<img alt="MedTator" src="https://raw.githubusercontent.com/wiki/OHNLP/MedTator/img/logo.png">

MedTator is a serverless text annotation tool for corpus development. It is built on HTML5 techniques and many open-source packages, and was designed to be easy-to-use for your annotation task.

No Java, no Python, no PHP, no Docker, no MySQL, and no need to install any server or client runtime for corpus annotation! Check Here to Start Annotation Now!

MedTator Demo

If you're having trouble using MedTator, you can use Issues to tell us about the issue you're experiencing.

Documentation

New to MedTator? Let's have a Quick Start.
More samples? Check our Sample Datasets.
No internet access? Check this Standalone version
Effective strategies for annotating? Check this Annotation best practices
Design annotation schema? Check this Annotation Schema Design.
Parse annotation data? Here is the Annotation File Format.
Use annotated files for machine learning? We have some Python Sample Scripts.
Having issues? Check the Issues.
More details about MedTator? We have a Manual.
And more contents in the Wiki

MedTator Development

MedTator itself doesn't require Python runtime environment, so you don't need to install any runtime environment to run MedTator for corpus annotation. If you are interested in the MedTator development or just want to try the development version, a Python 3+ runtime environment is needed to run a debugging server.

You can install a Python 3+ or Miniconda / Anaconda, then download the source code of MedTator and install the requirements (just Python Flask, that's all):

pip install -r requirements.txt

Then, run the following command to start a local server which is binding port 8086:

python web.py

Now you can open web browser and check the http://localhost:8086/.

For more details of the parameters for web.py, run python web.py -h and it will show the details as follows.

usage: web.py [-h] [--mode {build,run,release}] [--lib {local,cdn}]
              [--path PATH] [--fn FN]

MedTator Development Server and Toolkit

optional arguments:
  -h, --help            show this help message and exit
  --mode {build,run,release}
                        What do you want to do? `run` for starting the
                        development server. `build` for generating a static
                        HTML page for public release or local release.
  --lib {local,cdn}     Where to get third party libs in the HTML page? If
                        choose local, please make sure to copy the `static`
                        folder after generated the HTML file.
  --path PATH           Which folder to be used for the output page? The
                        default folder is the docs/ folder for public release.
  --fn FN               What file name to be used for the output page? The
                        default file name is the `index.html` which could be
                        accessed directly by browser.

Build the static version

To update the static version for publication (e.g., GitHub Pages), run the following command. It will generate a static HTML file in the docs/ folder and copy other files. In addition, as the default filename is index.html, the build script will automatically create a index.VERSION.html in the build path for backup. So that the user can access the old version for comparison or checking old functions.

python web.py --mode build

Or you can build a dev version for public testing, run the following command:

python web.py --mode build --fn dev.html

Or you can build a standalone version for local use, run the following command:

python web.py --mode build --lib local --fn standalone.html

Then, you can create a release zip file:

python web.py --mode release

License

Apache-2.0 License

Citation

If you use MedTator in scientific work or want to learn more about it, please take a look at our paper:

He H, Fu S, Wang L, Liu S, Wen A, Liu H. MedTator: a serverless annotation tool for corpus development. Bioinformatics, Volume 38, Issue 6, 15 March 2022, Pages 1776–1778, DOI: 10.1093/bioinformatics/btab880, PMID: 34983060

Change log

1.3.x (2023-05)

Research on IOB2/BIO format editing
Research on UMAP algorithm
Research on in-browser text embedding
Add sample dataset for error analysis
Update icon for error analysis
Update Cohen's Kappa calculation
Update README for new features
Update documents for error analysis
Update documents for new schema
Update UI for error analysis
Update demo script for inter-sentence

1.3.16 (2023-04-03)

Added example Python script for masking entities
Updated medtator_kits.py for saving xml
Updated relation annotation example schema and data
Fixed one-offset bug in first-line newline sign
Fixed cross-line entity render bug

1.3.15 (2023-02-26)

Added workspace JSON drag and drop on file list
Added workspace saving function
Added workspace loading function
Added schema drag and drop on file list
Added shortcut ALT + ↑ / ↓ to move to prev / next file
Added Toolkit/MedTaggerVis for checking .ann files (experimental)
Added local setting cache for auto save/load (experimental)
Fixed error analysis Sankey link bug
Fixed error analysis SVG height bug
Fixed error analysis popup box bug
Updated design for .ann/.txt conversion
Updated FAQ in MedTator Wiki
Updated scripts for downstream tasks
Updated sample datasets for new settings

1.3.11 (2022-12-08)

Added annotation visualization based on brat
Added Python scripts for read/parse MedTator XML format
Added Jupyter notebook for downstream tasks with MedTator XML files.
Developed functions for brat vis format conversion
Developed tag extraction based offset spans
Updated style for link/relation display

1.3.8 (2022-10-27)

Added schema of .yml extension support
Added auto-save (experimental) feature
Fixed scheme editor open bug

1.3.7 (2022-09-29)

Update the UI for IAA

1.3.6 (2022-09-15)

Updated a data sample for error analysis

1.3.5 (2022-08-18)

Added label panel for error labeling
Added error sankey diagram for error analysis
Added token scatter for error analysis
Added heatmap of error distribution for error analysis
Added bar charts of error statistics for error analysis
Added tag list and menu items for error analysis
Updated scripts for text embedding web services
Fixed IOB2/BIO empty export bug
Fixed exporter window height bug
Fixed BioC format export annotation text encoding bug
Fixed BioC format export attribute text encoding bug

1.3.2 (2022-08-04)

Added functions for error analysis
Added Math.js for statistics and matrix
Added ECharts for visualization
Added a sample dataset for error analysis
Updated the UI design for adjudication tab
Updated the packaged used to reduce loading time
Fixed open annotation files dialog bug
Fixed IAA download bug

1.3.0 (2022-07-21)

Refactored file reading workflow with asynchronous processing
Refactored annotation file loading workflow
Refactored code structure to reduce code size
Designed JSON/YAML format schema
Added tokenization exceptions
Added pagination for large dataset
Added loading dataset annimation
Added drag and drop folder for adjudication
Added drag and drop folder for converter
Added converting text files to MedTator xml
Added a float text content viewer
Added reading JSON/YAML for schema editor
Added JSON/YAML download option for schema editor
Added cmd/ctrl + s shortcut key for saving current file
Updated annotation UI design for bigger drag&drop area
Updated converter UI design for bigger buttons
Updated converter for downloading individual result file
Updated converter with support of viewing contents
Updated event handlers for drag and drop events
Updated license files of imported libraries
Updated the sample schemas with JSON/YAML format

1.2.48 (2022-07-07)

Added function for customizing sample text
Added changelog information on UI
Added sorting for corpus token list in statistics
Added tag details for corpus summary in statistics
Added filter options for token statistics
Added filtered count in token summaryies
Added a remote corpus sample
Updated all sample datasets
Updated the visual design for corpus summary in statistics
Updated the color encoding for annotated tags in statistics
Updated scripts for experimental tasks
Fixed ribbon menu resize bug

1.2.41 (2022-06-23)

Added meta-data structure for annotation file
Added color label to annotation file
Added functions for updating annotator for adjudication
Added download all tags for adjudication
Added sorting by label color
Added MedTagger ann format converter
Added UI for converting MedTagger results
Added folder drag an

MedTator

Install / Use

README