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carechronicle-mcp

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🏥 CareChronicle — Patient Record Intelligence

License: MIT FastAPI Groq Ollama FHIR

CareChronicle is a clinical document workspace and information retrieval platform that structures unstructured clinical documents (PDF, DOCX, TXT, MD, PNG, JPG) into a flat-file database format called Open Knowledge Format (OKF). It provides clinicians with a unified patient timeline, automated sidebar summarization, and a secure Q&A interface grounded strictly in patient documentation.

⚡ Core System Architecture

graph TD
    User([User Document / Query]) -->|Upload PDF/DOCX/TXT/PNG/JPG| Parser[extractors.py & okf_builder.py]
    Parser -->|Parse Frontmatter & Facts| OKF[(OKF Markdown Directory)]
    OKF -->|Build Patient Profile| Wiki[wiki.py Profiler]
    Wiki -->|LLM NER Extraction| Profile[lib/ner.py]
    Profile -->|Render Dashboard Stats & Timeline| UI[Front-End Web UI]

    User -->|Ask Question| QueryPipeline[llm.py: run_qa_pipeline]
    QueryPipeline -->|Classify Query| Classifier{Is Document Query?}
    
    Classifier -->|No: General Health Q| GenAns[1x Ollama/Groq/Gemini Call]
    Classifier -->|Yes: Patient Chart Q| Plan[Local Query Planner: 0 LLM Calls]
    
    Plan -->|Rank & Retrieve| Retrieval[rank_records_smarter]
    Retrieval -->|Cited Answer Generation| DocAns[1x Ollama/Groq/Gemini Call]
    
    GenAns --> UI
    DocAns --> UI

Related MCP server: FhirMCP

🚀 Hospital-Grade & EHR Readiness Upgrades

We have implemented five critical features to prepare CareChronicle for production-grade clinical environments:

1. 🔒 Data Privacy: Ollama Local LLM Support (HIPAA-Safe)

To protect Patient Health Information (PHI) under strict compliance guidelines (e.g. HIPAA), CareChronicle can run entirely offline without calling public cloud APIs.

  • How it works: By configuring OLLAMA_HOST in .env, the Q&A engine, general question classifier, and clinical entity extractor route all requests to your local secure Ollama instance.

  • Recommended Models: Use biomistral (clinical fine-tune) or llama3 / llama3.1 (general).

2. 📄 Scanned OCR: 4-Tier Intelligent OCR Fallback

Real hospital prescriptions are often handwritten, printed scans, or image files. CareChronicle handles this gracefully via an automated 4-tier fallback pipeline:

  1. Local Tesseract OCR: First tries running fast, local Tesseract OCR to process files without any external network request.

  2. Local Ollama Vision LLM (HIPAA-safe): If Tesseract is not installed or returns empty text, it calls your local running Ollama instance using a vision model (e.g. moondream or llava).

  3. Google Gemini Vision Fallback: Routes to Google's Gemini cloud vision engine (gemini-3.5-flash) via the Generative AI SDK using your GEMINI_API_KEY.

  4. Groq Vision Cloud Fallback: If local LLM/Ollama and Gemini fallback are offline, it securely routes to Groq's high-speed cloud vision engine using models like llava-v1.5-7b-4096-preview or llama-4-scout-17b-16e-instruct.

3. 🧠 Clinical NER: LLM-Based Entity Extraction

Replaces brittle keyword regular expression searches with an advanced LLM Clinical Named Entity Recognition (NER) prompt.

  • How it works: When loading patient dashboards, the engine invokes a fast clinical NER pipeline to identify diagnoses, drug schedules, dosage frequencies, lab values, reference ranges, and abnormal flags, falling back to regex rules if offline.

4. 🏥 EHR Integration: FHIR R4 Patient Import

Sync CareChronicle directly with medical records in hospital EHR networks like Epic, Cerner, or Athena.

  • How it works: A dedicated modal interface lets clinicians point to a standard HL7 FHIR endpoint, specify a patient ID, and sync Observation (lab results) and MedicationRequest resources into OKF Markdown files in one click.

5. 🔌 Model Context Protocol (MCP) Integration

CareChronicle runs a parallel Model Context Protocol (MCP) server. Any agentic LLM (like Claude Desktop) can connect directly to CareChronicle using the following exposed tools:

  • convert_text_to_okf — Convert raw medical text input into structured OKF format.

  • ingest_document_file — Ingest local files automatically.

  • get_patient_wiki_profile — Compile current patient conditions, tests, and medications.

  • list_patient_records — List all stored OKF records for a specific patient.

  • search_okf_records — Query planner search tool.

  • query_patient_records — Run full safety-first answering tool over records.

💡 System Design & Cost Optimization

1. Open Knowledge Format (OKF)

CareChronicle stores patient health records as structured markdown documents containing rich YAML frontmatter. This format eliminates heavy database dependencies, keeping patient history fully human-readable, auditable, and version-controlled.

---
id: lab-report-2026-07-01-diabetic-check-2026-07-01
type: lab-report
patient_id: patient-002
date: 2026-07-01
hospital: "Apex Diagnostics"
doctor: "Dr. Patel"
source_file: "diabetic-check-2026-07-01.txt"
links:
  - patient-002
  - glucose-fasting
  - hba1c
---
# Lab Report
## Extracted factual details
- Glucose (Fasting): 140 mg/dL
- HbA1c: 7.4 %

2. LLM Cost Optimization & Routing

Standard clinical Retrieval-Augmented Generation (RAG) platforms make multiple LLM calls to check safety, generate query keywords, determine matching record types, and formulate answers. CareChronicle optimizes this cost flow to a maximum of 1 LLM call per user turn:

  • Local Keyword Classifier (is_document_query): Determines if the question is a general health question or requires patient records.

  • General Health Questions: Bypasses the query planner and safety filter LLM calls completely. Uses exactly 1 LLM call to produce a patient-friendly summary.

  • Document-Related Questions:

    • Uses a 0-cost local parser (fallback_plan) to parse keywords and map targeted clinical document types (Prescriptions, Lab Reports, Discharge Summaries).

    • Performs keyword matching and TF-IDF-inspired ranking locally.

    • Sends the compiled, top-matching OKF documents into exactly 1 LLM call to synthesize a cited answer.

  • Cost Savings: Reductions of up to 75% in token consumption and 80% in latency compared to standard multi-agent RAG implementations.

🛠️ Installation & Local Setup

1. Prerequisites

  • Python 3.10 or higher installed.

  • Active Groq API Key (Primary & OCR Fallback).

  • Active Gemini API Key (Secondary Fallback).

  • Ollama running locally for HIPAA mode and local OCR.

  • (Optional) Tesseract OCR installed on your system PATH for local OCR ingestion.

2. Install Project Dependencies

Clone the repository, create a virtual environment, and install requirements:

git clone https://github.com/Ankithraj-1312/carechronicle.git
cd carechronicle

# Create virtual environment
python -m venv venv

# Activate virtual environment
# On Windows (PowerShell):
venv\Scripts\Activate.ps1
# On Linux/MacOS:
source venv/bin/activate

# Install required packages
pip install -r requirements.txt

3. Environment Configuration

Create a file named .env in the root directory:

PORT=3005
Groq_API_KEY=your_groq_api_key_here
GEMINI_API_KEY=your_gemini_api_key_here

# Local HIPAA / Offline Configuration (Optional)
# OLLAMA_HOST=http://localhost:11434
# OLLAMA_MODEL=moondream

4. Running the Platform

Start the FastAPI server:

python main.py

The server will bind and run on http://localhost:3005.

🎬 Live Demo & Step-by-Step Walkthrough

Follow these steps to run a full demonstration of CareChronicle's clinical capabilities:

Scenario 1: FHIR EHR Record Sync

  1. Click + in the left sidebar and register a new patient named "EHR Import Demo".

  2. Click Import from FHIR EHR at the bottom of the Document Ingestion card.

  3. Keep the default open public sandbox server URL (https://hapi.fhir.org/baseR4).

  4. Type test patient ID: example (or 1185012) and click Start FHIR Sync.

  5. Result: CareChronicle fetches observation/prescription history from the public server, builds OKF Markdown files, and dynamically updates the patient profile and timeline in the UI.

Scenario 2: Prescription Image OCR Ingestion

  1. Select any active patient.

  2. Drag and drop prescription_demo.png (provided in the repository root) into the ingestion dropzone.

  3. Result: The system converts the PNG image, runs OCR text extraction, and processes it through the Clinical NER model to index medications (Atorvastatin, Aspirin) automatically.

Scenario 3: Custom Patient Ingestion (Priya Nair Case Study)

Test the document converter using these sample raw clinical files.

  1. Click + in the left sidebar and register a new patient named Priya Nair.

  2. Select Priya Nair in the sidebar.

  3. Under the Document Ingestion card on the right, paste the text from Discharge Summary (below) into the text input, set the filename as discharge_summary.txt, and click Convert & Save.

  4. Repeat the ingestion step for the Lab Report and Outpatient Prescription files.

  5. Go to the Q&A Panel at the bottom and ask:

    • "What are Priya Nair's active blood pressure medications?"

    • "What was Priya's ferritin level on July 14?"

  6. Result: You will get precise answers with clickable citations referencing the specific OKF documents.

📂 Priya Nair Demo Files

METRO HEART & GENERAL HOSPITAL
DEPARTMENT OF GENERAL MEDICINE
12, Rajiv Gandhi Nagar, Bangalore - 560 001

====================================================
          INPATIENT DISCHARGE SUMMARY
====================================================

ADMISSION DETAILS
-----------------
Patient Name       : Priya Nair
Patient ID         : PAT-2026-004
Age / Gender       : 38 Years / Female
Date of Admission  : 10-July-2026
Date of Discharge  : 13-July-2026
Ward               : General Medicine - Ward B, Bed 14
IP Number          : MHH-IP-2026-00714
Consultant         : Dr. Meera Krishnan, MD (General Medicine)

====================================================
REASON FOR ADMISSION
====================================================
Patient presented to the Emergency Department on 10-July-2026 with
complaints of:
  - Severe fatigue and generalised weakness for 3 weeks
  - Persistent headache (frontal, non-throbbing) for 10 days
  - Palpitations on mild exertion for 5 days
  - Breathlessness on climbing stairs (Grade II dyspnoea)
  - Occasional dizziness on standing
  - Pallor noted by family members over 1 month

No chest pain, no syncope, no pedal oedema reported.

====================================================
SIGNIFICANT HISTORY
====================================================
Past Medical History   : Nil significant
Surgical History       : Appendectomy (2019, Manipal Hospital)
Family History         : Father - Hypertension, Diabetes
Menstrual History      : Heavy menstrual cycles (Menorrhagia) since 6 months
Allergies              : NKDA (No Known Drug Allergies)
Occupation             : Software Engineer
Lifestyle              : Predominantly sedentary, low dietary iron intake

====================================================
CLINICAL FINDINGS ON ADMISSION
====================================================
General Condition  : Conscious, oriented, mild pallor, no icterus
Pulse              : 96 bpm, regular
Blood Pressure     : 150 / 96 mmHg
Respiratory Rate   : 18 breaths/min
SpO2               : 98% on room air
Temperature        : 98.4 F (Afebrile)
Pallor             : Present (conjunctival and palmar)
Koilonychia        : Present (bilateral)
Cardiovascular     : S1 S2 heard, soft systolic murmur at apex (grade 2/6)
Respiratory        : Clear air entry bilaterally
Abdomen            : Soft, non-tender, no organomegaly

====================================================
INVESTIGATIONS DURING ADMISSION
====================================================
CBC (10-July-2026):
  Haemoglobin: 9.6 g/dL (LOW)         WBC: 8,100 /uL (Normal)
  RBC: 3.7 million/uL                 Platelets: 198,000 /uL (Normal)
  PCV: 31.4% (LOW)                    MCV: 78 fL (Microcytic)

Serum Ferritin: 5 ng/mL (Severely LOW - Normal: 12-150 ng/mL)
Serum Iron: 44 ug/dL (LOW)
TIBC: 410 ug/dL (HIGH)

Peripheral Blood Smear: Microcytic hypochromic red cells, pencil cells noted.
  Consistent with Iron Deficiency Anaemia.

ECG (12-Lead): Sinus tachycardia. No ST-T changes. No LVH pattern.

Renal Function Test: Serum Creatinine 0.8 mg/dL (Normal)
                     Serum Potassium 4.1 mEq/L (Normal)
Thyroid Function     TSH 2.4 mIU/L (Normal)
Gynaecology Consult  : Confirmed Menorrhagia. Tranexamic Acid initiated.
                       Pelvic ultrasound: No fibroids, no polyps.
                       Advised haematology correlation.

====================================================
DIAGNOSIS (FINAL)
====================================================
PRIMARY   : Iron Deficiency Anaemia (IDA) secondary to Menorrhagia
SECONDARY : Stage 1 Hypertension (newly detected)

====================================================
TREATMENT GIVEN DURING STAY
====================================================
1. IV Iron Sucrose 200 mg in 100 mL Normal Saline over 30 min
   - Administered on Days 1, 2, and 3 of admission (10, 11, 12 July 2026)
   - Total parenteral iron given: 600 mg
   - Tolerated well, no adverse reactions

2. Tab Amlodipine 5 mg once daily (initiated Day 2 for hypertension)

3. Tab Tranexamic Acid 500 mg thrice daily for menorrhagia control

4. Dietary iron supplementation advised by hospital dietitian

====================================================
CONDITION AT DISCHARGE
====================================================
Patient clinically improved. Haemoglobin at discharge: 10.2 g/dL (rising).
BP stabilised at 136/88 mmHg on Amlodipine.
Palpitations resolved. Fatigue significantly reduced.
Discharged in stable condition.

====================================================
DISCHARGE INSTRUCTIONS
====================================================
1. Continue Ferrous Sulphate 150 mg twice daily for 3 months.
2. Continue Vitamin C 500 mg twice daily with iron tablet.
3. Continue Amlodipine 5 mg once daily in the morning.
4. Continue Losartan 50 mg once daily in the evening.
5. Avoid tea/coffee within 1 hour of iron tablet.
6. Eat iron-rich foods: spinach, lentils, rajma, lean meat, jaggery.
7. Return to ER immediately if: chest pain, severe headache, BP > 180/110.
8. Follow up with Dr. Meera Krishnan on 20-August-2026 with repeat CBC
   and iron studies.
9. Gynaecology follow-up: 25-July-2026 (Appointment confirmed).

====================================================
ATTENDING PHYSICIAN
====================================================
Dr. Meera Krishnan, MD (General Medicine)
Registration No: KMC-45821
Metro Heart & General Hospital, Bangalore

====================================================
    ** DISCHARGE SUMMARY GENERATED ON 13-JULY-2026 **
          Authorised Signatory & Hospital Seal
====================================================
METRO HEART & GENERAL HOSPITAL
DEPARTMENT OF PATHOLOGY & LABORATORY MEDICINE
12, Rajiv Gandhi Nagar, Bangalore - 560 001
Ph: +91-80-4123-7890 | Lab License No: KAR/LAB/2019/00872

====================================================
        COMPREHENSIVE BLOOD INVESTIGATION REPORT
====================================================

Patient Name   : Priya Nair
Patient ID     : PAT-2026-004
Age / Gender   : 38 Years / Female
Referred By    : Dr. Meera Krishnan, MD (General Medicine)
Sample Type    : Venous Blood (EDTA)
Sample ID      : MHH-BL-20260714-0041
Collection Date: 14-July-2026   Time: 08:35 AM
Report Date    : 14-July-2026   Time: 01:15 PM

----------------------------------------------------
 COMPLETE BLOOD COUNT (CBC)
----------------------------------------------------
Test                        Result     Unit       Reference Range   Flag
Haemoglobin (Hb)           10.8       g/dL       12.0 - 15.5       LOW
Red Blood Cells (RBC)       3.9        million/uL  3.8 - 5.2
Packed Cell Volume (PCV)    34.2       %          36.0 - 46.0       LOW
Mean Corpuscular Volume     82.5       fL         80.0 - 100.0
MCH                         27.7       pg         27.0 - 33.0
MCHC                        31.6       g/dL       31.5 - 35.0
White Blood Cells (WBC)     8,400      /uL        4,000 - 11,000
Neutrophils                 62         %          40 - 70
Lymphocytes                 28         %          20 - 40
Monocytes                    6         %          2 - 10
Eosinophils                  3         %          1 - 6
Basophils                    1         %          0 - 1
Platelet Count             210,000    /uL        1,50,000 - 4,00,000

----------------------------------------------------
 SERUM IRON STUDIES
----------------------------------------------------
Serum Iron                  52         ug/dL      60 - 170          LOW
Total Iron Binding Capacity 390        ug/dL      250 - 370         HIGH
Transferrin Saturation      13.3       %          20 - 50           LOW
Serum Ferritin              8          ng/mL      12 - 150          LOW

----------------------------------------------------
 BLOOD PRESSURE (Recorded at Clinic)
----------------------------------------------------
Reading 1 (08:40 AM):   148 / 94 mmHg
Reading 2 (08:55 AM):   145 / 92 mmHg
Average:                146 / 93 mmHg          [ELEVATED - Stage 1 Hypertension]

----------------------------------------------------
 INTERPRETATION (Pathologist's Note)
----------------------------------------------------
Findings are consistent with Iron Deficiency Anaemia. Low serum ferritin (8 ng/mL)
and low transferrin saturation (13.3%) strongly support iron store depletion.
Blood pressure readings indicate Stage 1 Hypertension. Clinical correlation advised.

Reported by: Dr. Sunita Rao, MD Pathology
Verified by:  Metro Heart & General Hospital, Bangalore
====================================================
      ** THIS IS A COMPUTER-GENERATED REPORT **
      Report valid only with authorized signatory.
====================================================
METRO HEART & GENERAL HOSPITAL
OUTPATIENT PRESCRIPTION
OPD Receipt No: MHH-OPD-2026-07-16-00318
Date: 16-July-2026

====================================================
PHYSICIAN DETAILS
====================================================
Name     : Dr. Meera Krishnan
Degree   : MD (General Medicine), MBBS
Reg. No  : KMC-45821
Facility : Metro Heart & General Hospital, Bangalore

====================================================
PATIENT DETAILS
====================================================
Name        : Priya Nair
Patient ID  : PAT-2026-004
Age / Gender: 38 Years / Female
Weight      : 58 kg
Diagnosis   : Iron Deficiency Anaemia | Stage 1 Hypertension

====================================================
Rx  (PRESCRIPTION)
====================================================

1. Ferrous Sulphate 150 mg
   - Take 1 tablet TWICE daily (morning and evening)
   - To be taken on EMPTY STOMACH with a glass of water
   - Avoid taking with tea, coffee, or dairy products
   - Duration: 90 days

2. Ascorbic Acid (Vitamin C) 500 mg
   - Take 1 tablet TWICE daily along with Ferrous Sulphate
   - Helps improve iron absorption
   - Duration: 90 days

3. Amlodipine 5 mg
   - Take 1 tablet ONCE daily in the MORNING
   - For blood pressure control
   - Do NOT stop without consulting physician
   - Duration: Ongoing (review at next visit)

4. Losartan 50 mg
   - Take 1 tablet ONCE daily in the EVENING
   - For blood pressure control, combined with Amlodipine
   - Monitor for dizziness especially when standing up
   - Duration: Ongoing (review at next visit)

====================================================
CLINICAL NOTES
====================================================
- Repeat CBC and Iron Studies after 8 weeks of iron therapy.
- Monitor BP at home; target BP < 130/80 mmHg.
- Dietary counselling: increase intake of green leafy vegetables,
  lentils, and lean red meat. Avoid high-sodium processed foods.
- Avoid NSAIDs (e.g. Ibuprofen) which may elevate BP.

====================================================
FOLLOW-UP
====================================================
Next Appointment: 20-August-2026
Department: General Medicine OPD
Time: 10:00 AM (Please carry this prescription and lab reports)

Dr. Meera Krishnan
Metro Heart & General Hospital
Bangalore - 560 001
Signature & Stamp
====================================================

📂 Directory Layout

├── data/
│   ├── okf/
│   │   └── patients/        # Human-readable OKF patient records
│   └── patients.json        # Persistent patient profiles registry
├── lib/
│   ├── extractors.py        # PDF/DOCX/TXT/Image Tesseract text OCR parsers
│   ├── fhir_client.py       # Client for connecting to FHIR HL7 EHR servers
│   ├── llm.py               # Classification, routing, Q&A prompts, API fallbacks
│   ├── ner.py               # LLM clinical entity extraction (NER) helper
│   ├── okf_builder.py       # Converts raw documents into OKF schemas
│   └── wiki.py              # Compiles sidebar stats and patient profiles
├── public/
│   ├── app.js               # Frontend UI interactions and typewriter effect
│   ├── index.html           # Main dashboard template
│   └── styles.css           # Glassmorphic dark styling
├── main.py                  # API endpoints and server setup
├── mcp_server.py            # FastMCP tools definitions
├── requirements.txt         # Project dependencies
└── README.md                # Documentation

📝 License

This project is licensed under the MIT License - see the LICENSE file for details.

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