Manuscript - PanglaoDB and Wikidata

Project manuscript for "Analysing the extent of cell type information present in Wikidata: A case study on PanglaoDB"

Wikidata, a freely editable knowledge graph database, presents a great opportunity for the integration of biomedical knowledge, it’s well thought linked data model can improve significantly the handling and distribution of scientific information. On the other hand, Wikidata is still lacking in various aspects, in particular to what pertains to cell type information. This study aims to analyse how cell type knowledge is currently modelled in Wikidata and how it differs from other type of biological information, using, as a reference point, metadata from the well known single cell RNA sequencing database, PanglaoDB.

Written using Manubot

Repository directories & files

The directories are as follows:

• content contains the manuscript source, which includes markdown files as well as inputs for citations and references. See USAGE.md for more information.
• output contains the outputs (generated files) from Manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
• webpage is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
• build contains commands and tools for building the manuscript.
• ci contains files necessary for deployment via continuous integration.

Local execution

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 build. 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:

bash build/autobuild.sh

Continuous Integration

Whenever a pull request is opened, CI (continuous integration) 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 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), CI builds the manuscript and writes the results to the gh-pages and output branches. The gh-pages branch uses GitHub Pages to host the following URLs:

• HTML manuscript at https://jvfe.github.io/project_panglaodb/
• PDF manuscript at https://jvfe.github.io/project_panglaodb/manuscript.pdf

For continuous integration configuration details, see .github/workflows/manubot.yaml.