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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

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)

1.3.16 (2023-04-03)

1.3.15 (2023-02-26)

1.3.11 (2022-12-08)

1.3.8 (2022-10-27)

1.3.7 (2022-09-29)

1.3.6 (2022-09-15)

1.3.5 (2022-08-18)

1.3.2 (2022-08-04)

1.3.0 (2022-07-21)

1.2.48 (2022-07-07)

1.2.41 (2022-06-23)

1.2.32 (2022-05-26)

1.2.30 (2022-05-12)

1.2.29 (2022-04-28)

1.2.27 (2022-04-14)

1.2.24 (2022-03-31)

1.2.15 (2022-03-17)

1.2.13 (2022-03-03)

1.2.10 (2022-02-17)

1.2.6 (2022-02-03)

1.2.5 (2022-01-20)

1.2.3 (2022-01-06)

1.2.0 (2021-12-20)

1.1.3 (2021-12-13)

1.1.0 (2021-11-28)

1.0.2 (2021-11-08)

1.0.1 (2021-10-15)

1.0.0

Release Highlights

Acknowledgements

We thank all of our team members for their insights and contributions.