This repository and the corresponding DO_uses-published_2022 Google Sheet used for curation serve as an example implementing the public resource use assessment workflow described in:
J. Allen Baron, Lynn M Schriml, Assessing resource use: a case study with the Human Disease Ontology, Database, Volume 2023, 2023, baad007. PMID:36856688, https://doi.org/10.1093/database/baad007.
All the code, data, and figures for the case study with the Human Disease Ontology (DO; disease-ontology.org) are included.
All the data, figures and code for the publication can be found in the data/, graphics/, and scripts/ folders of this repository on Github (https://github.com/DiseaseOntology/assessing_DO_use) or the persistent, open-access repository Zenodo (DOI: 10.5281/zenodo.7467640). Re-executing the code requires R and a number of R packages, including the DO.utils package (DOI: 10.5281/zenodo.7467668), designed to support this workflow (as well as, analysis and improvement of the DO more specifically). The version of each R package has been tracked using the 'renv' R package.
The easiest way to get all dependencies and re-execute the code here is to download this repository from Github or Zenodo and R from CRAN. Then, install the 'renv' package (within R, run install.packages("renv")) and download all packages with versions matching those originally used to create this repository using 'renv' (within R, run renv::restore()).
The DO_uses-published_2022 Google Sheet used for curation as described in the publication remains in the same state used for code execution in this repository and is open for public viewing.
Details describing the purpose, input and output of each script in this repository can be found in the script_descriptions.md file.