-      "type": "ENTITY",
-      "start": 3431,
-      "end": 3440
-    },
-    {
-      "text": "maximal",
-      "type": "ENTITY",
-      "start": 3466,
-      "end": 3473
-    },
-    {
-      "text": "mitotic count",
-      "type": "ENTITY",
-      "start": 3474,
-      "end": 3487
-    },
-    {
-      "text": "mitotic figures",
-      "type": "ENTITY",
-      "start": 3498,
-      "end": 3513
-    },
-    {
-      "text": "power",
-      "type": "ENTITY",
-      "start": 3526,
-      "end": 3531
-    },
-    {
-      "text": "fields",
-      "type": "ENTITY",
-      "start": 3532,
-      "end": 3538
-    },
-    {
-      "text": "hypercellular foci",
-      "type": "ENTITY",
-      "start": 3547,
-      "end": 3565
-    },
-    {
-      "text": "MIs",
-      "type": "ENTITY",
-      "start": 3570,
-      "end": 3573
-    },
-    {
-      "text": "proliferation index",
-      "type": "ENTITY",
-      "start": 3587,
-      "end": 3606
-    },
-    {
-      "text": "findings",
-      "type": "ENTITY",
-      "start": 3640,
-      "end": 3648
-    },
-    {
-      "text": "int amount",
-      "type": "ENTITY",
-      "start": 3653,
-      "end": 3663
-    },
-    {
-      "text": "wHo grade III oligoastrocytoma",
-      "type": "ENTITY",
-      "start": 3669,
-      "end": 3699
-    },
-    {
-      "text": "PATHOLOrr",
-      "type": "ENTITY",
-      "start": 3701,
-      "end": 3710
-    },
-    {
-      "text": "DATED",
-      "type": "ENTITY",
-      "start": 3715,
-      "end": 3720
-    },
-    {
-      "text": "ELECTRONICALLY VALIDATED",
-      "type": "ENTITY",
-      "start": 3722,
-      "end": 3746
-    },
-    {
-      "text": "END",
-      "type": "ENTITY",
-      "start": 3748,
-      "end": 3751
-    },
-    {
-      "text": "COLL",
-      "type": "ENTITY",
-      "start": 3793,
-      "end": 3797
-    },
-    {
-      "text": "HISTOPATHOLOGY REPORI COPY TO",
-      "type": "ENTITY",
-      "start": 3829,
-      "end": 3858
-    },
-    {
-      "text": "A. Right frontal tumour",
-      "type": "ENTITY",
-      "start": 3870,
-      "end": 3893
-    },
-    {
-      "text": "B. Right",
-      "type": "ENTITY",
-      "start": 3895,
-      "end": 3903
-    },
-    {
-      "text": "C. Tumour",
-      "type": "ENTITY",
-      "start": 3920,
-      "end": 3929
-    },
-    {
-      "text": "Low grade frontal glioma",
-      "type": "ENTITY",
-      "start": 3941,
-      "end": 3965
-    },
-    {
-      "text": "A.  One piece",
-      "type": "ENTITY",
-      "start": 3981,
-      "end": 3994
-    },
-    {
-      "text": "grey-white tissue",
-      "type": "ENTITY",
-      "start": 3998,
-      "end": 4015
-    },
-    {
-      "text": "piece",
-      "type": "ENTITY",
-      "start": 4078,
-      "end": 4083
-    },
-    {
-      "text": "frozen sections",
-      "type": "ENTITY",
-      "start": 4098,
-      "end": 4113
-    },
-    {
-      "text": "imprint cytology",
-      "type": "ENTITY",
-      "start": 4118,
-      "end": 4134
-    },
-    {
-      "text": "ASSESSMENT",
-      "type": "ENTITY",
-      "start": 4154,
-      "end": 4164
-    },
-    {
-      "text": "FROZEN SECTION",
-      "type": "ENTITY",
-      "start": 4167,
-      "end": 4181
-    },
-    {
-      "text": "IMPRINT",
-      "type": "ENTITY",
-      "start": 4184,
-      "end": 4191
-    },
-    {
-      "text": "CYTOLOGY",
-      "type": "ENTITY",
-      "start": 4192,
-      "end": 4200
-    },
-    {
-      "text": "Glial neoplasm",
-      "type": "ENTITY",
-      "start": 4202,
-      "end": 4216
-    },
-    {
-      "text": "Result",
-      "type": "ENTITY",
-      "start": 4230,
-      "end": 4236
-    },
-    {
-      "text": "B.  Multiple",
-      "type": "ENTITY",
-      "start": 4247,
-      "end": 4259
-    },
-    {
-      "text": "fragments",
-      "type": "ENTITY",
-      "start": 4270,
-      "end": 4279
-    },
-    {
-      "text": "tan coloured tissue",
-      "type": "ENTITY",
-      "start": 4283,
-      "end": 4302
-    },
-    {
-      "text": "haemorrhage",
-      "type": "ENTITY",
-      "start": 4317,
-      "end": 4328
-    },
-    {
-      "text": "myxoid change",
-      "type": "ENTITY",
-      "start": 4333,
-      "end": 4346
-    },
-    {
-      "text": "Specimen",
-      "type": "ENTITY",
-      "start": 4348,
-      "end": 4356
-    },
-    {
-      "text": "sectioned",
-      "type": "ENTITY",
-      "start": 4360,
-      "end": 4369
-    },
-    {
-      "text": "white",
-      "type": "ENTITY",
-      "start": 4384,
-      "end": 4389
-    },
-    {
-      "text": "grey matter",
-      "type": "ENTITY",
-      "start": 4394,
-      "end": 4405
-    },
-    {
-      "text": "differentiation",
-      "type": "ENTITY",
-      "start": 4406,
-      "end": 4421
-    },
-    {
-      "text": "pieces",
-      "type": "ENTITY",
-      "start": 4432,
-      "end": 4438
-    },
-    {
-      "text": "brain tissue",
-      "type": "ENTITY",
-      "start": 4442,
-      "end": 4454
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 4468,
-      "end": 4476
-    },
-    {
-      "text": "Tissue",
-      "type": "ENTITY",
-      "start": 4497,
-      "end": 4503
-    },
-    {
-      "text": "creamy",
-      "type": "ENTITY",
-      "start": 4540,
-      "end": 4546
-    },
-    {
-      "text": "areas",
-      "type": "ENTITY",
-      "start": 4564,
-      "end": 4569
-    },
-    {
-      "text": "myxoid change",
-      "type": "ENTITY",
-      "start": 4578,
-      "end": 4591
-    },
-    {
-      "text": "haemorrhage",
-      "type": "ENTITY",
-      "start": 4596,
-      "end": 4607
-    },
-    {
-      "text": "Centrally",
-      "type": "ENTITY",
-      "start": 4609,
-      "end": 4618
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 4624,
-      "end": 4632
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 4657,
-      "end": 4663
-    },
-    {
-      "text": "soft consistency",
-      "type": "ENTITY",
-      "start": 4670,
-      "end": 4686
-    },
-    {
-      "text": "A. C.  ",
-      "type": "ENTITY",
-      "start": 4702,
-      "end": 4709
-    },
-    {
-      "text": "specimens",
-      "type": "ENTITY",
-      "start": 4713,
-      "end": 4722
-    },
-    {
-      "text": "sampled",
-      "type": "ENTITY",
-      "start": 4744,
-      "end": 4751
-    },
-    {
-      "text": "extensive",
-      "type": "ENTITY",
-      "start": 4761,
-      "end": 4770
-    },
-    {
-      "text": "malignancy",
-      "type": "ENTITY",
-      "start": 4771,
-      "end": 4781
-    },
-    {
-      "text": "oedematous",
-      "type": "ENTITY",
-      "start": 4810,
-      "end": 4820
-    },
-    {
-      "text": "appearance",
-      "type": "ENTITY",
-      "start": 4821,
-      "end": 4831
-    },
-    {
-      "text": "\"fried",
-      "type": "ENTITY",
-      "start": 4839,
-      "end": 4845
-    },
-    {
-      "text": "pattern",
-      "type": "ENTITY",
-      "start": 4851,
-      "end": 4858
-    },
-    {
-      "text": "infiltration",
-      "type": "ENTITY",
-      "start": 4872,
-      "end": 4884
-    },
-    {
-      "text": "grey matter",
-      "type": "ENTITY",
-      "start": 4890,
-      "end": 4901
-    },
-    {
-      "text": "peri-neuronal satellitosis",
-      "type": "ENTITY",
-      "start": 4907,
-      "end": 4933
-    },
-    {
-      "text": "cells",
-      "type": "ENTITY",
-      "start": 4939,
-      "end": 4944
-    },
-    {
-      "text": "oval",
-      "type": "ENTITY",
-      "start": 4959,
-      "end": 4963
-    },
-    {
-      "text": "irregular",
-      "type": "ENTITY",
-      "start": 4973,
-      "end": 4982
-    },
-    {
-      "text": "nuclei",
-      "type": "ENTITY",
-      "start": 4983,
-      "end": 4989
-    },
-    {
-      "text": "granular",
-      "type": "ENTITY",
-      "start": 4995,
-      "end": 5003
-    },
-    {
-      "text": "chromatin",
-      "type": "ENTITY",
-      "start": 5004,
-      "end": 5013
-    },
-    {
-      "text": "inconspicuous nucleoli",
-      "type": "ENTITY",
-      "start": 5018,
-      "end": 5040
-    },
-    {
-      "text": "Mini-gemistocytes",
-      "type": "ENTITY",
-      "start": 5042,
-      "end": 5059
-    },
-    {
-      "text": "fibrillary",
-      "type": "ENTITY",
-      "start": 5098,
-      "end": 5108
-    },
-    {
-      "text": "tumour",
-      "type": "ENTITY",
-      "start": 5124,
-      "end": 5130
-    },
-    {
-      "text": "cellular",
-      "type": "ENTITY",
-      "start": 5139,
-      "end": 5147
-    },
-    {
-      "text": "sheets",
-      "type": "ENTITY",
-      "start": 5171,
-      "end": 5177
-    },
-    {
-      "text": "alternating hyper",
-      "type": "ENTITY",
-      "start": 5184,
-      "end": 5201
-    },
-    {
-      "text": "hypocellular areas",
-      "type": "ENTITY",
-      "start": 5206,
-      "end": 5224
-    },
-    {
-      "text": "cells",
-      "type": "ENTITY",
-      "start": 5230,
-      "end": 5235
-    },
-    {
-      "text": "larger",
-      "type": "ENTITY",
-      "start": 5241,
-      "end": 5247
-    },
-    {
-      "text": "pleomorphic nuclei",
-      "type": "ENTITY",
-      "start": 5254,
-      "end": 5272
-    },
-    {
-      "text": "granular",
-      "type": "ENTITY",
-      "start": 5283,
-      "end": 5291
-    },
-    {
-      "text": "chromatin",
-      "type": "ENTITY",
-      "start": 5292,
-      "end": 5301
-    },
-    {
-      "text": "inconspicuous nucleoli",
-      "type": "ENTITY",
-      "start": 5306,
-      "end": 5328
-    },
-    {
-      "text": "Mini-gemistocytes",
-      "type": "ENTITY",
-      "start": 5331,
-      "end": 5348
-    },
-    {
-      "text": "background",
-      "type": "ENTITY",
-      "start": 5373,
-      "end": 5383
-    },
-    {
-      "text": "myxoid",
-      "type": "ENTITY",
-      "start": 5392,
-      "end": 5398
-    },
-    {
-      "text": "microcystic change",
-      "type": "ENTITY",
-      "start": 5412,
-      "end": 5430
-    },
-    {
-      "text": "mucoid",
-      "type": "ENTITY",
-      "start": 5442,
-      "end": 5448
-    },
-    {
-      "text": "material",
-      "type": "ENTITY",
-      "start": 5449,
-      "end": 5457
-    },
-    {
-      "text": "mitotic figures",
-      "type": "ENTITY",
-      "start": 5469,
-      "end": 5484
-    },
-    {
-      "text": "endothelial proliferation",
-      "type": "ENTITY",
-      "start": 5509,
-      "end": 5534
-    },
-    {
-      "text": "necrosis",
-      "type": "ENTITY",
-      "start": 5538,
-      "end": 5546
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 5547,
-      "end": 5557
-    },
-    {
-      "text": "C. Right",
-      "type": "ENTITY",
-      "start": 5592,
-      "end": 5600
-    },
-    {
-      "text": "Glial series tumour",
-      "type": "ENTITY",
-      "start": 5617,
-      "end": 5636
-    },
-    {
-      "text": "oligodendroglial features",
-      "type": "ENTITY",
-      "start": 5642,
-      "end": 5667
-    },
-    {
-      "text": "cellularity",
-      "type": "ENTITY",
-      "start": 5673,
-      "end": 5684
-    },
-    {
-      "text": "atypia",
-      "type": "ENTITY",
-      "start": 5686,
-      "end": 5692
-    },
-    {
-      "text": "mitotic activity",
-      "type": "ENTITY",
-      "start": 5697,
-      "end": 5713
-    },
-    {
-      "text": "consistent with",
-      "type": "ENTITY",
-      "start": 5718,
-      "end": 5733
-    },
-    {
-      "text": "anaplastic oligodendroglioma",
-      "type": "ENTITY",
-      "start": 5737,
-      "end": 5765
-    },
-    {
-      "text": "grade IIl",
-      "type": "ENTITY",
-      "start": 5771,
-      "end": 5780
-    },
-    {
-      "text": "cytogenetic",
-      "type": "ENTITY",
-      "start": 5783,
-      "end": 5794
-    },
-    {
-      "text": "studies",
-      "type": "ENTITY",
-      "start": 5796,
-      "end": 5803
-    },
-    {
-      "text": "proceding",
-      "type": "ENTITY",
-      "start": 5808,
-      "end": 5817
-    },
-    {
-      "text": "PATHOLOGIST",
-      "type": "ENTITY",
-      "start": 5888,
-      "end": 5899
-    },
-    {
-      "text": "DATED",
-      "type": "ENTITY",
-      "start": 5901,
-      "end": 5906
-    },
-    {
-      "text": "ELECTRONICALLY",
-      "type": "ENTITY",
-      "start": 5911,
-      "end": 5925
-    },
-    {
-      "text": "END",
-      "type": "ENTITY",
-      "start": 5937,
-      "end": 5940
-    }
-  ],
-  "entity_count": 242,
-  "has_embedding": true
-}

output/biomedbert_output/004e158d-aac7-461f-be6e-f3bdcde20224_nlp.json

@@ -1,176 +0,0 @@
-{
-  "filename": "004e158d-aac7-461f-be6e-f3bdcde20224",
-  "timestamp": "2026-01-05T14:44:02.948021",
-  "entities": [
-    {
-      "text": "Diagnosis",
-      "type": "ENTITY",
-      "start": 16,
-      "end": 25
-    },
-    {
-      "text": "Resected ileocolic material",
-      "type": "ENTITY",
-      "start": 27,
-      "end": 54
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 73,
-      "end": 78
-    },
-    {
-      "text": "ascendens",
-      "type": "ENTITY",
-      "start": 79,
-      "end": 88
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 103,
-      "end": 109
-    },
-    {
-      "text": "ileocecal valve",
-      "type": "ENTITY",
-      "start": 117,
-      "end": 132
-    },
-    {
-      "text": "adenocarcinoma",
-      "type": "ENTITY",
-      "start": 137,
-      "end": 151
-    },
-    {
-      "text": "colorectal type",
-      "type": "ENTITY",
-      "start": 155,
-      "end": 170
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 171,
-      "end": 180
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 202,
-      "end": 210
-    },
-    {
-      "text": "ulcerated",
-      "type": "ENTITY",
-      "start": 212,
-      "end": 221
-    },
-    {
-      "text": "differentiated",
-      "type": "ENTITY",
-      "start": 234,
-      "end": 248
-    },
-    {
-      "text": "infiltration",
-      "type": "ENTITY",
-      "start": 258,
-      "end": 270
-    },
-    {
-      "text": "perifocal",
-      "type": "ENTITY",
-      "start": 278,
-      "end": 287
-    },
-    {
-      "text": "Tumor-free lymph nodes",
-      "type": "ENTITY",
-      "start": 304,
-      "end": 326
-    },
-    {
-      "text": "region",
-      "type": "ENTITY",
-      "start": 335,
-      "end": 341
-    },
-    {
-      "text": "Tumor-free small",
-      "type": "ENTITY",
-      "start": 343,
-      "end": 359
-    },
-    {
-      "text": "intestine resection",
-      "type": "ENTITY",
-      "start": 370,
-      "end": 389
-    },
-    {
-      "text": "Tumor-free mesenteric resection margin",
-      "type": "ENTITY",
-      "start": 399,
-      "end": 437
-    },
-    {
-      "text": "Tumor-free appendix",
-      "type": "ENTITY",
-      "start": 439,
-      "end": 458
-    },
-    {
-      "text": "Tumor-",
-      "type": "ENTITY",
-      "start": 460,
-      "end": 466
-    },
-    {
-      "text": "omental",
-      "type": "ENTITY",
-      "start": 473,
-      "end": 480
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 481,
-      "end": 495
-    },
-    {
-      "text": "Tumor stage",
-      "type": "ENTITY",
-      "start": 497,
-      "end": 508
-    },
-    {
-      "text": "pT3",
-      "type": "ENTITY",
-      "start": 519,
-      "end": 522
-    },
-    {
-      "text": "pMX",
-      "type": "ENTITY",
-      "start": 535,
-      "end": 538
-    },
-    {
-      "text": "V0",
-      "type": "ENTITY",
-      "start": 548,
-      "end": 550
-    },
-    {
-      "text": "local R0",
-      "type": "ENTITY",
-      "start": 552,
-      "end": 560
-    }
-  ],
-  "entity_count": 28,
-  "has_embedding": true
-}

output/biomedbert_output/0077ff5b-55d3-4dca-80c0-fe5527b77362_nlp.json

@@ -1,272 +0,0 @@
-{
-  "filename": "0077ff5b-55d3-4dca-80c0-fe5527b77362",
-  "timestamp": "2026-01-05T14:40:48.691753",
-  "entities": [
-    {
-      "text": "UUID:5A59F9F1-9F37-",
-      "type": "ENTITY",
-      "start": 23,
-      "end": 42
-    },
-    {
-      "text": "TCGA-VR-AA4D-01A-PR Redacted Site",
-      "type": "ENTITY",
-      "start": 65,
-      "end": 98
-    },
-    {
-      "text": "Espnagus",
-      "type": "ENTITY",
-      "start": 100,
-      "end": 108
-    },
-    {
-      "text": "olstal",
-      "type": "ENTITY",
-      "start": 110,
-      "end": 116
-    },
-    {
-      "text": "C15.5 Q0s3|5/14",
-      "type": "ENTITY",
-      "start": 122,
-      "end": 137
-    },
-    {
-      "text": "Collect",
-      "type": "ENTITY",
-      "start": 138,
-      "end": 145
-    },
-    {
-      "text": "MM/DD/YYYY",
-      "type": "ENTITY",
-      "start": 153,
-      "end": 163
-    },
-    {
-      "text": "PRIMARY SITE",
-      "type": "ENTITY",
-      "start": 183,
-      "end": 195
-    },
-    {
-      "text": "Esophagus",
-      "type": "ENTITY",
-      "start": 197,
-      "end": 206
-    },
-    {
-      "text": "Distal",
-      "type": "ENTITY",
-      "start": 208,
-      "end": 214
-    },
-    {
-      "text": "esophagogastrectomy",
-      "type": "ENTITY",
-      "start": 230,
-      "end": 249
-    },
-    {
-      "text": "Moderately differentiated adenocarcinoma",
-      "type": "ENTITY",
-      "start": 254,
-      "end": 294
-    },
-    {
-      "text": "papillary areas",
-      "type": "ENTITY",
-      "start": 300,
-      "end": 315
-    },
-    {
-      "text": "infiltrative up to",
-      "type": "ENTITY",
-      "start": 316,
-      "end": 334
-    },
-    {
-      "text": "submucosa",
-      "type": "ENTITY",
-      "start": 335,
-      "end": 344
-    },
-    {
-      "text": "Presence",
-      "type": "ENTITY",
-      "start": 346,
-      "end": 354
-    },
-    {
-      "text": "lymphatic invasion",
-      "type": "ENTITY",
-      "start": 358,
-      "end": 376
-    },
-    {
-      "text": "Perineural infiltration",
-      "type": "ENTITY",
-      "start": 378,
-      "end": 401
-    },
-    {
-      "text": "detected",
-      "type": "ENTITY",
-      "start": 406,
-      "end": 414
-    },
-    {
-      "text": "Infiltrative growth pattern",
-      "type": "ENTITY",
-      "start": 417,
-      "end": 444
-    },
-    {
-      "text": "Absence",
-      "type": "ENTITY",
-      "start": 446,
-      "end": 453
-    },
-    {
-      "text": "necrosis",
-      "type": "ENTITY",
-      "start": 457,
-      "end": 465
-    },
-    {
-      "text": "peritumoral",
-      "type": "ENTITY",
-      "start": 476,
-      "end": 487
-    },
-    {
-      "text": "inflammatory infiltrate",
-      "type": "ENTITY",
-      "start": 488,
-      "end": 511
-    },
-    {
-      "text": "Surgical margins free",
-      "type": "ENTITY",
-      "start": 513,
-      "end": 534
-    },
-    {
-      "text": "neoplastic",
-      "type": "ENTITY",
-      "start": 538,
-      "end": 548
-    },
-    {
-      "text": "standardization",
-      "type": "ENTITY",
-      "start": 593,
-      "end": 608
-    },
-    {
-      "text": "Metastatic adenocarcinoma",
-      "type": "ENTITY",
-      "start": 612,
-      "end": 637
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 649,
-      "end": 659
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 660,
-      "end": 671
-    },
-    {
-      "text": "capsular",
-      "type": "ENTITY",
-      "start": 688,
-      "end": 696
-    },
-    {
-      "text": "compromise",
-      "type": "ENTITY",
-      "start": 697,
-      "end": 707
-    },
-    {
-      "text": "distributed",
-      "type": "ENTITY",
-      "start": 709,
-      "end": 720
-    },
-    {
-      "text": "right cardiac",
-      "type": "ENTITY",
-      "start": 738,
-      "end": 751
-    },
-    {
-      "text": "left cardiac",
-      "type": "ENTITY",
-      "start": 757,
-      "end": 769
-    },
-    {
-      "text": "lesser",
-      "type": "ENTITY",
-      "start": 776,
-      "end": 782
-    },
-    {
-      "text": "curvature",
-      "type": "ENTITY",
-      "start": 783,
-      "end": 792
-    },
-    {
-      "text": "left gastric artery",
-      "type": "ENTITY",
-      "start": 798,
-      "end": 817
-    },
-    {
-      "text": "celiac trunk",
-      "type": "ENTITY",
-      "start": 823,
-      "end": 835
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 841,
-      "end": 849
-    },
-    {
-      "text": "para-esophageal",
-      "type": "ENTITY",
-      "start": 850,
-      "end": 865
-    },
-    {
-      "text": "Greater",
-      "type": "ENTITY",
-      "start": 871,
-      "end": 878
-    },
-    {
-      "text": "neoplastic",
-      "type": "ENTITY",
-      "start": 897,
-      "end": 907
-    },
-    {
-      "text": "neoplastic",
-      "type": "ENTITY",
-      "start": 951,
-      "end": 961
-    }
-  ],
-  "entity_count": 44,
-  "has_embedding": true
-}

output/biomedbert_output/00a7f79f-49bd-46b9-bde2-1a28ac6eecce_nlp.json

@@ -1,1304 +0,0 @@
-{
-  "filename": "00a7f79f-49bd-46b9-bde2-1a28ac6eecce",
-  "timestamp": "2026-01-05T14:45:14.065668",
-  "entities": [
-    {
-      "text": "TCGA-LL-A73Y-01A-PR",
-      "type": "ENTITY",
-      "start": 58,
-      "end": 77
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 87,
-      "end": 90
-    },
-    {
-      "text": "PAGE",
-      "type": "ENTITY",
-      "start": 97,
-      "end": 101
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 104,
-      "end": 107
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 114,
-      "end": 117
-    },
-    {
-      "text": "PATIENT",
-      "type": "ENTITY",
-      "start": 126,
-      "end": 133
-    },
-    {
-      "text": "ACCT",
-      "type": "ENTITY",
-      "start": 135,
-      "end": 139
-    },
-    {
-      "text": "LOC",
-      "type": "ENTITY",
-      "start": 143,
-      "end": 146
-    },
-    {
-      "text": "AGE/SX",
-      "type": "ENTITY",
-      "start": 148,
-      "end": 154
-    },
-    {
-      "text": "REG DR",
-      "type": "ENTITY",
-      "start": 164,
-      "end": 170
-    },
-    {
-      "text": "DOB",
-      "type": "ENTITY",
-      "start": 172,
-      "end": 175
-    },
-    {
-      "text": "BED",
-      "type": "ENTITY",
-      "start": 177,
-      "end": 180
-    },
-    {
-      "text": "SPEC",
-      "type": "ENTITY",
-      "start": 191,
-      "end": 195
-    },
-    {
-      "text": "RECD",
-      "type": "ENTITY",
-      "start": 199,
-      "end": 203
-    },
-    {
-      "text": "COLL",
-      "type": "ENTITY",
-      "start": 213,
-      "end": 217
-    },
-    {
-      "text": "TIME",
-      "type": "ENTITY",
-      "start": 219,
-      "end": 223
-    },
-    {
-      "text": "FORMALIN",
-      "type": "ENTITY",
-      "start": 227,
-      "end": 235
-    },
-    {
-      "text": "COLD ISCHEMA",
-      "type": "ENTITY",
-      "start": 243,
-      "end": 255
-    },
-    {
-      "text": "Pre-Op Diagnosis",
-      "type": "ENTITY",
-      "start": 290,
-      "end": 306
-    },
-    {
-      "text": "Remarks",
-      "type": "ENTITY",
-      "start": 308,
-      "end": 315
-    },
-    {
-      "text": "Specimen(s): A. Right sentinel node",
-      "type": "ENTITY",
-      "start": 317,
-      "end": 352
-    },
-    {
-      "text": "B. Right breast",
-      "type": "ENTITY",
-      "start": 353,
-      "end": 368
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 373,
-      "end": 379
-    },
-    {
-      "text": "Ecd-6.3",
-      "type": "ENTITY",
-      "start": 388,
-      "end": 395
-    },
-    {
-      "text": "scnima",
-      "type": "ENTITY",
-      "start": 396,
-      "end": 402
-    },
-    {
-      "text": "yiltetis",
-      "type": "ENTITY",
-      "start": 406,
-      "end": 414
-    },
-    {
-      "text": "ductNDS U",
-      "type": "ENTITY",
-      "start": 415,
-      "end": 424
-    },
-    {
-      "text": "ICROSCPIC",
-      "type": "ENTITY",
-      "start": 432,
-      "end": 441
-    },
-    {
-      "text": "IIAGNOSIS",
-      "type": "ENTITY",
-      "start": 442,
-      "end": 451
-    },
-    {
-      "text": "RIGHT SENTINEL NODE",
-      "type": "ENTITY",
-      "start": 492,
-      "end": 511
-    },
-    {
-      "text": "IMMUNOCHEMICAL STAINS B. RIGHT",
-      "type": "ENTITY",
-      "start": 530,
-      "end": 560
-    },
-    {
-      "text": "BREAST",
-      "type": "ENTITY",
-      "start": 561,
-      "end": 567
-    },
-    {
-      "text": "INFILTRATING DUCTAL",
-      "type": "ENTITY",
-      "start": 587,
-      "end": 606
-    },
-    {
-      "text": "NOTTINGHAM",
-      "type": "ENTITY",
-      "start": 626,
-      "end": 636
-    },
-    {
-      "text": "NUCLEAR SCORE",
-      "type": "ENTITY",
-      "start": 662,
-      "end": 675
-    },
-    {
-      "text": "TUBULAR FORMATION",
-      "type": "ENTITY",
-      "start": 684,
-      "end": 701
-    },
-    {
-      "text": "SCORE",
-      "type": "ENTITY",
-      "start": 702,
-      "end": 707
-    },
-    {
-      "text": "SCORE",
-      "type": "ENTITY",
-      "start": 724,
-      "end": 729
-    },
-    {
-      "text": "FIGURES",
-      "type": "ENTITY",
-      "start": 748,
-      "end": 755
-    },
-    {
-      "text": "PER SQUARE MILLIMETER",
-      "type": "ENTITY",
-      "start": 756,
-      "end": 777
-    },
-    {
-      "text": "NO DUCTAL CARCINOMA",
-      "type": "ENTITY",
-      "start": 779,
-      "end": 798
-    },
-    {
-      "text": "FREE",
-      "type": "ENTITY",
-      "start": 865,
-      "end": 869
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 873,
-      "end": 878
-    },
-    {
-      "text": "NEAREST",
-      "type": "ENTITY",
-      "start": 884,
-      "end": 891
-    },
-    {
-      "text": "MM",
-      "type": "ENTITY",
-      "start": 901,
-      "end": 903
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 909,
-      "end": 914
-    },
-    {
-      "text": "DEEP MARGIN",
-      "type": "ENTITY",
-      "start": 920,
-      "end": 931
-    },
-    {
-      "text": "COMMENT",
-      "type": "ENTITY",
-      "start": 936,
-      "end": 943
-    },
-    {
-      "text": "SYNOPTIC",
-      "type": "ENTITY",
-      "start": 948,
-      "end": 956
-    },
-    {
-      "text": "SUMMARY",
-      "type": "ENTITY",
-      "start": 1006,
-      "end": 1013
-    },
-    {
-      "text": "APPROVED",
-      "type": "ENTITY",
-      "start": 1016,
-      "end": 1024
-    },
-    {
-      "text": "Total mastectomy",
-      "type": "ENTITY",
-      "start": 1073,
-      "end": 1089
-    },
-    {
-      "text": "Sentinel lymph node(s) SPECIMEN",
-      "type": "ENTITY",
-      "start": 1111,
-      "end": 1142
-    },
-    {
-      "text": "Right TUMOR SIZE",
-      "type": "ENTITY",
-      "start": 1155,
-      "end": 1171
-    },
-    {
-      "text": "dimension",
-      "type": "ENTITY",
-      "start": 1182,
-      "end": 1191
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 1212,
-      "end": 1220
-    },
-    {
-      "text": "NOTTINGHAM",
-      "type": "ENTITY",
-      "start": 1247,
-      "end": 1257
-    },
-    {
-      "text": "SCORE",
-      "type": "ENTITY",
-      "start": 1269,
-      "end": 1274
-    },
-    {
-      "text": "Glandular/tubular differentiation",
-      "type": "ENTITY",
-      "start": 1278,
-      "end": 1311
-    },
-    {
-      "text": "score",
-      "type": "ENTITY",
-      "start": 1313,
-      "end": 1318
-    },
-    {
-      "text": "Nuclear pleomorphism",
-      "type": "ENTITY",
-      "start": 1322,
-      "end": 1342
-    },
-    {
-      "text": "score",
-      "type": "ENTITY",
-      "start": 1344,
-      "end": 1349
-    },
-    {
-      "text": "Mitotic rate",
-      "type": "ENTITY",
-      "start": 1352,
-      "end": 1364
-    },
-    {
-      "text": "score",
-      "type": "ENTITY",
-      "start": 1366,
-      "end": 1371
-    },
-    {
-      "text": "grade 3 TUMOR FOCALITY",
-      "type": "ENTITY",
-      "start": 1389,
-      "end": 1411
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1429,
-      "end": 1447
-    },
-    {
-      "text": "DUCTAL CARCINOMA",
-      "type": "ENTITY",
-      "start": 1449,
-      "end": 1465
-    },
-    {
-      "text": "DcIs",
-      "type": "ENTITY",
-      "start": 1478,
-      "end": 1482
-    },
-    {
-      "text": "** CONTINUED",
-      "type": "ENTITY",
-      "start": 1494,
-      "end": 1506
-    },
-    {
-      "text": "PAGE",
-      "type": "ENTITY",
-      "start": 1549,
-      "end": 1553
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 1556,
-      "end": 1559
-    },
-    {
-      "text": "TIME",
-      "type": "ENTITY",
-      "start": 1560,
-      "end": 1564
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 1566,
-      "end": 1569
-    },
-    {
-      "text": "USER",
-      "type": "ENTITY",
-      "start": 1570,
-      "end": 1574
-    },
-    {
-      "text": "SPEC",
-      "type": "ENTITY",
-      "start": 1576,
-      "end": 1580
-    },
-    {
-      "text": "PATIENT",
-      "type": "ENTITY",
-      "start": 1584,
-      "end": 1591
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1639,
-      "end": 1657
-    },
-    {
-      "text": "Margins uninvolved",
-      "type": "ENTITY",
-      "start": 1659,
-      "end": 1677
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1681,
-      "end": 1699
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 1700,
-      "end": 1708
-    },
-    {
-      "text": "margin",
-      "type": "ENTITY",
-      "start": 1722,
-      "end": 1728
-    },
-    {
-      "text": "deep LYMPH",
-      "type": "ENTITY",
-      "start": 1736,
-      "end": 1746
-    },
-    {
-      "text": "sentinel lymph nodes",
-      "type": "ENTITY",
-      "start": 1764,
-      "end": 1784
-    },
-    {
-      "text": "Number",
-      "type": "ENTITY",
-      "start": 1795,
-      "end": 1801
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1805,
-      "end": 1816
-    },
-    {
-      "text": "macrometastases",
-      "type": "ENTITY",
-      "start": 1822,
-      "end": 1837
-    },
-    {
-      "text": "Number",
-      "type": "ENTITY",
-      "start": 1841,
-      "end": 1847
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1851,
-      "end": 1862
-    },
-    {
-      "text": "micrometastases",
-      "type": "ENTITY",
-      "start": 1868,
-      "end": 1883
-    },
-    {
-      "text": "Primary tumor",
-      "type": "ENTITY",
-      "start": 1905,
-      "end": 1918
-    },
-    {
-      "text": "Regional lymph nodes",
-      "type": "ENTITY",
-      "start": 1925,
-      "end": 1945
-    },
-    {
-      "text": "Distant metastases",
-      "type": "ENTITY",
-      "start": 1956,
-      "end": 1974
-    },
-    {
-      "text": "Estrogen receptor",
-      "type": "ENTITY",
-      "start": 2010,
-      "end": 2027
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 2038,
-      "end": 2046
-    },
-    {
-      "text": "tumor cells",
-      "type": "ENTITY",
-      "start": 2055,
-      "end": 2066
-    },
-    {
-      "text": "nuclear positivity",
-      "type": "ENTITY",
-      "start": 2072,
-      "end": 2090
-    },
-    {
-      "text": "Progesterone receptor",
-      "type": "ENTITY",
-      "start": 2092,
-      "end": 2113
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 2124,
-      "end": 2132
-    },
-    {
-      "text": "tumor cells",
-      "type": "ENTITY",
-      "start": 2141,
-      "end": 2152
-    },
-    {
-      "text": "nuclear positivity",
-      "type": "ENTITY",
-      "start": 2158,
-      "end": 2176
-    },
-    {
-      "text": "HER-3",
-      "type": "ENTITY",
-      "start": 2178,
-      "end": 2183
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 2220,
-      "end": 2228
-    },
-    {
-      "text": "score",
-      "type": "ENTITY",
-      "start": 2230,
-      "end": 2235
-    },
-    {
-      "text": "GROSS DESCRIPTION",
-      "type": "ENTITY",
-      "start": 2239,
-      "end": 2256
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2262,
-      "end": 2270
-    },
-    {
-      "text": "parts",
-      "type": "ENTITY",
-      "start": 2290,
-      "end": 2295
-    },
-    {
-      "text": "parts",
-      "type": "ENTITY",
-      "start": 2302,
-      "end": 2307
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 2321,
-      "end": 2328
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 2338,
-      "end": 2347
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 2369,
-      "end": 2377
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 2379,
-      "end": 2386
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 2396,
-      "end": 2405
-    },
-    {
-      "text": "\"right sentinel node",
-      "type": "ENTITY",
-      "start": 2415,
-      "end": 2435
-    },
-    {
-      "text": "portion of yellow",
-      "type": "ENTITY",
-      "start": 2462,
-      "end": 2479
-    },
-    {
-      "text": "lobulated adipose",
-      "type": "ENTITY",
-      "start": 2481,
-      "end": 2498
-    },
-    {
-      "text": "adipose",
-      "type": "ENTITY",
-      "start": 2504,
-      "end": 2511
-    },
-    {
-      "text": "flattened",
-      "type": "ENTITY",
-      "start": 2534,
-      "end": 2543
-    },
-    {
-      "text": "nodular",
-      "type": "ENTITY",
-      "start": 2564,
-      "end": 2571
-    },
-    {
-      "text": "fatty lymph node",
-      "type": "ENTITY",
-      "start": 2573,
-      "end": 2589
-    },
-    {
-      "text": "node",
-      "type": "ENTITY",
-      "start": 2595,
-      "end": 2599
-    },
-    {
-      "text": "sectioned perpendicular",
-      "type": "ENTITY",
-      "start": 2603,
-      "end": 2626
-    },
-    {
-      "text": "long axis",
-      "type": "ENTITY",
-      "start": 2634,
-      "end": 2643
-    },
-    {
-      "text": "sentinel lymph node protocol",
-      "type": "ENTITY",
-      "start": 2673,
-      "end": 2701
-    },
-    {
-      "text": "cassettes Al-A3",
-      "type": "ENTITY",
-      "start": 2702,
-      "end": 2717
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 2731,
-      "end": 2736
-    },
-    {
-      "text": "tissue banking",
-      "type": "ENTITY",
-      "start": 2741,
-      "end": 2755
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 2757,
-      "end": 2764
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 2774,
-      "end": 2783
-    },
-    {
-      "text": "\"right breast",
-      "type": "ENTITY",
-      "start": 2793,
-      "end": 2806
-    },
-    {
-      "text": "gram",
-      "type": "ENTITY",
-      "start": 2817,
-      "end": 2821
-    },
-    {
-      "text": "fibrofatty",
-      "type": "ENTITY",
-      "start": 2844,
-      "end": 2854
-    },
-    {
-      "text": "breast",
-      "type": "ENTITY",
-      "start": 2855,
-      "end": 2861
-    },
-    {
-      "text": "consistent with",
-      "type": "ENTITY",
-      "start": 2862,
-      "end": 2877
-    },
-    {
-      "text": "mastectomy",
-      "type": "ENTITY",
-      "start": 2885,
-      "end": 2895
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2896,
-      "end": 2904
-    },
-    {
-      "text": "suture",
-      "type": "ENTITY",
-      "start": 2917,
-      "end": 2923
-    },
-    {
-      "text": "region",
-      "type": "ENTITY",
-      "start": 2940,
-      "end": 2946
-    },
-    {
-      "text": "axilla",
-      "type": "ENTITY",
-      "start": 2954,
-      "end": 2960
-    },
-    {
-      "text": "overlying",
-      "type": "ENTITY",
-      "start": 2968,
-      "end": 2977
-    },
-    {
-      "text": "black-brown skin ellipse",
-      "type": "ENTITY",
-      "start": 2992,
-      "end": 3016
-    },
-    {
-      "text": "skin ellipse",
-      "type": "ENTITY",
-      "start": 3022,
-      "end": 3034
-    },
-    {
-      "text": "central",
-      "type": "ENTITY",
-      "start": 3041,
-      "end": 3048
-    },
-    {
-      "text": "areola",
-      "type": "ENTITY",
-      "start": 3063,
-      "end": 3069
-    },
-    {
-      "text": "skin margins",
-      "type": "ENTITY",
-      "start": 3091,
-      "end": 3103
-    },
-    {
-      "text": "erect",
-      "type": "ENTITY",
-      "start": 3125,
-      "end": 3130
-    },
-    {
-      "text": "nipple",
-      "type": "ENTITY",
-      "start": 3131,
-      "end": 3137
-    },
-    {
-      "text": "deep margin",
-      "type": "ENTITY",
-      "start": 3143,
-      "end": 3154
-    },
-    {
-      "text": "smooth",
-      "type": "ENTITY",
-      "start": 3172,
-      "end": 3178
-    },
-    {
-      "text": "intact",
-      "type": "ENTITY",
-      "start": 3183,
-      "end": 3189
-    },
-    {
-      "text": "focal",
-      "type": "ENTITY",
-      "start": 3197,
-      "end": 3202
-    },
-    {
-      "text": "inferior medial area",
-      "type": "ENTITY",
-      "start": 3211,
-      "end": 3231
-    },
-    {
-      "text": "disruption",
-      "type": "ENTITY",
-      "start": 3235,
-      "end": 3245
-    },
-    {
-      "text": "deep margin",
-      "type": "ENTITY",
-      "start": 3251,
-      "end": 3262
-    },
-    {
-      "text": "inked blue",
-      "type": "ENTITY",
-      "start": 3271,
-      "end": 3281
-    },
-    {
-      "text": "breast",
-      "type": "ENTITY",
-      "start": 3290,
-      "end": 3296
-    },
-    {
-      "text": "diffusely",
-      "type": "ENTITY",
-      "start": 3329,
-      "end": 3338
-    },
-    {
-      "text": "fatty parenchyma",
-      "type": "ENTITY",
-      "start": 3339,
-      "end": 3355
-    },
-    {
-      "text": "upper inner quadrant",
-      "type": "ENTITY",
-      "start": 3361,
-      "end": 3381
-    },
-    {
-      "text": "tumor mass",
-      "type": "ENTITY",
-      "start": 3407,
-      "end": 3417
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 3423,
-      "end": 3427
-    },
-    {
-      "text": "peripheral margin",
-      "type": "ENTITY",
-      "start": 3457,
-      "end": 3474
-    },
-    {
-      "text": "inferior peripheral margin",
-      "type": "ENTITY",
-      "start": 3500,
-      "end": 3526
-    },
-    {
-      "text": "medial peripheral margin",
-      "type": "ENTITY",
-      "start": 3559,
-      "end": 3583
-    },
-    {
-      "text": "lateral peripheral margin",
-      "type": "ENTITY",
-      "start": 3614,
-      "end": 3639
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 3645,
-      "end": 3650
-    },
-    {
-      "text": "deep margin",
-      "type": "ENTITY",
-      "start": 3681,
-      "end": 3692
-    },
-    {
-      "text": "breast",
-      "type": "ENTITY",
-      "start": 3715,
-      "end": 3721
-    },
-    {
-      "text": "glistening",
-      "type": "ENTITY",
-      "start": 3726,
-      "end": 3736
-    },
-    {
-      "text": "yellow adipose",
-      "type": "ENTITY",
-      "start": 3738,
-      "end": 3752
-    },
-    {
-      "text": "diffuse",
-      "type": "ENTITY",
-      "start": 3758,
-      "end": 3765
-    },
-    {
-      "text": "delicate",
-      "type": "ENTITY",
-      "start": 3767,
-      "end": 3775
-    },
-    {
-      "text": "focal scant dense-white",
-      "type": "ENTITY",
-      "start": 3780,
-      "end": 3803
-    },
-    {
-      "text": "fibrous tissue",
-      "type": "ENTITY",
-      "start": 3804,
-      "end": 3818
-    },
-    {
-      "text": "central area",
-      "type": "ENTITY",
-      "start": 3831,
-      "end": 3843
-    },
-    {
-      "text": "fibrocystic change",
-      "type": "ENTITY",
-      "start": 3856,
-      "end": 3874
-    },
-    {
-      "text": "white fibrous tissue",
-      "type": "ENTITY",
-      "start": 3880,
-      "end": 3900
-    },
-    {
-      "text": "parenchyma",
-      "type": "ENTITY",
-      "start": 3936,
-      "end": 3946
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 3982,
-      "end": 3988
-    },
-    {
-      "text": "aspect",
-      "type": "ENTITY",
-      "start": 3989,
-      "end": 3995
-    },
-    {
-      "text": "breast",
-      "type": "ENTITY",
-      "start": 4003,
-      "end": 4009
-    },
-    {
-      "text": "indurated",
-      "type": "ENTITY",
-      "start": 4025,
-      "end": 4034
-    },
-    {
-      "text": "lesions",
-      "type": "ENTITY",
-      "start": 4035,
-      "end": 4042
-    },
-    {
-      "text": "tumor-like masses",
-      "type": "ENTITY",
-      "start": 4046,
-      "end": 4063
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 4068,
-      "end": 4078
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 4080,
-      "end": 4103
-    },
-    {
-      "text": "sampled",
-      "type": "ENTITY",
-      "start": 4108,
-      "end": 4115
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 4119,
-      "end": 4126
-    },
-    {
-      "text": "B1 perpendicular section",
-      "type": "ENTITY",
-      "start": 4128,
-      "end": 4152
-    },
-    {
-      "text": "nipple B2 section",
-      "type": "ENTITY",
-      "start": 4156,
-      "end": 4173
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 4177,
-      "end": 4182
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 4195,
-      "end": 4200
-    },
-    {
-      "text": "tissue banking",
-      "type": "ENTITY",
-      "start": 4215,
-      "end": 4229
-    },
-    {
-      "text": "** CONTINUED",
-      "type": "ENTITY",
-      "start": 4230,
-      "end": 4242
-    },
-    {
-      "text": "PAGE",
-      "type": "ENTITY",
-      "start": 4294,
-      "end": 4298
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 4301,
-      "end": 4304
-    },
-    {
-      "text": "RUN",
-      "type": "ENTITY",
-      "start": 4311,
-      "end": 4314
-    },
-    {
-      "text": "SPEC",
-      "type": "ENTITY",
-      "start": 4333,
-      "end": 4337
-    },
-    {
-      "text": "GROSS DESCRIPTION",
-      "type": "ENTITY",
-      "start": 4341,
-      "end": 4358
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 4390,
-      "end": 4395
-    },
-    {
-      "text": "deep margin",
-      "type": "ENTITY",
-      "start": 4399,
-      "end": 4410
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4429,
-      "end": 4437
-    },
-    {
-      "text": "upper outer quadrant",
-      "type": "ENTITY",
-      "start": 4441,
-      "end": 4461
-    },
-    {
-      "text": "B7",
-      "type": "ENTITY",
-      "start": 4463,
-      "end": 4465
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4481,
-      "end": 4489
-    },
-    {
-      "text": "B8",
-      "type": "ENTITY",
-      "start": 4515,
-      "end": 4517
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4533,
-      "end": 4541
-    },
-    {
-      "text": "upper inner quadrant",
-      "type": "ENTITY",
-      "start": 4545,
-      "end": 4565
-    },
-    {
-      "text": "quadrant near tumor",
-      "type": "ENTITY",
-      "start": 4567,
-      "end": 4586
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4606,
-      "end": 4614
-    },
-    {
-      "text": "sampled",
-      "type": "ENTITY",
-      "start": 4639,
-      "end": 4646
-    },
-    {
-      "text": "GROSS EVALUATION RIGHT BREAST",
-      "type": "ENTITY",
-      "start": 4687,
-      "end": 4716
-    },
-    {
-      "text": "INVASIVE CARCINOMA",
-      "type": "ENTITY",
-      "start": 4718,
-      "end": 4736
-    },
-    {
-      "text": "TUMOR BANKING",
-      "type": "ENTITY",
-      "start": 4752,
-      "end": 4765
-    },
-    {
-      "text": "TUMOR PHOTO DOCUMENTATION Image Image Signed",
-      "type": "ENTITY",
-      "start": 4791,
-      "end": 4835
-    },
-    {
-      "text": "signature",
-      "type": "ENTITY",
-      "start": 4837,
-      "end": 4846
-    },
-    {
-      "text": "END",
-      "type": "ENTITY",
-      "start": 4859,
-      "end": 4862
-    }
-  ],
-  "entity_count": 216,
-  "has_embedding": true
-}

output/biomedbert_output/00ae28ec-fe97-47c3-8283-16c828c576b7_nlp.json

@@ -1,362 +0,0 @@
-{
-  "filename": "00ae28ec-fe97-47c3-8283-16c828c576b7",
-  "timestamp": "2026-01-05T14:42:24.957795",
-  "entities": [
-    {
-      "text": "1 Department of Cancer",
-      "type": "ENTITY",
-      "start": 25,
-      "end": 47
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 59,
-      "end": 70
-    },
-    {
-      "text": "Histopathological",
-      "type": "ENTITY",
-      "start": 72,
-      "end": 89
-    },
-    {
-      "text": "examination",
-      "type": "ENTITY",
-      "start": 90,
-      "end": 101
-    },
-    {
-      "text": "Internal invoice No. Cost",
-      "type": "ENTITY",
-      "start": 102,
-      "end": 127
-    },
-    {
-      "text": "diagnostic procedure Examination No.",
-      "type": "ENTITY",
-      "start": 131,
-      "end": 167
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 169,
-      "end": 176
-    },
-    {
-      "text": "XXX",
-      "type": "ENTITY",
-      "start": 178,
-      "end": 181
-    },
-    {
-      "text": "PESEL",
-      "type": "ENTITY",
-      "start": 182,
-      "end": 187
-    },
-    {
-      "text": "XXX Age",
-      "type": "ENTITY",
-      "start": 189,
-      "end": 196
-    },
-    {
-      "text": "Gender",
-      "type": "ENTITY",
-      "start": 198,
-      "end": 204
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 206,
-      "end": 214
-    },
-    {
-      "text": "Multiple",
-      "type": "ENTITY",
-      "start": 219,
-      "end": 227
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 234,
-      "end": 243
-    },
-    {
-      "text": "sigmoid colon Unit",
-      "type": "ENTITY",
-      "start": 246,
-      "end": 264
-    },
-    {
-      "text": "charge",
-      "type": "ENTITY",
-      "start": 290,
-      "end": 296
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 298,
-      "end": 306
-    },
-    {
-      "text": "collected",
-      "type": "ENTITY",
-      "start": 307,
-      "end": 316
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 321,
-      "end": 329
-    },
-    {
-      "text": "Expected time",
-      "type": "ENTITY",
-      "start": 342,
-      "end": 355
-    },
-    {
-      "text": "examination",
-      "type": "ENTITY",
-      "start": 359,
-      "end": 370
-    },
-    {
-      "text": "Clinical diagnosis",
-      "type": "ENTITY",
-      "start": 372,
-      "end": 390
-    },
-    {
-      "text": "Sigmoid colon",
-      "type": "ENTITY",
-      "start": 392,
-      "end": 405
-    },
-    {
-      "text": "tumour Examination",
-      "type": "ENTITY",
-      "start": 411,
-      "end": 429
-    },
-    {
-      "text": "Macroscopic",
-      "type": "ENTITY",
-      "start": 444,
-      "end": 455
-    },
-    {
-      "text": "description",
-      "type": "ENTITY",
-      "start": 456,
-      "end": 467
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 479,
-      "end": 485
-    },
-    {
-      "text": "intestine",
-      "type": "ENTITY",
-      "start": 499,
-      "end": 508
-    },
-    {
-      "text": "piece",
-      "type": "ENTITY",
-      "start": 516,
-      "end": 521
-    },
-    {
-      "text": "mesentery",
-      "type": "ENTITY",
-      "start": 525,
-      "end": 534
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 535,
-      "end": 540
-    },
-    {
-      "text": "Tumour",
-      "type": "ENTITY",
-      "start": 556,
-      "end": 562
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 563,
-      "end": 568
-    },
-    {
-      "text": "mucosa",
-      "type": "ENTITY",
-      "start": 598,
-      "end": 604
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 610,
-      "end": 616
-    },
-    {
-      "text": "intestine circumference",
-      "type": "ENTITY",
-      "start": 639,
-      "end": 662
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 694,
-      "end": 702
-    },
-    {
-      "text": "distal incision line",
-      "type": "ENTITY",
-      "start": 738,
-      "end": 758
-    },
-    {
-      "text": "Microscopic description",
-      "type": "ENTITY",
-      "start": 760,
-      "end": 783
-    },
-    {
-      "text": "Adenocarcinoma tubulopapillare",
-      "type": "ENTITY",
-      "start": 785,
-      "end": 815
-    },
-    {
-      "text": "GI",
-      "type": "ENTITY",
-      "start": 817,
-      "end": 819
-    },
-    {
-      "text": "Infiltratio carcinomatosa telae",
-      "type": "ENTITY",
-      "start": 823,
-      "end": 854
-    },
-    {
-      "text": "adiposae",
-      "type": "ENTITY",
-      "start": 855,
-      "end": 863
-    },
-    {
-      "text": "neoplastic lesions",
-      "type": "ENTITY",
-      "start": 901,
-      "end": 919
-    },
-    {
-      "text": "Lymphonodulitis reactiva",
-      "type": "ENTITY",
-      "start": 921,
-      "end": 945
-    },
-    {
-      "text": "NO viII",
-      "type": "ENTITY",
-      "start": 947,
-      "end": 954
-    },
-    {
-      "text": "Histopathological",
-      "type": "ENTITY",
-      "start": 958,
-      "end": 975
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 976,
-      "end": 985
-    },
-    {
-      "text": "Adenocarcinoma tubulopapillare coli",
-      "type": "ENTITY",
-      "start": 987,
-      "end": 1022
-    },
-    {
-      "text": "Tubulopapillar adenocarcinoma",
-      "type": "ENTITY",
-      "start": 1024,
-      "end": 1053
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 1061,
-      "end": 1066
-    },
-    {
-      "text": "GI",
-      "type": "ENTITY",
-      "start": 1069,
-      "end": 1071
-    },
-    {
-      "text": "Dukes B",
-      "type": "ENTITY",
-      "start": 1073,
-      "end": 1080
-    },
-    {
-      "text": "Astler",
-      "type": "ENTITY",
-      "start": 1082,
-      "end": 1088
-    },
-    {
-      "text": "Coller B2",
-      "type": "ENTITY",
-      "start": 1091,
-      "end": 1100
-    },
-    {
-      "text": "pT3",
-      "type": "ENTITY",
-      "start": 1102,
-      "end": 1105
-    },
-    {
-      "text": "pNO",
-      "type": "ENTITY",
-      "start": 1107,
-      "end": 1110
-    },
-    {
-      "text": "Compliance",
-      "type": "ENTITY",
-      "start": 1113,
-      "end": 1123
-    },
-    {
-      "text": "CONTACT YOUR DOCTOR",
-      "type": "ENTITY",
-      "start": 1138,
-      "end": 1157
-    }
-  ],
-  "entity_count": 59,
-  "has_embedding": true
-}

output/biomedbert_output/00b5b8bc-4d91-4e8c-925b-1c6c91430b13_nlp.json

@@ -1,818 +0,0 @@
-{
-  "filename": "00b5b8bc-4d91-4e8c-925b-1c6c91430b13",
-  "timestamp": "2026-01-05T14:41:38.917107",
-  "entities": [
-    {
-      "text": "TCGA-A7-A0C-01A-PR",
-      "type": "ENTITY",
-      "start": 66,
-      "end": 84
-    },
-    {
-      "text": "Carcioma mfiltrstig",
-      "type": "ENTITY",
-      "start": 94,
-      "end": 113
-    },
-    {
-      "text": "oluct",
-      "type": "ENTITY",
-      "start": 114,
-      "end": 119
-    },
-    {
-      "text": "A. Left",
-      "type": "ENTITY",
-      "start": 141,
-      "end": 148
-    },
-    {
-      "text": "Left breast biopsy",
-      "type": "ENTITY",
-      "start": 181,
-      "end": 199
-    },
-    {
-      "text": "NOTES",
-      "type": "ENTITY",
-      "start": 210,
-      "end": 215
-    },
-    {
-      "text": "CLINICAL HISTORY",
-      "type": "ENTITY",
-      "start": 216,
-      "end": 232
-    },
-    {
-      "text": "white",
-      "type": "ENTITY",
-      "start": 246,
-      "end": 251
-    },
-    {
-      "text": "female",
-      "type": "ENTITY",
-      "start": 252,
-      "end": 258
-    },
-    {
-      "text": "left breast cancer",
-      "type": "ENTITY",
-      "start": 264,
-      "end": 282
-    },
-    {
-      "text": "FROZEN SECTION",
-      "type": "ENTITY",
-      "start": 284,
-      "end": 298
-    },
-    {
-      "text": "AFs",
-      "type": "ENTITY",
-      "start": 309,
-      "end": 312
-    },
-    {
-      "text": "Left axillary sentinel node",
-      "type": "ENTITY",
-      "start": 314,
-      "end": 341
-    },
-    {
-      "text": "excision",
-      "type": "ENTITY",
-      "start": 343,
-      "end": 351
-    },
-    {
-      "text": "One lymph node",
-      "type": "ENTITY",
-      "start": 354,
-      "end": 368
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 377,
-      "end": 387
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 388,
-      "end": 398
-    },
-    {
-      "text": "DEscRIpTIon A. Container",
-      "type": "ENTITY",
-      "start": 407,
-      "end": 431
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 437,
-      "end": 444
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 454,
-      "end": 463
-    },
-    {
-      "text": "medical record number",
-      "type": "ENTITY",
-      "start": 470,
-      "end": 491
-    },
-    {
-      "text": "\"left axillary sentinel node",
-      "type": "ENTITY",
-      "start": 496,
-      "end": 524
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 531,
-      "end": 539
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 597,
-      "end": 606
-    },
-    {
-      "text": "AFs",
-      "type": "ENTITY",
-      "start": 625,
-      "end": 628
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 629,
-      "end": 637
-    },
-    {
-      "text": "B. Container B",
-      "type": "ENTITY",
-      "start": 639,
-      "end": 653
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 657,
-      "end": 664
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 674,
-      "end": 683
-    },
-    {
-      "text": "medical record number",
-      "type": "ENTITY",
-      "start": 690,
-      "end": 711
-    },
-    {
-      "text": "long anterior",
-      "type": "ENTITY",
-      "start": 737,
-      "end": 750
-    },
-    {
-      "text": "short superior",
-      "type": "ENTITY",
-      "start": 752,
-      "end": 766
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 773,
-      "end": 781
-    },
-    {
-      "text": "piece",
-      "type": "ENTITY",
-      "start": 803,
-      "end": 808
-    },
-    {
-      "text": "fibrous adipose tissue",
-      "type": "ENTITY",
-      "start": 812,
-      "end": 834
-    },
-    {
-      "text": "sutures",
-      "type": "ENTITY",
-      "start": 851,
-      "end": 858
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 863,
-      "end": 872
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 883,
-      "end": 889
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 893,
-      "end": 900
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 926,
-      "end": 934
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 949,
-      "end": 957
-    },
-    {
-      "text": "posterior",
-      "type": "ENTITY",
-      "start": 961,
-      "end": 970
-    },
-    {
-      "text": "specimen margins",
-      "type": "ENTITY",
-      "start": 976,
-      "end": 992
-    },
-    {
-      "text": "Blue",
-      "type": "ENTITY",
-      "start": 1015,
-      "end": 1019
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 1023,
-      "end": 1031
-    },
-    {
-      "text": "black",
-      "type": "ENTITY",
-      "start": 1033,
-      "end": 1038
-    },
-    {
-      "text": "posterior",
-      "type": "ENTITY",
-      "start": 1042,
-      "end": 1051
-    },
-    {
-      "text": "yellow",
-      "type": "ENTITY",
-      "start": 1053,
-      "end": 1059
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 1063,
-      "end": 1070
-    },
-    {
-      "text": "orange medial",
-      "type": "ENTITY",
-      "start": 1072,
-      "end": 1085
-    },
-    {
-      "text": "red",
-      "type": "ENTITY",
-      "start": 1087,
-      "end": 1090
-    },
-    {
-      "text": "superior",
-      "type": "ENTITY",
-      "start": 1094,
-      "end": 1102
-    },
-    {
-      "text": "green",
-      "type": "ENTITY",
-      "start": 1104,
-      "end": 1109
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 1113,
-      "end": 1121
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1127,
-      "end": 1135
-    },
-    {
-      "text": "cut section",
-      "type": "ENTITY",
-      "start": 1162,
-      "end": 1173
-    },
-    {
-      "text": "tumor mass",
-      "type": "ENTITY",
-      "start": 1214,
-      "end": 1224
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 1225,
-      "end": 1234
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 1259,
-      "end": 1263
-    },
-    {
-      "text": "posterior margin",
-      "type": "ENTITY",
-      "start": 1289,
-      "end": 1305
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 1309,
-      "end": 1318
-    },
-    {
-      "text": "portion",
-      "type": "ENTITY",
-      "start": 1322,
-      "end": 1329
-    },
-    {
-      "text": "tissue procurement",
-      "type": "ENTITY",
-      "start": 1347,
-      "end": 1365
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 1388,
-      "end": 1394
-    },
-    {
-      "text": "blocks",
-      "type": "ENTITY",
-      "start": 1411,
-      "end": 1417
-    },
-    {
-      "text": "A. Sections",
-      "type": "ENTITY",
-      "start": 1448,
-      "end": 1459
-    },
-    {
-      "text": "left axillary sentinel lymph node",
-      "type": "ENTITY",
-      "start": 1467,
-      "end": 1500
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 1515,
-      "end": 1525
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 1534,
-      "end": 1542
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 1546,
-      "end": 1556
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 1562,
-      "end": 1572
-    },
-    {
-      "text": "multilevel",
-      "type": "ENTITY",
-      "start": 1590,
-      "end": 1600
-    },
-    {
-      "text": "sectioning",
-      "type": "ENTITY",
-      "start": 1601,
-      "end": 1611
-    },
-    {
-      "text": "H&E stain",
-      "type": "ENTITY",
-      "start": 1617,
-      "end": 1626
-    },
-    {
-      "text": "immunohistochemistry",
-      "type": "ENTITY",
-      "start": 1638,
-      "end": 1658
-    },
-    {
-      "text": "pankeratin",
-      "type": "ENTITY",
-      "start": 1663,
-      "end": 1673
-    },
-    {
-      "text": "template",
-      "type": "ENTITY",
-      "start": 1692,
-      "end": 1700
-    },
-    {
-      "text": "left breast biopsy",
-      "type": "ENTITY",
-      "start": 1716,
-      "end": 1734
-    },
-    {
-      "text": "Invasive Carcinoma",
-      "type": "ENTITY",
-      "start": 1736,
-      "end": 1754
-    },
-    {
-      "text": "Histologic type",
-      "type": "ENTITY",
-      "start": 1765,
-      "end": 1780
-    },
-    {
-      "text": "Infiltrating ductal carcinoma",
-      "type": "ENTITY",
-      "start": 1782,
-      "end": 1811
-    },
-    {
-      "text": "Histologic grade",
-      "type": "ENTITY",
-      "start": 1812,
-      "end": 1828
-    },
-    {
-      "text": "Overall grade",
-      "type": "ENTITY",
-      "start": 1830,
-      "end": 1843
-    },
-    {
-      "text": "Architectural score",
-      "type": "ENTITY",
-      "start": 1847,
-      "end": 1866
-    },
-    {
-      "text": "Nuclear score",
-      "type": "ENTITY",
-      "start": 1870,
-      "end": 1883
-    },
-    {
-      "text": "Mitotic score",
-      "type": "ENTITY",
-      "start": 1887,
-      "end": 1900
-    },
-    {
-      "text": "dimension",
-      "type": "ENTITY",
-      "start": 1929,
-      "end": 1938
-    },
-    {
-      "text": "Specimen margins",
-      "type": "ENTITY",
-      "start": 1959,
-      "end": 1975
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 1977,
-      "end": 1985
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1987,
-      "end": 2005
-    },
-    {
-      "text": "green ink",
-      "type": "ENTITY",
-      "start": 2022,
-      "end": 2031
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 2047,
-      "end": 2062
-    },
-    {
-      "text": "Vessel",
-      "type": "ENTITY",
-      "start": 2064,
-      "end": 2070
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 2071,
-      "end": 2079
-    },
-    {
-      "text": "Calcification",
-      "type": "ENTITY",
-      "start": 2098,
-      "end": 2111
-    },
-    {
-      "text": "Ductal carcinoma",
-      "type": "ENTITY",
-      "start": 2121,
-      "end": 2137
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 2138,
-      "end": 2145
-    },
-    {
-      "text": "Histologic pattern",
-      "type": "ENTITY",
-      "start": 2156,
-      "end": 2174
-    },
-    {
-      "text": "Solid",
-      "type": "ENTITY",
-      "start": 2176,
-      "end": 2181
-    },
-    {
-      "text": "cribriform",
-      "type": "ENTITY",
-      "start": 2186,
-      "end": 2196
-    },
-    {
-      "text": "Nuclear grade",
-      "type": "ENTITY",
-      "start": 2198,
-      "end": 2211
-    },
-    {
-      "text": "Central necrosis",
-      "type": "ENTITY",
-      "start": 2217,
-      "end": 2233
-    },
-    {
-      "text": "Focally",
-      "type": "ENTITY",
-      "start": 2235,
-      "end": 2242
-    },
-    {
-      "text": "Specimen margins",
-      "type": "ENTITY",
-      "start": 2336,
-      "end": 2352
-    },
-    {
-      "text": "Close",
-      "type": "ENTITY",
-      "start": 2354,
-      "end": 2359
-    },
-    {
-      "text": "In situ carcinoma",
-      "type": "ENTITY",
-      "start": 2361,
-      "end": 2378
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 2406,
-      "end": 2414
-    },
-    {
-      "text": "posterior",
-      "type": "ENTITY",
-      "start": 2416,
-      "end": 2425
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 2427,
-      "end": 2433
-    },
-    {
-      "text": "inferior margins",
-      "type": "ENTITY",
-      "start": 2438,
-      "end": 2454
-    },
-    {
-      "text": "Calcification",
-      "type": "ENTITY",
-      "start": 2456,
-      "end": 2469
-    },
-    {
-      "text": "Description",
-      "type": "ENTITY",
-      "start": 2479,
-      "end": 2490
-    },
-    {
-      "text": "non-tumorous breast",
-      "type": "ENTITY",
-      "start": 2494,
-      "end": 2513
-    },
-    {
-      "text": "Proliferative changes",
-      "type": "ENTITY",
-      "start": 2515,
-      "end": 2536
-    },
-    {
-      "text": "Comments",
-      "type": "ENTITY",
-      "start": 2539,
-      "end": 2547
-    },
-    {
-      "text": "Prognostic",
-      "type": "ENTITY",
-      "start": 2579,
-      "end": 2589
-    },
-    {
-      "text": "markers",
-      "type": "ENTITY",
-      "start": 2590,
-      "end": 2597
-    },
-    {
-      "text": "DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 2630,
-      "end": 2639
-    },
-    {
-      "text": "A. Left",
-      "type": "ENTITY",
-      "start": 2640,
-      "end": 2647
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 2678,
-      "end": 2687
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 2693,
-      "end": 2701
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 2705,
-      "end": 2715
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 2723,
-      "end": 2733
-    },
-    {
-      "text": "B. Left breast",
-      "type": "ENTITY",
-      "start": 2742,
-      "end": 2756
-    },
-    {
-      "text": "excisional biopsy",
-      "type": "ENTITY",
-      "start": 2758,
-      "end": 2775
-    },
-    {
-      "text": "Infiltrating ductal carcinoma",
-      "type": "ENTITY",
-      "start": 2778,
-      "end": 2807
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 2843,
-      "end": 2858
-    },
-    {
-      "text": "ductal carcinoma",
-      "type": "ENTITY",
-      "start": 2870,
-      "end": 2886
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 2887,
-      "end": 2894
-    },
-    {
-      "text": "solid",
-      "type": "ENTITY",
-      "start": 2896,
-      "end": 2901
-    },
-    {
-      "text": "cribriforming",
-      "type": "ENTITY",
-      "start": 2906,
-      "end": 2919
-    },
-    {
-      "text": "subtypes",
-      "type": "ENTITY",
-      "start": 2921,
-      "end": 2929
-    },
-    {
-      "text": "nuclear grade 2-3",
-      "type": "ENTITY",
-      "start": 2931,
-      "end": 2948
-    },
-    {
-      "text": "multiple margins",
-      "type": "ENTITY",
-      "start": 2970,
-      "end": 2986
-    },
-    {
-      "text": "Electronic Signature",
-      "type": "ENTITY",
-      "start": 2994,
-      "end": 3014
-    }
-  ],
-  "entity_count": 135,
-  "has_embedding": true
-}

output/biomedbert_output/00c0279c-c926-4899-909f-b1c77798e3fa_nlp.json

@@ -1,1892 +0,0 @@
-{
-  "filename": "00c0279c-c926-4899-909f-b1c77798e3fa",
-  "timestamp": "2026-01-05T14:45:21.999890",
-  "entities": [
-    {
-      "text": "right colon mass",
-      "type": "ENTITY",
-      "start": 21,
-      "end": 37
-    },
-    {
-      "text": "Specimens",
-      "type": "ENTITY",
-      "start": 42,
-      "end": 51
-    },
-    {
-      "text": "Sp",
-      "type": "ENTITY",
-      "start": 66,
-      "end": 68
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 77,
-      "end": 82
-    },
-    {
-      "text": "hemicolectomy",
-      "type": "ENTITY",
-      "start": 84,
-      "end": 97
-    },
-    {
-      "text": "DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 99,
-      "end": 108
-    },
-    {
-      "text": "Colon",
-      "type": "ENTITY",
-      "start": 117,
-      "end": 122
-    },
-    {
-      "text": "hemicolectomy",
-      "type": "ENTITY",
-      "start": 131,
-      "end": 144
-    },
-    {
-      "text": "Tumor Type",
-      "type": "ENTITY",
-      "start": 146,
-      "end": 156
-    },
-    {
-      "text": "Adenocarcinoma",
-      "type": "ENTITY",
-      "start": 158,
-      "end": 172
-    },
-    {
-      "text": "Histologic Grade",
-      "type": "ENTITY",
-      "start": 173,
-      "end": 189
-    },
-    {
-      "text": "Tumox",
-      "type": "ENTITY",
-      "start": 217,
-      "end": 222
-    },
-    {
-      "text": "Location",
-      "type": "ENTITY",
-      "start": 223,
-      "end": 231
-    },
-    {
-      "text": "Ascending colon",
-      "type": "ENTITY",
-      "start": 233,
-      "end": 248
-    },
-    {
-      "text": "Tumor Size",
-      "type": "ENTITY",
-      "start": 249,
-      "end": 259
-    },
-    {
-      "text": "Length",
-      "type": "ENTITY",
-      "start": 261,
-      "end": 267
-    },
-    {
-      "text": "width",
-      "type": "ENTITY",
-      "start": 278,
-      "end": 283
-    },
-    {
-      "text": "Tumor Budding",
-      "type": "ENTITY",
-      "start": 294,
-      "end": 307
-    },
-    {
-      "text": "Absent",
-      "type": "ENTITY",
-      "start": 309,
-      "end": 315
-    },
-    {
-      "text": "Increased",
-      "type": "ENTITY",
-      "start": 316,
-      "end": 325
-    },
-    {
-      "text": "Tumor Infiltrating",
-      "type": "ENTITY",
-      "start": 326,
-      "end": 344
-    },
-    {
-      "text": "Lymphocytes",
-      "type": "ENTITY",
-      "start": 345,
-      "end": 356
-    },
-    {
-      "text": "Absent Precursor Leslone",
-      "type": "ENTITY",
-      "start": 358,
-      "end": 382
-    },
-    {
-      "text": "Tumor Invasion",
-      "type": "ENTITY",
-      "start": 407,
-      "end": 421
-    },
-    {
-      "text": "Subserosal adipose tissue",
-      "type": "ENTITY",
-      "start": 423,
-      "end": 448
-    },
-    {
-      "text": "mesentexic fat",
-      "type": "ENTITY",
-      "start": 456,
-      "end": 470
-    },
-    {
-      "text": "Perforation",
-      "type": "ENTITY",
-      "start": 483,
-      "end": 494
-    },
-    {
-      "text": "Lymphovascular Invasion",
-      "type": "ENTITY",
-      "start": 511,
-      "end": 534
-    },
-    {
-      "text": "Identified",
-      "type": "ENTITY",
-      "start": 536,
-      "end": 546
-    },
-    {
-      "text": "Venous Invaslon",
-      "type": "ENTITY",
-      "start": 553,
-      "end": 568
-    },
-    {
-      "text": "Perineuxal Invasion",
-      "type": "ENTITY",
-      "start": 585,
-      "end": 604
-    },
-    {
-      "text": "Surgical Margins",
-      "type": "ENTITY",
-      "start": 621,
-      "end": 637
-    },
-    {
-      "text": "Free of",
-      "type": "ENTITY",
-      "start": 639,
-      "end": 646
-    },
-    {
-      "text": "Dysplasia",
-      "type": "ENTITY",
-      "start": 667,
-      "end": 676
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 692,
-      "end": 701
-    },
-    {
-      "text": "Tubular adenoma",
-      "type": "ENTITY",
-      "start": 704,
-      "end": 719
-    },
-    {
-      "text": "Hyperplastic polyp",
-      "type": "ENTITY",
-      "start": 731,
-      "end": 749
-    },
-    {
-      "text": "Non-Neoplastic Bowel",
-      "type": "ENTITY",
-      "start": 761,
-      "end": 781
-    },
-    {
-      "text": "Unremarkable",
-      "type": "ENTITY",
-      "start": 783,
-      "end": 795
-    },
-    {
-      "text": "Appendix Fibrous obliteration",
-      "type": "ENTITY",
-      "start": 850,
-      "end": 879
-    },
-    {
-      "text": "lumen",
-      "type": "ENTITY",
-      "start": 887,
-      "end": 892
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 893,
-      "end": 904
-    },
-    {
-      "text": "Number",
-      "type": "ENTITY",
-      "start": 906,
-      "end": 912
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 918,
-      "end": 928
-    },
-    {
-      "text": "Tumor deposits",
-      "type": "ENTITY",
-      "start": 959,
-      "end": 973
-    },
-    {
-      "text": "pericolorectal",
-      "type": "ENTITY",
-      "start": 977,
-      "end": 991
-    },
-    {
-      "text": "soft tissue",
-      "type": "ENTITY",
-      "start": 992,
-      "end": 1003
-    },
-    {
-      "text": "Identieied Tumor Staging",
-      "type": "ENTITY",
-      "start": 1005,
-      "end": 1029
-    },
-    {
-      "text": "pT3",
-      "type": "ENTITY",
-      "start": 1049,
-      "end": 1052
-    },
-    {
-      "text": "Tumor",
-      "type": "ENTITY",
-      "start": 1054,
-      "end": 1059
-    },
-    {
-      "text": "muscularis propria",
-      "type": "ENTITY",
-      "start": 1080,
-      "end": 1098
-    },
-    {
-      "text": "pexicolorectal tissues",
-      "type": "ENTITY",
-      "start": 1104,
-      "end": 1126
-    },
-    {
-      "text": "Lymph Node Stage",
-      "type": "ENTITY",
-      "start": 1128,
-      "end": 1144
-    },
-    {
-      "text": "N1",
-      "type": "ENTITY",
-      "start": 1165,
-      "end": 1167
-    },
-    {
-      "text": "Metastasig",
-      "type": "ENTITY",
-      "start": 1169,
-      "end": 1179
-    },
-    {
-      "text": "regional lymph nodes",
-      "type": "ENTITY",
-      "start": 1187,
-      "end": 1207
-    },
-    {
-      "text": "K-RAS",
-      "type": "ENTITY",
-      "start": 1217,
-      "end": 1222
-    },
-    {
-      "text": "ATTEST",
-      "type": "ENTITY",
-      "start": 1226,
-      "end": 1232
-    },
-    {
-      "text": "ABOVE DIAGNOSIS IS",
-      "type": "ENTITY",
-      "start": 1242,
-      "end": 1260
-    },
-    {
-      "text": "THAT I",
-      "type": "ENTITY",
-      "start": 1339,
-      "end": 1345
-    },
-    {
-      "text": "KRAS",
-      "type": "ENTITY",
-      "start": 1415,
-      "end": 1419
-    },
-    {
-      "text": "Gross Description",
-      "type": "ENTITY",
-      "start": 1420,
-      "end": 1437
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1446,
-      "end": 1454
-    },
-    {
-      "text": "freah",
-      "type": "ENTITY",
-      "start": 1467,
-      "end": 1472
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 1474,
-      "end": 1481
-    },
-    {
-      "text": "Right hemicolectomy colon'",
-      "type": "ENTITY",
-      "start": 1483,
-      "end": 1509
-    },
-    {
-      "text": "segment",
-      "type": "ENTITY",
-      "start": 1528,
-      "end": 1535
-    },
-    {
-      "text": "terminal",
-      "type": "ENTITY",
-      "start": 1539,
-      "end": 1547
-    },
-    {
-      "text": "ileun",
-      "type": "ENTITY",
-      "start": 1548,
-      "end": 1553
-    },
-    {
-      "text": "cecum",
-      "type": "ENTITY",
-      "start": 1555,
-      "end": 1560
-    },
-    {
-      "text": "appendix",
-      "type": "ENTITY",
-      "start": 1575,
-      "end": 1583
-    },
-    {
-      "text": "ascending colon",
-      "type": "ENTITY",
-      "start": 1589,
-      "end": 1604
-    },
-    {
-      "text": "terminal",
-      "type": "ENTITY",
-      "start": 1610,
-      "end": 1618
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 1619,
-      "end": 1624
-    },
-    {
-      "text": "measuxes",
-      "type": "ENTITY",
-      "start": 1625,
-      "end": 1633
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 1644,
-      "end": 1650
-    },
-    {
-      "text": "circumference",
-      "type": "ENTITY",
-      "start": 1665,
-      "end": 1678
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 1686,
-      "end": 1694
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 1727,
-      "end": 1732
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 1733,
-      "end": 1741
-    },
-    {
-      "text": "length with",
-      "type": "ENTITY",
-      "start": 1749,
-      "end": 1760
-    },
-    {
-      "text": "circumference",
-      "type": "ENTITY",
-      "start": 1763,
-      "end": 1776
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 1792,
-      "end": 1798
-    },
-    {
-      "text": "appendix",
-      "type": "ENTITY",
-      "start": 1829,
-      "end": 1837
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 1838,
-      "end": 1846
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 1857,
-      "end": 1863
-    },
-    {
-      "text": "averages",
-      "type": "ENTITY",
-      "start": 1868,
-      "end": 1876
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 1888,
-      "end": 1896
-    },
-    {
-      "text": "appendiceal",
-      "type": "ENTITY",
-      "start": 1902,
-      "end": 1913
-    },
-    {
-      "text": "intestinal serosa",
-      "type": "ENTITY",
-      "start": 1918,
-      "end": 1935
-    },
-    {
-      "text": "pink tan",
-      "type": "ENTITY",
-      "start": 1939,
-      "end": 1947
-    },
-    {
-      "text": "smooth",
-      "type": "ENTITY",
-      "start": 1952,
-      "end": 1958
-    },
-    {
-      "text": "Focally hemorrhagic lobulated yellow tan adipose tissue",
-      "type": "ENTITY",
-      "start": 1961,
-      "end": 2016
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 2027,
-      "end": 2033
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2041,
-      "end": 2049
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2050,
-      "end": 2059
-    },
-    {
-      "text": "thickness",
-      "type": "ENTITY",
-      "start": 2075,
-      "end": 2084
-    },
-    {
-      "text": "gpecimen",
-      "type": "ENTITY",
-      "start": 2090,
-      "end": 2098
-    },
-    {
-      "text": "circumferential",
-      "type": "ENTITY",
-      "start": 2122,
-      "end": 2137
-    },
-    {
-      "text": "centrally ulcerative",
-      "type": "ENTITY",
-      "start": 2139,
-      "end": 2159
-    },
-    {
-      "text": "fungating",
-      "type": "ENTITY",
-      "start": 2161,
-      "end": 2170
-    },
-    {
-      "text": "brown tan tumor",
-      "type": "ENTITY",
-      "start": 2172,
-      "end": 2187
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2188,
-      "end": 2197
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 2208,
-      "end": 2214
-    },
-    {
-      "text": "width",
-      "type": "ENTITY",
-      "start": 2226,
-      "end": 2231
-    },
-    {
-      "text": "height",
-      "type": "ENTITY",
-      "start": 2247,
-      "end": 2253
-    },
-    {
-      "text": "cut section",
-      "type": "ENTITY",
-      "start": 2258,
-      "end": 2269
-    },
-    {
-      "text": "tunox",
-      "type": "ENTITY",
-      "start": 2277,
-      "end": 2282
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 2287,
-      "end": 2295
-    },
-    {
-      "text": "maximun depth",
-      "type": "ENTITY",
-      "start": 2306,
-      "end": 2319
-    },
-    {
-      "text": "abuts",
-      "type": "ENTITY",
-      "start": 2324,
-      "end": 2329
-    },
-    {
-      "text": "black inked radial margin",
-      "type": "ENTITY",
-      "start": 2335,
-      "end": 2360
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2368,
-      "end": 2373
-    },
-    {
-      "text": "ileocecal valve",
-      "type": "ENTITY",
-      "start": 2401,
-      "end": 2416
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 2435,
-      "end": 2441
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 2464,
-      "end": 2474
-    },
-    {
-      "text": "ileocecal valve",
-      "type": "ENTITY",
-      "start": 2493,
-      "end": 2508
-    },
-    {
-      "text": "tumor mass",
-      "type": "ENTITY",
-      "start": 2534,
-      "end": 2544
-    },
-    {
-      "text": "brown-tan polypoid structure",
-      "type": "ENTITY",
-      "start": 2557,
-      "end": 2585
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2586,
-      "end": 2595
-    },
-    {
-      "text": "mucosa",
-      "type": "ENTITY",
-      "start": 2631,
-      "end": 2637
-    },
-    {
-      "text": "brown-tan folded",
-      "type": "ENTITY",
-      "start": 2644,
-      "end": 2660
-    },
-    {
-      "text": "appearance",
-      "type": "ENTITY",
-      "start": 2661,
-      "end": 2671
-    },
-    {
-      "text": "polypoid areas",
-      "type": "ENTITY",
-      "start": 2684,
-      "end": 2698
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2699,
-      "end": 2708
-    },
-    {
-      "text": "dimensions",
-      "type": "ENTITY",
-      "start": 2740,
-      "end": 2750
-    },
-    {
-      "text": "Submitted",
-      "type": "ENTITY",
-      "start": 2771,
-      "end": 2780
-    },
-    {
-      "text": "apecimen",
-      "type": "ENTITY",
-      "start": 2786,
-      "end": 2794
-    },
-    {
-      "text": "fox lymph node dissection",
-      "type": "ENTITY",
-      "start": 2808,
-      "end": 2833
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 2848,
-      "end": 2862
-    },
-    {
-      "text": "examined",
-      "type": "ENTITY",
-      "start": 2877,
-      "end": 2885
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 2894,
-      "end": 2904
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2905,
-      "end": 2916
-    },
-    {
-      "text": "aubmitted",
-      "type": "ENTITY",
-      "start": 2921,
-      "end": 2930
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 2932,
-      "end": 2955
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2963,
-      "end": 2971
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 3042,
-      "end": 3050
-    },
-    {
-      "text": "PM",
-      "type": "ENTITY",
-      "start": 3052,
-      "end": 3054
-    },
-    {
-      "text": "proximal",
-      "type": "ENTITY",
-      "start": 3057,
-      "end": 3065
-    },
-    {
-      "text": "margin shave",
-      "type": "ENTITY",
-      "start": 3066,
-      "end": 3078
-    },
-    {
-      "text": "DM",
-      "type": "ENTITY",
-      "start": 3079,
-      "end": 3081
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 3084,
-      "end": 3090
-    },
-    {
-      "text": "margin shave T",
-      "type": "ENTITY",
-      "start": 3091,
-      "end": 3105
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 3108,
-      "end": 3113
-    },
-    {
-      "text": "full-thickness",
-      "type": "ENTITY",
-      "start": 3144,
-      "end": 3158
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 3170,
-      "end": 3175
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 3201,
-      "end": 3211
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 3213,
-      "end": 3221
-    },
-    {
-      "text": "APP",
-      "type": "ENTITY",
-      "start": 3223,
-      "end": 3226
-    },
-    {
-      "text": "appendix",
-      "type": "ENTITY",
-      "start": 3229,
-      "end": 3237
-    },
-    {
-      "text": "representative",
-      "type": "ENTITY",
-      "start": 3238,
-      "end": 3252
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 3253,
-      "end": 3261
-    },
-    {
-      "text": "RS",
-      "type": "ENTITY",
-      "start": 3262,
-      "end": 3264
-    },
-    {
-      "text": "LN",
-      "type": "ENTITY",
-      "start": 3290,
-      "end": 3292
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 3295,
-      "end": 3306
-    },
-    {
-      "text": "LPOL-largest polypoid",
-      "type": "ENTITY",
-      "start": 3307,
-      "end": 3328
-    },
-    {
-      "text": "POL-polypoid",
-      "type": "ENTITY",
-      "start": 3334,
-      "end": 3346
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 3364,
-      "end": 3372
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 3382,
-      "end": 3384
-    },
-    {
-      "text": "Colon",
-      "type": "ENTITY",
-      "start": 3386,
-      "end": 3391
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 3393,
-      "end": 3398
-    },
-    {
-      "text": "hemic ectomy",
-      "type": "ENTITY",
-      "start": 3400,
-      "end": 3412
-    },
-    {
-      "text": "Block Sect",
-      "type": "ENTITY",
-      "start": 3413,
-      "end": 3423
-    },
-    {
-      "text": "Report",
-      "type": "ENTITY",
-      "start": 3495,
-      "end": 3501
-    },
-    {
-      "text": "DM",
-      "type": "ENTITY",
-      "start": 3547,
-      "end": 3549
-    },
-    {
-      "text": "UNSTAINED SLIDES",
-      "type": "ENTITY",
-      "start": 3563,
-      "end": 3579
-    },
-    {
-      "text": "H&E",
-      "type": "ENTITY",
-      "start": 3586,
-      "end": 3589
-    },
-    {
-      "text": "RIGHT COLON Test",
-      "type": "ENTITY",
-      "start": 3591,
-      "end": 3607
-    },
-    {
-      "text": "KRAs",
-      "type": "ENTITY",
-      "start": 3620,
-      "end": 3624
-    },
-    {
-      "text": "Gene Exon 2 mutation analyais",
-      "type": "ENTITY",
-      "start": 3625,
-      "end": 3654
-    },
-    {
-      "text": "codons",
-      "type": "ENTITY",
-      "start": 3656,
-      "end": 3662
-    },
-    {
-      "text": "DNA quality",
-      "type": "ENTITY",
-      "start": 3674,
-      "end": 3685
-    },
-    {
-      "text": "Methodology",
-      "type": "ENTITY",
-      "start": 3693,
-      "end": 3704
-    },
-    {
-      "text": "PCR",
-      "type": "ENTITY",
-      "start": 3706,
-      "end": 3709
-    },
-    {
-      "text": "exon 2",
-      "type": "ENTITY",
-      "start": 3735,
-      "end": 3741
-    },
-    {
-      "text": "KRAs",
-      "type": "ENTITY",
-      "start": 3749,
-      "end": 3753
-    },
-    {
-      "text": "gene",
-      "type": "ENTITY",
-      "start": 3754,
-      "end": 3758
-    },
-    {
-      "text": "genomic DNA",
-      "type": "ENTITY",
-      "start": 3764,
-      "end": 3775
-    },
-    {
-      "text": "pcr product",
-      "type": "ENTITY",
-      "start": 3816,
-      "end": 3827
-    },
-    {
-      "text": "analyzed",
-      "type": "ENTITY",
-      "start": 3832,
-      "end": 3840
-    },
-    {
-      "text": "ABI DIAGNOSTIC",
-      "type": "ENTITY",
-      "start": 3847,
-      "end": 3861
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 3878,
-      "end": 3886
-    },
-    {
-      "text": "KRAs",
-      "type": "ENTITY",
-      "start": 3891,
-      "end": 3895
-    },
-    {
-      "text": "exon 2 mutation",
-      "type": "ENTITY",
-      "start": 3896,
-      "end": 3911
-    },
-    {
-      "text": "Technical",
-      "type": "ENTITY",
-      "start": 3914,
-      "end": 3923
-    },
-    {
-      "text": "sensitivity",
-      "type": "ENTITY",
-      "start": 3924,
-      "end": 3935
-    },
-    {
-      "text": "asaay'cannot detect",
-      "type": "ENTITY",
-      "start": 3942,
-      "end": 3961
-    },
-    {
-      "text": "exon 2 mutation",
-      "type": "ENTITY",
-      "start": 3969,
-      "end": 3984
-    },
-    {
-      "text": "proportion",
-      "type": "ENTITY",
-      "start": 3992,
-      "end": 4002
-    },
-    {
-      "text": "tumor cells",
-      "type": "ENTITY",
-      "start": 4006,
-      "end": 4017
-    },
-    {
-      "text": "sample",
-      "type": "ENTITY",
-      "start": 4025,
-      "end": 4031
-    },
-    {
-      "text": "result",
-      "type": "ENTITY",
-      "start": 4066,
-      "end": 4072
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 4096,
-      "end": 4104
-    },
-    {
-      "text": "cancer",
-      "type": "ENTITY",
-      "start": 4120,
-      "end": 4126
-    },
-    {
-      "text": "interpreted",
-      "type": "ENTITY",
-      "start": 4141,
-      "end": 4152
-    },
-    {
-      "text": "context",
-      "type": "ENTITY",
-      "start": 4160,
-      "end": 4167
-    },
-    {
-      "text": "clinical",
-      "type": "ENTITY",
-      "start": 4185,
-      "end": 4193
-    },
-    {
-      "text": "pathological",
-      "type": "ENTITY",
-      "start": 4198,
-      "end": 4210
-    },
-    {
-      "text": "information",
-      "type": "ENTITY",
-      "start": 4211,
-      "end": 4222
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 4232,
-      "end": 4236
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 4259,
-      "end": 4270
-    },
-    {
-      "text": "characteristics",
-      "type": "ENTITY",
-      "start": 4271,
-      "end": 4286
-    },
-    {
-      "text": "Laboratory",
-      "type": "ENTITY",
-      "start": 4305,
-      "end": 4315
-    },
-    {
-      "text": "cleared",
-      "type": "ENTITY",
-      "start": 4367,
-      "end": 4374
-    },
-    {
-      "text": "U.S.",
-      "type": "ENTITY",
-      "start": 4395,
-      "end": 4399
-    },
-    {
-      "text": "Fba",
-      "type": "ENTITY",
-      "start": 4431,
-      "end": 4434
-    },
-    {
-      "text": "FDa",
-      "type": "ENTITY",
-      "start": 4441,
-      "end": 4444
-    },
-    {
-      "text": "clearance",
-      "type": "ENTITY",
-      "start": 4470,
-      "end": 4479
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 4503,
-      "end": 4507
-    },
-    {
-      "text": "clinical purposes",
-      "type": "ENTITY",
-      "start": 4520,
-      "end": 4537
-    },
-    {
-      "text": "Pursuant",
-      "type": "ENTITY",
-      "start": 4540,
-      "end": 4548
-    },
-    {
-      "text": "requirements",
-      "type": "ENTITY",
-      "start": 4556,
-      "end": 4568
-    },
-    {
-      "text": "CLia",
-      "type": "ENTITY",
-      "start": 4572,
-      "end": 4576
-    },
-    {
-      "text": "laboratory",
-      "type": "ENTITY",
-      "start": 4588,
-      "end": 4598
-    },
-    {
-      "text": "accuracy",
-      "type": "ENTITY",
-      "start": 4619,
-      "end": 4627
-    },
-    {
-      "text": "precision",
-      "type": "ENTITY",
-      "start": 4632,
-      "end": 4641
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 4650,
-      "end": 4654
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 4661,
-      "end": 4665
-    },
-    {
-      "text": "laboratory",
-      "type": "ENTITY",
-      "start": 4692,
-      "end": 4702
-    },
-    {
-      "text": "ATTEST",
-      "type": "ENTITY",
-      "start": 4722,
-      "end": 4728
-    },
-    {
-      "text": "DIAGNOSTS",
-      "type": "ENTITY",
-      "start": 4744,
-      "end": 4753
-    },
-    {
-      "text": "IS",
-      "type": "ENTITY",
-      "start": 4754,
-      "end": 4756
-    },
-    {
-      "text": "THAT I",
-      "type": "ENTITY",
-      "start": 4893,
-      "end": 4899
-    },
-    {
-      "text": "Date",
-      "type": "ENTITY",
-      "start": 4998,
-      "end": 5002
-    },
-    {
-      "text": "Reported",
-      "type": "ENTITY",
-      "start": 5003,
-      "end": 5011
-    },
-    {
-      "text": "Diagnosis",
-      "type": "ENTITY",
-      "start": 5021,
-      "end": 5030
-    },
-    {
-      "text": "THESE MOTATIONS",
-      "type": "ENTITY",
-      "start": 5039,
-      "end": 5054
-    },
-    {
-      "text": "CLINICAL PANEL Gene",
-      "type": "ENTITY",
-      "start": 5083,
-      "end": 5102
-    },
-    {
-      "text": "Codon BRAF V600 EGFR L858",
-      "type": "ENTITY",
-      "start": 5103,
-      "end": 5128
-    },
-    {
-      "text": "Codon Gene",
-      "type": "ENTITY",
-      "start": 5156,
-      "end": 5166
-    },
-    {
-      "text": "Codon Gene",
-      "type": "ENTITY",
-      "start": 5167,
-      "end": 5177
-    },
-    {
-      "text": "Codon AKT1",
-      "type": "ENTITY",
-      "start": 5178,
-      "end": 5188
-    },
-    {
-      "text": "BRAF G469",
-      "type": "ENTITY",
-      "start": 5212,
-      "end": 5221
-    },
-    {
-      "text": "ERBB2",
-      "type": "ENTITY",
-      "start": 5222,
-      "end": 5227
-    },
-    {
-      "text": "L755 NRAS G13 BRAF D594 ERBB2",
-      "type": "ENTITY",
-      "start": 5228,
-      "end": 5257
-    },
-    {
-      "text": "Q61 EGFR",
-      "type": "ENTITY",
-      "start": 5268,
-      "end": 5276
-    },
-    {
-      "text": "ERBB2",
-      "type": "ENTITY",
-      "start": 5282,
-      "end": 5287
-    },
-    {
-      "text": "PIK3CA R88 EGFR G719",
-      "type": "ENTITY",
-      "start": 5293,
-      "end": 5313
-    },
-    {
-      "text": "KRAS",
-      "type": "ENTITY",
-      "start": 5314,
-      "end": 5318
-    },
-    {
-      "text": "Q61 PIK3CA N345 EGFR D761 KRAS K117 PIK3CA C420 EGFR S768 KRAS A146 PIK3CA E542 EGFR R776",
-      "type": "ENTITY",
-      "start": 5319,
-      "end": 5408
-    },
-    {
-      "text": "MEKL",
-      "type": "ENTITY",
-      "start": 5409,
-      "end": 5413
-    },
-    {
-      "text": "Q56 PIK3CA E545 EGFR T790",
-      "type": "ENTITY",
-      "start": 5414,
-      "end": 5439
-    },
-    {
-      "text": "MEK1",
-      "type": "ENTITY",
-      "start": 5440,
-      "end": 5444
-    },
-    {
-      "text": "K57 PIK3CA",
-      "type": "ENTITY",
-      "start": 5445,
-      "end": 5455
-    },
-    {
-      "text": "EGFR",
-      "type": "ENTITY",
-      "start": 5462,
-      "end": 5466
-    },
-    {
-      "text": "T854",
-      "type": "ENTITY",
-      "start": 5467,
-      "end": 5471
-    },
-    {
-      "text": "MEKL",
-      "type": "ENTITY",
-      "start": 5472,
-      "end": 5476
-    },
-    {
-      "text": "PIK3CA H1047",
-      "type": "ENTITY",
-      "start": 5481,
-      "end": 5493
-    },
-    {
-      "text": "Diagnoatic sensitivity",
-      "type": "ENTITY",
-      "start": 5494,
-      "end": 5516
-    },
-    {
-      "text": "finding",
-      "type": "ENTITY",
-      "start": 5523,
-      "end": 5530
-    },
-    {
-      "text": "poasibility",
-      "type": "ENTITY",
-      "start": 5552,
-      "end": 5563
-    },
-    {
-      "text": "mutations",
-      "type": "ENTITY",
-      "start": 5573,
-      "end": 5582
-    },
-    {
-      "text": "Technical",
-      "type": "ENTITY",
-      "start": 5584,
-      "end": 5593
-    },
-    {
-      "text": "sensitivity",
-      "type": "ENTITY",
-      "start": 5594,
-      "end": 5605
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 5612,
-      "end": 5616
-    },
-    {
-      "text": "detect",
-      "type": "ENTITY",
-      "start": 5625,
-      "end": 5631
-    },
-    {
-      "text": "mutations",
-      "type": "ENTITY",
-      "start": 5640,
-      "end": 5649
-    },
-    {
-      "text": "proportion",
-      "type": "ENTITY",
-      "start": 5657,
-      "end": 5667
-    },
-    {
-      "text": "tunor cells",
-      "type": "ENTITY",
-      "start": 5671,
-      "end": 5682
-    },
-    {
-      "text": "sample",
-      "type": "ENTITY",
-      "start": 5690,
-      "end": 5696
-    },
-    {
-      "text": "Sequenom masa-spectrometry",
-      "type": "ENTITY",
-      "start": 5741,
-      "end": 5767
-    },
-    {
-      "text": "genotyping",
-      "type": "ENTITY",
-      "start": 5768,
-      "end": 5778
-    },
-    {
-      "text": "mutations",
-      "type": "ENTITY",
-      "start": 5792,
-      "end": 5801
-    },
-    {
-      "text": "genes",
-      "type": "ENTITY",
-      "start": 5807,
-      "end": 5812
-    },
-    {
-      "text": "AKT1",
-      "type": "ENTITY",
-      "start": 5815,
-      "end": 5819
-    },
-    {
-      "text": "BRAF",
-      "type": "ENTITY",
-      "start": 5821,
-      "end": 5825
-    },
-    {
-      "text": "EGFR",
-      "type": "ENTITY",
-      "start": 5827,
-      "end": 5831
-    },
-    {
-      "text": "ERBB2",
-      "type": "ENTITY",
-      "start": 5833,
-      "end": 5838
-    },
-    {
-      "text": "KRAS",
-      "type": "ENTITY",
-      "start": 5840,
-      "end": 5844
-    },
-    {
-      "text": "MEK1",
-      "type": "ENTITY",
-      "start": 5846,
-      "end": 5850
-    },
-    {
-      "text": "MAP2KI",
-      "type": "ENTITY",
-      "start": 5852,
-      "end": 5858
-    },
-    {
-      "text": "NRAS",
-      "type": "ENTITY",
-      "start": 5861,
-      "end": 5865
-    },
-    {
-      "text": "PIK3CA Methodology",
-      "type": "ENTITY",
-      "start": 5871,
-      "end": 5889
-    },
-    {
-      "text": "mutations",
-      "type": "ENTITY",
-      "start": 5904,
-      "end": 5913
-    },
-    {
-      "text": "detected",
-      "type": "ENTITY",
-      "start": 5918,
-      "end": 5926
-    },
-    {
-      "text": "amplification",
-      "type": "ENTITY",
-      "start": 5930,
-      "end": 5943
-    },
-    {
-      "text": "exons",
-      "type": "ENTITY",
-      "start": 5966,
-      "end": 5971
-    },
-    {
-      "text": "polymerase chain reaction",
-      "type": "ENTITY",
-      "start": 5975,
-      "end": 6000
-    },
-    {
-      "text": "pcr",
-      "type": "ENTITY",
-      "start": 6002,
-      "end": 6005
-    },
-    {
-      "text": "extension",
-      "type": "ENTITY",
-      "start": 6035,
-      "end": 6044
-    },
-    {
-      "text": "site",
-      "type": "ENTITY",
-      "start": 6052,
-      "end": 6056
-    },
-    {
-      "text": "point mutation",
-      "type": "ENTITY",
-      "start": 6064,
-      "end": 6078
-    },
-    {
-      "text": "single base extension product",
-      "type": "ENTITY",
-      "start": 6084,
-      "end": 6113
-    },
-    {
-      "text": "detected",
-      "type": "ENTITY",
-      "start": 6117,
-      "end": 6125
-    },
-    {
-      "text": "mass-spectrometry",
-      "type": "ENTITY",
-      "start": 6136,
-      "end": 6153
-    },
-    {
-      "text": "Sequenom MassArray Spectrometer",
-      "type": "ENTITY",
-      "start": 6159,
-      "end": 6190
-    },
-    {
-      "text": "result",
-      "type": "ENTITY",
-      "start": 6285,
-      "end": 6291
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 6315,
-      "end": 6323
-    },
-    {
-      "text": "cancer",
-      "type": "ENTITY",
-      "start": 6339,
-      "end": 6345
-    },
-    {
-      "text": "interpreted",
-      "type": "ENTITY",
-      "start": 6360,
-      "end": 6371
-    },
-    {
-      "text": "context",
-      "type": "ENTITY",
-      "start": 6379,
-      "end": 6386
-    },
-    {
-      "text": "clinical",
-      "type": "ENTITY",
-      "start": 6404,
-      "end": 6412
-    },
-    {
-      "text": "pathological",
-      "type": "ENTITY",
-      "start": 6417,
-      "end": 6429
-    },
-    {
-      "text": "information",
-      "type": "ENTITY",
-      "start": 6431,
-      "end": 6442
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 6449,
-      "end": 6453
-    },
-    {
-      "text": "ita",
-      "type": "ENTITY",
-      "start": 6473,
-      "end": 6476
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 6477,
-      "end": 6488
-    },
-    {
-      "text": "detexmined",
-      "type": "ENTITY",
-      "start": 6505,
-      "end": 6515
-    },
-    {
-      "text": "cleared",
-      "type": "ENTITY",
-      "start": 6541,
-      "end": 6548
-    },
-    {
-      "text": "U.S. Food and Drug Administration",
-      "type": "ENTITY",
-      "start": 6568,
-      "end": 6601
-    },
-    {
-      "text": "FDA",
-      "type": "ENTITY",
-      "start": 6603,
-      "end": 6606
-    },
-    {
-      "text": "FDA",
-      "type": "ENTITY",
-      "start": 6613,
-      "end": 6616
-    },
-    {
-      "text": "clearance",
-      "type": "ENTITY",
-      "start": 6642,
-      "end": 6651
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 6675,
-      "end": 6679
-    },
-    {
-      "text": "clinical purposes",
-      "type": "ENTITY",
-      "start": 6692,
-      "end": 6709
-    },
-    {
-      "text": "laboratory",
-      "type": "ENTITY",
-      "start": 6714,
-      "end": 6724
-    },
-    {
-      "text": "accuracy",
-      "type": "ENTITY",
-      "start": 6745,
-      "end": 6753
-    },
-    {
-      "text": "precision",
-      "type": "ENTITY",
-      "start": 6758,
-      "end": 6767
-    },
-    {
-      "text": "test",
-      "type": "ENTITY",
-      "start": 6776,
-      "end": 6780
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 6786,
-      "end": 6793
-    },
-    {
-      "text": "inveetigational panel",
-      "type": "ENTITY",
-      "start": 6801,
-      "end": 6822
-    },
-    {
-      "text": "investigational",
-      "type": "ENTITY",
-      "start": 6831,
-      "end": 6846
-    },
-    {
-      "text": "Report",
-      "type": "ENTITY",
-      "start": 6868,
-      "end": 6874
-    },
-    {
-      "text": "**",
-      "type": "ENTITY",
-      "start": 6875,
-      "end": 6877
-    }
-  ],
-  "entity_count": 314,
-  "has_embedding": true
-}

output/biomedbert_output/0101a550-8206-4187-8ee9-6bcbfb499b7e_nlp.json

@@ -1,2642 +0,0 @@
-{
-  "filename": "0101a550-8206-4187-8ee9-6bcbfb499b7e",
-  "timestamp": "2026-01-05T14:45:18.729455",
-  "entities": [
-    {
-      "text": "TCGA-AC-A7VB-01A-PR",
-      "type": "ENTITY",
-      "start": 59,
-      "end": 78
-    },
-    {
-      "text": "DOB",
-      "type": "ENTITY",
-      "start": 110,
-      "end": 113
-    },
-    {
-      "text": "Age",
-      "type": "ENTITY",
-      "start": 115,
-      "end": 118
-    },
-    {
-      "text": "Gender",
-      "type": "ENTITY",
-      "start": 120,
-      "end": 126
-    },
-    {
-      "text": "Provider Group",
-      "type": "ENTITY",
-      "start": 142,
-      "end": 156
-    },
-    {
-      "text": "Date of Service",
-      "type": "ENTITY",
-      "start": 159,
-      "end": 174
-    },
-    {
-      "text": "ase Date",
-      "type": "ENTITY",
-      "start": 191,
-      "end": 199
-    },
-    {
-      "text": "PATHOLOGy",
-      "type": "ENTITY",
-      "start": 225,
-      "end": 234
-    },
-    {
-      "text": "Diagnosis",
-      "type": "ENTITY",
-      "start": 242,
-      "end": 251
-    },
-    {
-      "text": "A.",
-      "type": "ENTITY",
-      "start": 253,
-      "end": 255
-    },
-    {
-      "text": "rIght breast",
-      "type": "ENTITY",
-      "start": 261,
-      "end": 273
-    },
-    {
-      "text": "noDes",
-      "type": "ENTITY",
-      "start": 293,
-      "end": 298
-    },
-    {
-      "text": "mastectomy",
-      "type": "ENTITY",
-      "start": 300,
-      "end": 310
-    },
-    {
-      "text": "Sentinel LYMPH NODE",
-      "type": "ENTITY",
-      "start": 312,
-      "end": 331
-    },
-    {
-      "text": "BIOPSIES",
-      "type": "ENTITY",
-      "start": 332,
-      "end": 340
-    },
-    {
-      "text": "AXILLARY LYMPH NODE",
-      "type": "ENTITY",
-      "start": 346,
-      "end": 365
-    },
-    {
-      "text": "Multifocal",
-      "type": "ENTITY",
-      "start": 380,
-      "end": 390
-    },
-    {
-      "text": "Nottingham grades 2-3",
-      "type": "ENTITY",
-      "start": 418,
-      "end": 439
-    },
-    {
-      "text": "Largest",
-      "type": "ENTITY",
-      "start": 456,
-      "end": 463
-    },
-    {
-      "text": "tumor nodule",
-      "type": "ENTITY",
-      "start": 464,
-      "end": 476
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 488,
-      "end": 496
-    },
-    {
-      "text": "o'clock aspect",
-      "type": "ENTITY",
-      "start": 500,
-      "end": 514
-    },
-    {
-      "text": "nodules",
-      "type": "ENTITY",
-      "start": 531,
-      "end": 538
-    },
-    {
-      "text": "o'clock",
-      "type": "ENTITY",
-      "start": 560,
-      "end": 567
-    },
-    {
-      "text": "Ductal carcinoma",
-      "type": "ENTITY",
-      "start": 579,
-      "end": 595
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 596,
-      "end": 603
-    },
-    {
-      "text": "DciS",
-      "type": "ENTITY",
-      "start": 605,
-      "end": 609
-    },
-    {
-      "text": "high nuclear grade",
-      "type": "ENTITY",
-      "start": 612,
-      "end": 630
-    },
-    {
-      "text": "solid type",
-      "type": "ENTITY",
-      "start": 632,
-      "end": 642
-    },
-    {
-      "text": "DCIS",
-      "type": "ENTITY",
-      "start": 646,
-      "end": 650
-    },
-    {
-      "text": "biopsy tissue",
-      "type": "ENTITY",
-      "start": 678,
-      "end": 691
-    },
-    {
-      "text": "volume",
-      "type": "ENTITY",
-      "start": 692,
-      "end": 698
-    },
-    {
-      "text": "associated with",
-      "type": "ENTITY",
-      "start": 707,
-      "end": 722
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 733,
-      "end": 741
-    },
-    {
-      "text": "tumor nodules",
-      "type": "ENTITY",
-      "start": 742,
-      "end": 755
-    },
-    {
-      "text": "Mastectomy",
-      "type": "ENTITY",
-      "start": 759,
-      "end": 769
-    },
-    {
-      "text": "margins",
-      "type": "ENTITY",
-      "start": 770,
-      "end": 777
-    },
-    {
-      "text": "free of tumor",
-      "type": "ENTITY",
-      "start": 782,
-      "end": 795
-    },
-    {
-      "text": "Carcinoma",
-      "type": "ENTITY",
-      "start": 800,
-      "end": 809
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 827,
-      "end": 842
-    },
-    {
-      "text": "margins",
-      "type": "ENTITY",
-      "start": 879,
-      "end": 886
-    },
-    {
-      "text": "Metastatic carcinoma",
-      "type": "ENTITY",
-      "start": 891,
-      "end": 911
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 932,
-      "end": 943
-    },
-    {
-      "text": "Largest",
-      "type": "ENTITY",
-      "start": 954,
-      "end": 961
-    },
-    {
-      "text": "metastatic",
-      "type": "ENTITY",
-      "start": 962,
-      "end": 972
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 990,
-      "end": 998
-    },
-    {
-      "text": "Extranodal",
-      "type": "ENTITY",
-      "start": 1002,
-      "end": 1012
-    },
-    {
-      "text": "extension",
-      "type": "ENTITY",
-      "start": 1013,
-      "end": 1022
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 1035,
-      "end": 1043
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1044,
-      "end": 1055
-    },
-    {
-      "text": "sentinel lymph nodes",
-      "type": "ENTITY",
-      "start": 1060,
-      "end": 1080
-    },
-    {
-      "text": "Type",
-      "type": "ENTITY",
-      "start": 1131,
-      "end": 1135
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 1147,
-      "end": 1155
-    },
-    {
-      "text": "Invasive ductal carcinoma",
-      "type": "ENTITY",
-      "start": 1158,
-      "end": 1183
-    },
-    {
-      "text": "Nottingham grade 2-3",
-      "type": "ENTITY",
-      "start": 1185,
-      "end": 1205
-    },
-    {
-      "text": "Type",
-      "type": "ENTITY",
-      "start": 1207,
-      "end": 1211
-    },
-    {
-      "text": "grade",
-      "type": "ENTITY",
-      "start": 1216,
-      "end": 1221
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 1223,
-      "end": 1230
-    },
-    {
-      "text": "Dcis",
-      "type": "ENTITY",
-      "start": 1233,
-      "end": 1237
-    },
-    {
-      "text": "high-nuclear grade",
-      "type": "ENTITY",
-      "start": 1239,
-      "end": 1257
-    },
-    {
-      "text": "Primary tumor",
-      "type": "ENTITY",
-      "start": 1268,
-      "end": 1281
-    },
-    {
-      "text": "Regional",
-      "type": "ENTITY",
-      "start": 1292,
-      "end": 1300
-    },
-    {
-      "text": "pN1c",
-      "type": "ENTITY",
-      "start": 1314,
-      "end": 1318
-    },
-    {
-      "text": "iryiltatiy oluct NoS Distant metastasis",
-      "type": "ENTITY",
-      "start": 1329,
-      "end": 1368
-    },
-    {
-      "text": "Stage",
-      "type": "ENTITY",
-      "start": 1394,
-      "end": 1399
-    },
-    {
-      "text": "IIA",
-      "type": "ENTITY",
-      "start": 1401,
-      "end": 1404
-    },
-    {
-      "text": "Lymphovascular invasion",
-      "type": "ENTITY",
-      "start": 1406,
-      "end": 1429
-    },
-    {
-      "text": "Indeterminate",
-      "type": "ENTITY",
-      "start": 1431,
-      "end": 1444
-    },
-    {
-      "text": "Margin status",
-      "type": "ENTITY",
-      "start": 1454,
-      "end": 1467
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 1469,
-      "end": 1477
-    },
-    {
-      "text": "foci",
-      "type": "ENTITY",
-      "start": 1511,
-      "end": 1515
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1519,
-      "end": 1537
-    },
-    {
-      "text": "histologic features",
-      "type": "ENTITY",
-      "start": 1551,
-      "end": 1570
-    },
-    {
-      "text": "tumor grade",
-      "type": "ENTITY",
-      "start": 1585,
-      "end": 1596
-    },
-    {
-      "text": "variable",
-      "type": "ENTITY",
-      "start": 1609,
-      "end": 1617
-    },
-    {
-      "text": "tumor nodule",
-      "type": "ENTITY",
-      "start": 1633,
-      "end": 1645
-    },
-    {
-      "text": "variable rate",
-      "type": "ENTITY",
-      "start": 1664,
-      "end": 1677
-    },
-    {
-      "text": "mitosis",
-      "type": "ENTITY",
-      "start": 1681,
-      "end": 1688
-    },
-    {
-      "text": "nuclear pleomorphism",
-      "type": "ENTITY",
-      "start": 1694,
-      "end": 1714
-    },
-    {
-      "text": "intermediate",
-      "type": "ENTITY",
-      "start": 1728,
-      "end": 1740
-    },
-    {
-      "text": "high-grade",
-      "type": "ENTITY",
-      "start": 1744,
-      "end": 1754
-    },
-    {
-      "text": "tumor nodules",
-      "type": "ENTITY",
-      "start": 1768,
-      "end": 1781
-    },
-    {
-      "text": "high-grade malignant Case",
-      "type": "ENTITY",
-      "start": 1790,
-      "end": 1815
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 1840,
-      "end": 1846
-    },
-    {
-      "text": "No.",
-      "type": "ENTITY",
-      "start": 1880,
-      "end": 1883
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 1886,
-      "end": 1893
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 1900,
-      "end": 1909
-    },
-    {
-      "text": "Page",
-      "type": "ENTITY",
-      "start": 1912,
-      "end": 1916
-    },
-    {
-      "text": "Doc#1\n\n",
-      "type": "ENTITY",
-      "start": 1929,
-      "end": 1936
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 1951,
-      "end": 1958
-    },
-    {
-      "text": "epithelial cells",
-      "type": "ENTITY",
-      "start": 2000,
-      "end": 2016
-    },
-    {
-      "text": "solid sheets",
-      "type": "ENTITY",
-      "start": 2029,
-      "end": 2041
-    },
-    {
-      "text": "frequent",
-      "type": "ENTITY",
-      "start": 2047,
-      "end": 2055
-    },
-    {
-      "text": "mitoses",
-      "type": "ENTITY",
-      "start": 2056,
-      "end": 2063
-    },
-    {
-      "text": "Nottingham grade 3",
-      "type": "ENTITY",
-      "start": 2081,
-      "end": 2099
-    },
-    {
-      "text": "morphologic similarity",
-      "type": "ENTITY",
-      "start": 2117,
-      "end": 2139
-    },
-    {
-      "text": "nodules",
-      "type": "ENTITY",
-      "start": 2154,
-      "end": 2161
-    },
-    {
-      "text": "origin",
-      "type": "ENTITY",
-      "start": 2197,
-      "end": 2203
-    },
-    {
-      "text": "Intradepartmental consultation",
-      "type": "ENTITY",
-      "start": 2205,
-      "end": 2235
-    },
-    {
-      "text": "impression",
-      "type": "ENTITY",
-      "start": 2255,
-      "end": 2265
-    },
-    {
-      "text": "Invasive",
-      "type": "ENTITY",
-      "start": 2267,
-      "end": 2275
-    },
-    {
-      "text": "CAP",
-      "type": "ENTITY",
-      "start": 2359,
-      "end": 2362
-    },
-    {
-      "text": "pathology",
-      "type": "ENTITY",
-      "start": 2402,
-      "end": 2411
-    },
-    {
-      "text": "specimens",
-      "type": "ENTITY",
-      "start": 2412,
-      "end": 2421
-    },
-    {
-      "text": "Page 2 Case",
-      "type": "ENTITY",
-      "start": 2423,
-      "end": 2434
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 2443,
-      "end": 2449
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 2480,
-      "end": 2487
-    },
-    {
-      "text": "MR",
-      "type": "ENTITY",
-      "start": 2495,
-      "end": 2497
-    },
-    {
-      "text": "No.",
-      "type": "ENTITY",
-      "start": 2498,
-      "end": 2501
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 2518,
-      "end": 2527
-    },
-    {
-      "text": "Page",
-      "type": "ENTITY",
-      "start": 2530,
-      "end": 2534
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 2555,
-      "end": 2562
-    },
-    {
-      "text": "Modified radical mastectomy",
-      "type": "ENTITY",
-      "start": 2621,
-      "end": 2648
-    },
-    {
-      "text": "Laterality",
-      "type": "ENTITY",
-      "start": 2650,
-      "end": 2660
-    },
-    {
-      "text": "Right",
-      "type": "ENTITY",
-      "start": 2662,
-      "end": 2667
-    },
-    {
-      "text": "Lymph node sampling",
-      "type": "ENTITY",
-      "start": 2669,
-      "end": 2688
-    },
-    {
-      "text": "Sentinel lymph node biopsies",
-      "type": "ENTITY",
-      "start": 2690,
-      "end": 2718
-    },
-    {
-      "text": "lymph node dissection",
-      "type": "ENTITY",
-      "start": 2731,
-      "end": 2752
-    },
-    {
-      "text": "INVASIVE",
-      "type": "ENTITY",
-      "start": 2754,
-      "end": 2762
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 2773,
-      "end": 2778
-    },
-    {
-      "text": "Histologic type",
-      "type": "ENTITY",
-      "start": 2795,
-      "end": 2810
-    },
-    {
-      "text": "Invasive ductal carcinoma",
-      "type": "ENTITY",
-      "start": 2812,
-      "end": 2837
-    },
-    {
-      "text": "multifocal",
-      "type": "ENTITY",
-      "start": 2839,
-      "end": 2849
-    },
-    {
-      "text": "Tumor sites",
-      "type": "ENTITY",
-      "start": 2852,
-      "end": 2863
-    },
-    {
-      "text": "Tumor size",
-      "type": "ENTITY",
-      "start": 2876,
-      "end": 2886
-    },
-    {
-      "text": "Largest",
-      "type": "ENTITY",
-      "start": 2888,
-      "end": 2895
-    },
-    {
-      "text": "tumor nodule",
-      "type": "ENTITY",
-      "start": 2896,
-      "end": 2908
-    },
-    {
-      "text": "Tumor focality",
-      "type": "ENTITY",
-      "start": 2918,
-      "end": 2932
-    },
-    {
-      "text": "Multifocal",
-      "type": "ENTITY",
-      "start": 2934,
-      "end": 2944
-    },
-    {
-      "text": "Histologic grade",
-      "type": "ENTITY",
-      "start": 2946,
-      "end": 2962
-    },
-    {
-      "text": "Nottingham Score",
-      "type": "ENTITY",
-      "start": 2964,
-      "end": 2980
-    },
-    {
-      "text": "Tubule formation",
-      "type": "ENTITY",
-      "start": 2993,
-      "end": 3009
-    },
-    {
-      "text": "Nuclear pleomorphism",
-      "type": "ENTITY",
-      "start": 3019,
-      "end": 3039
-    },
-    {
-      "text": "Mitotic rate",
-      "type": "ENTITY",
-      "start": 3051,
-      "end": 3063
-    },
-    {
-      "text": "mitotic rate",
-      "type": "ENTITY",
-      "start": 3084,
-      "end": 3096
-    },
-    {
-      "text": "Lymphovascular invasion",
-      "type": "ENTITY",
-      "start": 3099,
-      "end": 3122
-    },
-    {
-      "text": "Indeterminate",
-      "type": "ENTITY",
-      "start": 3124,
-      "end": 3137
-    },
-    {
-      "text": "Macroscopic",
-      "type": "ENTITY",
-      "start": 3139,
-      "end": 3150
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 3155,
-      "end": 3166
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 3177,
-      "end": 3182
-    },
-    {
-      "text": "No skin",
-      "type": "ENTITY",
-      "start": 3184,
-      "end": 3191
-    },
-    {
-      "text": "chest wall invasion",
-      "type": "ENTITY",
-      "start": 3195,
-      "end": 3214
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 3215,
-      "end": 3225
-    },
-    {
-      "text": "DUCTAL CARCINOMA INSITU",
-      "type": "ENTITY",
-      "start": 3227,
-      "end": 3250
-    },
-    {
-      "text": "DCIS",
-      "type": "ENTITY",
-      "start": 3252,
-      "end": 3256
-    },
-    {
-      "text": "association with",
-      "type": "ENTITY",
-      "start": 3270,
-      "end": 3286
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 3293,
-      "end": 3301
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 3326,
-      "end": 3344
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 3346,
-      "end": 3354
-    },
-    {
-      "text": "Ductal carcinoma",
-      "type": "ENTITY",
-      "start": 3356,
-      "end": 3372
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 3373,
-      "end": 3380
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 3382,
-      "end": 3390
-    },
-    {
-      "text": "Total lymph nodes",
-      "type": "ENTITY",
-      "start": 3404,
-      "end": 3421
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 3445,
-      "end": 3456
-    },
-    {
-      "text": "Size",
-      "type": "ENTITY",
-      "start": 3469,
-      "end": 3473
-    },
-    {
-      "text": "metastatic",
-      "type": "ENTITY",
-      "start": 3485,
-      "end": 3495
-    },
-    {
-      "text": "Extranodal extension",
-      "type": "ENTITY",
-      "start": 3513,
-      "end": 3533
-    },
-    {
-      "text": "Primary Tumor",
-      "type": "ENTITY",
-      "start": 3564,
-      "end": 3577
-    },
-    {
-      "text": "Regional lymph nodes",
-      "type": "ENTITY",
-      "start": 3593,
-      "end": 3613
-    },
-    {
-      "text": "Distant metastasis",
-      "type": "ENTITY",
-      "start": 3626,
-      "end": 3644
-    },
-    {
-      "text": "AJCC Stage",
-      "type": "ENTITY",
-      "start": 3667,
-      "end": 3677
-    },
-    {
-      "text": "IIA",
-      "type": "ENTITY",
-      "start": 3679,
-      "end": 3682
-    },
-    {
-      "text": "Performed",
-      "type": "ENTITY",
-      "start": 3703,
-      "end": 3712
-    },
-    {
-      "text": "biopsies",
-      "type": "ENTITY",
-      "start": 3730,
-      "end": 3738
-    },
-    {
-      "text": "HER2 studies",
-      "type": "ENTITY",
-      "start": 3751,
-      "end": 3763
-    },
-    {
-      "text": "addendum",
-      "type": "ENTITY",
-      "start": 3794,
-      "end": 3802
-    },
-    {
-      "text": "Estrogen receptor",
-      "type": "ENTITY",
-      "start": 3805,
-      "end": 3822
-    },
-    {
-      "text": "positive cells",
-      "type": "ENTITY",
-      "start": 3831,
-      "end": 3845
-    },
-    {
-      "text": "strong",
-      "type": "ENTITY",
-      "start": 3847,
-      "end": 3853
-    },
-    {
-      "text": "intensity",
-      "type": "ENTITY",
-      "start": 3854,
-      "end": 3863
-    },
-    {
-      "text": "Progesterone receptor",
-      "type": "ENTITY",
-      "start": 3865,
-      "end": 3886
-    },
-    {
-      "text": "positive cells",
-      "type": "ENTITY",
-      "start": 3891,
-      "end": 3905
-    },
-    {
-      "text": "HER2",
-      "type": "ENTITY",
-      "start": 3907,
-      "end": 3911
-    },
-    {
-      "text": "studies",
-      "type": "ENTITY",
-      "start": 3924,
-      "end": 3931
-    },
-    {
-      "text": "addendum",
-      "type": "ENTITY",
-      "start": 3962,
-      "end": 3970
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 4000,
-      "end": 4006
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 4046,
-      "end": 4053
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 4061,
-      "end": 4070
-    },
-    {
-      "text": "Page",
-      "type": "ENTITY",
-      "start": 4073,
-      "end": 4077
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 4112,
-      "end": 4119
-    },
-    {
-      "text": "PATHOLOGY REPORT",
-      "type": "ENTITY",
-      "start": 4144,
-      "end": 4160
-    },
-    {
-      "text": "Variable",
-      "type": "ENTITY",
-      "start": 4161,
-      "end": 4169
-    },
-    {
-      "text": "Ki-67",
-      "type": "ENTITY",
-      "start": 4198,
-      "end": 4203
-    },
-    {
-      "text": "A. Sentinel",
-      "type": "ENTITY",
-      "start": 4225,
-      "end": 4236
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 4253,
-      "end": 4258
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 4296,
-      "end": 4301
-    },
-    {
-      "text": "axillary right",
-      "type": "ENTITY",
-      "start": 4302,
-      "end": 4316
-    },
-    {
-      "text": "D. Sentinel",
-      "type": "ENTITY",
-      "start": 4354,
-      "end": 4365
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 4382,
-      "end": 4387
-    },
-    {
-      "text": "axillary E. Breast",
-      "type": "ENTITY",
-      "start": 4388,
-      "end": 4406
-    },
-    {
-      "text": "Axillary nodes right Clinical History/Operative Dx",
-      "type": "ENTITY",
-      "start": 4425,
-      "end": 4475
-    },
-    {
-      "text": "Right breast cancer",
-      "type": "ENTITY",
-      "start": 4478,
-      "end": 4497
-    },
-    {
-      "text": "Intraoperative Diagnosis",
-      "type": "ENTITY",
-      "start": 4499,
-      "end": 4523
-    },
-    {
-      "text": "A. Sentinel node",
-      "type": "ENTITY",
-      "start": 4526,
-      "end": 4542
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 4548,
-      "end": 4557
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 4559,
-      "end": 4567
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 4572,
-      "end": 4581
-    },
-    {
-      "text": "B. Sentinel node",
-      "type": "ENTITY",
-      "start": 4583,
-      "end": 4599
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 4605,
-      "end": 4614
-    },
-    {
-      "text": "atypical cells",
-      "type": "ENTITY",
-      "start": 4621,
-      "end": 4635
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 4652,
-      "end": 4661
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 4694,
-      "end": 4703
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 4705,
-      "end": 4713
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 4718,
-      "end": 4727
-    },
-    {
-      "text": "D. Sentinel node",
-      "type": "ENTITY",
-      "start": 4729,
-      "end": 4745
-    },
-    {
-      "text": "intraoperative",
-      "type": "ENTITY",
-      "start": 4753,
-      "end": 4767
-    },
-    {
-      "text": "interpretation(s) was/were",
-      "type": "ENTITY",
-      "start": 4768,
-      "end": 4794
-    },
-    {
-      "text": "performed",
-      "type": "ENTITY",
-      "start": 4795,
-      "end": 4804
-    },
-    {
-      "text": "Gross Description",
-      "type": "ENTITY",
-      "start": 4822,
-      "end": 4839
-    },
-    {
-      "text": "touch prep",
-      "type": "ENTITY",
-      "start": 4856,
-      "end": 4866
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 4894,
-      "end": 4899
-    },
-    {
-      "text": "A. Part A",
-      "type": "ENTITY",
-      "start": 4901,
-      "end": 4910
-    },
-    {
-      "text": "sentinel node",
-      "type": "ENTITY",
-      "start": 4928,
-      "end": 4941
-    },
-    {
-      "text": "frozen section/touch prep",
-      "type": "ENTITY",
-      "start": 4956,
-      "end": 4981
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 4982,
-      "end": 4992
-    },
-    {
-      "text": "piece",
-      "type": "ENTITY",
-      "start": 5017,
-      "end": 5022
-    },
-    {
-      "text": "red-tan soft tissue",
-      "type": "ENTITY",
-      "start": 5026,
-      "end": 5045
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 5047,
-      "end": 5058
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 5088,
-      "end": 5098
-    },
-    {
-      "text": "cut surfaces",
-      "type": "ENTITY",
-      "start": 5104,
-      "end": 5116
-    },
-    {
-      "text": "fatty",
-      "type": "ENTITY",
-      "start": 5121,
-      "end": 5126
-    },
-    {
-      "text": "rubbery",
-      "type": "ENTITY",
-      "start": 5131,
-      "end": 5138
-    },
-    {
-      "text": "pink",
-      "type": "ENTITY",
-      "start": 5140,
-      "end": 5144
-    },
-    {
-      "text": "tan",
-      "type": "ENTITY",
-      "start": 5149,
-      "end": 5152
-    },
-    {
-      "text": "touch",
-      "type": "ENTITY",
-      "start": 5158,
-      "end": 5163
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 5196,
-      "end": 5207
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 5208,
-      "end": 5218
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 5224,
-      "end": 5234
-    },
-    {
-      "text": "Page 4 Case",
-      "type": "ENTITY",
-      "start": 5248,
-      "end": 5259
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 5268,
-      "end": 5274
-    },
-    {
-      "text": "Acct",
-      "type": "ENTITY",
-      "start": 5305,
-      "end": 5309
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 5316,
-      "end": 5323
-    },
-    {
-      "text": "MR",
-      "type": "ENTITY",
-      "start": 5331,
-      "end": 5333
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 5351,
-      "end": 5360
-    },
-    {
-      "text": "Page",
-      "type": "ENTITY",
-      "start": 5363,
-      "end": 5367
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 5388,
-      "end": 5395
-    },
-    {
-      "text": "routine",
-      "type": "ENTITY",
-      "start": 5451,
-      "end": 5458
-    },
-    {
-      "text": "histology",
-      "type": "ENTITY",
-      "start": 5459,
-      "end": 5468
-    },
-    {
-      "text": "A1",
-      "type": "ENTITY",
-      "start": 5472,
-      "end": 5474
-    },
-    {
-      "text": "sentinel node protocol",
-      "type": "ENTITY",
-      "start": 5482,
-      "end": 5504
-    },
-    {
-      "text": "B. Part B",
-      "type": "ENTITY",
-      "start": 5516,
-      "end": 5525
-    },
-    {
-      "text": "sentinel node",
-      "type": "ENTITY",
-      "start": 5529,
-      "end": 5542
-    },
-    {
-      "text": "fresh state",
-      "type": "ENTITY",
-      "start": 5574,
-      "end": 5585
-    },
-    {
-      "text": "touch",
-      "type": "ENTITY",
-      "start": 5590,
-      "end": 5595
-    },
-    {
-      "text": "prep/frozen section",
-      "type": "ENTITY",
-      "start": 5596,
-      "end": 5615
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 5616,
-      "end": 5626
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 5682,
-      "end": 5693
-    },
-    {
-      "text": "Iymph node",
-      "type": "ENTITY",
-      "start": 5723,
-      "end": 5733
-    },
-    {
-      "text": "Sectioning",
-      "type": "ENTITY",
-      "start": 5735,
-      "end": 5745
-    },
-    {
-      "text": "rubbery",
-      "type": "ENTITY",
-      "start": 5761,
-      "end": 5768
-    },
-    {
-      "text": "pink",
-      "type": "ENTITY",
-      "start": 5770,
-      "end": 5774
-    },
-    {
-      "text": "tan cut",
-      "type": "ENTITY",
-      "start": 5779,
-      "end": 5786
-    },
-    {
-      "text": "surfaces",
-      "type": "ENTITY",
-      "start": 5787,
-      "end": 5795
-    },
-    {
-      "text": "touch",
-      "type": "ENTITY",
-      "start": 5801,
-      "end": 5806
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 5840,
-      "end": 5851
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 5852,
-      "end": 5862
-    },
-    {
-      "text": "Iymph node",
-      "type": "ENTITY",
-      "start": 5868,
-      "end": 5878
-    },
-    {
-      "text": "routine",
-      "type": "ENTITY",
-      "start": 5905,
-      "end": 5912
-    },
-    {
-      "text": "histology",
-      "type": "ENTITY",
-      "start": 5913,
-      "end": 5922
-    },
-    {
-      "text": "B1",
-      "type": "ENTITY",
-      "start": 5926,
-      "end": 5928
-    },
-    {
-      "text": "sentinel node protocol",
-      "type": "ENTITY",
-      "start": 5936,
-      "end": 5958
-    },
-    {
-      "text": "C. Part C",
-      "type": "ENTITY",
-      "start": 5970,
-      "end": 5979
-    },
-    {
-      "text": "sentinel node",
-      "type": "ENTITY",
-      "start": 5994,
-      "end": 6007
-    },
-    {
-      "text": "axillary",
-      "type": "ENTITY",
-      "start": 6018,
-      "end": 6026
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 6040,
-      "end": 6048
-    },
-    {
-      "text": "fragment of fat",
-      "type": "ENTITY",
-      "start": 6073,
-      "end": 6088
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 6090,
-      "end": 6101
-    },
-    {
-      "text": "apparent",
-      "type": "ENTITY",
-      "start": 6123,
-      "end": 6131
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 6132,
-      "end": 6143
-    },
-    {
-      "text": "Iymph node",
-      "type": "ENTITY",
-      "start": 6174,
-      "end": 6184
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 6234,
-      "end": 6245
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 6246,
-      "end": 6256
-    },
-    {
-      "text": "C1",
-      "type": "ENTITY",
-      "start": 6260,
-      "end": 6262
-    },
-    {
-      "text": "sentinel Iymph node protocol",
-      "type": "ENTITY",
-      "start": 6270,
-      "end": 6298
-    },
-    {
-      "text": "D. Part D",
-      "type": "ENTITY",
-      "start": 6310,
-      "end": 6319
-    },
-    {
-      "text": "sentinel node",
-      "type": "ENTITY",
-      "start": 6337,
-      "end": 6350
-    },
-    {
-      "text": "axillary",
-      "type": "ENTITY",
-      "start": 6360,
-      "end": 6368
-    },
-    {
-      "text": "fresh state",
-      "type": "ENTITY",
-      "start": 6396,
-      "end": 6407
-    },
-    {
-      "text": "frozen section/touch",
-      "type": "ENTITY",
-      "start": 6413,
-      "end": 6433
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 6442,
-      "end": 6452
-    },
-    {
-      "text": "fatty soft tissue",
-      "type": "ENTITY",
-      "start": 6501,
-      "end": 6518
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 6535,
-      "end": 6542
-    },
-    {
-      "text": "frozen section",
-      "type": "ENTITY",
-      "start": 6560,
-      "end": 6574
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 6575,
-      "end": 6585
-    },
-    {
-      "text": "residual",
-      "type": "ENTITY",
-      "start": 6591,
-      "end": 6599
-    },
-    {
-      "text": "frozen tissue",
-      "type": "ENTITY",
-      "start": 6600,
-      "end": 6613
-    },
-    {
-      "text": "D1",
-      "type": "ENTITY",
-      "start": 6630,
-      "end": 6632
-    },
-    {
-      "text": "permanent",
-      "type": "ENTITY",
-      "start": 6637,
-      "end": 6646
-    },
-    {
-      "text": "touch",
-      "type": "ENTITY",
-      "start": 6664,
-      "end": 6669
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 6692,
-      "end": 6702
-    },
-    {
-      "text": "D2",
-      "type": "ENTITY",
-      "start": 6719,
-      "end": 6721
-    },
-    {
-      "text": "permanent",
-      "type": "ENTITY",
-      "start": 6726,
-      "end": 6735
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 6736,
-      "end": 6744
-    },
-    {
-      "text": "sentinel lymph node protocol",
-      "type": "ENTITY",
-      "start": 6752,
-      "end": 6780
-    },
-    {
-      "text": "E.",
-      "type": "ENTITY",
-      "start": 6791,
-      "end": 6793
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 6803,
-      "end": 6808
-    },
-    {
-      "text": "Sutures",
-      "type": "ENTITY",
-      "start": 6833,
-      "end": 6840
-    },
-    {
-      "text": "orientation",
-      "type": "ENTITY",
-      "start": 6853,
-      "end": 6864
-    },
-    {
-      "text": "portion of tumor",
-      "type": "ENTITY",
-      "start": 6877,
-      "end": 6893
-    },
-    {
-      "text": "Laterality",
-      "type": "ENTITY",
-      "start": 6911,
-      "end": 6921
-    },
-    {
-      "text": "Right",
-      "type": "ENTITY",
-      "start": 6923,
-      "end": 6928
-    },
-    {
-      "text": "Specimen",
-      "type": "ENTITY",
-      "start": 6930,
-      "end": 6938
-    },
-    {
-      "text": "Mastectomy",
-      "type": "ENTITY",
-      "start": 6940,
-      "end": 6950
-    },
-    {
-      "text": "Size of mastectomy",
-      "type": "ENTITY",
-      "start": 6952,
-      "end": 6970
-    },
-    {
-      "text": "A-P",
-      "type": "ENTITY",
-      "start": 6985,
-      "end": 6988
-    },
-    {
-      "text": "Axillary tail",
-      "type": "ENTITY",
-      "start": 7009,
-      "end": 7022
-    },
-    {
-      "text": "Skin",
-      "type": "ENTITY",
-      "start": 7037,
-      "end": 7041
-    },
-    {
-      "text": "pigmented",
-      "type": "ENTITY",
-      "start": 7055,
-      "end": 7064
-    },
-    {
-      "text": "skin",
-      "type": "ENTITY",
-      "start": 7065,
-      "end": 7069
-    },
-    {
-      "text": "Nipple/areola",
-      "type": "ENTITY",
-      "start": 7070,
-      "end": 7083
-    },
-    {
-      "text": "center of skin",
-      "type": "ENTITY",
-      "start": 7090,
-      "end": 7104
-    },
-    {
-      "text": "Specimen weight",
-      "type": "ENTITY",
-      "start": 7106,
-      "end": 7121
-    },
-    {
-      "text": "grams",
-      "type": "ENTITY",
-      "start": 7127,
-      "end": 7132
-    },
-    {
-      "text": "Ink code",
-      "type": "ENTITY",
-      "start": 7134,
-      "end": 7142
-    },
-    {
-      "text": "Blue",
-      "type": "ENTITY",
-      "start": 7144,
-      "end": 7148
-    },
-    {
-      "text": "superior-anterior",
-      "type": "ENTITY",
-      "start": 7152,
-      "end": 7169
-    },
-    {
-      "text": "orange",
-      "type": "ENTITY",
-      "start": 7171,
-      "end": 7177
-    },
-    {
-      "text": "inferior-anterior",
-      "type": "ENTITY",
-      "start": 7181,
-      "end": 7198
-    },
-    {
-      "text": "black",
-      "type": "ENTITY",
-      "start": 7200,
-      "end": 7205
-    },
-    {
-      "text": "deep",
-      "type": "ENTITY",
-      "start": 7208,
-      "end": 7212
-    },
-    {
-      "text": "M-1=1",
-      "type": "ENTITY",
-      "start": 7232,
-      "end": 7237
-    },
-    {
-      "text": "L-S= 11",
-      "type": "ENTITY",
-      "start": 7239,
-      "end": 7246
-    },
-    {
-      "text": "Nipple",
-      "type": "ENTITY",
-      "start": 7248,
-      "end": 7254
-    },
-    {
-      "text": "slab",
-      "type": "ENTITY",
-      "start": 7258,
-      "end": 7262
-    },
-    {
-      "text": "Time",
-      "type": "ENTITY",
-      "start": 7267,
-      "end": 7271
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 7275,
-      "end": 7284
-    },
-    {
-      "text": "Time",
-      "type": "ENTITY",
-      "start": 7286,
-      "end": 7290
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 7303,
-      "end": 7311
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 7325,
-      "end": 7333
-    },
-    {
-      "text": "Lesion",
-      "type": "ENTITY",
-      "start": 7336,
-      "end": 7342
-    },
-    {
-      "text": "Biopsy site",
-      "type": "ENTITY",
-      "start": 7346,
-      "end": 7357
-    },
-    {
-      "text": "Size",
-      "type": "ENTITY",
-      "start": 7367,
-      "end": 7371
-    },
-    {
-      "text": "stellate",
-      "type": "ENTITY",
-      "start": 7393,
-      "end": 7401
-    },
-    {
-      "text": "gray-white",
-      "type": "ENTITY",
-      "start": 7403,
-      "end": 7413
-    },
-    {
-      "text": "firm",
-      "type": "ENTITY",
-      "start": 7415,
-      "end": 7419
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 7420,
-      "end": 7424
-    },
-    {
-      "text": "Location",
-      "type": "ENTITY",
-      "start": 7426,
-      "end": 7434
-    },
-    {
-      "text": "slabs",
-      "type": "ENTITY",
-      "start": 7451,
-      "end": 7456
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 7464,
-      "end": 7472
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 7505,
-      "end": 7520
-    },
-    {
-      "text": "deep margin",
-      "type": "ENTITY",
-      "start": 7532,
-      "end": 7543
-    },
-    {
-      "text": "Lesion",
-      "type": "ENTITY",
-      "start": 7545,
-      "end": 7551
-    },
-    {
-      "text": "Biopsy site",
-      "type": "ENTITY",
-      "start": 7556,
-      "end": 7567
-    },
-    {
-      "text": "Size",
-      "type": "ENTITY",
-      "start": 7577,
-      "end": 7581
-    },
-    {
-      "text": "Location",
-      "type": "ENTITY",
-      "start": 7603,
-      "end": 7611
-    },
-    {
-      "text": "slabs",
-      "type": "ENTITY",
-      "start": 7628,
-      "end": 7633
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 7640,
-      "end": 7648
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 7681,
-      "end": 7689
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 7720,
-      "end": 7726
-    },
-    {
-      "text": "No.",
-      "type": "ENTITY",
-      "start": 7751,
-      "end": 7754
-    },
-    {
-      "text": "Acct",
-      "type": "ENTITY",
-      "start": 7757,
-      "end": 7761
-    },
-    {
-      "text": "No.",
-      "type": "ENTITY",
-      "start": 7762,
-      "end": 7765
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 7768,
-      "end": 7775
-    },
-    {
-      "text": "Name",
-      "type": "ENTITY",
-      "start": 7776,
-      "end": 7780
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 7783,
-      "end": 7792
-    },
-    {
-      "text": "Page",
-      "type": "ENTITY",
-      "start": 7795,
-      "end": 7799
-    },
-    {
-      "text": "Page 5 Doc",
-      "type": "ENTITY",
-      "start": 7807,
-      "end": 7817
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 7837,
-      "end": 7844
-    },
-    {
-      "text": "PATHOLOGY REPORT",
-      "type": "ENTITY",
-      "start": 7869,
-      "end": 7885
-    },
-    {
-      "text": "Lesion",
-      "type": "ENTITY",
-      "start": 7886,
-      "end": 7892
-    },
-    {
-      "text": "No biopsy site",
-      "type": "ENTITY",
-      "start": 7897,
-      "end": 7911
-    },
-    {
-      "text": "Size",
-      "type": "ENTITY",
-      "start": 7921,
-      "end": 7925
-    },
-    {
-      "text": "Location",
-      "type": "ENTITY",
-      "start": 7947,
-      "end": 7955
-    },
-    {
-      "text": "slabs",
-      "type": "ENTITY",
-      "start": 7972,
-      "end": 7977
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 7982,
-      "end": 7990
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 8023,
-      "end": 8031
-    },
-    {
-      "text": "Non-lesional breast",
-      "type": "ENTITY",
-      "start": 8033,
-      "end": 8052
-    },
-    {
-      "text": "Fibrofatty",
-      "type": "ENTITY",
-      "start": 8054,
-      "end": 8064
-    },
-    {
-      "text": "breast tissue",
-      "type": "ENTITY",
-      "start": 8065,
-      "end": 8078
-    },
-    {
-      "text": "Cassette summary",
-      "type": "ENTITY",
-      "start": 8080,
-      "end": 8096
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 8117,
-      "end": 8122
-    },
-    {
-      "text": "biopsied",
-      "type": "ENTITY",
-      "start": 8135,
-      "end": 8143
-    },
-    {
-      "text": "portion of the",
-      "type": "ENTITY",
-      "start": 8145,
-      "end": 8159
-    },
-    {
-      "text": "small tumor",
-      "type": "ENTITY",
-      "start": 8160,
-      "end": 8171
-    },
-    {
-      "text": "E2-E4",
-      "type": "ENTITY",
-      "start": 8186,
-      "end": 8191
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 8206,
-      "end": 8212
-    },
-    {
-      "text": "central breast tissue",
-      "type": "ENTITY",
-      "start": 8218,
-      "end": 8239
-    },
-    {
-      "text": "E6-E7",
-      "type": "ENTITY",
-      "start": 8241,
-      "end": 8246
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 8248,
-      "end": 8255
-    },
-    {
-      "text": "E8",
-      "type": "ENTITY",
-      "start": 8271,
-      "end": 8273
-    },
-    {
-      "text": "E9",
-      "type": "ENTITY",
-      "start": 8308,
-      "end": 8310
-    },
-    {
-      "text": "breast tissue",
-      "type": "ENTITY",
-      "start": 8327,
-      "end": 8340
-    },
-    {
-      "text": "E10-E11",
-      "type": "ENTITY",
-      "start": 8342,
-      "end": 8349
-    },
-    {
-      "text": "fibrous tissue",
-      "type": "ENTITY",
-      "start": 8351,
-      "end": 8365
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 8366,
-      "end": 8372
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 8384,
-      "end": 8389
-    },
-    {
-      "text": "E12",
-      "type": "ENTITY",
-      "start": 8391,
-      "end": 8394
-    },
-    {
-      "text": "medial breast tissue",
-      "type": "ENTITY",
-      "start": 8411,
-      "end": 8431
-    },
-    {
-      "text": "central posterior breast tissue",
-      "type": "ENTITY",
-      "start": 8462,
-      "end": 8493
-    },
-    {
-      "text": "F. Part F",
-      "type": "ENTITY",
-      "start": 8495,
-      "end": 8504
-    },
-    {
-      "text": "axillary nodes",
-      "type": "ENTITY",
-      "start": 8514,
-      "end": 8528
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 8530,
-      "end": 8535
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 8549,
-      "end": 8557
-    },
-    {
-      "text": "gram partially",
-      "type": "ENTITY",
-      "start": 8567,
-      "end": 8581
-    },
-    {
-      "text": "yellow-tan fatty soft tissue",
-      "type": "ENTITY",
-      "start": 8602,
-      "end": 8630
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 8653,
-      "end": 8664
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 8680,
-      "end": 8691
-    },
-    {
-      "text": "dimension",
-      "type": "ENTITY",
-      "start": 8746,
-      "end": 8755
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 8761,
-      "end": 8772
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 8800,
-      "end": 8811
-    },
-    {
-      "text": "evaluation",
-      "type": "ENTITY",
-      "start": 8812,
-      "end": 8822
-    },
-    {
-      "text": "Cassette summary",
-      "type": "ENTITY",
-      "start": 8824,
-      "end": 8840
-    },
-    {
-      "text": "F1",
-      "type": "ENTITY",
-      "start": 8847,
-      "end": 8849
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 8856,
-      "end": 8867
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 8879,
-      "end": 8890
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 8901,
-      "end": 8911
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 8913,
-      "end": 8921
-    },
-    {
-      "text": "F4",
-      "type": "ENTITY",
-      "start": 8923,
-      "end": 8925
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 8931,
-      "end": 8941
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 8943,
-      "end": 8951
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 8968,
-      "end": 8978
-    },
-    {
-      "text": "serially sectioned",
-      "type": "ENTITY",
-      "start": 8980,
-      "end": 8998
-    },
-    {
-      "text": "Microscopic Description",
-      "type": "ENTITY",
-      "start": 9003,
-      "end": 9026
-    },
-    {
-      "text": "A.",
-      "type": "ENTITY",
-      "start": 9028,
-      "end": 9030
-    },
-    {
-      "text": "C. Immunohistochemical stain",
-      "type": "ENTITY",
-      "start": 9033,
-      "end": 9061
-    },
-    {
-      "text": "CK",
-      "type": "ENTITY",
-      "start": 9063,
-      "end": 9065
-    },
-    {
-      "text": "focal metastatic carcinoma",
-      "type": "ENTITY",
-      "start": 9081,
-      "end": 9107
-    },
-    {
-      "text": "specimens B",
-      "type": "ENTITY",
-      "start": 9111,
-      "end": 9122
-    },
-    {
-      "text": "C. D. Immunohistochemical stain",
-      "type": "ENTITY",
-      "start": 9127,
-      "end": 9158
-    },
-    {
-      "text": "CK",
-      "type": "ENTITY",
-      "start": 9160,
-      "end": 9162
-    },
-    {
-      "text": "OSCAR",
-      "type": "ENTITY",
-      "start": 9163,
-      "end": 9168
-    },
-    {
-      "text": "metastatic carcinoma",
-      "type": "ENTITY",
-      "start": 9183,
-      "end": 9203
-    },
-    {
-      "text": "HER2",
-      "type": "ENTITY",
-      "start": 9205,
-      "end": 9209
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 9212,
-      "end": 9219
-    },
-    {
-      "text": "addendum",
-      "type": "ENTITY",
-      "start": 9250,
-      "end": 9258
-    },
-    {
-      "text": "E. Immunohistochemical stain",
-      "type": "ENTITY",
-      "start": 9260,
-      "end": 9288
-    },
-    {
-      "text": "HER2",
-      "type": "ENTITY",
-      "start": 9290,
-      "end": 9294
-    },
-    {
-      "text": "addendum",
-      "type": "ENTITY",
-      "start": 9317,
-      "end": 9325
-    },
-    {
-      "text": "Microscopic sections",
-      "type": "ENTITY",
-      "start": 9330,
-      "end": 9350
-    },
-    {
-      "text": "microscopic",
-      "type": "ENTITY",
-      "start": 9375,
-      "end": 9386
-    },
-    {
-      "text": "findings",
-      "type": "ENTITY",
-      "start": 9387,
-      "end": 9395
-    },
-    {
-      "text": "retlected",
-      "type": "ENTITY",
-      "start": 9400,
-      "end": 9409
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 9417,
-      "end": 9426
-    },
-    {
-      "text": "END",
-      "type": "ENTITY",
-      "start": 9461,
-      "end": 9464
-    },
-    {
-      "text": "No.",
-      "type": "ENTITY",
-      "start": 9486,
-      "end": 9489
-    },
-    {
-      "text": "Acct",
-      "type": "ENTITY",
-      "start": 9492,
-      "end": 9496
-    },
-    {
-      "text": "No. 'atient Name",
-      "type": "ENTITY",
-      "start": 9497,
-      "end": 9513
-    },
-    {
-      "text": "Pathology",
-      "type": "ENTITY",
-      "start": 9516,
-      "end": 9525
-    },
-    {
-      "text": "Page 6/6",
-      "type": "ENTITY",
-      "start": 9528,
-      "end": 9536
-    }
-  ],
-  "entity_count": 439,
-  "has_embedding": true
-}

output/biomedbert_output/01192b42-c386-43af-961c-9d6b28670770_nlp.json

@@ -1,452 +0,0 @@
-{
-  "filename": "01192b42-c386-43af-961c-9d6b28670770",
-  "timestamp": "2026-01-05T14:45:21.057513",
-  "entities": [
-    {
-      "text": "CHROMOPHOBE RENAL CELL CARCINOMA",
-      "type": "ENTITY",
-      "start": 61,
-      "end": 93
-    },
-    {
-      "text": "FUHRMAN'S NUCLEAR",
-      "type": "ENTITY",
-      "start": 95,
-      "end": 112
-    },
-    {
-      "text": "CM",
-      "type": "ENTITY",
-      "start": 155,
-      "end": 157
-    },
-    {
-      "text": "MAXIMUM",
-      "type": "ENTITY",
-      "start": 161,
-      "end": 168
-    },
-    {
-      "text": "LYMPHATIC/VASCULAR",
-      "type": "ENTITY",
-      "start": 186,
-      "end": 204
-    },
-    {
-      "text": "Multilocular cyst",
-      "type": "ENTITY",
-      "start": 227,
-      "end": 244
-    },
-    {
-      "text": "Margins",
-      "type": "ENTITY",
-      "start": 255,
-      "end": 262
-    },
-    {
-      "text": "resection free of tumor",
-      "type": "ENTITY",
-      "start": 266,
-      "end": 289
-    },
-    {
-      "text": "Immunoperoxidase studies",
-      "type": "ENTITY",
-      "start": 300,
-      "end": 324
-    },
-    {
-      "text": "tumor cells",
-      "type": "ENTITY",
-      "start": 341,
-      "end": 352
-    },
-    {
-      "text": "positive",
-      "type": "ENTITY",
-      "start": 359,
-      "end": 367
-    },
-    {
-      "text": "CK7",
-      "type": "ENTITY",
-      "start": 372,
-      "end": 375
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 380,
-      "end": 388
-    },
-    {
-      "text": "CD10",
-      "type": "ENTITY",
-      "start": 393,
-      "end": 397
-    },
-    {
-      "text": "Vimentin",
-      "type": "ENTITY",
-      "start": 402,
-      "end": 410
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 427,
-      "end": 436
-    },
-    {
-      "text": "Chromophobe renal cell carcinoma",
-      "type": "ENTITY",
-      "start": 440,
-      "end": 472
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 478,
-      "end": 483
-    },
-    {
-      "text": "pushing border",
-      "type": "ENTITY",
-      "start": 490,
-      "end": 504
-    },
-    {
-      "text": "invade",
-      "type": "ENTITY",
-      "start": 518,
-      "end": 524
-    },
-    {
-      "text": "sinus",
-      "type": "ENTITY",
-      "start": 529,
-      "end": 534
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 535,
-      "end": 549
-    },
-    {
-      "text": "perinephric fat",
-      "type": "ENTITY",
-      "start": 553,
-      "end": 568
-    },
-    {
-      "text": "renal vein",
-      "type": "ENTITY",
-      "start": 574,
-      "end": 584
-    },
-    {
-      "text": "free of tumor",
-      "type": "ENTITY",
-      "start": 588,
-      "end": 601
-    },
-    {
-      "text": "GROSS DESCRIPTION",
-      "type": "ENTITY",
-      "start": 604,
-      "end": 621
-    },
-    {
-      "text": "KIDNEY",
-      "type": "ENTITY",
-      "start": 631,
-      "end": 637
-    },
-    {
-      "text": "A",
-      "type": "ENTITY",
-      "start": 640,
-      "end": 641
-    },
-    {
-      "text": "nephrectomy",
-      "type": "ENTITY",
-      "start": 642,
-      "end": 653
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 654,
-      "end": 662
-    },
-    {
-      "text": "kidney",
-      "type": "ENTITY",
-      "start": 700,
-      "end": 706
-    },
-    {
-      "text": "attached ureter",
-      "type": "ENTITY",
-      "start": 733,
-      "end": 748
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 760,
-      "end": 766
-    },
-    {
-      "text": "mid-portion",
-      "type": "ENTITY",
-      "start": 784,
-      "end": 795
-    },
-    {
-      "text": "kidney",
-      "type": "ENTITY",
-      "start": 803,
-      "end": 809
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 852,
-      "end": 861
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 880,
-      "end": 885
-    },
-    {
-      "text": "kidney",
-      "type": "ENTITY",
-      "start": 924,
-      "end": 930
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 935,
-      "end": 943
-    },
-    {
-      "text": "renal vein",
-      "type": "ENTITY",
-      "start": 951,
-      "end": 961
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 965,
-      "end": 975
-    },
-    {
-      "text": "inferior pole",
-      "type": "ENTITY",
-      "start": 992,
-      "end": 1005
-    },
-    {
-      "text": "kidney",
-      "type": "ENTITY",
-      "start": 1013,
-      "end": 1019
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 1042,
-      "end": 1046
-    },
-    {
-      "text": "multilocular cyst",
-      "type": "ENTITY",
-      "start": 1059,
-      "end": 1076
-    },
-    {
-      "text": "fluid",
-      "type": "ENTITY",
-      "start": 1115,
-      "end": 1120
-    },
-    {
-      "text": "cyst",
-      "type": "ENTITY",
-      "start": 1126,
-      "end": 1130
-    },
-    {
-      "text": "capsule",
-      "type": "ENTITY",
-      "start": 1142,
-      "end": 1149
-    },
-    {
-      "text": "smooth lining",
-      "type": "ENTITY",
-      "start": 1154,
-      "end": 1167
-    },
-    {
-      "text": "SECTION",
-      "type": "ENTITY",
-      "start": 1170,
-      "end": 1177
-    },
-    {
-      "text": "CODE",
-      "type": "ENTITY",
-      "start": 1178,
-      "end": 1182
-    },
-    {
-      "text": "A1",
-      "type": "ENTITY",
-      "start": 1184,
-      "end": 1186
-    },
-    {
-      "text": "vascular",
-      "type": "ENTITY",
-      "start": 1188,
-      "end": 1196
-    },
-    {
-      "text": "ureteric resection margin",
-      "type": "ENTITY",
-      "start": 1201,
-      "end": 1226
-    },
-    {
-      "text": "A2-A7",
-      "type": "ENTITY",
-      "start": 1238,
-      "end": 1243
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 1245,
-      "end": 1250
-    },
-    {
-      "text": "adjacent kidney",
-      "type": "ENTITY",
-      "start": 1256,
-      "end": 1271
-    },
-    {
-      "text": "A8",
-      "type": "ENTITY",
-      "start": 1273,
-      "end": 1275
-    },
-    {
-      "text": "A9",
-      "type": "ENTITY",
-      "start": 1277,
-      "end": 1279
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 1281,
-      "end": 1286
-    },
-    {
-      "text": "adjacent",
-      "type": "ENTITY",
-      "start": 1292,
-      "end": 1300
-    },
-    {
-      "text": "renal sinus",
-      "type": "ENTITY",
-      "start": 1301,
-      "end": 1312
-    },
-    {
-      "text": "A10-A14",
-      "type": "ENTITY",
-      "start": 1314,
-      "end": 1321
-    },
-    {
-      "text": "renal cysts",
-      "type": "ENTITY",
-      "start": 1323,
-      "end": 1334
-    },
-    {
-      "text": "adjacent",
-      "type": "ENTITY",
-      "start": 1340,
-      "end": 1348
-    },
-    {
-      "text": "renal parenchyma",
-      "type": "ENTITY",
-      "start": 1349,
-      "end": 1365
-    },
-    {
-      "text": "cassette A10",
-      "type": "ENTITY",
-      "start": 1396,
-      "end": 1408
-    },
-    {
-      "text": "A15",
-      "type": "ENTITY",
-      "start": 1410,
-      "end": 1413
-    },
-    {
-      "text": "renal pelvis",
-      "type": "ENTITY",
-      "start": 1415,
-      "end": 1427
-    },
-    {
-      "text": "A16",
-      "type": "ENTITY",
-      "start": 1429,
-      "end": 1432
-    },
-    {
-      "text": "normal kidney",
-      "type": "ENTITY",
-      "start": 1434,
-      "end": 1447
-    },
-    {
-      "text": "CLINICAL HISTORY",
-      "type": "ENTITY",
-      "start": 1457,
-      "end": 1473
-    },
-    {
-      "text": "Left renal mass",
-      "type": "ENTITY",
-      "start": 1474,
-      "end": 1489
-    },
-    {
-      "text": "SNOMED CODES",
-      "type": "ENTITY",
-      "start": 1491,
-      "end": 1503
-    }
-  ],
-  "entity_count": 74,
-  "has_embedding": true
-}

output/biomedbert_output/0126a9bb-8172-4c8c-b333-4509fe5cddc5_nlp.json

@@ -1,1568 +0,0 @@
-{
-  "filename": "0126a9bb-8172-4c8c-b333-4509fe5cddc5",
-  "timestamp": "2026-01-05T14:43:23.560857",
-  "entities": [
-    {
-      "text": "LcD o-3 Carcinoma",
-      "type": "ENTITY",
-      "start": 94,
-      "end": 111
-    },
-    {
-      "text": "bular inf",
-      "type": "ENTITY",
-      "start": 116,
-      "end": 125
-    },
-    {
-      "text": "Sentinel node biopsy",
-      "type": "ENTITY",
-      "start": 169,
-      "end": 189
-    },
-    {
-      "text": "partial mastectomy",
-      "type": "ENTITY",
-      "start": 194,
-      "end": 212
-    },
-    {
-      "text": "S",
-      "type": "ENTITY",
-      "start": 214,
-      "end": 215
-    },
-    {
-      "text": "Path-Brast UOQ",
-      "type": "ENTITY",
-      "start": 221,
-      "end": 235
-    },
-    {
-      "text": "A. Right",
-      "type": "ENTITY",
-      "start": 236,
-      "end": 244
-    },
-    {
-      "text": "axillary sentinel node",
-      "type": "ENTITY",
-      "start": 245,
-      "end": 267
-    },
-    {
-      "text": "Single lymph node",
-      "type": "ENTITY",
-      "start": 271,
-      "end": 288
-    },
-    {
-      "text": "no tumor",
-      "type": "ENTITY",
-      "start": 290,
-      "end": 298
-    },
-    {
-      "text": "B. Right",
-      "type": "ENTITY",
-      "start": 311,
-      "end": 319
-    },
-    {
-      "text": "C$cF B Brash N6s",
-      "type": "ENTITY",
-      "start": 347,
-      "end": 363
-    },
-    {
-      "text": "Invasive",
-      "type": "ENTITY",
-      "start": 366,
-      "end": 374
-    },
-    {
-      "text": "lobular carcinoma",
-      "type": "ENTITY",
-      "start": 375,
-      "end": 392
-    },
-    {
-      "text": "SBR grade II",
-      "type": "ENTITY",
-      "start": 394,
-      "end": 406
-    },
-    {
-      "text": "focal necrosis",
-      "type": "ENTITY",
-      "start": 413,
-      "end": 427
-    },
-    {
-      "text": "Focal",
-      "type": "ENTITY",
-      "start": 438,
-      "end": 443
-    },
-    {
-      "text": "atypical",
-      "type": "ENTITY",
-      "start": 476,
-      "end": 484
-    },
-    {
-      "text": "columnar cell",
-      "type": "ENTITY",
-      "start": 485,
-      "end": 498
-    },
-    {
-      "text": "Uninvolved",
-      "type": "ENTITY",
-      "start": 509,
-      "end": 519
-    },
-    {
-      "text": "breast parenchyma",
-      "type": "ENTITY",
-      "start": 520,
-      "end": 537
-    },
-    {
-      "text": "apocrine metaplasia",
-      "type": "ENTITY",
-      "start": 543,
-      "end": 562
-    },
-    {
-      "text": "Breast Pathologic Parameters",
-      "type": "ENTITY",
-      "start": 564,
-      "end": 592
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 596,
-      "end": 614
-    },
-    {
-      "text": "A. Combined",
-      "type": "ENTITY",
-      "start": 616,
-      "end": 627
-    },
-    {
-      "text": "gross",
-      "type": "ENTITY",
-      "start": 628,
-      "end": 633
-    },
-    {
-      "text": "microscopic measurement",
-      "type": "ENTITY",
-      "start": 638,
-      "end": 661
-    },
-    {
-      "text": "B. Composite",
-      "type": "ENTITY",
-      "start": 669,
-      "end": 681
-    },
-    {
-      "text": "histologic",
-      "type": "ENTITY",
-      "start": 682,
-      "end": 692
-    },
-    {
-      "text": "grade II",
-      "type": "ENTITY",
-      "start": 708,
-      "end": 716
-    },
-    {
-      "text": "Architecture",
-      "type": "ENTITY",
-      "start": 719,
-      "end": 731
-    },
-    {
-      "text": "Nuclear",
-      "type": "ENTITY",
-      "start": 737,
-      "end": 744
-    },
-    {
-      "text": "Mitotic",
-      "type": "ENTITY",
-      "start": 756,
-      "end": 763
-    },
-    {
-      "text": "C. Associated ductal carcinoma",
-      "type": "ENTITY",
-      "start": 773,
-      "end": 803
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 804,
-      "end": 811
-    },
-    {
-      "text": "DCIS",
-      "type": "ENTITY",
-      "start": 813,
-      "end": 817
-    },
-    {
-      "text": "Absent 2",
-      "type": "ENTITY",
-      "start": 820,
-      "end": 828
-    },
-    {
-      "text": "Excisional biopsy margins",
-      "type": "ENTITY",
-      "start": 830,
-      "end": 855
-    },
-    {
-      "text": "Free of",
-      "type": "ENTITY",
-      "start": 857,
-      "end": 864
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 865,
-      "end": 870
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 873,
-      "end": 891
-    },
-    {
-      "text": "superior",
-      "type": "ENTITY",
-      "start": 901,
-      "end": 909
-    },
-    {
-      "text": "slide B14",
-      "type": "ENTITY",
-      "start": 928,
-      "end": 937
-    },
-    {
-      "text": "Additional",
-      "type": "ENTITY",
-      "start": 941,
-      "end": 951
-    },
-    {
-      "text": "margins",
-      "type": "ENTITY",
-      "start": 952,
-      "end": 959
-    },
-    {
-      "text": "Blood vessel",
-      "type": "ENTITY",
-      "start": 985,
-      "end": 997
-    },
-    {
-      "text": "lymphatic invasion",
-      "type": "ENTITY",
-      "start": 1002,
-      "end": 1020
-    },
-    {
-      "text": "Absent 4",
-      "type": "ENTITY",
-      "start": 1022,
-      "end": 1030
-    },
-    {
-      "text": "Axillary lymph nodes",
-      "type": "ENTITY",
-      "start": 1032,
-      "end": 1052
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 1054,
-      "end": 1062
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 1067,
-      "end": 1072
-    },
-    {
-      "text": "Special studies",
-      "type": "ENTITY",
-      "start": 1076,
-      "end": 1091
-    },
-    {
-      "text": "Expression",
-      "type": "ENTITY",
-      "start": 1099,
-      "end": 1109
-    },
-    {
-      "text": "ER",
-      "type": "ENTITY",
-      "start": 1113,
-      "end": 1115
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 1126,
-      "end": 1134
-    },
-    {
-      "text": "tumor nuclei",
-      "type": "ENTITY",
-      "start": 1135,
-      "end": 1147
-    },
-    {
-      "text": "Expression",
-      "type": "ENTITY",
-      "start": 1150,
-      "end": 1160
-    },
-    {
-      "text": "PR",
-      "type": "ENTITY",
-      "start": 1164,
-      "end": 1166
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 1177,
-      "end": 1185
-    },
-    {
-      "text": "tumor nuclei",
-      "type": "ENTITY",
-      "start": 1186,
-      "end": 1198
-    },
-    {
-      "text": "Her2/neu antigen",
-      "type": "ENTITY",
-      "start": 1201,
-      "end": 1217
-    },
-    {
-      "text": "FISH",
-      "type": "ENTITY",
-      "start": 1219,
-      "end": 1223
-    },
-    {
-      "text": "Non-amplified",
-      "type": "ENTITY",
-      "start": 1226,
-      "end": 1239
-    },
-    {
-      "text": "ratio",
-      "type": "ENTITY",
-      "start": 1241,
-      "end": 1246
-    },
-    {
-      "text": "pTNM",
-      "type": "ENTITY",
-      "start": 1254,
-      "end": 1258
-    },
-    {
-      "text": "pT2",
-      "type": "ENTITY",
-      "start": 1260,
-      "end": 1263
-    },
-    {
-      "text": "NO(sn",
-      "type": "ENTITY",
-      "start": 1265,
-      "end": 1270
-    },
-    {
-      "text": "MX Clinical History",
-      "type": "ENTITY",
-      "start": 1273,
-      "end": 1292
-    },
-    {
-      "text": "patient",
-      "type": "ENTITY",
-      "start": 1299,
-      "end": 1306
-    },
-    {
-      "text": "female",
-      "type": "ENTITY",
-      "start": 1324,
-      "end": 1330
-    },
-    {
-      "text": "right breast mass",
-      "type": "ENTITY",
-      "start": 1338,
-      "end": 1355
-    },
-    {
-      "text": "patient",
-      "type": "ENTITY",
-      "start": 1361,
-      "end": 1368
-    },
-    {
-      "text": "self-palpated",
-      "type": "ENTITY",
-      "start": 1369,
-      "end": 1382
-    },
-    {
-      "text": "breast mass",
-      "type": "ENTITY",
-      "start": 1385,
-      "end": 1396
-    },
-    {
-      "text": "right upper outer quadrant",
-      "type": "ENTITY",
-      "start": 1404,
-      "end": 1430
-    },
-    {
-      "text": "diagnostic mammography",
-      "type": "ENTITY",
-      "start": 1448,
-      "end": 1470
-    },
-    {
-      "text": "ultrasound",
-      "type": "ENTITY",
-      "start": 1475,
-      "end": 1485
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 1513,
-      "end": 1517
-    },
-    {
-      "text": "size",
-      "type": "ENTITY",
-      "start": 1542,
-      "end": 1546
-    },
-    {
-      "text": "ultrasound-guided core biopsy",
-      "type": "ENTITY",
-      "start": 1551,
-      "end": 1580
-    },
-    {
-      "text": "clip",
-      "type": "ENTITY",
-      "start": 1585,
-      "end": 1589
-    },
-    {
-      "text": "placement",
-      "type": "ENTITY",
-      "start": 1590,
-      "end": 1599
-    },
-    {
-      "text": "lobular features4",
-      "type": "ENTITY",
-      "start": 1660,
-      "end": 1677
-    },
-    {
-      "text": "patient",
-      "type": "ENTITY",
-      "start": 1685,
-      "end": 1692
-    },
-    {
-      "text": "breast MRI",
-      "type": "ENTITY",
-      "start": 1705,
-      "end": 1715
-    },
-    {
-      "text": "irregularly",
-      "type": "ENTITY",
-      "start": 1745,
-      "end": 1756
-    },
-    {
-      "text": "shaped",
-      "type": "ENTITY",
-      "start": 1757,
-      "end": 1763
-    },
-    {
-      "text": "posteriorly positioned",
-      "type": "ENTITY",
-      "start": 1765,
-      "end": 1787
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 1788,
-      "end": 1792
-    },
-    {
-      "text": "o'clock",
-      "type": "ENTITY",
-      "start": 1799,
-      "end": 1806
-    },
-    {
-      "text": "right breast",
-      "type": "ENTITY",
-      "start": 1814,
-      "end": 1826
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 1827,
-      "end": 1836
-    },
-    {
-      "text": "bilateral axillae",
-      "type": "ENTITY",
-      "start": 1887,
-      "end": 1904
-    },
-    {
-      "text": "patient",
-      "type": "ENTITY",
-      "start": 1922,
-      "end": 1929
-    },
-    {
-      "text": "right sentinel lymph node biopsy",
-      "type": "ENTITY",
-      "start": 1940,
-      "end": 1972
-    },
-    {
-      "text": "right breast partial mastectomy",
-      "type": "ENTITY",
-      "start": 1977,
-      "end": 2008
-    },
-    {
-      "text": "needle",
-      "type": "ENTITY",
-      "start": 2014,
-      "end": 2020
-    },
-    {
-      "text": "localization",
-      "type": "ENTITY",
-      "start": 2021,
-      "end": 2033
-    },
-    {
-      "text": "tumor cells",
-      "type": "ENTITY",
-      "start": 2047,
-      "end": 2058
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 2063,
-      "end": 2071
-    },
-    {
-      "text": "E-cadherin",
-      "type": "ENTITY",
-      "start": 2076,
-      "end": 2086
-    },
-    {
-      "text": "consistent with",
-      "type": "ENTITY",
-      "start": 2087,
-      "end": 2102
-    },
-    {
-      "text": "lobular",
-      "type": "ENTITY",
-      "start": 2105,
-      "end": 2112
-    },
-    {
-      "text": "phenotype",
-      "type": "ENTITY",
-      "start": 2113,
-      "end": 2122
-    },
-    {
-      "text": "AE1/AE3 stain",
-      "type": "ENTITY",
-      "start": 2124,
-      "end": 2137
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 2141,
-      "end": 2149
-    },
-    {
-      "text": "sentinel node",
-      "type": "ENTITY",
-      "start": 2157,
-      "end": 2170
-    },
-    {
-      "text": "Specimens",
-      "type": "ENTITY",
-      "start": 2173,
-      "end": 2182
-    },
-    {
-      "text": "Received",
-      "type": "ENTITY",
-      "start": 2183,
-      "end": 2191
-    },
-    {
-      "text": "Right axillary sentinel lymph node B",
-      "type": "ENTITY",
-      "start": 2196,
-      "end": 2232
-    },
-    {
-      "text": "Right Breast Partial Mastectomy",
-      "type": "ENTITY",
-      "start": 2234,
-      "end": 2265
-    },
-    {
-      "text": "Gross Description",
-      "type": "ENTITY",
-      "start": 2266,
-      "end": 2283
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2289,
-      "end": 2297
-    },
-    {
-      "text": "containers",
-      "type": "ENTITY",
-      "start": 2317,
-      "end": 2327
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 2333,
-      "end": 2340
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 2350,
-      "end": 2359
-    },
-    {
-      "text": "medical record number",
-      "type": "ENTITY",
-      "start": 2369,
-      "end": 2390
-    },
-    {
-      "text": "A. Part A",
-      "type": "ENTITY",
-      "start": 2392,
-      "end": 2401
-    },
-    {
-      "text": "right axillary sentinel node",
-      "type": "ENTITY",
-      "start": 2432,
-      "end": 2460
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 2475,
-      "end": 2480
-    },
-    {
-      "text": "frozen diagnosis",
-      "type": "ENTITY",
-      "start": 2485,
-      "end": 2501
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 2526,
-      "end": 2536
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 2546,
-      "end": 2554
-    },
-    {
-      "text": "frozen",
-      "type": "ENTITY",
-      "start": 2568,
-      "end": 2574
-    },
-    {
-      "text": "read",
-      "type": "ENTITY",
-      "start": 2579,
-      "end": 2583
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 2591,
-      "end": 2599
-    },
-    {
-      "text": "metastatic tumor4",
-      "type": "ENTITY",
-      "start": 2603,
-      "end": 2620
-    },
-    {
-      "text": "remnant",
-      "type": "ENTITY",
-      "start": 2629,
-      "end": 2636
-    },
-    {
-      "text": "frozen tissue",
-      "type": "ENTITY",
-      "start": 2640,
-      "end": 2653
-    },
-    {
-      "text": "cassette",
-      "type": "ENTITY",
-      "start": 2679,
-      "end": 2687
-    },
-    {
-      "text": "A1FS",
-      "type": "ENTITY",
-      "start": 2688,
-      "end": 2692
-    },
-    {
-      "text": "B. Part B",
-      "type": "ENTITY",
-      "start": 2694,
-      "end": 2703
-    },
-    {
-      "text": "right breast partial mastectomy4",
-      "type": "ENTITY",
-      "start": 2735,
-      "end": 2767
-    },
-    {
-      "text": "fresh",
-      "type": "ENTITY",
-      "start": 2778,
-      "end": 2783
-    },
-    {
-      "text": "AccuGrid",
-      "type": "ENTITY",
-      "start": 2790,
-      "end": 2798
-    },
-    {
-      "text": "radiograph",
-      "type": "ENTITY",
-      "start": 2817,
-      "end": 2827
-    },
-    {
-      "text": "partial",
-      "type": "ENTITY",
-      "start": 2842,
-      "end": 2849
-    },
-    {
-      "text": "mastectomy",
-      "type": "ENTITY",
-      "start": 2850,
-      "end": 2860
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2861,
-      "end": 2869
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2875,
-      "end": 2883
-    },
-    {
-      "text": "needle",
-      "type": "ENTITY",
-      "start": 2894,
-      "end": 2900
-    },
-    {
-      "text": "double long stitch",
-      "type": "ENTITY",
-      "start": 2926,
-      "end": 2944
-    },
-    {
-      "text": "orientation",
-      "type": "ENTITY",
-      "start": 2980,
-      "end": 2991
-    },
-    {
-      "text": "overall",
-      "type": "ENTITY",
-      "start": 2997,
-      "end": 3004
-    },
-    {
-      "text": "measurements",
-      "type": "ENTITY",
-      "start": 3005,
-      "end": 3017
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 3046,
-      "end": 3054
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 3063,
-      "end": 3069
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 3089,
-      "end": 3097
-    },
-    {
-      "text": "posterior",
-      "type": "ENTITY",
-      "start": 3101,
-      "end": 3110
-    },
-    {
-      "text": "requisition designates",
-      "type": "ENTITY",
-      "start": 3123,
-      "end": 3145
-    },
-    {
-      "text": "stitch",
-      "type": "ENTITY",
-      "start": 3163,
-      "end": 3169
-    },
-    {
-      "text": "lateral margin",
-      "type": "ENTITY",
-      "start": 3173,
-      "end": 3187
-    },
-    {
-      "text": "short stitch",
-      "type": "ENTITY",
-      "start": 3192,
-      "end": 3204
-    },
-    {
-      "text": "radiograph",
-      "type": "ENTITY",
-      "start": 3242,
-      "end": 3252
-    },
-    {
-      "text": "stellate",
-      "type": "ENTITY",
-      "start": 3288,
-      "end": 3296
-    },
-    {
-      "text": "partial mastectomy",
-      "type": "ENTITY",
-      "start": 3313,
-      "end": 3331
-    },
-    {
-      "text": "C3",
-      "type": "ENTITY",
-      "start": 3364,
-      "end": 3366
-    },
-    {
-      "text": "D3",
-      "type": "ENTITY",
-      "start": 3368,
-      "end": 3370
-    },
-    {
-      "text": "D2",
-      "type": "ENTITY",
-      "start": 3375,
-      "end": 3377
-    },
-    {
-      "text": "needle",
-      "type": "ENTITY",
-      "start": 3390,
-      "end": 3396
-    },
-    {
-      "text": "localization",
-      "type": "ENTITY",
-      "start": 3397,
-      "end": 3409
-    },
-    {
-      "text": "wire",
-      "type": "ENTITY",
-      "start": 3410,
-      "end": 3414
-    },
-    {
-      "text": "A3",
-      "type": "ENTITY",
-      "start": 3431,
-      "end": 3433
-    },
-    {
-      "text": "terminates",
-      "type": "ENTITY",
-      "start": 3438,
-      "end": 3448
-    },
-    {
-      "text": "E1",
-      "type": "ENTITY",
-      "start": 3452,
-      "end": 3454
-    },
-    {
-      "text": "needle",
-      "type": "ENTITY",
-      "start": 3474,
-      "end": 3480
-    },
-    {
-      "text": "localization",
-      "type": "ENTITY",
-      "start": 3481,
-      "end": 3493
-    },
-    {
-      "text": "A5",
-      "type": "ENTITY",
-      "start": 3512,
-      "end": 3514
-    },
-    {
-      "text": "terminates",
-      "type": "ENTITY",
-      "start": 3519,
-      "end": 3529
-    },
-    {
-      "text": "E4",
-      "type": "ENTITY",
-      "start": 3533,
-      "end": 3535
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 3541,
-      "end": 3545
-    },
-    {
-      "text": "wires",
-      "type": "ENTITY",
-      "start": 3570,
-      "end": 3575
-    },
-    {
-      "text": "Thereis",
-      "type": "ENTITY",
-      "start": 3577,
-      "end": 3584
-    },
-    {
-      "text": "clip",
-      "type": "ENTITY",
-      "start": 3594,
-      "end": 3598
-    },
-    {
-      "text": "quadrant D2",
-      "type": "ENTITY",
-      "start": 3602,
-      "end": 3613
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 3620,
-      "end": 3628
-    },
-    {
-      "text": "anterior-black",
-      "type": "ENTITY",
-      "start": 3650,
-      "end": 3664
-    },
-    {
-      "text": "lateral-violet",
-      "type": "ENTITY",
-      "start": 3681,
-      "end": 3695
-    },
-    {
-      "text": "medial-yellow",
-      "type": "ENTITY",
-      "start": 3697,
-      "end": 3710
-    },
-    {
-      "text": "superior-blue",
-      "type": "ENTITY",
-      "start": 3712,
-      "end": 3725
-    },
-    {
-      "text": "inferior-green",
-      "type": "ENTITY",
-      "start": 3730,
-      "end": 3744
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 3750,
-      "end": 3758
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 3786,
-      "end": 3793
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 3797,
-      "end": 3803
-    },
-    {
-      "text": "slices",
-      "type": "ENTITY",
-      "start": 3814,
-      "end": 3820
-    },
-    {
-      "text": "irregularly",
-      "type": "ENTITY",
-      "start": 3839,
-      "end": 3850
-    },
-    {
-      "text": "shaped",
-      "type": "ENTITY",
-      "start": 3851,
-      "end": 3857
-    },
-    {
-      "text": "firm",
-      "type": "ENTITY",
-      "start": 3859,
-      "end": 3863
-    },
-    {
-      "text": "white-tan mass",
-      "type": "ENTITY",
-      "start": 3865,
-      "end": 3879
-    },
-    {
-      "text": "slices",
-      "type": "ENTITY",
-      "start": 3891,
-      "end": 3897
-    },
-    {
-      "text": "Needle",
-      "type": "ENTITY",
-      "start": 3913,
-      "end": 3919
-    },
-    {
-      "text": "localization",
-      "type": "ENTITY",
-      "start": 3921,
-      "end": 3933
-    },
-    {
-      "text": "terminate",
-      "type": "ENTITY",
-      "start": 3940,
-      "end": 3949
-    },
-    {
-      "text": "slices",
-      "type": "ENTITY",
-      "start": 3953,
-      "end": 3959
-    },
-    {
-      "text": "clip",
-      "type": "ENTITY",
-      "start": 3975,
-      "end": 3979
-    },
-    {
-      "text": "dimensions",
-      "type": "ENTITY",
-      "start": 4018,
-      "end": 4028
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4036,
-      "end": 4040
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4069,
-      "end": 4073
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 4101,
-      "end": 4109
-    },
-    {
-      "text": "margin",
-      "type": "ENTITY",
-      "start": 4110,
-      "end": 4116
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 4134,
-      "end": 4149
-    },
-    {
-      "text": "superior margin",
-      "type": "ENTITY",
-      "start": 4167,
-      "end": 4182
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 4216,
-      "end": 4223
-    },
-    {
-      "text": "medial margins",
-      "type": "ENTITY",
-      "start": 4228,
-      "end": 4242
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 4265,
-      "end": 4273
-    },
-    {
-      "text": "breast parenchyma",
-      "type": "ENTITY",
-      "start": 4308,
-      "end": 4325
-    },
-    {
-      "text": "lobular",
-      "type": "ENTITY",
-      "start": 4340,
-      "end": 4347
-    },
-    {
-      "text": "soft",
-      "type": "ENTITY",
-      "start": 4349,
-      "end": 4353
-    },
-    {
-      "text": "yellow-tan tissue",
-      "type": "ENTITY",
-      "start": 4355,
-      "end": 4372
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 4411,
-      "end": 4434
-    },
-    {
-      "text": "lateral margin",
-      "type": "ENTITY",
-      "start": 4469,
-      "end": 4483
-    },
-    {
-      "text": "serially sectioned",
-      "type": "ENTITY",
-      "start": 4485,
-      "end": 4503
-    },
-    {
-      "text": "medial margin",
-      "type": "ENTITY",
-      "start": 4531,
-      "end": 4544
-    },
-    {
-      "text": "serially sectioned",
-      "type": "ENTITY",
-      "start": 4546,
-      "end": 4564
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4610,
-      "end": 4614
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 4618,
-      "end": 4626
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4635,
-      "end": 4640
-    },
-    {
-      "text": "margin",
-      "type": "ENTITY",
-      "start": 4677,
-      "end": 4683
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4685,
-      "end": 4690
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4719,
-      "end": 4723
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 4727,
-      "end": 4742
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4744,
-      "end": 4749
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4757,
-      "end": 4761
-    },
-    {
-      "text": "representative",
-      "type": "ENTITY",
-      "start": 4763,
-      "end": 4777
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 4778,
-      "end": 4785
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4786,
-      "end": 4791
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 4826,
-      "end": 4833
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 4837,
-      "end": 4841
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4843,
-      "end": 4848
-    },
-    {
-      "text": "representative",
-      "type": "ENTITY",
-      "start": 4857,
-      "end": 4871
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 4872,
-      "end": 4879
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 4883,
-      "end": 4889
-    },
-    {
-      "text": "termination",
-      "type": "ENTITY",
-      "start": 4893,
-      "end": 4904
-    },
-    {
-      "text": "localization",
-      "type": "ENTITY",
-      "start": 4908,
-      "end": 4920
-    },
-    {
-      "text": "wire",
-      "type": "ENTITY",
-      "start": 4921,
-      "end": 4925
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4927,
-      "end": 4932
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 4945,
-      "end": 4951
-    },
-    {
-      "text": "needle",
-      "type": "ENTITY",
-      "start": 4955,
-      "end": 4961
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 4993,
-      "end": 4998
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 5027,
-      "end": 5035
-    },
-    {
-      "text": "nodular tan-white",
-      "type": "ENTITY",
-      "start": 5039,
-      "end": 5056
-    },
-    {
-      "text": "B15,B16",
-      "type": "ENTITY",
-      "start": 5084,
-      "end": 5091
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 5108,
-      "end": 5116
-    },
-    {
-      "text": "nodular tan-white breast parenchyma",
-      "type": "ENTITY",
-      "start": 5120,
-      "end": 5155
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 5157,
-      "end": 5162
-    },
-    {
-      "text": "representative",
-      "type": "ENTITY",
-      "start": 5172,
-      "end": 5186
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 5187,
-      "end": 5194
-    },
-    {
-      "text": "unremarkable",
-      "type": "ENTITY",
-      "start": 5198,
-      "end": 5210
-    },
-    {
-      "text": "breast parenchyma",
-      "type": "ENTITY",
-      "start": 5211,
-      "end": 5228
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 5230,
-      "end": 5235
-    },
-    {
-      "text": "representative",
-      "type": "ENTITY",
-      "start": 5244,
-      "end": 5258
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 5259,
-      "end": 5266
-    },
-    {
-      "text": "unremarkable",
-      "type": "ENTITY",
-      "start": 5270,
-      "end": 5282
-    },
-    {
-      "text": "breast parenchyma",
-      "type": "ENTITY",
-      "start": 5283,
-      "end": 5300
-    },
-    {
-      "text": "slice",
-      "type": "ENTITY",
-      "start": 5302,
-      "end": 5307
-    },
-    {
-      "text": "Intraoperative",
-      "type": "ENTITY",
-      "start": 5312,
-      "end": 5326
-    },
-    {
-      "text": "Diagnosis",
-      "type": "ENTITY",
-      "start": 5335,
-      "end": 5344
-    },
-    {
-      "text": "A1FS",
-      "type": "ENTITY",
-      "start": 5346,
-      "end": 5350
-    },
-    {
-      "text": "No evidence",
-      "type": "ENTITY",
-      "start": 5388,
-      "end": 5399
-    },
-    {
-      "text": "metastatic tumor",
-      "type": "ENTITY",
-      "start": 5403,
-      "end": 5419
-    }
-  ],
-  "entity_count": 260,
-  "has_embedding": true
-}

output/biomedbert_output/013643d8-723f-48a9-a315-0f7c6f766c58_nlp.json

@@ -1,200 +0,0 @@
-{
-  "filename": "013643d8-723f-48a9-a315-0f7c6f766c58",
-  "timestamp": "2026-01-05T14:43:24.408231",
-  "entities": [
-    {
-      "text": "Sits",
-      "type": "ENTITY",
-      "start": 24,
-      "end": 28
-    },
-    {
-      "text": "Breast",
-      "type": "ENTITY",
-      "start": 68,
-      "end": 74
-    },
-    {
-      "text": "right",
-      "type": "ENTITY",
-      "start": 76,
-      "end": 81
-    },
-    {
-      "text": "excision",
-      "type": "ENTITY",
-      "start": 83,
-      "end": 91
-    },
-    {
-      "text": "Infiltrating lobular carcinoma",
-      "type": "ENTITY",
-      "start": 93,
-      "end": 123
-    },
-    {
-      "text": "Nottingham I",
-      "type": "ENTITY",
-      "start": 125,
-      "end": 137
-    },
-    {
-      "text": "mass",
-      "type": "ENTITY",
-      "start": 176,
-      "end": 180
-    },
-    {
-      "text": "AJcc pTlc",
-      "type": "ENTITY",
-      "start": 182,
-      "end": 191
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 198,
-      "end": 207
-    },
-    {
-      "text": "ductular",
-      "type": "ENTITY",
-      "start": 214,
-      "end": 222
-    },
-    {
-      "text": "involvement",
-      "type": "ENTITY",
-      "start": 223,
-      "end": 234
-    },
-    {
-      "text": "angiolymphatic",
-      "type": "ENTITY",
-      "start": 239,
-      "end": 253
-    },
-    {
-      "text": "involvement",
-      "type": "ENTITY",
-      "start": 254,
-      "end": 265
-    },
-    {
-      "text": "surgical resection margins",
-      "type": "ENTITY",
-      "start": 282,
-      "end": 308
-    },
-    {
-      "text": "margins",
-      "type": "ENTITY",
-      "start": 345,
-      "end": 352
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 358,
-      "end": 366
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 371,
-      "end": 376
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 378,
-      "end": 389
-    },
-    {
-      "text": "right sentinel",
-      "type": "ENTITY",
-      "start": 391,
-      "end": 405
-    },
-    {
-      "text": "excision",
-      "type": "ENTITY",
-      "start": 407,
-      "end": 415
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 417,
-      "end": 425
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 430,
-      "end": 435
-    },
-    {
-      "text": "sentinel lymph node tissue",
-      "type": "ENTITY",
-      "start": 446,
-      "end": 472
-    },
-    {
-      "text": "H&E",
-      "type": "ENTITY",
-      "start": 490,
-      "end": 493
-    },
-    {
-      "text": "impression",
-      "type": "ENTITY",
-      "start": 494,
-      "end": 504
-    },
-    {
-      "text": "infiltrating",
-      "type": "ENTITY",
-      "start": 510,
-      "end": 522
-    },
-    {
-      "text": "breast carcinoma",
-      "type": "ENTITY",
-      "start": 523,
-      "end": 539
-    },
-    {
-      "text": "positive",
-      "type": "ENTITY",
-      "start": 543,
-      "end": 551
-    },
-    {
-      "text": "estrogen receptor",
-      "type": "ENTITY",
-      "start": 556,
-      "end": 573
-    },
-    {
-      "text": "negative",
-      "type": "ENTITY",
-      "start": 578,
-      "end": 586
-    },
-    {
-      "text": "progesterone receptor",
-      "type": "ENTITY",
-      "start": 591,
-      "end": 612
-    },
-    {
-      "text": "TCGA-AR-A2LE-01A-PR",
-      "type": "ENTITY",
-      "start": 656,
-      "end": 675
-    }
-  ],
-  "entity_count": 32,
-  "has_embedding": true
-}

output/biomedbert_output/0138414a-aa54-4ad7-813a-c01fae2abec9_nlp.json

@@ -1,368 +0,0 @@
-{
-  "filename": "0138414a-aa54-4ad7-813a-c01fae2abec9",
-  "timestamp": "2026-01-05T14:42:43.658383",
-  "entities": [
-    {
-      "text": "TCGA-AZ-4682 Parts 1",
-      "type": "ENTITY",
-      "start": 34,
-      "end": 54
-    },
-    {
-      "text": "SIGMOID COLON",
-      "type": "ENTITY",
-      "start": 65,
-      "end": 78
-    },
-    {
-      "text": "COLECTOMY",
-      "type": "ENTITY",
-      "start": 80,
-      "end": 89
-    },
-    {
-      "text": "A.  INVASIVE MODERATELY DIFFERENTIATED",
-      "type": "ENTITY",
-      "start": 93,
-      "end": 131
-    },
-    {
-      "text": "ADENOCARCINOMA",
-      "type": "ENTITY",
-      "start": 132,
-      "end": 146
-    },
-    {
-      "text": "CM",
-      "type": "ENTITY",
-      "start": 152,
-      "end": 154
-    },
-    {
-      "text": "MUSCULARIS Propria",
-      "type": "ENTITY",
-      "start": 164,
-      "end": 182
-    },
-    {
-      "text": "into.perirectal fat",
-      "type": "ENTITY",
-      "start": 183,
-      "end": 202
-    },
-    {
-      "text": "ANGIOLYMPHATICINVASION",
-      "type": "ENTITY",
-      "start": 208,
-      "end": 230
-    },
-    {
-      "text": "IDENTIFIED",
-      "type": "ENTITY",
-      "start": 231,
-      "end": 241
-    },
-    {
-      "text": "C.  SURGICAL RESECTION MARGINS FREE OF",
-      "type": "ENTITY",
-      "start": 243,
-      "end": 281
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 282,
-      "end": 287
-    },
-    {
-      "text": "pericolonic",
-      "type": "ENTITY",
-      "start": 299,
-      "end": 310
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 311,
-      "end": 322
-    },
-    {
-      "text": "free Of tumor",
-      "type": "ENTITY",
-      "start": 324,
-      "end": 337
-    },
-    {
-      "text": "E. pATHOLOGIC STAGE pT3 N0 M1",
-      "type": "ENTITY",
-      "start": 345,
-      "end": 374
-    },
-    {
-      "text": "HYPERPLASTIC.POLYPS",
-      "type": "ENTITY",
-      "start": 376,
-      "end": 395
-    },
-    {
-      "text": "Liver",
-      "type": "ENTITY",
-      "start": 405,
-      "end": 410
-    },
-    {
-      "text": "biopsy",
-      "type": "ENTITY",
-      "start": 412,
-      "end": 418
-    },
-    {
-      "text": "MICROSCOPIC",
-      "type": "ENTITY",
-      "start": 422,
-      "end": 433
-    },
-    {
-      "text": "SYNOPTIC",
-      "type": "ENTITY",
-      "start": 435,
-      "end": 443
-    },
-    {
-      "text": "DATA",
-      "type": "ENTITY",
-      "start": 444,
-      "end": 448
-    },
-    {
-      "text": "PRIMARY",
-      "type": "ENTITY",
-      "start": 451,
-      "end": 458
-    },
-    {
-      "text": "RECTAL TUMORS",
-      "type": "ENTITY",
-      "start": 469,
-      "end": 482
-    },
-    {
-      "text": "SPECImen",
-      "type": "ENTITY",
-      "start": 483,
-      "end": 491
-    },
-    {
-      "text": "Rectal/rectosigmoid colon",
-      "type": "ENTITY",
-      "start": 500,
-      "end": 525
-    },
-    {
-      "text": "low anterior resection",
-      "type": "ENTITY",
-      "start": 527,
-      "end": 549
-    },
-    {
-      "text": "Rectosigmoid",
-      "type": "ENTITY",
-      "start": 578,
-      "end": 590
-    },
-    {
-      "text": "TuMOR SITE",
-      "type": "ENTITY",
-      "start": 591,
-      "end": 601
-    },
-    {
-      "text": "TUMOR CONFIGURATION",
-      "type": "ENTITY",
-      "start": 603,
-      "end": 622
-    },
-    {
-      "text": "Uicerating",
-      "type": "ENTITY",
-      "start": 624,
-      "end": 634
-    },
-    {
-      "text": "dimension",
-      "type": "ENTITY",
-      "start": 656,
-      "end": 665
-    },
-    {
-      "text": "INTACTNESS",
-      "type": "ENTITY",
-      "start": 674,
-      "end": 684
-    },
-    {
-      "text": "MESORECTUM",
-      "type": "ENTITY",
-      "start": 688,
-      "end": 698
-    },
-    {
-      "text": "HISTOLOgIC TyPE",
-      "type": "ENTITY",
-      "start": 716,
-      "end": 731
-    },
-    {
-      "text": "Adenocarcinoma",
-      "type": "ENTITY",
-      "start": 733,
-      "end": 747
-    },
-    {
-      "text": "Low-grade",
-      "type": "ENTITY",
-      "start": 770,
-      "end": 779
-    },
-    {
-      "text": "differentiated",
-      "type": "ENTITY",
-      "start": 800,
-      "end": 814
-    },
-    {
-      "text": "pTNM",
-      "type": "ENTITY",
-      "start": 836,
-      "end": 840
-    },
-    {
-      "text": "pT3",
-      "type": "ENTITY",
-      "start": 844,
-      "end": 847
-    },
-    {
-      "text": "nodes",
-      "type": "ENTITY",
-      "start": 862,
-      "end": 867
-    },
-    {
-      "text": "nodes",
-      "type": "ENTITY",
-      "start": 890,
-      "end": 895
-    },
-    {
-      "text": "Proxima! margin",
-      "type": "ENTITY",
-      "start": 921,
-      "end": 936
-    },
-    {
-      "text": "uninvolved",
-      "type": "ENTITY",
-      "start": 937,
-      "end": 947
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 951,
-      "end": 969
-    },
-    {
-      "text": "Dista!",
-      "type": "ENTITY",
-      "start": 970,
-      "end": 976
-    },
-    {
-      "text": "uninvolved",
-      "type": "ENTITY",
-      "start": 984,
-      "end": 994
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 998,
-      "end": 1016
-    },
-    {
-      "text": "Circumferential (radial) margin",
-      "type": "ENTITY",
-      "start": 1017,
-      "end": 1048
-    },
-    {
-      "text": "uninvolved",
-      "type": "ENTITY",
-      "start": 1049,
-      "end": 1059
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 1063,
-      "end": 1081
-    },
-    {
-      "text": "Mesenteric margin",
-      "type": "ENTITY",
-      "start": 1083,
-      "end": 1100
-    },
-    {
-      "text": "assessed",
-      "type": "ENTITY",
-      "start": 1111,
-      "end": 1119
-    },
-    {
-      "text": "ANGIOLYMPHATIC",
-      "type": "ENTITY",
-      "start": 1120,
-      "end": 1134
-    },
-    {
-      "text": "INVASION",
-      "type": "ENTITY",
-      "start": 1135,
-      "end": 1143
-    },
-    {
-      "text": "Absent PERINEURAL INVASION",
-      "type": "ENTITY",
-      "start": 1145,
-      "end": 1171
-    },
-    {
-      "text": "Absent TUMORAL LYMPHOCYTIC",
-      "type": "ENTITY",
-      "start": 1173,
-      "end": 1199
-    },
-    {
-      "text": "moderate",
-      "type": "ENTITY",
-      "start": 1218,
-      "end": 1226
-    },
-    {
-      "text": "polyps",
-      "type": "ENTITY",
-      "start": 1233,
-      "end": 1239
-    },
-    {
-      "text": "(type[s]):Hyperplastic polyps",
-      "type": "ENTITY",
-      "start": 1240,
-      "end": 1269
-    }
-  ],
-  "entity_count": 60,
-  "has_embedding": true
-}

output/biomedbert_output/01461646-e769-4f18-a157-40560d7c327d_nlp.json

@@ -1,524 +0,0 @@
-{
-  "filename": "01461646-e769-4f18-a157-40560d7c327d",
-  "timestamp": "2026-01-05T14:40:56.659144",
-  "entities": [
-    {
-      "text": "Caucinome.mfi1tnsHny dutl",
-      "type": "ENTITY",
-      "start": 24,
-      "end": 49
-    },
-    {
-      "text": "Sr+",
-      "type": "ENTITY",
-      "start": 62,
-      "end": 65
-    },
-    {
-      "text": "buast",
-      "type": "ENTITY",
-      "start": 68,
-      "end": 73
-    },
-    {
-      "text": "page",
-      "type": "ENTITY",
-      "start": 88,
-      "end": 92
-    },
-    {
-      "text": "1 Department of Cancer",
-      "type": "ENTITY",
-      "start": 97,
-      "end": 119
-    },
-    {
-      "text": "Pathologye",
-      "type": "ENTITY",
-      "start": 120,
-      "end": 130
-    },
-    {
-      "text": "copy No. Date",
-      "type": "ENTITY",
-      "start": 131,
-      "end": 144
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 146,
-      "end": 157
-    },
-    {
-      "text": "Histopathological",
-      "type": "ENTITY",
-      "start": 159,
-      "end": 176
-    },
-    {
-      "text": "examination",
-      "type": "ENTITY",
-      "start": 177,
-      "end": 188
-    },
-    {
-      "text": "Internal invoice No. Cost",
-      "type": "ENTITY",
-      "start": 190,
-      "end": 215
-    },
-    {
-      "text": "diagnostic proceduree Examination No.",
-      "type": "ENTITY",
-      "start": 219,
-      "end": 256
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 258,
-      "end": 265
-    },
-    {
-      "text": "XXX",
-      "type": "ENTITY",
-      "start": 267,
-      "end": 270
-    },
-    {
-      "text": "PESEL",
-      "type": "ENTITY",
-      "start": 271,
-      "end": 276
-    },
-    {
-      "text": "XXX Age",
-      "type": "ENTITY",
-      "start": 278,
-      "end": 285
-    },
-    {
-      "text": "Gender",
-      "type": "ENTITY",
-      "start": 287,
-      "end": 293
-    },
-    {
-      "text": "Multiple organ",
-      "type": "ENTITY",
-      "start": 307,
-      "end": 321
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 322,
-      "end": 331
-    },
-    {
-      "text": "left breast",
-      "type": "ENTITY",
-      "start": 335,
-      "end": 346
-    },
-    {
-      "text": "charge",
-      "type": "ENTITY",
-      "start": 378,
-      "end": 384
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 386,
-      "end": 394
-    },
-    {
-      "text": "collected",
-      "type": "ENTITY",
-      "start": 395,
-      "end": 404
-    },
-    {
-      "text": "Material",
-      "type": "ENTITY",
-      "start": 409,
-      "end": 417
-    },
-    {
-      "text": "Expected time",
-      "type": "ENTITY",
-      "start": 430,
-      "end": 443
-    },
-    {
-      "text": "examination",
-      "type": "ENTITY",
-      "start": 447,
-      "end": 458
-    },
-    {
-      "text": "working days",
-      "type": "ENTITY",
-      "start": 468,
-      "end": 480
-    },
-    {
-      "text": "Clinical diagnosis",
-      "type": "ENTITY",
-      "start": 482,
-      "end": 500
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 502,
-      "end": 513
-    },
-    {
-      "text": "performed",
-      "type": "ENTITY",
-      "start": 514,
-      "end": 523
-    },
-    {
-      "text": "immunohistochemical examination",
-      "type": "ENTITY",
-      "start": 540,
-      "end": 571
-    },
-    {
-      "text": "estrogen receptors",
-      "type": "ENTITY",
-      "start": 576,
-      "end": 594
-    },
-    {
-      "text": "neoplastic cell",
-      "type": "ENTITY",
-      "start": 608,
-      "end": 623
-    },
-    {
-      "text": "progesterone receptors",
-      "type": "ENTITY",
-      "start": 635,
-      "end": 657
-    },
-    {
-      "text": "neoplastic cell",
-      "type": "ENTITY",
-      "start": 671,
-      "end": 686
-    },
-    {
-      "text": "HER2  protein stained with",
-      "type": "ENTITY",
-      "start": 695,
-      "end": 721
-    },
-    {
-      "text": "HercepTestTM",
-      "type": "ENTITY",
-      "start": 722,
-      "end": 734
-    },
-    {
-      "text": "DAKo",
-      "type": "ENTITY",
-      "start": 738,
-      "end": 742
-    },
-    {
-      "text": "Negative reaction",
-      "type": "ENTITY",
-      "start": 744,
-      "end": 761
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 765,
-      "end": 773
-    },
-    {
-      "text": "Score",
-      "type": "ENTITY",
-      "start": 791,
-      "end": 796
-    },
-    {
-      "text": "Compliance",
-      "type": "ENTITY",
-      "start": 804,
-      "end": 814
-    },
-    {
-      "text": "Examination",
-      "type": "ENTITY",
-      "start": 829,
-      "end": 840
-    },
-    {
-      "text": "performed",
-      "type": "ENTITY",
-      "start": 841,
-      "end": 850
-    },
-    {
-      "text": "Macroscopic",
-      "type": "ENTITY",
-      "start": 854,
-      "end": 865
-    },
-    {
-      "text": "description",
-      "type": "ENTITY",
-      "start": 866,
-      "end": 877
-    },
-    {
-      "text": "Right breast",
-      "type": "ENTITY",
-      "start": 879,
-      "end": 891
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 892,
-      "end": 897
-    },
-    {
-      "text": "removed",
-      "type": "ENTITY",
-      "start": 913,
-      "end": 920
-    },
-    {
-      "text": "axillary tissues",
-      "type": "ENTITY",
-      "start": 932,
-      "end": 948
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 949,
-      "end": 954
-    },
-    {
-      "text": "skin flap",
-      "type": "ENTITY",
-      "start": 975,
-      "end": 984
-    },
-    {
-      "text": "Tumour",
-      "type": "ENTITY",
-      "start": 1000,
-      "end": 1006
-    },
-    {
-      "text": "sized",
-      "type": "ENTITY",
-      "start": 1007,
-      "end": 1012
-    },
-    {
-      "text": "border",
-      "type": "ENTITY",
-      "start": 1039,
-      "end": 1045
-    },
-    {
-      "text": "lower edge",
-      "type": "ENTITY",
-      "start": 1099,
-      "end": 1109
-    },
-    {
-      "text": "base",
-      "type": "ENTITY",
-      "start": 1127,
-      "end": 1131
-    },
-    {
-      "text": "skin",
-      "type": "ENTITY",
-      "start": 1153,
-      "end": 1157
-    },
-    {
-      "text": "Microscopic description",
-      "type": "ENTITY",
-      "start": 1159,
-      "end": 1182
-    },
-    {
-      "text": "Carcinoma",
-      "type": "ENTITY",
-      "start": 1184,
-      "end": 1193
-    },
-    {
-      "text": "ductale",
-      "type": "ENTITY",
-      "start": 1194,
-      "end": 1201
-    },
-    {
-      "text": "invasivum",
-      "type": "ENTITY",
-      "start": 1202,
-      "end": 1211
-    },
-    {
-      "text": "NHG3",
-      "type": "ENTITY",
-      "start": 1212,
-      "end": 1216
-    },
-    {
-      "text": "HPF",
-      "type": "ENTITY",
-      "start": 1243,
-      "end": 1246
-    },
-    {
-      "text": "visual",
-      "type": "ENTITY",
-      "start": 1249,
-      "end": 1255
-    },
-    {
-      "text": "Glandular tissue",
-      "type": "ENTITY",
-      "start": 1274,
-      "end": 1290
-    },
-    {
-      "text": "tumour",
-      "type": "ENTITY",
-      "start": 1299,
-      "end": 1305
-    },
-    {
-      "text": "lesions",
-      "type": "ENTITY",
-      "start": 1314,
-      "end": 1321
-    },
-    {
-      "text": "type mastopathia fibrosa",
-      "type": "ENTITY",
-      "start": 1329,
-      "end": 1353
-    },
-    {
-      "text": "cystica",
-      "type": "ENTITY",
-      "start": 1357,
-      "end": 1364
-    },
-    {
-      "text": "hyperplasia ductalis simplex",
-      "type": "ENTITY",
-      "start": 1366,
-      "end": 1394
-    },
-    {
-      "text": "UDH",
-      "type": "ENTITY",
-      "start": 1396,
-      "end": 1399
-    },
-    {
-      "text": "Axillary lymph nodes",
-      "type": "ENTITY",
-      "start": 1402,
-      "end": 1422
-    },
-    {
-      "text": "Sinus histiocytosis lymphonodorum",
-      "type": "ENTITY",
-      "start": 1424,
-      "end": 1457
-    },
-    {
-      "text": "No XI",
-      "type": "ENTITY",
-      "start": 1459,
-      "end": 1464
-    },
-    {
-      "text": "Histopathological",
-      "type": "ENTITY",
-      "start": 1467,
-      "end": 1484
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 1485,
-      "end": 1494
-    },
-    {
-      "text": "Carcinoma",
-      "type": "ENTITY",
-      "start": 1496,
-      "end": 1505
-    },
-    {
-      "text": "ductale",
-      "type": "ENTITY",
-      "start": 1506,
-      "end": 1513
-    },
-    {
-      "text": "Invasive ductal carcinoma",
-      "type": "ENTITY",
-      "start": 1540,
-      "end": 1565
-    },
-    {
-      "text": "right'breast",
-      "type": "ENTITY",
-      "start": 1573,
-      "end": 1585
-    },
-    {
-      "text": "NHG3",
-      "type": "ENTITY",
-      "start": 1588,
-      "end": 1592
-    },
-    {
-      "text": "pT2",
-      "type": "ENTITY",
-      "start": 1594,
-      "end": 1597
-    },
-    {
-      "text": "Compliance",
-      "type": "ENTITY",
-      "start": 1605,
-      "end": 1615
-    },
-    {
-      "text": "THIS REPORT! UUID",
-      "type": "ENTITY",
-      "start": 1653,
-      "end": 1670
-    },
-    {
-      "text": "TCGA-D8-A13L-01A-PR",
-      "type": "ENTITY",
-      "start": 1709,
-      "end": 1728
-    }
-  ],
-  "entity_count": 86,
-  "has_embedding": true
-}

output/biomedbert_output/016d474a-b6f5-40ec-a9d4-f9345f170965_nlp.json

@@ -1,920 +0,0 @@
-{
-  "filename": "016d474a-b6f5-40ec-a9d4-f9345f170965",
-  "timestamp": "2026-01-05T14:42:11.116813",
-  "entities": [
-    {
-      "text": "UUID",
-      "type": "ENTITY",
-      "start": 40,
-      "end": 44
-    },
-    {
-      "text": "FFA18E29-2CC3-48F3-A7F2-88FC092E5606",
-      "type": "ENTITY",
-      "start": 45,
-      "end": 81
-    },
-    {
-      "text": "TCGA-P4-A5E7-01A-PR",
-      "type": "ENTITY",
-      "start": 82,
-      "end": 101
-    },
-    {
-      "text": "Redacted Tissue Source Site",
-      "type": "ENTITY",
-      "start": 102,
-      "end": 129
-    },
-    {
-      "text": "TsS",
-      "type": "ENTITY",
-      "start": 131,
-      "end": 134
-    },
-    {
-      "text": "Patholgy Accession",
-      "type": "ENTITY",
-      "start": 139,
-      "end": 157
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 162,
-      "end": 169
-    },
-    {
-      "text": "ID",
-      "type": "ENTITY",
-      "start": 170,
-      "end": 172
-    },
-    {
-      "text": "Normal Sample",
-      "type": "ENTITY",
-      "start": 174,
-      "end": 187
-    },
-    {
-      "text": "Pathology Report",
-      "type": "ENTITY",
-      "start": 192,
-      "end": 208
-    },
-    {
-      "text": "LCD-O-3",
-      "type": "ENTITY",
-      "start": 209,
-      "end": 216
-    },
-    {
-      "text": "REVIEW",
-      "type": "ENTITY",
-      "start": 243,
-      "end": 249
-    },
-    {
-      "text": "ADDENDUM SECTION",
-      "type": "ENTITY",
-      "start": 250,
-      "end": 266
-    },
-    {
-      "text": "comment",
-      "type": "ENTITY",
-      "start": 328,
-      "end": 335
-    },
-    {
-      "text": "papillary renal cell carcinoma",
-      "type": "ENTITY",
-      "start": 351,
-      "end": 381
-    },
-    {
-      "text": "original",
-      "type": "ENTITY",
-      "start": 415,
-      "end": 423
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 424,
-      "end": 430
-    },
-    {
-      "text": "diagnosis",
-      "type": "ENTITY",
-      "start": 460,
-      "end": 469
-    },
-    {
-      "text": "C64.9",
-      "type": "ENTITY",
-      "start": 476,
-      "end": 481
-    },
-    {
-      "text": "review",
-      "type": "ENTITY",
-      "start": 488,
-      "end": 494
-    },
-    {
-      "text": "H&E slides",
-      "type": "ENTITY",
-      "start": 502,
-      "end": 512
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 519,
-      "end": 524
-    },
-    {
-      "text": "type 2 papillary renal cell",
-      "type": "ENTITY",
-      "start": 542,
-      "end": 569
-    },
-    {
-      "text": "H1/io113 carcinoma",
-      "type": "ENTITY",
-      "start": 570,
-      "end": 588
-    },
-    {
-      "text": "DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 590,
-      "end": 599
-    },
-    {
-      "text": "FUHRMAN'S NUCLEAR",
-      "type": "ENTITY",
-      "start": 661,
-      "end": 678
-    },
-    {
-      "text": "CM",
-      "type": "ENTITY",
-      "start": 733,
-      "end": 735
-    },
-    {
-      "text": "MAXIMUM",
-      "type": "ENTITY",
-      "start": 739,
-      "end": 746
-    },
-    {
-      "text": "DIMENSION",
-      "type": "ENTITY",
-      "start": 747,
-      "end": 756
-    },
-    {
-      "text": "Margins",
-      "type": "ENTITY",
-      "start": 758,
-      "end": 765
-    },
-    {
-      "text": "resection free of tumor",
-      "type": "ENTITY",
-      "start": 769,
-      "end": 792
-    },
-    {
-      "text": "NEPHRECTOMY II",
-      "type": "ENTITY",
-      "start": 811,
-      "end": 825
-    },
-    {
-      "text": "Renal parenchyma",
-      "type": "ENTITY",
-      "start": 827,
-      "end": 843
-    },
-    {
-      "text": "focal glomerulosclerosis",
-      "type": "ENTITY",
-      "start": 849,
-      "end": 873
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 878,
-      "end": 883
-    },
-    {
-      "text": "Adrenal",
-      "type": "ENTITY",
-      "start": 927,
-      "end": 934
-    },
-    {
-      "text": "cortical tissue",
-      "type": "ENTITY",
-      "start": 935,
-      "end": 950
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 978,
-      "end": 986
-    },
-    {
-      "text": "left partial nephrectomy",
-      "type": "ENTITY",
-      "start": 998,
-      "end": 1022
-    },
-    {
-      "text": "specimen B",
-      "type": "ENTITY",
-      "start": 1024,
-      "end": 1034
-    },
-    {
-      "text": "fragment",
-      "type": "ENTITY",
-      "start": 1051,
-      "end": 1059
-    },
-    {
-      "text": "renal parenchyma",
-      "type": "ENTITY",
-      "start": 1063,
-      "end": 1079
-    },
-    {
-      "text": "focal glomerulosclerosis",
-      "type": "ENTITY",
-      "start": 1085,
-      "end": 1109
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 1138,
-      "end": 1146
-    },
-    {
-      "text": "examined",
-      "type": "ENTITY",
-      "start": 1152,
-      "end": 1160
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1167,
-      "end": 1175
-    },
-    {
-      "text": "adrenal biopsy",
-      "type": "ENTITY",
-      "start": 1187,
-      "end": 1201
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1203,
-      "end": 1211
-    },
-    {
-      "text": "fragment",
-      "type": "ENTITY",
-      "start": 1230,
-      "end": 1238
-    },
-    {
-      "text": "adrenal",
-      "type": "ENTITY",
-      "start": 1242,
-      "end": 1249
-    },
-    {
-      "text": "cortical tissue",
-      "type": "ENTITY",
-      "start": 1250,
-      "end": 1265
-    },
-    {
-      "text": "metastatic carcinoma",
-      "type": "ENTITY",
-      "start": 1270,
-      "end": 1290
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 1294,
-      "end": 1304
-    },
-    {
-      "text": "Correlation",
-      "type": "ENTITY",
-      "start": 1306,
-      "end": 1317
-    },
-    {
-      "text": "clinical findings",
-      "type": "ENTITY",
-      "start": 1327,
-      "end": 1344
-    },
-    {
-      "text": "GROSS DESCRIPTION",
-      "type": "ENTITY",
-      "start": 1359,
-      "end": 1376
-    },
-    {
-      "text": "LEFT",
-      "type": "ENTITY",
-      "start": 1381,
-      "end": 1385
-    },
-    {
-      "text": "NEPHRECTOMY",
-      "type": "ENTITY",
-      "start": 1394,
-      "end": 1405
-    },
-    {
-      "text": "DEEP",
-      "type": "ENTITY",
-      "start": 1408,
-      "end": 1412
-    },
-    {
-      "text": "MARGIN",
-      "type": "ENTITY",
-      "start": 1413,
-      "end": 1419
-    },
-    {
-      "text": "INK",
-      "type": "ENTITY",
-      "start": 1422,
-      "end": 1425
-    },
-    {
-      "text": "FROZEN SECTION",
-      "type": "ENTITY",
-      "start": 1426,
-      "end": 1440
-    },
-    {
-      "text": "MARGIN",
-      "type": "ENTITY",
-      "start": 1447,
-      "end": 1453
-    },
-    {
-      "text": "A",
-      "type": "ENTITY",
-      "start": 1456,
-      "end": 1457
-    },
-    {
-      "text": "partial",
-      "type": "ENTITY",
-      "start": 1458,
-      "end": 1465
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1478,
-      "end": 1486
-    },
-    {
-      "text": "perinephric fat",
-      "type": "ENTITY",
-      "start": 1501,
-      "end": 1516
-    },
-    {
-      "text": "overall",
-      "type": "ENTITY",
-      "start": 1537,
-      "end": 1544
-    },
-    {
-      "text": "portion of kidney",
-      "type": "ENTITY",
-      "start": 1551,
-      "end": 1568
-    },
-    {
-      "text": "blue surgical ink",
-      "type": "ENTITY",
-      "start": 1623,
-      "end": 1640
-    },
-    {
-      "text": "parenchymal resection margin",
-      "type": "ENTITY",
-      "start": 1659,
-      "end": 1687
-    },
-    {
-      "text": "friable",
-      "type": "ENTITY",
-      "start": 1710,
-      "end": 1717
-    },
-    {
-      "text": "orange-brown",
-      "type": "ENTITY",
-      "start": 1718,
-      "end": 1730
-    },
-    {
-      "text": "focally hemorrhagic",
-      "type": "ENTITY",
-      "start": 1735,
-      "end": 1754
-    },
-    {
-      "text": "tumor mass",
-      "type": "ENTITY",
-      "start": 1755,
-      "end": 1765
-    },
-    {
-      "text": "kidney parenchyma",
-      "type": "ENTITY",
-      "start": 1788,
-      "end": 1805
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 1811,
-      "end": 1816
-    },
-    {
-      "text": "parenchymal margin",
-      "type": "ENTITY",
-      "start": 1854,
-      "end": 1872
-    },
-    {
-      "text": "gross extension",
-      "type": "ENTITY",
-      "start": 1877,
-      "end": 1892
-    },
-    {
-      "text": "perinephric fat",
-      "type": "ENTITY",
-      "start": 1898,
-      "end": 1913
-    },
-    {
-      "text": "renal parenchyma",
-      "type": "ENTITY",
-      "start": 1940,
-      "end": 1956
-    },
-    {
-      "text": "light tan",
-      "type": "ENTITY",
-      "start": 1960,
-      "end": 1969
-    },
-    {
-      "text": "unremarkable",
-      "type": "ENTITY",
-      "start": 1974,
-      "end": 1986
-    },
-    {
-      "text": "INK",
-      "type": "ENTITY",
-      "start": 1988,
-      "end": 1991
-    },
-    {
-      "text": "CODE",
-      "type": "ENTITY",
-      "start": 1992,
-      "end": 1996
-    },
-    {
-      "text": "Black",
-      "type": "ENTITY",
-      "start": 1998,
-      "end": 2003
-    },
-    {
-      "text": "parenchymal",
-      "type": "ENTITY",
-      "start": 2006,
-      "end": 2017
-    },
-    {
-      "text": "blue",
-      "type": "ENTITY",
-      "start": 2036,
-      "end": 2040
-    },
-    {
-      "text": "surgically",
-      "type": "ENTITY",
-      "start": 2043,
-      "end": 2053
-    },
-    {
-      "text": "parenchymal margin",
-      "type": "ENTITY",
-      "start": 2061,
-      "end": 2079
-    },
-    {
-      "text": "CODE",
-      "type": "ENTITY",
-      "start": 2089,
-      "end": 2093
-    },
-    {
-      "text": "A1",
-      "type": "ENTITY",
-      "start": 2095,
-      "end": 2097
-    },
-    {
-      "text": "A2",
-      "type": "ENTITY",
-      "start": 2099,
-      "end": 2101
-    },
-    {
-      "text": "frozen sections",
-      "type": "ENTITY",
-      "start": 2103,
-      "end": 2118
-    },
-    {
-      "text": "parenchymal margin",
-      "type": "ENTITY",
-      "start": 2122,
-      "end": 2140
-    },
-    {
-      "text": "A3-A6",
-      "type": "ENTITY",
-      "start": 2142,
-      "end": 2147
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2149,
-      "end": 2154
-    },
-    {
-      "text": "margin",
-      "type": "ENTITY",
-      "start": 2160,
-      "end": 2166
-    },
-    {
-      "text": "A7-A9",
-      "type": "ENTITY",
-      "start": 2168,
-      "end": 2173
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2175,
-      "end": 2180
-    },
-    {
-      "text": "surrounding",
-      "type": "ENTITY",
-      "start": 2186,
-      "end": 2197
-    },
-    {
-      "text": "adipose",
-      "type": "ENTITY",
-      "start": 2198,
-      "end": 2205
-    },
-    {
-      "text": "normal kidney",
-      "type": "ENTITY",
-      "start": 2210,
-      "end": 2223
-    },
-    {
-      "text": "A10",
-      "type": "ENTITY",
-      "start": 2225,
-      "end": 2228
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2230,
-      "end": 2235
-    },
-    {
-      "text": "blue surgical ink",
-      "type": "ENTITY",
-      "start": 2241,
-      "end": 2258
-    },
-    {
-      "text": "tumor section",
-      "type": "ENTITY",
-      "start": 2280,
-      "end": 2293
-    },
-    {
-      "text": "MARGIN FREE",
-      "type": "ENTITY",
-      "start": 2318,
-      "end": 2329
-    },
-    {
-      "text": "TUMOR",
-      "type": "ENTITY",
-      "start": 2333,
-      "end": 2338
-    },
-    {
-      "text": "LEFT PARTIAL",
-      "type": "ENTITY",
-      "start": 2344,
-      "end": 2356
-    },
-    {
-      "text": "NEPHRECTOMY",
-      "type": "ENTITY",
-      "start": 2357,
-      "end": 2368
-    },
-    {
-      "text": "portion",
-      "type": "ENTITY",
-      "start": 2395,
-      "end": 2402
-    },
-    {
-      "text": "renal parenchyma",
-      "type": "ENTITY",
-      "start": 2406,
-      "end": 2422
-    },
-    {
-      "text": "apparent",
-      "type": "ENTITY",
-      "start": 2428,
-      "end": 2436
-    },
-    {
-      "text": "cortical",
-      "type": "ENTITY",
-      "start": 2437,
-      "end": 2445
-    },
-    {
-      "text": "vague nodularity",
-      "type": "ENTITY",
-      "start": 2487,
-      "end": 2503
-    },
-    {
-      "text": "apparent",
-      "type": "ENTITY",
-      "start": 2509,
-      "end": 2517
-    },
-    {
-      "text": "parenchymal margin",
-      "type": "ENTITY",
-      "start": 2518,
-      "end": 2536
-    },
-    {
-      "text": "tan",
-      "type": "ENTITY",
-      "start": 2540,
-      "end": 2543
-    },
-    {
-      "text": "unremarkable",
-      "type": "ENTITY",
-      "start": 2548,
-      "end": 2560
-    },
-    {
-      "text": "cut surface",
-      "type": "ENTITY",
-      "start": 2566,
-      "end": 2577
-    },
-    {
-      "text": "grossly invasive tumor",
-      "type": "ENTITY",
-      "start": 2592,
-      "end": 2614
-    },
-    {
-      "text": "Tissue Source Site",
-      "type": "ENTITY",
-      "start": 2657,
-      "end": 2675
-    },
-    {
-      "text": "TSs",
-      "type": "ENTITY",
-      "start": 2677,
-      "end": 2680
-    },
-    {
-      "text": "Patholgy Accession",
-      "type": "ENTITY",
-      "start": 2685,
-      "end": 2703
-    },
-    {
-      "text": "Patient",
-      "type": "ENTITY",
-      "start": 2708,
-      "end": 2715
-    },
-    {
-      "text": "ID",
-      "type": "ENTITY",
-      "start": 2716,
-      "end": 2718
-    },
-    {
-      "text": "Normal Sample",
-      "type": "ENTITY",
-      "start": 2720,
-      "end": 2733
-    },
-    {
-      "text": "Tumor Sample",
-      "type": "ENTITY",
-      "start": 2738,
-      "end": 2750
-    },
-    {
-      "text": "INK",
-      "type": "ENTITY",
-      "start": 2755,
-      "end": 2758
-    },
-    {
-      "text": "CODE",
-      "type": "ENTITY",
-      "start": 2759,
-      "end": 2763
-    },
-    {
-      "text": "Blue-apparent",
-      "type": "ENTITY",
-      "start": 2765,
-      "end": 2778
-    },
-    {
-      "text": "cortical surface",
-      "type": "ENTITY",
-      "start": 2779,
-      "end": 2795
-    },
-    {
-      "text": "orange-apparent",
-      "type": "ENTITY",
-      "start": 2797,
-      "end": 2812
-    },
-    {
-      "text": "CODE",
-      "type": "ENTITY",
-      "start": 2843,
-      "end": 2847
-    },
-    {
-      "text": "B",
-      "type": "ENTITY",
-      "start": 2849,
-      "end": 2850
-    },
-    {
-      "text": "left partial nephrectomy",
-      "type": "ENTITY",
-      "start": 2859,
-      "end": 2883
-    },
-    {
-      "text": "RULE",
-      "type": "ENTITY",
-      "start": 2905,
-      "end": 2909
-    },
-    {
-      "text": "METASTASIS",
-      "type": "ENTITY",
-      "start": 2914,
-      "end": 2924
-    },
-    {
-      "text": "yellow tissue",
-      "type": "ENTITY",
-      "start": 2953,
-      "end": 2966
-    },
-    {
-      "text": "frozen section",
-      "type": "ENTITY",
-      "start": 3014,
-      "end": 3028
-    },
-    {
-      "text": "C. *FS/DX",
-      "type": "ENTITY",
-      "start": 3032,
-      "end": 3041
-    },
-    {
-      "text": "NO",
-      "type": "ENTITY",
-      "start": 3068,
-      "end": 3070
-    },
-    {
-      "text": "HISTORYS",
-      "type": "ENTITY",
-      "start": 3102,
-      "end": 3110
-    },
-    {
-      "text": "SNOMED",
-      "type": "ENTITY",
-      "start": 3123,
-      "end": 3129
-    },
-    {
-      "text": "T-71000",
-      "type": "ENTITY",
-      "start": 3136,
-      "end": 3143
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 3160,
-      "end": 3165
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 3208,
-      "end": 3219
-    },
-    {
-      "text": "characteristics",
-      "type": "ENTITY",
-      "start": 3221,
-      "end": 3236
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 3259,
-      "end": 3264
-    },
-    {
-      "text": "cleared",
-      "type": "ENTITY",
-      "start": 3292,
-      "end": 3299
-    },
-    {
-      "text": "U.S. Food and Drug Administration",
-      "type": "ENTITY",
-      "start": 3319,
-      "end": 3352
-    }
-  ],
-  "entity_count": 152,
-  "has_embedding": true
-}

output/biomedbert_output/0172007d-ca4b-473d-aef1-0373f8e18886_nlp.json

@@ -1,1484 +0,0 @@
-{
-  "filename": "0172007d-ca4b-473d-aef1-0373f8e18886",
-  "timestamp": "2026-01-05T14:41:55.959582",
-  "entities": [
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 27,
-      "end": 35
-    },
-    {
-      "text": "COLON AMENDMENT",
-      "type": "ENTITY",
-      "start": 36,
-      "end": 51
-    },
-    {
-      "text": "REASON",
-      "type": "ENTITY",
-      "start": 52,
-      "end": 58
-    },
-    {
-      "text": "case",
-      "type": "ENTITY",
-      "start": 64,
-      "end": 68
-    },
-    {
-      "text": "formatting error",
-      "type": "ENTITY",
-      "start": 94,
-      "end": 110
-    },
-    {
-      "text": "changes",
-      "type": "ENTITY",
-      "start": 121,
-      "end": 128
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 147,
-      "end": 153
-    },
-    {
-      "text": "SPECIMEN(S",
-      "type": "ENTITY",
-      "start": 155,
-      "end": 165
-    },
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 168,
-      "end": 176
-    },
-    {
-      "text": "A. RIGHT",
-      "type": "ENTITY",
-      "start": 202,
-      "end": 210
-    },
-    {
-      "text": "Received",
-      "type": "ENTITY",
-      "start": 217,
-      "end": 225
-    },
-    {
-      "text": "fixative",
-      "type": "ENTITY",
-      "start": 234,
-      "end": 242
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 244,
-      "end": 251
-    },
-    {
-      "text": "ilealcolectomy",
-      "type": "ENTITY",
-      "start": 273,
-      "end": 287
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 288,
-      "end": 296
-    },
-    {
-      "text": "segment",
-      "type": "ENTITY",
-      "start": 311,
-      "end": 318
-    },
-    {
-      "text": "long",
-      "type": "ENTITY",
-      "start": 328,
-      "end": 332
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 333,
-      "end": 338
-    },
-    {
-      "text": "cecum",
-      "type": "ENTITY",
-      "start": 347,
-      "end": 352
-    },
-    {
-      "text": "long appendix",
-      "type": "ENTITY",
-      "start": 372,
-      "end": 385
-    },
-    {
-      "text": "long colon",
-      "type": "ENTITY",
-      "start": 393,
-      "end": 403
-    },
-    {
-      "text": "mesenteric fat",
-      "type": "ENTITY",
-      "start": 419,
-      "end": 433
-    },
-    {
-      "text": "colon",
-      "type": "ENTITY",
-      "start": 439,
-      "end": 444
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 472,
-      "end": 480
-    },
-    {
-      "text": "resection margins",
-      "type": "ENTITY",
-      "start": 487,
-      "end": 504
-    },
-    {
-      "text": "stapled closed",
-      "type": "ENTITY",
-      "start": 509,
-      "end": 523
-    },
-    {
-      "text": "removal",
-      "type": "ENTITY",
-      "start": 531,
-      "end": 538
-    },
-    {
-      "text": "stapled line",
-      "type": "ENTITY",
-      "start": 546,
-      "end": 558
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 564,
-      "end": 572
-    },
-    {
-      "text": "polypoid",
-      "type": "ENTITY",
-      "start": 599,
-      "end": 607
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 633,
-      "end": 641
-    },
-    {
-      "text": "elevated",
-      "type": "ENTITY",
-      "start": 659,
-      "end": 667
-    },
-    {
-      "text": "colonic mucosa",
-      "type": "ENTITY",
-      "start": 678,
-      "end": 692
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 709,
-      "end": 715
-    },
-    {
-      "text": "colonic resection margin",
-      "type": "ENTITY",
-      "start": 733,
-      "end": 757
-    },
-    {
-      "text": "ileal",
-      "type": "ENTITY",
-      "start": 771,
-      "end": 776
-    },
-    {
-      "text": "resection margin",
-      "type": "ENTITY",
-      "start": 777,
-      "end": 793
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 799,
-      "end": 805
-    },
-    {
-      "text": "superficial",
-      "type": "ENTITY",
-      "start": 820,
-      "end": 831
-    },
-    {
-      "text": "colonic wall",
-      "type": "ENTITY",
-      "start": 857,
-      "end": 869
-    },
-    {
-      "text": "polypoid",
-      "type": "ENTITY",
-      "start": 888,
-      "end": 896
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 924,
-      "end": 933
-    },
-    {
-      "text": "dimension",
-      "type": "ENTITY",
-      "start": 964,
-      "end": 973
-    },
-    {
-      "text": "8.0-cm",
-      "type": "ENTITY",
-      "start": 1004,
-      "end": 1010
-    },
-    {
-      "text": "colonic resection margin",
-      "type": "ENTITY",
-      "start": 1018,
-      "end": 1042
-    },
-    {
-      "text": "colonic mucosa",
-      "type": "ENTITY",
-      "start": 1059,
-      "end": 1073
-    },
-    {
-      "text": "ileal",
-      "type": "ENTITY",
-      "start": 1078,
-      "end": 1083
-    },
-    {
-      "text": "unremarkable",
-      "type": "ENTITY",
-      "start": 1095,
-      "end": 1107
-    },
-    {
-      "text": "appendix",
-      "type": "ENTITY",
-      "start": 1113,
-      "end": 1121
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 1134,
-      "end": 1140
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 1155,
-      "end": 1163
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1211,
-      "end": 1222
-    },
-    {
-      "text": "mesentery fat",
-      "type": "ENTITY",
-      "start": 1243,
-      "end": 1256
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 1258,
-      "end": 1281
-    },
-    {
-      "text": "A1",
-      "type": "ENTITY",
-      "start": 1309,
-      "end": 1311
-    },
-    {
-      "text": "Distal colonic resection margin A2",
-      "type": "ENTITY",
-      "start": 1313,
-      "end": 1347
-    },
-    {
-      "text": "Proximal",
-      "type": "ENTITY",
-      "start": 1349,
-      "end": 1357
-    },
-    {
-      "text": "thickness",
-      "type": "ENTITY",
-      "start": 1393,
-      "end": 1402
-    },
-    {
-      "text": "ulcerated polypoid",
-      "type": "ENTITY",
-      "start": 1406,
-      "end": 1424
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 1425,
-      "end": 1431
-    },
-    {
-      "text": "mesenteric fat",
-      "type": "ENTITY",
-      "start": 1446,
-      "end": 1460
-    },
-    {
-      "text": "inked black",
-      "type": "ENTITY",
-      "start": 1462,
-      "end": 1473
-    },
-    {
-      "text": "bisected A5",
-      "type": "ENTITY",
-      "start": 1476,
-      "end": 1487
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 1500,
-      "end": 1507
-    },
-    {
-      "text": "ulcerated polypoid lesion A6",
-      "type": "ENTITY",
-      "start": 1511,
-      "end": 1539
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 1541,
-      "end": 1549
-    },
-    {
-      "text": "polypoid area",
-      "type": "ENTITY",
-      "start": 1555,
-      "end": 1568
-    },
-    {
-      "text": "colonic resection margin A7",
-      "type": "ENTITY",
-      "start": 1584,
-      "end": 1611
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 1613,
-      "end": 1621
-    },
-    {
-      "text": "polypoid area",
-      "type": "ENTITY",
-      "start": 1627,
-      "end": 1640
-    },
-    {
-      "text": "colonic resection margin",
-      "type": "ENTITY",
-      "start": 1656,
-      "end": 1680
-    },
-    {
-      "text": "A8",
-      "type": "ENTITY",
-      "start": 1681,
-      "end": 1683
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 1685,
-      "end": 1693
-    },
-    {
-      "text": "polypoid area",
-      "type": "ENTITY",
-      "start": 1699,
-      "end": 1712
-    },
-    {
-      "text": "colonic resection margin A9",
-      "type": "ENTITY",
-      "start": 1728,
-      "end": 1755
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 1757,
-      "end": 1765
-    },
-    {
-      "text": "ileum",
-      "type": "ENTITY",
-      "start": 1769,
-      "end": 1774
-    },
-    {
-      "text": "A10",
-      "type": "ENTITY",
-      "start": 1776,
-      "end": 1779
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 1781,
-      "end": 1789
-    },
-    {
-      "text": "cecum",
-      "type": "ENTITY",
-      "start": 1793,
-      "end": 1798
-    },
-    {
-      "text": "appendix A11",
-      "type": "ENTITY",
-      "start": 1803,
-      "end": 1815
-    },
-    {
-      "text": "Ileocecal valve A12-A14: Random sections",
-      "type": "ENTITY",
-      "start": 1817,
-      "end": 1857
-    },
-    {
-      "text": "uninvolved colon",
-      "type": "ENTITY",
-      "start": 1861,
-      "end": 1877
-    },
-    {
-      "text": "Multiple",
-      "type": "ENTITY",
-      "start": 1887,
-      "end": 1895
-    },
-    {
-      "text": "lymph nodes A28",
-      "type": "ENTITY",
-      "start": 1905,
-      "end": 1920
-    },
-    {
-      "text": "Tip",
-      "type": "ENTITY",
-      "start": 1922,
-      "end": 1925
-    },
-    {
-      "text": "appendix DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 1929,
-      "end": 1947
-    },
-    {
-      "text": "A. COLON",
-      "type": "ENTITY",
-      "start": 1949,
-      "end": 1957
-    },
-    {
-      "text": "TERMINAL",
-      "type": "ENTITY",
-      "start": 1962,
-      "end": 1970
-    },
-    {
-      "text": "RIGHT HEMICOLECTOMY",
-      "type": "ENTITY",
-      "start": 1978,
-      "end": 1997
-    },
-    {
-      "text": "SERRATED",
-      "type": "ENTITY",
-      "start": 2067,
-      "end": 2075
-    },
-    {
-      "text": "SURGICAL",
-      "type": "ENTITY",
-      "start": 2095,
-      "end": 2103
-    },
-    {
-      "text": "ARE",
-      "type": "ENTITY",
-      "start": 2112,
-      "end": 2115
-    },
-    {
-      "text": "METASTATIC",
-      "type": "ENTITY",
-      "start": 2132,
-      "end": 2142
-    },
-    {
-      "text": "INVOLVING",
-      "type": "ENTITY",
-      "start": 2153,
-      "end": 2162
-    },
-    {
-      "text": "THREE LYMPH NODES",
-      "type": "ENTITY",
-      "start": 2163,
-      "end": 2180
-    },
-    {
-      "text": "SYNOPTIC",
-      "type": "ENTITY",
-      "start": 2188,
-      "end": 2196
-    },
-    {
-      "text": "REPORT",
-      "type": "ENTITY",
-      "start": 2197,
-      "end": 2203
-    },
-    {
-      "text": "COLON",
-      "type": "ENTITY",
-      "start": 2206,
-      "end": 2211
-    },
-    {
-      "text": "RECTUM Specimens",
-      "type": "ENTITY",
-      "start": 2214,
-      "end": 2230
-    },
-    {
-      "text": "Involved",
-      "type": "ENTITY",
-      "start": 2231,
-      "end": 2239
-    },
-    {
-      "text": "Specimens",
-      "type": "ENTITY",
-      "start": 2240,
-      "end": 2249
-    },
-    {
-      "text": "RIGHT COLON Specimen Type",
-      "type": "ENTITY",
-      "start": 2254,
-      "end": 2279
-    },
-    {
-      "text": "Right hemicolectomy Tumor Site",
-      "type": "ENTITY",
-      "start": 2281,
-      "end": 2311
-    },
-    {
-      "text": "Cecum Tumor Configuration",
-      "type": "ENTITY",
-      "start": 2313,
-      "end": 2338
-    },
-    {
-      "text": "Exophytic (polypoid)",
-      "type": "ENTITY",
-      "start": 2340,
-      "end": 2360
-    },
-    {
-      "text": "Tumor size",
-      "type": "ENTITY",
-      "start": 2361,
-      "end": 2371
-    },
-    {
-      "text": "dimensions",
-      "type": "ENTITY",
-      "start": 2390,
-      "end": 2400
-    },
-    {
-      "text": "WHO",
-      "type": "ENTITY",
-      "start": 2415,
-      "end": 2418
-    },
-    {
-      "text": "Classification Adenocarcinoma",
-      "type": "ENTITY",
-      "start": 2419,
-      "end": 2448
-    },
-    {
-      "text": "Histologic Grade",
-      "type": "ENTITY",
-      "start": 2456,
-      "end": 2472
-    },
-    {
-      "text": "Moderately differentiated",
-      "type": "ENTITY",
-      "start": 2478,
-      "end": 2503
-    },
-    {
-      "text": "Invasion",
-      "type": "ENTITY",
-      "start": 2514,
-      "end": 2522
-    },
-    {
-      "text": "Muscularis propria",
-      "type": "ENTITY",
-      "start": 2524,
-      "end": 2542
-    },
-    {
-      "text": "Margins",
-      "type": "ENTITY",
-      "start": 2543,
-      "end": 2550
-    },
-    {
-      "text": "Margin(s",
-      "type": "ENTITY",
-      "start": 2552,
-      "end": 2560
-    },
-    {
-      "text": "uninvolved",
-      "type": "ENTITY",
-      "start": 2562,
-      "end": 2572
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 2576,
-      "end": 2594
-    },
-    {
-      "text": "Proximal",
-      "type": "ENTITY",
-      "start": 2596,
-      "end": 2604
-    },
-    {
-      "text": "Distal",
-      "type": "ENTITY",
-      "start": 2606,
-      "end": 2612
-    },
-    {
-      "text": "Radial",
-      "type": "ENTITY",
-      "start": 2614,
-      "end": 2620
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 2622,
-      "end": 2630
-    },
-    {
-      "text": "invasive carcinoma",
-      "type": "ENTITY",
-      "start": 2634,
-      "end": 2652
-    },
-    {
-      "text": "margin",
-      "type": "ENTITY",
-      "start": 2666,
-      "end": 2672
-    },
-    {
-      "text": "Margin",
-      "type": "ENTITY",
-      "start": 2679,
-      "end": 2685
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 2687,
-      "end": 2693
-    },
-    {
-      "text": "Venous/Lymphatic Invasion",
-      "type": "ENTITY",
-      "start": 2694,
-      "end": 2719
-    },
-    {
-      "text": "Absent\n\n--- Page 2 ---\nPerineural Invasion",
-      "type": "ENTITY",
-      "start": 2721,
-      "end": 2763
-    },
-    {
-      "text": "Pathologic",
-      "type": "ENTITY",
-      "start": 2784,
-      "end": 2794
-    },
-    {
-      "text": "Findings",
-      "type": "ENTITY",
-      "start": 2795,
-      "end": 2803
-    },
-    {
-      "text": "hyperplastic polyps",
-      "type": "ENTITY",
-      "start": 2811,
-      "end": 2830
-    },
-    {
-      "text": "Extent",
-      "type": "ENTITY",
-      "start": 2831,
-      "end": 2837
-    },
-    {
-      "text": "Resection",
-      "type": "ENTITY",
-      "start": 2841,
-      "end": 2850
-    },
-    {
-      "text": "Complete",
-      "type": "ENTITY",
-      "start": 2856,
-      "end": 2864
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 2865,
-      "end": 2874
-    },
-    {
-      "text": "grossly",
-      "type": "ENTITY",
-      "start": 2880,
-      "end": 2887
-    },
-    {
-      "text": "microscopically negative margins",
-      "type": "ENTITY",
-      "start": 2892,
-      "end": 2924
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 2925,
-      "end": 2936
-    },
-    {
-      "text": "Positive 3",
-      "type": "ENTITY",
-      "start": 2938,
-      "end": 2948
-    },
-    {
-      "text": "Extranodal extension",
-      "type": "ENTITY",
-      "start": 2954,
-      "end": 2974
-    },
-    {
-      "text": "Absent Implants",
-      "type": "ENTITY",
-      "start": 2976,
-      "end": 2991
-    },
-    {
-      "text": "Absent Pathological Staging",
-      "type": "ENTITY",
-      "start": 2993,
-      "end": 3020
-    },
-    {
-      "text": "pTNM",
-      "type": "ENTITY",
-      "start": 3022,
-      "end": 3026
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 3058,
-      "end": 3063
-    },
-    {
-      "text": "occasional",
-      "type": "ENTITY",
-      "start": 3100,
-      "end": 3110
-    },
-    {
-      "text": "rare",
-      "type": "ENTITY",
-      "start": 3112,
-      "end": 3116
-    },
-    {
-      "text": "signet ring cells",
-      "type": "ENTITY",
-      "start": 3117,
-      "end": 3134
-    },
-    {
-      "text": "Immunohistochemical studies",
-      "type": "ENTITY",
-      "start": 3146,
-      "end": 3173
-    },
-    {
-      "text": "blocks",
-      "type": "ENTITY",
-      "start": 3192,
-      "end": 3198
-    },
-    {
-      "text": "presence",
-      "type": "ENTITY",
-      "start": 3227,
-      "end": 3235
-    },
-    {
-      "text": "metastatic disease",
-      "type": "ENTITY",
-      "start": 3239,
-      "end": 3257
-    },
-    {
-      "text": "depth",
-      "type": "ENTITY",
-      "start": 3269,
-      "end": 3274
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 3278,
-      "end": 3286
-    },
-    {
-      "text": "studies",
-      "type": "ENTITY",
-      "start": 3296,
-      "end": 3303
-    },
-    {
-      "text": "microsatellite instability",
-      "type": "ENTITY",
-      "start": 3314,
-      "end": 3340
-    },
-    {
-      "text": "addendum",
-      "type": "ENTITY",
-      "start": 3365,
-      "end": 3373
-    },
-    {
-      "text": "IMMUNOHISTOCHEMISTRY/SPECIAL STAINS Material",
-      "type": "ENTITY",
-      "start": 3386,
-      "end": 3430
-    },
-    {
-      "text": "Block A3 Population",
-      "type": "ENTITY",
-      "start": 3432,
-      "end": 3451
-    },
-    {
-      "text": "Tumor Cells",
-      "type": "ENTITY",
-      "start": 3453,
-      "end": 3464
-    },
-    {
-      "text": "CYTOKERATIN",
-      "type": "ENTITY",
-      "start": 3494,
-      "end": 3505
-    },
-    {
-      "text": "AE1/3",
-      "type": "ENTITY",
-      "start": 3506,
-      "end": 3511
-    },
-    {
-      "text": "Block A4 Population",
-      "type": "ENTITY",
-      "start": 3531,
-      "end": 3550
-    },
-    {
-      "text": "Tumor Cells",
-      "type": "ENTITY",
-      "start": 3552,
-      "end": 3563
-    },
-    {
-      "text": "Comment",
-      "type": "ENTITY",
-      "start": 3585,
-      "end": 3592
-    },
-    {
-      "text": "CYTOKERATIN",
-      "type": "ENTITY",
-      "start": 3594,
-      "end": 3605
-    },
-    {
-      "text": "AE1/3",
-      "type": "ENTITY",
-      "start": 3606,
-      "end": 3611
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 3612,
-      "end": 3620
-    },
-    {
-      "text": "interpretation",
-      "type": "ENTITY",
-      "start": 3625,
-      "end": 3639
-    },
-    {
-      "text": "immunohistochemistry stain",
-      "type": "ENTITY",
-      "start": 3653,
-      "end": 3679
-    },
-    {
-      "text": "stains",
-      "type": "ENTITY",
-      "start": 3683,
-      "end": 3689
-    },
-    {
-      "text": "published results",
-      "type": "ENTITY",
-      "start": 3703,
-      "end": 3720
-    },
-    {
-      "text": "medical literature",
-      "type": "ENTITY",
-      "start": 3729,
-      "end": 3747
-    },
-    {
-      "text": "package information",
-      "type": "ENTITY",
-      "start": 3758,
-      "end": 3777
-    },
-    {
-      "text": "manufacturer",
-      "type": "ENTITY",
-      "start": 3787,
-      "end": 3799
-    },
-    {
-      "text": "internal review",
-      "type": "ENTITY",
-      "start": 3807,
-      "end": 3822
-    },
-    {
-      "text": "staining",
-      "type": "ENTITY",
-      "start": 3826,
-      "end": 3834
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 3835,
-      "end": 3846
-    },
-    {
-      "text": "assay",
-      "type": "ENTITY",
-      "start": 3851,
-      "end": 3856
-    },
-    {
-      "text": "validation",
-      "type": "ENTITY",
-      "start": 3857,
-      "end": 3867
-    },
-    {
-      "text": "Immunohistochemistry",
-      "type": "ENTITY",
-      "start": 3879,
-      "end": 3899
-    },
-    {
-      "text": "reagents",
-      "type": "ENTITY",
-      "start": 3939,
-      "end": 3947
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 3961,
-      "end": 3966
-    },
-    {
-      "text": "analyte",
-      "type": "ENTITY",
-      "start": 3986,
-      "end": 3993
-    },
-    {
-      "text": "AsR",
-      "type": "ENTITY",
-      "start": 4012,
-      "end": 4015
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 4024,
-      "end": 4029
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 4056,
-      "end": 4067
-    },
-    {
-      "text": "characteristic",
-      "type": "ENTITY",
-      "start": 4068,
-      "end": 4082
-    },
-    {
-      "text": "determined by",
-      "type": "ENTITY",
-      "start": 4083,
-      "end": 4096
-    },
-    {
-      "text": "Department of Pathology Laboratory",
-      "type": "ENTITY",
-      "start": 4101,
-      "end": 4135
-    },
-    {
-      "text": "cleared",
-      "type": "ENTITY",
-      "start": 4159,
-      "end": 4166
-    },
-    {
-      "text": "U.S. Food and Drug Administration",
-      "type": "ENTITY",
-      "start": 4186,
-      "end": 4219
-    },
-    {
-      "text": "FDA",
-      "type": "ENTITY",
-      "start": 4226,
-      "end": 4229
-    },
-    {
-      "text": "clearance",
-      "type": "ENTITY",
-      "start": 4255,
-      "end": 4264
-    },
-    {
-      "text": "approval",
-      "type": "ENTITY",
-      "start": 4268,
-      "end": 4276
-    },
-    {
-      "text": "Special stains",
-      "type": "ENTITY",
-      "start": 4295,
-      "end": 4309
-    },
-    {
-      "text": "immunohistochemical stains",
-      "type": "ENTITY",
-      "start": 4317,
-      "end": 4343
-    },
-    {
-      "text": "stained",
-      "type": "ENTITY",
-      "start": 4378,
-      "end": 4385
-    },
-    {
-      "text": "negative controls",
-      "type": "ENTITY",
-      "start": 4400,
-      "end": 4417
-    },
-    {
-      "text": "PRE-OPERATIVE DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 4448,
-      "end": 4471
-    },
-    {
-      "text": "Colon cancer",
-      "type": "ENTITY",
-      "start": 4473,
-      "end": 4485
-    },
-    {
-      "text": "IMMUNOHISTOCHEMISTRY/SPECIAL STAINS Material",
-      "type": "ENTITY",
-      "start": 4507,
-      "end": 4551
-    },
-    {
-      "text": "Specimen A Population",
-      "type": "ENTITY",
-      "start": 4553,
-      "end": 4574
-    },
-    {
-      "text": "Tumor Cells",
-      "type": "ENTITY",
-      "start": 4576,
-      "end": 4587
-    },
-    {
-      "text": "Comment",
-      "type": "ENTITY",
-      "start": 4625,
-      "end": 4632
-    },
-    {
-      "text": "MLH1",
-      "type": "ENTITY",
-      "start": 4634,
-      "end": 4638
-    },
-    {
-      "text": "PMS2",
-      "type": "ENTITY",
-      "start": 4662,
-      "end": 4666
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 4667,
-      "end": 4675
-    },
-    {
-      "text": "MSH6",
-      "type": "ENTITY",
-      "start": 4676,
-      "end": 4680
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 4681,
-      "end": 4689
-    },
-    {
-      "text": "interpretation",
-      "type": "ENTITY",
-      "start": 4694,
-      "end": 4708
-    },
-    {
-      "text": "immunohistochemistry stain",
-      "type": "ENTITY",
-      "start": 4722,
-      "end": 4748
-    },
-    {
-      "text": "stains",
-      "type": "ENTITY",
-      "start": 4752,
-      "end": 4758
-    },
-    {
-      "text": "published results",
-      "type": "ENTITY",
-      "start": 4772,
-      "end": 4789
-    },
-    {
-      "text": "medical literature",
-      "type": "ENTITY",
-      "start": 4797,
-      "end": 4815
-    },
-    {
-      "text": "package information",
-      "type": "ENTITY",
-      "start": 4826,
-      "end": 4845
-    },
-    {
-      "text": "manufacturer",
-      "type": "ENTITY",
-      "start": 4855,
-      "end": 4867
-    },
-    {
-      "text": "internal review",
-      "type": "ENTITY",
-      "start": 4875,
-      "end": 4890
-    },
-    {
-      "text": "staining",
-      "type": "ENTITY",
-      "start": 4894,
-      "end": 4902
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 4903,
-      "end": 4914
-    },
-    {
-      "text": "assay",
-      "type": "ENTITY",
-      "start": 4919,
-      "end": 4924
-    },
-    {
-      "text": "validation",
-      "type": "ENTITY",
-      "start": 4925,
-      "end": 4935
-    },
-    {
-      "text": "Immunohistochemistry Laboratory",
-      "type": "ENTITY",
-      "start": 4947,
-      "end": 4978
-    },
-    {
-      "text": "reagents",
-      "type": "ENTITY",
-      "start": 5010,
-      "end": 5018
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 5032,
-      "end": 5037
-    },
-    {
-      "text": "analyte",
-      "type": "ENTITY",
-      "start": 5057,
-      "end": 5064
-    },
-    {
-      "text": "ASR",
-      "type": "ENTITY",
-      "start": 5083,
-      "end": 5086
-    },
-    {
-      "text": "tests",
-      "type": "ENTITY",
-      "start": 5095,
-      "end": 5100
-    },
-    {
-      "text": "performance",
-      "type": "ENTITY",
-      "start": 5126,
-      "end": 5137
-    },
-    {
-      "text": "characteristic",
-      "type": "ENTITY",
-      "start": 5138,
-      "end": 5152
-    },
-    {
-      "text": "determined by",
-      "type": "ENTITY",
-      "start": 5153,
-      "end": 5166
-    },
-    {
-      "text": "Department of Pathology Laboratory",
-      "type": "ENTITY",
-      "start": 5171,
-      "end": 5205
-    },
-    {
-      "text": "cleared",
-      "type": "ENTITY",
-      "start": 5226,
-      "end": 5233
-    },
-    {
-      "text": "U.S. Food and Drug Administration",
-      "type": "ENTITY",
-      "start": 5253,
-      "end": 5286
-    },
-    {
-      "text": "FDA",
-      "type": "ENTITY",
-      "start": 5292,
-      "end": 5295
-    },
-    {
-      "text": "clearance",
-      "type": "ENTITY",
-      "start": 5321,
-      "end": 5330
-    },
-    {
-      "text": "approval",
-      "type": "ENTITY",
-      "start": 5334,
-      "end": 5342
-    },
-    {
-      "text": "Special stains",
-      "type": "ENTITY",
-      "start": 5361,
-      "end": 5375
-    },
-    {
-      "text": "immunohistochemical stains",
-      "type": "ENTITY",
-      "start": 5383,
-      "end": 5409
-    },
-    {
-      "text": "stained positive",
-      "type": "ENTITY",
-      "start": 5444,
-      "end": 5460
-    },
-    {
-      "text": "negative controls",
-      "type": "ENTITY",
-      "start": 5465,
-      "end": 5482
-    },
-    {
-      "text": "PMS2 proteins",
-      "type": "ENTITY",
-      "start": 5504,
-      "end": 5517
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 5518,
-      "end": 5528
-    },
-    {
-      "text": "immunohistochemistry",
-      "type": "ENTITY",
-      "start": 5532,
-      "end": 5552
-    },
-    {
-      "text": "results",
-      "type": "ENTITY",
-      "start": 5558,
-      "end": 5565
-    },
-    {
-      "text": "microsatellite instability testing",
-      "type": "ENTITY",
-      "start": 5569,
-      "end": 5603
-    },
-    {
-      "text": "report",
-      "type": "ENTITY",
-      "start": 5633,
-      "end": 5639
-    }
-  ],
-  "entity_count": 246,
-  "has_embedding": true
-}

output/biomedbert_output/01844833-aa33-4549-948b-3a08a50f0a35_nlp.json

@@ -1,1004 +0,0 @@
-{
-  "filename": "01844833-aa33-4549-948b-3a08a50f0a35",
-  "timestamp": "2026-01-05T14:42:50.261062",
-  "entities": [
-    {
-      "text": "SsiS",
-      "type": "ENTITY",
-      "start": 24,
-      "end": 28
-    },
-    {
-      "text": "SENTIneL",
-      "type": "ENTITY",
-      "start": 40,
-      "end": 48
-    },
-    {
-      "text": "LympH",
-      "type": "ENTITY",
-      "start": 49,
-      "end": 54
-    },
-    {
-      "text": "NODe",
-      "type": "ENTITY",
-      "start": 55,
-      "end": 59
-    },
-    {
-      "text": "BIOpSy",
-      "type": "ENTITY",
-      "start": 64,
-      "end": 70
-    },
-    {
-      "text": "one",
-      "type": "ENTITY",
-      "start": 73,
-      "end": 76
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 77,
-      "end": 87
-    },
-    {
-      "text": "metastatic carcinoma",
-      "type": "ENTITY",
-      "start": 93,
-      "end": 113
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 114,
-      "end": 123
-    },
-    {
-      "text": "Dimension",
-      "type": "ENTITY",
-      "start": 143,
-      "end": 152
-    },
-    {
-      "text": "NO",
-      "type": "ENTITY",
-      "start": 161,
-      "end": 163
-    },
-    {
-      "text": "ExTension",
-      "type": "ENTITY",
-      "start": 178,
-      "end": 187
-    },
-    {
-      "text": "identifieD.",
-      "type": "ENTITY",
-      "start": 191,
-      "end": 202
-    },
-    {
-      "text": "Right sreast",
-      "type": "ENTITY",
-      "start": 211,
-      "end": 223
-    },
-    {
-      "text": "O'clock",
-      "type": "ENTITY",
-      "start": 229,
-      "end": 236
-    },
-    {
-      "text": "segmental mastectomy",
-      "type": "ENTITY",
-      "start": 238,
-      "end": 258
-    },
-    {
-      "text": "A.  mUL",
-      "type": "ENTITY",
-      "start": 261,
-      "end": 268
-    },
-    {
-      "text": "TIfOCAl",
-      "type": "ENTITY",
-      "start": 269,
-      "end": 276
-    },
-    {
-      "text": "JNyASIVe",
-      "type": "ENTITY",
-      "start": 277,
-      "end": 285
-    },
-    {
-      "text": "DUctAL",
-      "type": "ENTITY",
-      "start": 286,
-      "end": 292
-    },
-    {
-      "text": "CArciNQMA",
-      "type": "ENTITY",
-      "start": 293,
-      "end": 302
-    },
-    {
-      "text": "GrADE 2",
-      "type": "ENTITY",
-      "start": 315,
-      "end": 322
-    },
-    {
-      "text": "nUCLEAr GrADe 3",
-      "type": "ENTITY",
-      "start": 324,
-      "end": 339
-    },
-    {
-      "text": "TUBULE Score 3",
-      "type": "ENTITY",
-      "start": 341,
-      "end": 355
-    },
-    {
-      "text": "mitotic activity score",
-      "type": "ENTITY",
-      "start": 357,
-      "end": 379
-    },
-    {
-      "text": "MASs",
-      "type": "ENTITY",
-      "start": 416,
-      "end": 420
-    },
-    {
-      "text": "MEAsURe8",
-      "type": "ENTITY",
-      "start": 421,
-      "end": 429
-    },
-    {
-      "text": "Cm",
-      "type": "ENTITY",
-      "start": 434,
-      "end": 436
-    },
-    {
-      "text": "SITe",
-      "type": "ENTITY",
-      "start": 467,
-      "end": 471
-    },
-    {
-      "text": "CHAnGES",
-      "type": "ENTITY",
-      "start": 472,
-      "end": 479
-    },
-    {
-      "text": "C. A",
-      "type": "ENTITY",
-      "start": 481,
-      "end": 485
-    },
-    {
-      "text": "SATELLITE",
-      "type": "ENTITY",
-      "start": 493,
-      "end": 502
-    },
-    {
-      "text": "nODUEE",
-      "type": "ENTITY",
-      "start": 503,
-      "end": 509
-    },
-    {
-      "text": "INVASIVE TUMOR IS",
-      "type": "ENTITY",
-      "start": 513,
-      "end": 530
-    },
-    {
-      "text": "THE Specimen",
-      "type": "ENTITY",
-      "start": 566,
-      "end": 578
-    },
-    {
-      "text": "tumor mass",
-      "type": "ENTITY",
-      "start": 599,
-      "end": 609
-    },
-    {
-      "text": "THiro tumOR FOcUS",
-      "type": "ENTITY",
-      "start": 614,
-      "end": 631
-    },
-    {
-      "text": "SEen",
-      "type": "ENTITY",
-      "start": 635,
-      "end": 639
-    },
-    {
-      "text": "PaRT",
-      "type": "ENTITY",
-      "start": 643,
-      "end": 647
-    },
-    {
-      "text": "soc comment",
-      "type": "ENTITY",
-      "start": 651,
-      "end": 662
-    },
-    {
-      "text": "E. LYMPHOVASCULAR",
-      "type": "ENTITY",
-      "start": 665,
-      "end": 682
-    },
-    {
-      "text": "IS",
-      "type": "ENTITY",
-      "start": 698,
-      "end": 700
-    },
-    {
-      "text": "IOENTIFIED",
-      "type": "ENTITY",
-      "start": 701,
-      "end": 711
-    },
-    {
-      "text": "F.  PERINEURAL INVASION",
-      "type": "ENTITY",
-      "start": 713,
-      "end": 736
-    },
-    {
-      "text": "G. TUMOR",
-      "type": "ENTITY",
-      "start": 752,
-      "end": 760
-    },
-    {
-      "text": "CENTRAL FIBROSIS",
-      "type": "ENTITY",
-      "start": 777,
-      "end": 793
-    },
-    {
-      "text": "PSEUDO DECiDUALIZEd STROmAL",
-      "type": "ENTITY",
-      "start": 799,
-      "end": 826
-    },
-    {
-      "text": "HYPERPI.ASIA",
-      "type": "ENTITY",
-      "start": 827,
-      "end": 839
-    },
-    {
-      "text": "StrOmal ReactiOn",
-      "type": "ENTITY",
-      "start": 852,
-      "end": 868
-    },
-    {
-      "text": "H. DuctaL CARcInOmA",
-      "type": "ENTITY",
-      "start": 870,
-      "end": 889
-    },
-    {
-      "text": "SiTU",
-      "type": "ENTITY",
-      "start": 893,
-      "end": 897
-    },
-    {
-      "text": "DCIS",
-      "type": "ENTITY",
-      "start": 899,
-      "end": 903
-    },
-    {
-      "text": "CALCIFICATIONS",
-      "type": "ENTITY",
-      "start": 946,
-      "end": 960
-    },
-    {
-      "text": "NEOPLASM",
-      "type": "ENTITY",
-      "start": 988,
-      "end": 996
-    },
-    {
-      "text": "INVASIVE CARCINOMA",
-      "type": "ENTITY",
-      "start": 1032,
-      "end": 1050
-    },
-    {
-      "text": "WAS",
-      "type": "ENTITY",
-      "start": 1051,
-      "end": 1054
-    },
-    {
-      "text": "CLOSEST",
-      "type": "ENTITY",
-      "start": 1055,
-      "end": 1062
-    },
-    {
-      "text": "THE ANTERIOR MARGiN",
-      "type": "ENTITY",
-      "start": 1066,
-      "end": 1085
-    },
-    {
-      "text": "INTRAVASCULAR TUmOR WAS CLOSEST",
-      "type": "ENTITY",
-      "start": 1097,
-      "end": 1128
-    },
-    {
-      "text": "SUPERIOR MARGIN",
-      "type": "ENTITY",
-      "start": 1136,
-      "end": 1151
-    },
-    {
-      "text": "consIstent with",
-      "type": "ENTITY",
-      "start": 1168,
-      "end": 1183
-    },
-    {
-      "text": "BiOp8y Site",
-      "type": "ENTITY",
-      "start": 1193,
-      "end": 1204
-    },
-    {
-      "text": "repORted",
-      "type": "ENTITY",
-      "start": 1226,
-      "end": 1234
-    },
-    {
-      "text": "AnD",
-      "type": "ENTITY",
-      "start": 1257,
-      "end": 1260
-    },
-    {
-      "text": "PR",
-      "type": "ENTITY",
-      "start": 1261,
-      "end": 1263
-    },
-    {
-      "text": "AnD nEgAtIVe fOr",
-      "type": "ENTITY",
-      "start": 1265,
-      "end": 1281
-    },
-    {
-      "text": "hEr-2/nEu PATHOLOGIC 8TAGE",
-      "type": "ENTITY",
-      "start": 1282,
-      "end": 1308
-    },
-    {
-      "text": "pT2 pN2a pMX",
-      "type": "ENTITY",
-      "start": 1310,
-      "end": 1322
-    },
-    {
-      "text": "Right axillary",
-      "type": "ENTITY",
-      "start": 1332,
-      "end": 1346
-    },
-    {
-      "text": "contents",
-      "type": "ENTITY",
-      "start": 1347,
-      "end": 1355
-    },
-    {
-      "text": "Di8section",
-      "type": "ENTITY",
-      "start": 1357,
-      "end": 1367
-    },
-    {
-      "text": "A. Satellite.noDule",
-      "type": "ENTITY",
-      "start": 1370,
-      "end": 1389
-    },
-    {
-      "text": "invasive ductal Carcinoma",
-      "type": "ENTITY",
-      "start": 1393,
-      "end": 1418
-    },
-    {
-      "text": "Ductal Carcinoma",
-      "type": "ENTITY",
-      "start": 1423,
-      "end": 1439
-    },
-    {
-      "text": "Situ",
-      "type": "ENTITY",
-      "start": 1443,
-      "end": 1447
-    },
-    {
-      "text": "TUmOR",
-      "type": "ENTITY",
-      "start": 1476,
-      "end": 1481
-    },
-    {
-      "text": "SEen",
-      "type": "ENTITY",
-      "start": 1482,
-      "end": 1486
-    },
-    {
-      "text": "PArt 2",
-      "type": "ENTITY",
-      "start": 1490,
-      "end": 1496
-    },
-    {
-      "text": "B.  SEVEN LYMPH NODES",
-      "type": "ENTITY",
-      "start": 1507,
-      "end": 1528
-    },
-    {
-      "text": "POSITIVEFOR",
-      "type": "ENTITY",
-      "start": 1530,
-      "end": 1541
-    },
-    {
-      "text": "AOENOCARCINOMA",
-      "type": "ENTITY",
-      "start": 1553,
-      "end": 1567
-    },
-    {
-      "text": "MEASURING UP",
-      "type": "ENTITY",
-      "start": 1568,
-      "end": 1580
-    },
-    {
-      "text": "AppROXImATELY",
-      "type": "ENTITY",
-      "start": 1584,
-      "end": 1597
-    },
-    {
-      "text": "Mm",
-      "type": "ENTITY",
-      "start": 1600,
-      "end": 1602
-    },
-    {
-      "text": "EACH",
-      "type": "ENTITY",
-      "start": 1603,
-      "end": 1607
-    },
-    {
-      "text": "C. ExtracapsuLar",
-      "type": "ENTITY",
-      "start": 1616,
-      "end": 1632
-    },
-    {
-      "text": "Ex'tensIonis",
-      "type": "ENTITY",
-      "start": 1633,
-      "end": 1645
-    },
-    {
-      "text": "Present",
-      "type": "ENTITY",
-      "start": 1646,
-      "end": 1653
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 1658,
-      "end": 1666
-    },
-    {
-      "text": "EXTeNSIVe",
-      "type": "ENTITY",
-      "start": 1686,
-      "end": 1695
-    },
-    {
-      "text": "intRAVASCULAK",
-      "type": "ENTITY",
-      "start": 1696,
-      "end": 1709
-    },
-    {
-      "text": "iumUR",
-      "type": "ENTITY",
-      "start": 1710,
-      "end": 1715
-    },
-    {
-      "text": "SYNOPTIC",
-      "type": "ENTITY",
-      "start": 1741,
-      "end": 1749
-    },
-    {
-      "text": "PRIMARY",
-      "type": "ENTITY",
-      "start": 1752,
-      "end": 1759
-    },
-    {
-      "text": "iNVASIVE",
-      "type": "ENTITY",
-      "start": 1760,
-      "end": 1768
-    },
-    {
-      "text": "BREASt",
-      "type": "ENTITY",
-      "start": 1782,
-      "end": 1788
-    },
-    {
-      "text": "Cnicii",
-      "type": "ENTITY",
-      "start": 1801,
-      "end": 1807
-    },
-    {
-      "text": "nifilr#ny ductl",
-      "type": "ENTITY",
-      "start": 1813,
-      "end": 1828
-    },
-    {
-      "text": "Nts 85oo/3 PROCEDURE",
-      "type": "ENTITY",
-      "start": 1829,
-      "end": 1849
-    },
-    {
-      "text": "Right  Sagmental Si#:buust",
-      "type": "ENTITY",
-      "start": 1851,
-      "end": 1877
-    },
-    {
-      "text": "Nos C5v.9 3/131n",
-      "type": "ENTITY",
-      "start": 1879,
-      "end": 1895
-    },
-    {
-      "text": "LOCATION",
-      "type": "ENTITY",
-      "start": 1899,
-      "end": 1907
-    },
-    {
-      "text": "Uppur nuter quadrant",
-      "type": "ENTITY",
-      "start": 1909,
-      "end": 1929
-    },
-    {
-      "text": "TumOR",
-      "type": "ENTITY",
-      "start": 1938,
-      "end": 1943
-    },
-    {
-      "text": "Lower outor quadrant",
-      "type": "ENTITY",
-      "start": 1945,
-      "end": 1965
-    },
-    {
-      "text": "MULTICENTRICITY/MULTIFOCALITY",
-      "type": "ENTITY",
-      "start": 1966,
-      "end": 1995
-    },
-    {
-      "text": "INVASIVE",
-      "type": "ENTITY",
-      "start": 1999,
-      "end": 2007
-    },
-    {
-      "text": "Maxirmiurn",
-      "type": "ENTITY",
-      "start": 2014,
-      "end": 2024
-    },
-    {
-      "text": "Qimcnsion",
-      "type": "ENTITY",
-      "start": 2025,
-      "end": 2034
-    },
-    {
-      "text": "Tumor",
-      "type": "ENTITY",
-      "start": 2062,
-      "end": 2067
-    },
-    {
-      "text": "Aggregate size",
-      "type": "ENTITY",
-      "start": 2068,
-      "end": 2082
-    },
-    {
-      "text": "Yes TUmOR TYPE",
-      "type": "ENTITY",
-      "start": 2084,
-      "end": 2098
-    },
-    {
-      "text": "invasive component",
-      "type": "ENTITY",
-      "start": 2100,
-      "end": 2118
-    },
-    {
-      "text": "Sum",
-      "type": "ENTITY",
-      "start": 2121,
-      "end": 2124
-    },
-    {
-      "text": "sizos",
-      "type": "ENTITY",
-      "start": 2132,
-      "end": 2137
-    },
-    {
-      "text": "multiple",
-      "type": "ENTITY",
-      "start": 2141,
-      "end": 2149
-    },
-    {
-      "text": "NOTTINGHAM",
-      "type": "ENTITY",
-      "start": 2174,
-      "end": 2184
-    },
-    {
-      "text": "SCORE",
-      "type": "ENTITY",
-      "start": 2185,
-      "end": 2190
-    },
-    {
-      "text": "Ductal adenocarcinoma",
-      "type": "ENTITY",
-      "start": 2192,
-      "end": 2213
-    },
-    {
-      "text": "NOS",
-      "type": "ENTITY",
-      "start": 2215,
-      "end": 2218
-    },
-    {
-      "text": "Nuclear grade",
-      "type": "ENTITY",
-      "start": 2219,
-      "end": 2232
-    },
-    {
-      "text": "Tubulo formatlon",
-      "type": "ENTITY",
-      "start": 2236,
-      "end": 2252
-    },
-    {
-      "text": "Nottinyham srnre",
-      "type": "ENTITY",
-      "start": 2262,
-      "end": 2278
-    },
-    {
-      "text": "UUID",
-      "type": "ENTITY",
-      "start": 2282,
-      "end": 2286
-    },
-    {
-      "text": "E4CBDC29-63E2-4CF0-B02F-16CA9C69F26E ANGIOLYMPHATIC",
-      "type": "ENTITY",
-      "start": 2287,
-      "end": 2338
-    },
-    {
-      "text": "INVASION",
-      "type": "ENTITY",
-      "start": 2339,
-      "end": 2347
-    },
-    {
-      "text": "Nottinyham grade",
-      "type": "ENTITY",
-      "start": 2349,
-      "end": 2365
-    },
-    {
-      "text": "TCGA-BH-A0DS-01A-PR",
-      "type": "ENTITY",
-      "start": 2379,
-      "end": 2398
-    },
-    {
-      "text": "LYMPhATIC INVASION",
-      "type": "ENTITY",
-      "start": 2406,
-      "end": 2424
-    },
-    {
-      "text": "Redacted",
-      "type": "ENTITY",
-      "start": 2430,
-      "end": 2438
-    },
-    {
-      "text": "Not applicahlc",
-      "type": "ENTITY",
-      "start": 2454,
-      "end": 2468
-    },
-    {
-      "text": "Tumor type",
-      "type": "ENTITY",
-      "start": 2469,
-      "end": 2479
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 2481,
-      "end": 2488
-    },
-    {
-      "text": "malignant zones",
-      "type": "ENTITY",
-      "start": 2495,
-      "end": 2510
-    },
-    {
-      "text": "Cribriform SURGICAL mARGINS",
-      "type": "ENTITY",
-      "start": 2511,
-      "end": 2538
-    },
-    {
-      "text": "Comedo",
-      "type": "ENTITY",
-      "start": 2571,
-      "end": 2577
-    },
-    {
-      "text": "SURG",
-      "type": "ENTITY",
-      "start": 2581,
-      "end": 2585
-    },
-    {
-      "text": "Distance",
-      "type": "ENTITY",
-      "start": 2625,
-      "end": 2633
-    },
-    {
-      "text": "invasive",
-      "type": "ENTITY",
-      "start": 2637,
-      "end": 2645
-    },
-    {
-      "text": "No LYMPH NODES",
-      "type": "ENTITY",
-      "start": 2676,
-      "end": 2690
-    },
-    {
-      "text": "Diytance",
-      "type": "ENTITY",
-      "start": 2701,
-      "end": 2709
-    },
-    {
-      "text": "in situ discaxe",
-      "type": "ENTITY",
-      "start": 2713,
-      "end": 2728
-    },
-    {
-      "text": "dosest margin",
-      "type": "ENTITY",
-      "start": 2732,
-      "end": 2745
-    },
-    {
-      "text": "LymPh nODeS ExAMINED",
-      "type": "ENTITY",
-      "start": 2752,
-      "end": 2772
-    },
-    {
-      "text": "B METHOD(S)",
-      "type": "ENTITY",
-      "start": 2774,
-      "end": 2785
-    },
-    {
-      "text": "LYMPH NODE",
-      "type": "ENTITY",
-      "start": 2789,
-      "end": 2799
-    },
-    {
-      "text": "Sentinel",
-      "type": "ENTITY",
-      "start": 2816,
-      "end": 2824
-    },
-    {
-      "text": "nOde",
-      "type": "ENTITY",
-      "start": 2825,
-      "end": 2829
-    },
-    {
-      "text": "metAstasis",
-      "type": "ENTITY",
-      "start": 2830,
-      "end": 2840
-    },
-    {
-      "text": "H/E stain  SIZE",
-      "type": "ENTITY",
-      "start": 2842,
-      "end": 2857
-    },
-    {
-      "text": "NODAL",
-      "type": "ENTITY",
-      "start": 2861,
-      "end": 2866
-    },
-    {
-      "text": "Lymph",
-      "type": "ENTITY",
-      "start": 2883,
-      "end": 2888
-    },
-    {
-      "text": "Diameter",
-      "type": "ENTITY",
-      "start": 2940,
-      "end": 2948
-    },
-    {
-      "text": "lymph node metastasis",
-      "type": "ENTITY",
-      "start": 2960,
-      "end": 2981
-    },
-    {
-      "text": "stage",
-      "type": "ENTITY",
-      "start": 2990,
-      "end": 2995
-    },
-    {
-      "text": "Pathologic",
-      "type": "ENTITY",
-      "start": 2997,
-      "end": 3007
-    },
-    {
-      "text": "stage",
-      "type": "ENTITY",
-      "start": 3040,
-      "end": 3045
-    },
-    {
-      "text": "pathologic",
-      "type": "ENTITY",
-      "start": 3047,
-      "end": 3057
-    },
-    {
-      "text": "pN2a ESTROGeN RECEPTOrS",
-      "type": "ENTITY",
-      "start": 3059,
-      "end": 3082
-    },
-    {
-      "text": "pMX",
-      "type": "ENTITY",
-      "start": 3084,
-      "end": 3087
-    },
-    {
-      "text": "HER2/NEU",
-      "type": "ENTITY",
-      "start": 3121,
-      "end": 3129
-    },
-    {
-      "text": "positivn",
-      "type": "ENTITY",
-      "start": 3131,
-      "end": 3139
-    },
-    {
-      "text": "rimary",
-      "type": "ENTITY",
-      "start": 3140,
-      "end": 3146
-    },
-    {
-      "text": "Tum HPAA Disc Zoro",
-      "type": "ENTITY",
-      "start": 3147,
-      "end": 3165
-    },
-    {
-      "text": "rior",
-      "type": "ENTITY",
-      "start": 3172,
-      "end": 3176
-    },
-    {
-      "text": "Malignan",
-      "type": "ENTITY",
-      "start": 3177,
-      "end": 3185
-    }
-  ],
-  "entity_count": 166,
-  "has_embedding": true
-}

output/biomedbert_output/0184b3ab-2ef7-44aa-98d0-260dc7657ac2_nlp.json

@@ -1,782 +0,0 @@
-{
-  "filename": "0184b3ab-2ef7-44aa-98d0-260dc7657ac2",
-  "timestamp": "2026-01-05T14:43:43.761869",
-  "entities": [
-    {
-      "text": "CaLcinvma",
-      "type": "ENTITY",
-      "start": 24,
-      "end": 33
-    },
-    {
-      "text": "metap|asft",
-      "type": "ENTITY",
-      "start": 35,
-      "end": 45
-    },
-    {
-      "text": "UUID:46A75AD3-BAD1-4A16-873E-0099BD10FA8C",
-      "type": "ENTITY",
-      "start": 57,
-      "end": 98
-    },
-    {
-      "text": "NOS",
-      "type": "ENTITY",
-      "start": 111,
-      "end": 114
-    },
-    {
-      "text": "TCGA-A7-A26F-01A-PR Redacted C",
-      "type": "ENTITY",
-      "start": 115,
-      "end": 145
-    },
-    {
-      "text": "LABORATORY MEDICINE",
-      "type": "ENTITY",
-      "start": 187,
-      "end": 206
-    },
-    {
-      "text": "Date",
-      "type": "ENTITY",
-      "start": 207,
-      "end": 211
-    },
-    {
-      "text": "A. Left",
-      "type": "ENTITY",
-      "start": 226,
-      "end": 233
-    },
-    {
-      "text": "Left breast",
-      "type": "ENTITY",
-      "start": 266,
-      "end": 277
-    },
-    {
-      "text": "CLINICAL HISTORY",
-      "type": "ENTITY",
-      "start": 293,
-      "end": 309
-    },
-    {
-      "text": "left breast metaplastic cancer",
-      "type": "ENTITY",
-      "start": 328,
-      "end": 358
-    },
-    {
-      "text": "FROZEN SECTION",
-      "type": "ENTITY",
-      "start": 360,
-      "end": 374
-    },
-    {
-      "text": "AFs",
-      "type": "ENTITY",
-      "start": 385,
-      "end": 388
-    },
-    {
-      "text": "Left axillary sentinel node",
-      "type": "ENTITY",
-      "start": 389,
-      "end": 416
-    },
-    {
-      "text": "excision",
-      "type": "ENTITY",
-      "start": 418,
-      "end": 426
-    },
-    {
-      "text": "No evidence",
-      "type": "ENTITY",
-      "start": 428,
-      "end": 439
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 443,
-      "end": 453
-    },
-    {
-      "text": "node",
-      "type": "ENTITY",
-      "start": 459,
-      "end": 463
-    },
-    {
-      "text": "GROSS DESCRIPTION",
-      "type": "ENTITY",
-      "start": 470,
-      "end": 487
-    },
-    {
-      "text": "container",
-      "type": "ENTITY",
-      "start": 505,
-      "end": 514
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 532,
-      "end": 541
-    },
-    {
-      "text": "medical record number",
-      "type": "ENTITY",
-      "start": 548,
-      "end": 569
-    },
-    {
-      "text": "\"left axillary sentinel lymph node",
-      "type": "ENTITY",
-      "start": 574,
-      "end": 608
-    },
-    {
-      "text": "specimen container",
-      "type": "ENTITY",
-      "start": 615,
-      "end": 633
-    },
-    {
-      "text": "single soft tan lymph node",
-      "type": "ENTITY",
-      "start": 642,
-      "end": 668
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 669,
-      "end": 678
-    },
-    {
-      "text": "AS",
-      "type": "ENTITY",
-      "start": 697,
-      "end": 699
-    },
-    {
-      "text": "Asf",
-      "type": "ENTITY",
-      "start": 706,
-      "end": 709
-    },
-    {
-      "text": "bisected",
-      "type": "ENTITY",
-      "start": 711,
-      "end": 719
-    },
-    {
-      "text": "B. Container B",
-      "type": "ENTITY",
-      "start": 721,
-      "end": 735
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 739,
-      "end": 746
-    },
-    {
-      "text": "patient's",
-      "type": "ENTITY",
-      "start": 756,
-      "end": 765
-    },
-    {
-      "text": "medical record number",
-      "type": "ENTITY",
-      "start": 772,
-      "end": 793
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 817,
-      "end": 825
-    },
-    {
-      "text": "excisional biopsy",
-      "type": "ENTITY",
-      "start": 841,
-      "end": 858
-    },
-    {
-      "text": "sutures",
-      "type": "ENTITY",
-      "start": 875,
-      "end": 882
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 887,
-      "end": 896
-    },
-    {
-      "text": "anterior",
-      "type": "ENTITY",
-      "start": 910,
-      "end": 918
-    },
-    {
-      "text": "posterior",
-      "type": "ENTITY",
-      "start": 922,
-      "end": 931
-    },
-    {
-      "text": "inferior",
-      "type": "ENTITY",
-      "start": 958,
-      "end": 966
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 984,
-      "end": 990
-    },
-    {
-      "text": "lateral",
-      "type": "ENTITY",
-      "start": 994,
-      "end": 1001
-    },
-    {
-      "text": "specimen margins",
-      "type": "ENTITY",
-      "start": 1007,
-      "end": 1023
-    },
-    {
-      "text": "blue-interior",
-      "type": "ENTITY",
-      "start": 1046,
-      "end": 1059
-    },
-    {
-      "text": "black-posterior",
-      "type": "ENTITY",
-      "start": 1061,
-      "end": 1076
-    },
-    {
-      "text": "red-superior",
-      "type": "ENTITY",
-      "start": 1078,
-      "end": 1090
-    },
-    {
-      "text": "green-inferior",
-      "type": "ENTITY",
-      "start": 1092,
-      "end": 1106
-    },
-    {
-      "text": "yellow-medial",
-      "type": "ENTITY",
-      "start": 1108,
-      "end": 1121
-    },
-    {
-      "text": "orange-lateral",
-      "type": "ENTITY",
-      "start": 1123,
-      "end": 1137
-    },
-    {
-      "text": "sectioned",
-      "type": "ENTITY",
-      "start": 1148,
-      "end": 1157
-    },
-    {
-      "text": "tan stellate",
-      "type": "ENTITY",
-      "start": 1179,
-      "end": 1191
-    },
-    {
-      "text": "lesion",
-      "type": "ENTITY",
-      "start": 1192,
-      "end": 1198
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1203,
-      "end": 1211
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 1215,
-      "end": 1224
-    },
-    {
-      "text": "direction",
-      "type": "ENTITY",
-      "start": 1271,
-      "end": 1280
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 1288,
-      "end": 1303
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 1307,
-      "end": 1316
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 1346,
-      "end": 1361
-    },
-    {
-      "text": "Asb1-b20",
-      "type": "ENTITY",
-      "start": 1363,
-      "end": 1371
-    },
-    {
-      "text": "evidence",
-      "type": "ENTITY",
-      "start": 1412,
-      "end": 1420
-    },
-    {
-      "text": "metastasis",
-      "type": "ENTITY",
-      "start": 1424,
-      "end": 1434
-    },
-    {
-      "text": "left axillary sentinel lymph node",
-      "type": "ENTITY",
-      "start": 1442,
-      "end": 1475
-    },
-    {
-      "text": "node",
-      "type": "ENTITY",
-      "start": 1481,
-      "end": 1485
-    },
-    {
-      "text": "multilevel",
-      "type": "ENTITY",
-      "start": 1501,
-      "end": 1511
-    },
-    {
-      "text": "sectioning",
-      "type": "ENTITY",
-      "start": 1512,
-      "end": 1522
-    },
-    {
-      "text": "H&E",
-      "type": "ENTITY",
-      "start": 1528,
-      "end": 1531
-    },
-    {
-      "text": "staining",
-      "type": "ENTITY",
-      "start": 1532,
-      "end": 1540
-    },
-    {
-      "text": "immunohistochemistry",
-      "type": "ENTITY",
-      "start": 1557,
-      "end": 1577
-    },
-    {
-      "text": "pankeratin",
-      "type": "ENTITY",
-      "start": 1582,
-      "end": 1592
-    },
-    {
-      "text": "B. Invasive Carcinoma",
-      "type": "ENTITY",
-      "start": 1594,
-      "end": 1615
-    },
-    {
-      "text": "Histologic type",
-      "type": "ENTITY",
-      "start": 1626,
-      "end": 1641
-    },
-    {
-      "text": "metaplastic",
-      "type": "ENTITY",
-      "start": 1643,
-      "end": 1654
-    },
-    {
-      "text": "Histologic grade",
-      "type": "ENTITY",
-      "start": 1656,
-      "end": 1672
-    },
-    {
-      "text": "Overall grade",
-      "type": "ENTITY",
-      "start": 1674,
-      "end": 1687
-    },
-    {
-      "text": "Architectural score",
-      "type": "ENTITY",
-      "start": 1691,
-      "end": 1710
-    },
-    {
-      "text": "Nuclear score",
-      "type": "ENTITY",
-      "start": 1712,
-      "end": 1725
-    },
-    {
-      "text": "Mitotic score",
-      "type": "ENTITY",
-      "start": 1729,
-      "end": 1742
-    },
-    {
-      "text": "Greatest dimension",
-      "type": "ENTITY",
-      "start": 1746,
-      "end": 1764
-    },
-    {
-      "text": "Positive",
-      "type": "ENTITY",
-      "start": 1802,
-      "end": 1810
-    },
-    {
-      "text": "Vessel",
-      "type": "ENTITY",
-      "start": 1812,
-      "end": 1818
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 1819,
-      "end": 1827
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 1858,
-      "end": 1873
-    },
-    {
-      "text": "distance",
-      "type": "ENTITY",
-      "start": 1881,
-      "end": 1889
-    },
-    {
-      "text": "Vessel",
-      "type": "ENTITY",
-      "start": 1912,
-      "end": 1918
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 1919,
-      "end": 1927
-    },
-    {
-      "text": "foci",
-      "type": "ENTITY",
-      "start": 1929,
-      "end": 1933
-    },
-    {
-      "text": "suspicious",
-      "type": "ENTITY",
-      "start": 1934,
-      "end": 1944
-    },
-    {
-      "text": "Calcification",
-      "type": "ENTITY",
-      "start": 1946,
-      "end": 1959
-    },
-    {
-      "text": "Ductal carcinoma",
-      "type": "ENTITY",
-      "start": 1970,
-      "end": 1986
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 1987,
-      "end": 1994
-    },
-    {
-      "text": "Histologic pattern",
-      "type": "ENTITY",
-      "start": 2005,
-      "end": 2023
-    },
-    {
-      "text": "Nuclear grade",
-      "type": "ENTITY",
-      "start": 2033,
-      "end": 2046
-    },
-    {
-      "text": "Central necrosis",
-      "type": "ENTITY",
-      "start": 2050,
-      "end": 2066
-    },
-    {
-      "text": "Absent",
-      "type": "ENTITY",
-      "start": 2132,
-      "end": 2138
-    },
-    {
-      "text": "intraductal component",
-      "type": "ENTITY",
-      "start": 2150,
-      "end": 2171
-    },
-    {
-      "text": "Specimen margins",
-      "type": "ENTITY",
-      "start": 2174,
-      "end": 2190
-    },
-    {
-      "text": "Negative",
-      "type": "ENTITY",
-      "start": 2192,
-      "end": 2200
-    },
-    {
-      "text": "Calcification",
-      "type": "ENTITY",
-      "start": 2202,
-      "end": 2215
-    },
-    {
-      "text": "Description",
-      "type": "ENTITY",
-      "start": 2226,
-      "end": 2237
-    },
-    {
-      "text": "non-tumorous breast",
-      "type": "ENTITY",
-      "start": 2241,
-      "end": 2260
-    },
-    {
-      "text": "Unremarkable",
-      "type": "ENTITY",
-      "start": 2263,
-      "end": 2275
-    },
-    {
-      "text": "Comments",
-      "type": "ENTITY",
-      "start": 2277,
-      "end": 2285
-    },
-    {
-      "text": "FISh",
-      "type": "ENTITY",
-      "start": 2304,
-      "end": 2308
-    },
-    {
-      "text": "HER-2",
-      "type": "ENTITY",
-      "start": 2313,
-      "end": 2318
-    },
-    {
-      "text": "Prognostic markers",
-      "type": "ENTITY",
-      "start": 2335,
-      "end": 2353
-    },
-    {
-      "text": "equivocal",
-      "type": "ENTITY",
-      "start": 2355,
-      "end": 2364
-    },
-    {
-      "text": "block",
-      "type": "ENTITY",
-      "start": 2371,
-      "end": 2376
-    },
-    {
-      "text": "HER-2",
-      "type": "ENTITY",
-      "start": 2411,
-      "end": 2416
-    },
-    {
-      "text": "FISH",
-      "type": "ENTITY",
-      "start": 2420,
-      "end": 2424
-    },
-    {
-      "text": "DIAGNOSISS",
-      "type": "ENTITY",
-      "start": 2426,
-      "end": 2436
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 2472,
-      "end": 2481
-    },
-    {
-      "text": "A. B. Left breast",
-      "type": "ENTITY",
-      "start": 2483,
-      "end": 2500
-    },
-    {
-      "text": "excisional biopsy",
-      "type": "ENTITY",
-      "start": 2502,
-      "end": 2519
-    },
-    {
-      "text": "carcinoma",
-      "type": "ENTITY",
-      "start": 2544,
-      "end": 2553
-    },
-    {
-      "text": "metaplastic features",
-      "type": "ENTITY",
-      "start": 2559,
-      "end": 2579
-    },
-    {
-      "text": "Invasive carcinoma",
-      "type": "ENTITY",
-      "start": 2597,
-      "end": 2615
-    },
-    {
-      "text": "inferior margin",
-      "type": "ENTITY",
-      "start": 2639,
-      "end": 2654
-    },
-    {
-      "text": "resection",
-      "type": "ENTITY",
-      "start": 2658,
-      "end": 2667
-    },
-    {
-      "text": "in situ",
-      "type": "ENTITY",
-      "start": 2687,
-      "end": 2694
-    },
-    {
-      "text": "solid",
-      "type": "ENTITY",
-      "start": 2696,
-      "end": 2701
-    },
-    {
-      "text": "comedo",
-      "type": "ENTITY",
-      "start": 2706,
-      "end": 2712
-    },
-    {
-      "text": "subtypes",
-      "type": "ENTITY",
-      "start": 2713,
-      "end": 2721
-    },
-    {
-      "text": "nuclear grade 3 with",
-      "type": "ENTITY",
-      "start": 2724,
-      "end": 2744
-    },
-    {
-      "text": "necrosis",
-      "type": "ENTITY",
-      "start": 2745,
-      "end": 2753
-    },
-    {
-      "text": "margins negative",
-      "type": "ENTITY",
-      "start": 2755,
-      "end": 2771
-    },
-    {
-      "text": "ctronic",
-      "type": "ENTITY",
-      "start": 2774,
-      "end": 2781
-    },
-    {
-      "text": "Signature",
-      "type": "ENTITY",
-      "start": 2782,
-      "end": 2791
-    },
-    {
-      "text": "Report Case",
-      "type": "ENTITY",
-      "start": 2801,
-      "end": 2812
-    },
-    {
-      "text": "circie",
-      "type": "ENTITY",
-      "start": 2817,
-      "end": 2823
-    }
-  ],
-  "entity_count": 129,
-  "has_embedding": true
-}

output/biomedbert_output/01ada9fd-11b3-4b62-bf75-7bf4c71f81a9_nlp.json

@@ -1,1544 +0,0 @@
-{
-  "filename": "01ada9fd-11b3-4b62-bf75-7bf4c71f81a9",
-  "timestamp": "2026-01-05T14:41:23.006503",
-  "entities": [
-    {
-      "text": "History",
-      "type": "ENTITY",
-      "start": 37,
-      "end": 44
-    },
-    {
-      "text": "Right renal mass",
-      "type": "ENTITY",
-      "start": 46,
-      "end": 62
-    },
-    {
-      "text": "Specimens",
-      "type": "ENTITY",
-      "start": 64,
-      "end": 73
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 103,
-      "end": 109
-    },
-    {
-      "text": "bladder cuff nephrouterectomy 2:SP",
-      "type": "ENTITY",
-      "start": 114,
-      "end": 148
-    },
-    {
-      "text": "Retroperitoneal lipoma",
-      "type": "ENTITY",
-      "start": 149,
-      "end": 171
-    },
-    {
-      "text": "rightexcision 3:SP",
-      "type": "ENTITY",
-      "start": 172,
-      "end": 190
-    },
-    {
-      "text": "Lymph nodes.paracavalexcision 4:SP",
-      "type": "ENTITY",
-      "start": 191,
-      "end": 225
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 226,
-      "end": 237
-    },
-    {
-      "text": "right common iliacexcision 5:SP",
-      "type": "ENTITY",
-      "start": 238,
-      "end": 269
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 270,
-      "end": 281
-    },
-    {
-      "text": "precaval",
-      "type": "ENTITY",
-      "start": 282,
-      "end": 290
-    },
-    {
-      "text": "interaortocavalexcision",
-      "type": "ENTITY",
-      "start": 295,
-      "end": 318
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 324,
-      "end": 335
-    },
-    {
-      "text": "suprahilar",
-      "type": "ENTITY",
-      "start": 337,
-      "end": 347
-    },
-    {
-      "text": "adrenal gland",
-      "type": "ENTITY",
-      "start": 352,
-      "end": 365
-    },
-    {
-      "text": "right excision DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 366,
-      "end": 390
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 392,
-      "end": 394
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 408,
-      "end": 414
-    },
-    {
-      "text": "bladder cuff",
-      "type": "ENTITY",
-      "start": 419,
-      "end": 431
-    },
-    {
-      "text": "nephrouterectomy",
-      "type": "ENTITY",
-      "start": 433,
-      "end": 449
-    },
-    {
-      "text": "Tumor Type",
-      "type": "ENTITY",
-      "start": 450,
-      "end": 460
-    },
-    {
-      "text": "Renal cell",
-      "type": "ENTITY",
-      "start": 462,
-      "end": 472
-    },
-    {
-      "text": "carcinoma-Chromophobe type",
-      "type": "ENTITY",
-      "start": 473,
-      "end": 499
-    },
-    {
-      "text": "Tumor Size",
-      "type": "ENTITY",
-      "start": 500,
-      "end": 510
-    },
-    {
-      "text": "diameter",
-      "type": "ENTITY",
-      "start": 521,
-      "end": 529
-    },
-    {
-      "text": "Local Invasion",
-      "type": "ENTITY",
-      "start": 541,
-      "end": 555
-    },
-    {
-      "text": "renal cortical types",
-      "type": "ENTITY",
-      "start": 561,
-      "end": 581
-    },
-    {
-      "text": "Involves",
-      "type": "ENTITY",
-      "start": 584,
-      "end": 592
-    },
-    {
-      "text": "renal sinus fat Renal Vein",
-      "type": "ENTITY",
-      "start": 593,
-      "end": 619
-    },
-    {
-      "text": "Invasion",
-      "type": "ENTITY",
-      "start": 620,
-      "end": 628
-    },
-    {
-      "text": "Small vessel",
-      "type": "ENTITY",
-      "start": 645,
-      "end": 657
-    },
-    {
-      "text": "angiolymphatic invasion",
-      "type": "ENTITY",
-      "start": 658,
-      "end": 681
-    },
-    {
-      "text": "Surgical Margins",
-      "type": "ENTITY",
-      "start": 705,
-      "end": 721
-    },
-    {
-      "text": "Free of",
-      "type": "ENTITY",
-      "start": 723,
-      "end": 730
-    },
-    {
-      "text": "Mild",
-      "type": "ENTITY",
-      "start": 760,
-      "end": 764
-    },
-    {
-      "text": "arteriosclerotic",
-      "type": "ENTITY",
-      "start": 765,
-      "end": 781
-    },
-    {
-      "text": "benign",
-      "type": "ENTITY",
-      "start": 794,
-      "end": 800
-    },
-    {
-      "text": "cortical cysts",
-      "type": "ENTITY",
-      "start": 801,
-      "end": 815
-    },
-    {
-      "text": "Adrenal Gland",
-      "type": "ENTITY",
-      "start": 816,
-      "end": 829
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 845,
-      "end": 856
-    },
-    {
-      "text": "renal cell",
-      "type": "ENTITY",
-      "start": 885,
-      "end": 895
-    },
-    {
-      "text": "Tumor",
-      "type": "ENTITY",
-      "start": 923,
-      "end": 928
-    },
-    {
-      "text": "invades",
-      "type": "ENTITY",
-      "start": 929,
-      "end": 936
-    },
-    {
-      "text": "adrenal gland",
-      "type": "ENTITY",
-      "start": 941,
-      "end": 954
-    },
-    {
-      "text": "perinephric tissues",
-      "type": "ENTITY",
-      "start": 958,
-      "end": 977
-    },
-    {
-      "text": "Gerota's",
-      "type": "ENTITY",
-      "start": 993,
-      "end": 1001
-    },
-    {
-      "text": "fascia",
-      "type": "ENTITY",
-      "start": 1002,
-      "end": 1008
-    },
-    {
-      "text": "Benign",
-      "type": "ENTITY",
-      "start": 1017,
-      "end": 1023
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 1050,
-      "end": 1056
-    },
-    {
-      "text": "Soft tissue",
-      "type": "ENTITY",
-      "start": 1062,
-      "end": 1073
-    },
-    {
-      "text": "retroperitoneumright;excision",
-      "type": "ENTITY",
-      "start": 1075,
-      "end": 1104
-    },
-    {
-      "text": "Mature",
-      "type": "ENTITY",
-      "start": 1105,
-      "end": 1111
-    },
-    {
-      "text": "PATHOLOGYREPORT",
-      "type": "ENTITY",
-      "start": 1170,
-      "end": 1185
-    },
-    {
-      "text": "atypia",
-      "type": "ENTITY",
-      "start": 1189,
-      "end": 1195
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 1196,
-      "end": 1206
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1234,
-      "end": 1242
-    },
-    {
-      "text": "consultation",
-      "type": "ENTITY",
-      "start": 1255,
-      "end": 1267
-    },
-    {
-      "text": "SPLymph nodes",
-      "type": "ENTITY",
-      "start": 1289,
-      "end": 1302
-    },
-    {
-      "text": "paracaval;excision",
-      "type": "ENTITY",
-      "start": 1303,
-      "end": 1321
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 1322,
-      "end": 1333
-    },
-    {
-      "text": "nodes",
-      "type": "ENTITY",
-      "start": 1358,
-      "end": 1363
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 1378,
-      "end": 1380
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 1381,
-      "end": 1392
-    },
-    {
-      "text": "right common iliac;excision",
-      "type": "ENTITY",
-      "start": 1393,
-      "end": 1420
-    },
-    {
-      "text": "Lymph Nodes",
-      "type": "ENTITY",
-      "start": 1421,
-      "end": 1432
-    },
-    {
-      "text": "nodes",
-      "type": "ENTITY",
-      "start": 1457,
-      "end": 1462
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 1479,
-      "end": 1490
-    },
-    {
-      "text": "precaval",
-      "type": "ENTITY",
-      "start": 1491,
-      "end": 1499
-    },
-    {
-      "text": "interaortocaval",
-      "type": "ENTITY",
-      "start": 1504,
-      "end": 1519
-    },
-    {
-      "text": "excision Lymph Nodes",
-      "type": "ENTITY",
-      "start": 1521,
-      "end": 1541
-    },
-    {
-      "text": "nodes",
-      "type": "ENTITY",
-      "start": 1565,
-      "end": 1570
-    },
-    {
-      "text": "Suprahilar nodes",
-      "type": "ENTITY",
-      "start": 1587,
-      "end": 1603
-    },
-    {
-      "text": "right adrenalgland;excision",
-      "type": "ENTITY",
-      "start": 1608,
-      "end": 1635
-    },
-    {
-      "text": "Benign adrenal gland",
-      "type": "ENTITY",
-      "start": 1636,
-      "end": 1656
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 1661,
-      "end": 1672
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 1673,
-      "end": 1683
-    },
-    {
-      "text": "IATTEST",
-      "type": "ENTITY",
-      "start": 1685,
-      "end": 1692
-    },
-    {
-      "text": "REVIEWEDANDAPPROVEDTHISREPORT",
-      "type": "ENTITY",
-      "start": 1809,
-      "end": 1838
-    },
-    {
-      "text": "Result",
-      "type": "ENTITY",
-      "start": 1857,
-      "end": 1863
-    },
-    {
-      "text": "SpecialStain",
-      "type": "ENTITY",
-      "start": 1864,
-      "end": 1876
-    },
-    {
-      "text": "RECUT",
-      "type": "ENTITY",
-      "start": 1885,
-      "end": 1890
-    },
-    {
-      "text": "Gross Description",
-      "type": "ENTITY",
-      "start": 1903,
-      "end": 1920
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 1929,
-      "end": 1937
-    },
-    {
-      "text": "fresh state",
-      "type": "ENTITY",
-      "start": 1953,
-      "end": 1964
-    },
-    {
-      "text": "intraoperative consultation",
-      "type": "ENTITY",
-      "start": 1969,
-      "end": 1996
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 1998,
-      "end": 2005
-    },
-    {
-      "text": "kidney",
-      "type": "ENTITY",
-      "start": 2015,
-      "end": 2021
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 2022,
-      "end": 2028
-    },
-    {
-      "text": "bladder",
-      "type": "ENTITY",
-      "start": 2034,
-      "end": 2041
-    },
-    {
-      "text": "total nephrectomy",
-      "type": "ENTITY",
-      "start": 2067,
-      "end": 2084
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2085,
-      "end": 2093
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2122,
-      "end": 2130
-    },
-    {
-      "text": "surface",
-      "type": "ENTITY",
-      "start": 2131,
-      "end": 2138
-    },
-    {
-      "text": "inked",
-      "type": "ENTITY",
-      "start": 2142,
-      "end": 2147
-    },
-    {
-      "text": "adrenal gland",
-      "type": "ENTITY",
-      "start": 2151,
-      "end": 2164
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 2168,
-      "end": 2178
-    },
-    {
-      "text": "Kidney measures",
-      "type": "ENTITY",
-      "start": 2180,
-      "end": 2195
-    },
-    {
-      "text": "segment",
-      "type": "ENTITY",
-      "start": 2221,
-      "end": 2228
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 2232,
-      "end": 2238
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 2239,
-      "end": 2247
-    },
-    {
-      "text": "length",
-      "type": "ENTITY",
-      "start": 2257,
-      "end": 2263
-    },
-    {
-      "text": "circumference",
-      "type": "ENTITY",
-      "start": 2278,
-      "end": 2291
-    },
-    {
-      "text": "distal",
-      "type": "ENTITY",
-      "start": 2296,
-      "end": 2302
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 2314,
-      "end": 2320
-    },
-    {
-      "text": "cuff",
-      "type": "ENTITY",
-      "start": 2353,
-      "end": 2357
-    },
-    {
-      "text": "Sectioning",
-      "type": "ENTITY",
-      "start": 2358,
-      "end": 2368
-    },
-    {
-      "text": "well-circumscribed",
-      "type": "ENTITY",
-      "start": 2379,
-      "end": 2397
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 2423,
-      "end": 2432
-    },
-    {
-      "text": "medial",
-      "type": "ENTITY",
-      "start": 2464,
-      "end": 2470
-    },
-    {
-      "text": "aspect",
-      "type": "ENTITY",
-      "start": 2471,
-      "end": 2477
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2485,
-      "end": 2493
-    },
-    {
-      "text": "tumor",
-      "type": "ENTITY",
-      "start": 2514,
-      "end": 2519
-    },
-    {
-      "text": "contact with",
-      "type": "ENTITY",
-      "start": 2532,
-      "end": 2544
-    },
-    {
-      "text": "sinus fat",
-      "type": "ENTITY",
-      "start": 2545,
-      "end": 2554
-    },
-    {
-      "text": "frank",
-      "type": "ENTITY",
-      "start": 2560,
-      "end": 2565
-    },
-    {
-      "text": "invasion",
-      "type": "ENTITY",
-      "start": 2566,
-      "end": 2574
-    },
-    {
-      "text": "Grossly",
-      "type": "ENTITY",
-      "start": 2602,
-      "end": 2609
-    },
-    {
-      "text": "venous invasion",
-      "type": "ENTITY",
-      "start": 2618,
-      "end": 2633
-    },
-    {
-      "text": "Perirenal fat",
-      "type": "ENTITY",
-      "start": 2647,
-      "end": 2660
-    },
-    {
-      "text": "uninvolved",
-      "type": "ENTITY",
-      "start": 2664,
-      "end": 2674
-    },
-    {
-      "text": "renal parenchyma",
-      "type": "ENTITY",
-      "start": 2687,
-      "end": 2703
-    },
-    {
-      "text": "mildly",
-      "type": "ENTITY",
-      "start": 2710,
-      "end": 2716
-    },
-    {
-      "text": "thinned cortex",
-      "type": "ENTITY",
-      "start": 2717,
-      "end": 2731
-    },
-    {
-      "text": "sharp cortical medullary junction",
-      "type": "ENTITY",
-      "start": 2746,
-      "end": 2779
-    },
-    {
-      "text": "Pelvic mucosa",
-      "type": "ENTITY",
-      "start": 2781,
-      "end": 2794
-    },
-    {
-      "text": "ureteral mucosa",
-      "type": "ENTITY",
-      "start": 2799,
-      "end": 2814
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 2856,
-      "end": 2867
-    },
-    {
-      "text": "identified",
-      "type": "ENTITY",
-      "start": 2872,
-      "end": 2882
-    },
-    {
-      "text": "perirenal fat",
-      "type": "ENTITY",
-      "start": 2890,
-      "end": 2903
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 2908,
-      "end": 2916
-    },
-    {
-      "text": "photographed",
-      "type": "ENTITY",
-      "start": 2920,
-      "end": 2932
-    },
-    {
-      "text": "TPS",
-      "type": "ENTITY",
-      "start": 2934,
-      "end": 2937
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 2959,
-      "end": 2967
-    },
-    {
-      "text": "FSC--frozen section control tumor",
-      "type": "ENTITY",
-      "start": 2969,
-      "end": 3002
-    },
-    {
-      "text": "UM- ureter margin",
-      "type": "ENTITY",
-      "start": 3004,
-      "end": 3021
-    },
-    {
-      "text": "VM--vascular margins",
-      "type": "ENTITY",
-      "start": 3074,
-      "end": 3094
-    },
-    {
-      "text": "TSF-tumor",
-      "type": "ENTITY",
-      "start": 3095,
-      "end": 3104
-    },
-    {
-      "text": "sinus fat T-tumor BG--background",
-      "type": "ENTITY",
-      "start": 3110,
-      "end": 3142
-    },
-    {
-      "text": "U--ureteral mucosa",
-      "type": "ENTITY",
-      "start": 3177,
-      "end": 3195
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 3203,
-      "end": 3211
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 3227,
-      "end": 3235
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 3237,
-      "end": 3244
-    },
-    {
-      "text": "right retroperitoneal",
-      "type": "ENTITY",
-      "start": 3249,
-      "end": 3270
-    },
-    {
-      "text": "encapsulated",
-      "type": "ENTITY",
-      "start": 3310,
-      "end": 3322
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 3333,
-      "end": 3347
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 3348,
-      "end": 3357
-    },
-    {
-      "text": "Sectioning",
-      "type": "ENTITY",
-      "start": 3376,
-      "end": 3386
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 3416,
-      "end": 3430
-    },
-    {
-      "text": "fibrosis",
-      "type": "ENTITY",
-      "start": 3439,
-      "end": 3447
-    },
-    {
-      "text": "hemorrhage",
-      "type": "ENTITY",
-      "start": 3451,
-      "end": 3461
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 3463,
-      "end": 3486
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 3513,
-      "end": 3521
-    },
-    {
-      "text": "U--undesignated",
-      "type": "ENTITY",
-      "start": 3523,
-      "end": 3538
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 3546,
-      "end": 3554
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 3570,
-      "end": 3578
-    },
-    {
-      "text": "paracaval lymph",
-      "type": "ENTITY",
-      "start": 3590,
-      "end": 3605
-    },
-    {
-      "text": "multiple",
-      "type": "ENTITY",
-      "start": 3632,
-      "end": 3640
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 3650,
-      "end": 3661
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 3662,
-      "end": 3671
-    },
-    {
-      "text": "Entire",
-      "type": "ENTITY",
-      "start": 3685,
-      "end": 3691
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 3692,
-      "end": 3703
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 3730,
-      "end": 3738
-    },
-    {
-      "text": "LN--",
-      "type": "ENTITY",
-      "start": 3740,
-      "end": 3744
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 3745,
-      "end": 3756
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 3765,
-      "end": 3773
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 3789,
-      "end": 3797
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 3799,
-      "end": 3806
-    },
-    {
-      "text": "iliac lymph",
-      "type": "ENTITY",
-      "start": 3824,
-      "end": 3835
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 3880,
-      "end": 3890
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 3891,
-      "end": 3900
-    },
-    {
-      "text": "Entire lymph node",
-      "type": "ENTITY",
-      "start": 3908,
-      "end": 3925
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 3950,
-      "end": 3958
-    },
-    {
-      "text": "LN--",
-      "type": "ENTITY",
-      "start": 3959,
-      "end": 3963
-    },
-    {
-      "text": "lymph node Akihiko Yoshida",
-      "type": "ENTITY",
-      "start": 3964,
-      "end": 3990
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 4003,
-      "end": 4011
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 4027,
-      "end": 4035
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 4037,
-      "end": 4044
-    },
-    {
-      "text": "precaval",
-      "type": "ENTITY",
-      "start": 4048,
-      "end": 4056
-    },
-    {
-      "text": "inter-aortocaval lymph node\",and",
-      "type": "ENTITY",
-      "start": 4061,
-      "end": 4093
-    },
-    {
-      "text": "multiple",
-      "type": "ENTITY",
-      "start": 4109,
-      "end": 4117
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 4127,
-      "end": 4138
-    },
-    {
-      "text": "measuring",
-      "type": "ENTITY",
-      "start": 4139,
-      "end": 4148
-    },
-    {
-      "text": "lymph node",
-      "type": "ENTITY",
-      "start": 4174,
-      "end": 4184
-    },
-    {
-      "text": "trisected",
-      "type": "ENTITY",
-      "start": 4188,
-      "end": 4197
-    },
-    {
-      "text": "Entire",
-      "type": "ENTITY",
-      "start": 4199,
-      "end": 4205
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 4206,
-      "end": 4217
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4244,
-      "end": 4252
-    },
-    {
-      "text": "TLN--trisected",
-      "type": "ENTITY",
-      "start": 4254,
-      "end": 4268
-    },
-    {
-      "text": "Akihiko Yoshida",
-      "type": "ENTITY",
-      "start": 4296,
-      "end": 4311
-    },
-    {
-      "text": "specimen",
-      "type": "ENTITY",
-      "start": 4323,
-      "end": 4331
-    },
-    {
-      "text": "formalin",
-      "type": "ENTITY",
-      "start": 4347,
-      "end": 4355
-    },
-    {
-      "text": "labeled",
-      "type": "ENTITY",
-      "start": 4357,
-      "end": 4364
-    },
-    {
-      "text": "suprahilar nodes",
-      "type": "ENTITY",
-      "start": 4369,
-      "end": 4385
-    },
-    {
-      "text": "right adrenal",
-      "type": "ENTITY",
-      "start": 4390,
-      "end": 4403
-    },
-    {
-      "text": "adrenal gland",
-      "type": "ENTITY",
-      "start": 4433,
-      "end": 4446
-    },
-    {
-      "text": "surrounding",
-      "type": "ENTITY",
-      "start": 4451,
-      "end": 4462
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 4463,
-      "end": 4477
-    },
-    {
-      "text": "Adrenal gland",
-      "type": "ENTITY",
-      "start": 4478,
-      "end": 4491
-    },
-    {
-      "text": "measures",
-      "type": "ENTITY",
-      "start": 4492,
-      "end": 4500
-    },
-    {
-      "text": "weighs",
-      "type": "ENTITY",
-      "start": 4524,
-      "end": 4530
-    },
-    {
-      "text": "removal",
-      "type": "ENTITY",
-      "start": 4548,
-      "end": 4555
-    },
-    {
-      "text": "fat",
-      "type": "ENTITY",
-      "start": 4559,
-      "end": 4562
-    },
-    {
-      "text": "Section",
-      "type": "ENTITY",
-      "start": 4564,
-      "end": 4571
-    },
-    {
-      "text": "adrenal tissue",
-      "type": "ENTITY",
-      "start": 4601,
-      "end": 4615
-    },
-    {
-      "text": "Surrounding",
-      "type": "ENTITY",
-      "start": 4617,
-      "end": 4628
-    },
-    {
-      "text": "adipose tissue",
-      "type": "ENTITY",
-      "start": 4629,
-      "end": 4643
-    },
-    {
-      "text": "lymph nodes",
-      "type": "ENTITY",
-      "start": 4677,
-      "end": 4688
-    },
-    {
-      "text": "Representative sections",
-      "type": "ENTITY",
-      "start": 4690,
-      "end": 4713
-    },
-    {
-      "text": "sections",
-      "type": "ENTITY",
-      "start": 4740,
-      "end": 4748
-    },
-    {
-      "text": "AD",
-      "type": "ENTITY",
-      "start": 4750,
-      "end": 4752
-    },
-    {
-      "text": "adrenal",
-      "type": "ENTITY",
-      "start": 4754,
-      "end": 4761
-    },
-    {
-      "text": "F-adipose tissue",
-      "type": "ENTITY",
-      "start": 4762,
-      "end": 4778
-    },
-    {
-      "text": "fibrotic area",
-      "type": "ENTITY",
-      "start": 4789,
-      "end": 4802
-    },
-    {
-      "text": "Sections",
-      "type": "ENTITY",
-      "start": 4814,
-      "end": 4822
-    },
-    {
-      "text": "Right kidney",
-      "type": "ENTITY",
-      "start": 4834,
-      "end": 4846
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 4848,
-      "end": 4854
-    },
-    {
-      "text": "bladder cuff",
-      "type": "ENTITY",
-      "start": 4859,
-      "end": 4871
-    },
-    {
-      "text": "nephrouterectomy Block Sect",
-      "type": "ENTITY",
-      "start": 4873,
-      "end": 4900
-    },
-    {
-      "text": "PCs",
-      "type": "ENTITY",
-      "start": 4906,
-      "end": 4909
-    },
-    {
-      "text": "tsf",
-      "type": "ENTITY",
-      "start": 4935,
-      "end": 4938
-    },
-    {
-      "text": "Retroperitoneal lipoma",
-      "type": "ENTITY",
-      "start": 5022,
-      "end": 5044
-    },
-    {
-      "text": "rightexcision Block Sect",
-      "type": "ENTITY",
-      "start": 5045,
-      "end": 5069
-    },
-    {
-      "text": "PCs",
-      "type": "ENTITY",
-      "start": 5075,
-      "end": 5078
-    },
-    {
-      "text": "Part 3:SP",
-      "type": "ENTITY",
-      "start": 5085,
-      "end": 5094
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 5095,
-      "end": 5106
-    },
-    {
-      "text": "paracaval;excision Block Sect",
-      "type": "ENTITY",
-      "start": 5107,
-      "end": 5136
-    },
-    {
-      "text": "PCs",
-      "type": "ENTITY",
-      "start": 5142,
-      "end": 5145
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 5161,
-      "end": 5163
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 5164,
-      "end": 5175
-    },
-    {
-      "text": "right common iliac;excision Block Sect",
-      "type": "ENTITY",
-      "start": 5176,
-      "end": 5214
-    },
-    {
-      "text": "PCs",
-      "type": "ENTITY",
-      "start": 5221,
-      "end": 5224
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 5240,
-      "end": 5242
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 5243,
-      "end": 5254
-    },
-    {
-      "text": "precaval",
-      "type": "ENTITY",
-      "start": 5255,
-      "end": 5263
-    },
-    {
-      "text": "interaortocaval;excision Block Sect",
-      "type": "ENTITY",
-      "start": 5268,
-      "end": 5303
-    },
-    {
-      "text": "PCs",
-      "type": "ENTITY",
-      "start": 5310,
-      "end": 5313
-    },
-    {
-      "text": "SP",
-      "type": "ENTITY",
-      "start": 5337,
-      "end": 5339
-    },
-    {
-      "text": "Lymph nodes",
-      "type": "ENTITY",
-      "start": 5340,
-      "end": 5351
-    },
-    {
-      "text": "suprahilar",
-      "type": "ENTITY",
-      "start": 5352,
-      "end": 5362
-    },
-    {
-      "text": "adrenal gland",
-      "type": "ENTITY",
-      "start": 5367,
-      "end": 5380
-    },
-    {
-      "text": "rightexcision Block Sect",
-      "type": "ENTITY",
-      "start": 5381,
-      "end": 5405
-    },
-    {
-      "text": "Intraoperative Consultation",
-      "type": "ENTITY",
-      "start": 5428,
-      "end": 5455
-    },
-    {
-      "text": "diagnoses",
-      "type": "ENTITY",
-      "start": 5467,
-      "end": 5476
-    },
-    {
-      "text": "section",
-      "type": "ENTITY",
-      "start": 5491,
-      "end": 5498
-    },
-    {
-      "text": "tissue",
-      "type": "ENTITY",
-      "start": 5519,
-      "end": 5525
-    },
-    {
-      "text": "time",
-      "type": "ENTITY",
-      "start": 5549,
-      "end": 5553
-    },
-    {
-      "text": "intraoperative consultation",
-      "type": "ENTITY",
-      "start": 5561,
-      "end": 5588
-    },
-    {
-      "text": "FROZEN SECTION",
-      "type": "ENTITY",
-      "start": 5590,
-      "end": 5604
-    },
-    {
-      "text": "DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 5605,
-      "end": 5614
-    },
-    {
-      "text": "ureter",
-      "type": "ENTITY",
-      "start": 5631,
-      "end": 5637
-    },
-    {
-      "text": "bladder",
-      "type": "ENTITY",
-      "start": 5642,
-      "end": 5649
-    },
-    {
-      "text": "PERMANENT DIAGNOSIS",
-      "type": "ENTITY",
-      "start": 5680,
-      "end": 5699
-    },
-    {
-      "text": "SAME",
-      "type": "ENTITY",
-      "start": 5701,
-      "end": 5705
-    },
-    {
-      "text": "END",
-      "type": "ENTITY",
-      "start": 5715,
-      "end": 5718
-    },
-    {
-      "text": "OFREPORT",
-      "type": "ENTITY",
-      "start": 5719,
-      "end": 5727
-    }
-  ],
-  "entity_count": 256,
-  "has_embedding": true
-}