watney 6.0.0

Interactive NiceGUI oncology annotation platform for reviewing LLM-extracted progression events and systemic therapy timelines.

WATNEY

Interactive Oncology Annotation Platform

WATNEY is a browser-based tool for reviewing and annotating LLM-extracted oncology progression events from longitudinal clinical notes. It runs locally, stores all annotations in a local SQLite database, and is designed for multi-user annotation workflows in oncology research.

Developed by Justin Vinh at Dana-Farber Cancer Institute.

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Features

• Side-by-side review of LLM-extracted progression events and source clinical notes
• Click Source on any progression card to jump to the supporting note and highlight the evidence quote
• Agent Intervals box with Start source / End source buttons linking directly to treatment date evidence
• Progression card highlighting — cards are highlighted in amber when the selected agent matches the treatment_plan_at_time field, identifying the most likely progression event for that agent
• Assign agents to progression events with auto-populated start/end dates (editable, auto-formatting)
• Add clinician-derived progression events manually
• Progression Summary table updates immediately on save or remove
• Undo the last annotation for any patient
• Arrow key navigation between patients
• Multi-user support with per-session usernames and logout
• Persistent configuration (CSV path, font size) via local JSON
• Export annotations to CSV (demo and real data are always separate)
• Demo mode — 3 synthetic brain cancer patients, fully isolated in-memory database
• Interactive tutorial — 10-step guided walkthrough, launches inside demo mode
• Multi-instance warning if more than one browser tab is open
• In-app update checker (Settings → Check for updates)

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Installation

pip install watney

Required dependencies are installed automatically: nicegui, pandas.

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Launching

watney

Opens the application in your browser at http://localhost:8080.

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First-Time Setup

1. Enter your username on the login screen
2. Enter the full path to your extraction CSV
3. WATNEY saves the path — subsequent logins go straight in

Configuration is stored at:

./watney_annotations/watney_config.json

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Required Input Format

WATNEY expects a CSV with these three columns:

Column	Description
DFCI_MRN	Patient identifier
all_notes	Concatenated longitudinal clinical notes
generation	LLM-extracted JSON (see schema below)

Note Format

Notes within all_notes must be separated by a line of at least 20 = characters, with metadata headers:

Note Number: 1
Note Report ID: RPT001
Note Date: 2024-01-15
Note Dept: Neuro-Oncology
Note Author: Dr. Smith

[note text here]

====================
Note Number: 2
Note Report ID: RPT002
...

JSON Schema (generation column)

The fields WATNEY reads from:

{
  "systemic_therapy": {
    "agents": [
      {
        "drug_name": "Temozolomide",
        "intervals": [
          {
            "start_date": "2023-01-01",
            "start_date_rationale": {
              "text": "initiated temozolomide 150 mg/m2",
              "report_id": "RPT001"
            },
            "end_date": "2023-06-01",
            "end_date_rationale": {
              "text": "discontinued due to progression",
              "report_id": "RPT004"
            }
          }
        ]
      }
    ]
  },
  "progression": {
    "progression_events": [
      {
        "progression_date": "2023-06-15",
        "confidence_level": "high",
        "treatment_plan_at_time": "Temozolomide",
        "treatment_plan_at_time_rationale": {
          "text": "patient was on temozolomide at time of imaging"
        },
        "progression_date_rationale": {
          "text": "new enhancing lesion at resection margin...",
          "report_id": "RPT005",
          "note_date": "2023-06-15",
          "author": "Dr. Smith"
        }
      }
    ]
  }
}

Only the fields above are used by WATNEY. The full schema supports additional fields (diagnosis, radiation, surgery, PFS) which are ignored.

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Workflow

1. Navigate patients

Control	Action
Prev / Next buttons	Move between patients
← → arrow keys	Move between patients
Patient List	See all patients; jump to any

2. Review Agent Intervals

Select an agent from the Agent Intervals dropdown to see its treatment intervals. Each interval row shows:

• Start date → End date
• Start source button — jumps to and highlights the supporting note for the start date
• End source button — jumps to and highlights the supporting note for the end date

3. Identify the progression event

Progression cards are highlighted in amber when the currently selected agent matches the treatment_plan_at_time field. A notice above the cards reads:

▶ Highlighted card: likely progression event for [Agent]

4. Assign an agent to a progression event

In each progression card:

1. Select the responsible agent from the dropdown
2. Review the auto-populated Start date and End date — these come from the LLM extraction
3. Edit either date if needed — blur the field to auto-format to YYYY-MM-DD
4. Click Save Agent Assignment

The Progression Summary table at the top of the left panel updates immediately.

5. Source navigation

Click Source on any progression card to scroll the right panel to the supporting note and highlight the evidence text. All evidence segments (separated by ... or …) are highlighted individually.

6. Add clinician progression events

Use the form at the bottom of the left panel to manually record:

• Agent (required)
• Progression Date (required, auto-formats to YYYY-MM-DD)
• Agent Start date and End date
• Supporting evidence and Report ID
• Who determined the progression

7. Remove or undo

• Remove Agent — clears the assignment from a specific card in place; summary updates immediately
• Undo (nav bar) — deletes the most recently modified annotation for the current patient

8. Export

Click Export on the nav bar to download all annotations as a timestamped CSV. In demo mode, only demo annotations are exported — your real database is never touched.

9. Logout

Click Logout (top-right of the left panel) to return to the login screen. Demo annotations are discarded permanently on logout.

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Demo Mode

Click Try Demo on the login screen to explore WATNEY with 3 synthetic brain cancer patients:

Patient	Diagnosis	Agents	Progression Events
MRN000001	GBM (IDH-wt, MGMT-meth)	Temozolomide → Bevacizumab	2
MRN000002	Anaplastic astrocytoma	PCV → Temozolomide	2
MRN000003	Grade 3 oligodendroglioma	Temozolomide → Lomustine	2

Demo annotations are stored in an isolated in-memory database and are permanently discarded on logout. They are never written to your real database.

Place watney_demo_data.csv in the same directory as watney3.py (or wherever WATNEY is installed).

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Tutorial

Click Tutorial + Demo on the login screen to launch demo mode with a guided 10-step walkthrough that opens automatically inside the app. Steps are navigated with Back / Next buttons or by clicking the dot indicators.

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Settings

Open Settings from the nav bar to:

• Adjust report text font size (8–20 px)
• View current file paths (CSV, database, annotations folder)
• Change the input CSV path
• Move the annotations folder (copies DB + config, removes old files)
• Rename the database file
• Check for and install WATNEY updates from PyPI

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Annotation Database

Stored at:

./watney_annotations/watney_annotations_database.db

Schema

Column	Description
DFCI_MRN	Patient identifier
progression_date	Date of the progression event
progression_source	LLM or manual
agent	Assigned therapeutic agent
agent_start	Agent start date
agent_start_source	LLM or manual
agent_end	Agent end date
agent_end_source	LLM or manual
evidence	Supporting text from the note
report_id	Source note report ID
determined_by	Who determined the event (clinician entries)
user	Annotator username
modification_timestamp	ISO timestamp of last change

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Multiple Browser Tabs

If more than one browser tab connects to the WATNEY server simultaneously, a warning banner appears on the login screen. Multiple active sessions sharing a single server can cause unexpected UI behavior — close any extra tabs before working.

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Citation

Justin Vinh. WATNEY: Interactive Oncology Annotation Platform.
https://github.com/justin-vinh/watney_project

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License

MIT License