Develop Python extension for ariadne

[RiboRings]

Given that ariadne is a general solution in principle independent of programming language, we could recreate it in Python to expand our potential user base.

Many of the R packages we use have equivalents in Python:

• igraph -> igraph
• data.table -> pandas
• arrow -> pyarrow
• httr2 -> requests (and others more advanced)

[RiboRings]

The ariadne database is hosted in Zenodo so there is no need to recreate the upstream pipeline in Python.

[RiboRings]

Multi-language docs: https://quarto.thecoatlessprofessor.com/tabby/

[RiboRings]

Action points to build a Python package:

• Implement an importer for the ariadne database (~ ariadne.R)
• Build logic to search graph and explore pathways (~ draw.R, search.R, plot.R)
• Implement weave functionality (~ weave.R, cache.R, sparql.R)

We can start simple with a minimal package and expand later.

[RiboRings]

In Python scikit-bio Table and AnnData are data structures for omic data equivalent to Bioconductor (Tree)SummarizedExperiment class. Ideally, ariadne would support them. Some ideas to integrate ariadne output with those objects are available in append.R and mia::agglomerateByModule.