Automated scholarly manuscripts on GitHub
This repository contains the manuscript "Reusing label functions to extract multiple types of biomedical relationships from biomedical abstracts at scale". Code to produce the results described in this manuscript can be found here.
Manubot is a system for writing scholarly manuscripts via GitHub.
Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub.
An overview manuscript presents the benefits of collaborative writing with Manubot and its unique features.
The rootstock repository is a general purpose template for creating new Manubot instances, as detailed in
USAGE.md for documentation how to write a manuscript.
Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.
Repository directories & files
The directories are as follows:
contentcontains the manuscript source, which includes markdown files as well as inputs for citations and references. See
USAGE.mdfor more information.
outputcontains the outputs (generated files) from Manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
webpageis a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
buildcontains commands and tools for building the manuscript.
cicontains files necessary for deployment via continuous integration. For the CI configuration, see
The easiest way to run Manubot is to use continuous integration to rebuild the manuscript when the content changes.
If you want to build a Manubot manuscript locally, install the conda environment as described in
Then, you can build the manuscript on POSIX systems by running the following commands from this root directory.
# Activate the manubot conda environment (assumes conda version >= 4.4) conda activate manubot # Build the manuscript, saving outputs to the output directory bash build/build.sh # At this point, the HTML & PDF outputs will have been created. The remaining # commands are for serving the webpage to view the HTML manuscript locally. # This is required to view local images in the HTML output. # Configure the webpage directory manubot webpage # You can now open the manuscript webpage/index.html in a web browser. # Alternatively, open a local webserver at http://localhost:8000/ with the # following commands. cd webpage python -m http.server
Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.
The following command, while running, will trigger both the
build.sh script and
manubot webpage command upon content changes:
Whenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.
When a commit to the
master branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the
gh-pages branch uses GitHub Pages to host the following URLs:
- HTML manuscript at https://greenelab.github.io/text_mined_hetnet_manuscript/
- PDF manuscript at https://greenelab.github.io/text_mined_hetnet_manuscript/manuscript.pdf
For continuous integration configuration details, see
Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (
LICENSE.md), which allows reuse with attribution.
Please attribute by linking to https://github.com/greenelab/text_mined_hetnet_manuscript.
Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (
All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:
All other files are only available under CC BY 4.0, including:
Please open an issue for any question related to licensing.