Wikidata to build 5-star Linked Open biological databases: A case study of PanglaoDB

Research compendium for the project "Wikidata to build 5-star Linked Open biological databases: A case study of PanglaoDB".

Repository brief descrition

Research-related directories:

analysis: Scripts and notebooks used for the main analysis. It also includes the subdirectories:
- data: Raw data from PanglaoDB and Wikidata is stored here.
- results: Processed data is stored here.
manuscripts: Manuscripts for this research project, each manuscript is a submodule of a GitHub repository that uses Manubot.
improvements: One-use code, creating Wikidata items from PanglaoDB's metadata and improving existing items. Subdiretories:
- go2cell: Prototype of a shiny app to match Gene Ontology terms to cell types. As of April, 2024, it's running here.

Software-related directories, they are structured similarly to a Python package:

wikidata_panglaodb: This is the source code for all author-defined functions used in the analysis.
tests: These are the unit tests for the wikidata_panglaodb "package" functions.
docs: This is a directory containing documentation for the wikidata_panglaodb functions, it is served as a live website in our github pages branch.

Pre-requisites:

Download the repository's zip file or clone it using:

git clone --recurse-submodules https://github.com/jvfe/wikidata_panglaodb

Then, at the project's root directory (wikidata_panglaodb/):

make repro

This will reproduce all steps of the analysis done after the reconciliation.

Pre-requisites:

Initiate the environment:

make develop

If you've already collaborated before but changes have been made to the conda enviroment/repository, run:

make update-proj