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Reed-CompBio / spras

Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
MIT License
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Pathway reconstruction algorithm attribution #5

Open agitter opened 3 years ago

agitter commented 3 years ago

We should think about how to provide credit to the original pathway reconstruction algorithm authors if their methods are run using our workflow and Docker images. One idea would be to include citation information in the algorithm class. Then we could print or log the recommended citation(s) when we call the run function.

That wouldn't work for providing attribution if someone uses the Docker image outside of our workflow. An alternative would be to print citation information as part of the Docker entrypoint.

agitter commented 2 months ago

I thought about this more and now recommend that we add a Snakemake workflow rule as well that generates citation information in multiple formats. It can have a .bib file for LaTeX users, a Markdown file, and a .docx file. We can use the Manubot package to manage a lot of the citation work if we include it as a conda environment dependency. It would take a list of citations with DOIs, URLs, or other standard identifiers for each pathway reconstruction algorithm or analysis step (Cytoscape visualization, clustering, etc.).

A good example is ColabFold. They produce a .bib file along with all of the other results showing which dependencies are used when running the Colab notebook.

agitter commented 3 weeks ago

Software Citation Station (https://arxiv.org/abs/2406.04405) is a related effort. The manuscript references Python projects for citing imported Python packages.