cpauvert/mi-atlas

Interactive and evolving catalogue of microbial interactions based on the framework of Pacheco and Segrè (2019)

mi-atlas's Issues

Set the Github Pages for the download of the formatted catalog

The catalog formatted in #1 should be made available in a website just like the mockrobiota

Enable a detailed exploration of a single entry

Within the Shiny app (#4), once an interaction in the catalog is selected through the dynamic table (#6), an action button should display a detailed view of the entry featuring the attributes of the interaction detailed in the framework

Include NCBI TaxID alongside the participants names

Deploy the Shiny App

Add the version number to the website

Export the catalog to the JSON format of MIND

Upon discussions with Alan Pacheco & Daniel Segrè, the catalog could be exported as a JSON towards the database of correlative interactions (MIND).
But NCBI TaxID are needed beforehand (#16)

Display the catalog in a dynamic table

In the Shiny app (#4), a summarised catalog should be displayed in a dynamic table with the following columns:

• Interaction number
• Interaction name
• Domain

using the DT R package

Improve documentation for new submission

Using:

• examples or tooltips around the form
• a dedicated step-by-step tutorial (using https://carlganz.github.io/rintrojs)
• a screencast to indicated how to add the new line to the repository

Integrate the existing catalog of Pachero and Segré

with the following modifications:

1. dedicated encoding of unknown values
2. and doi as references

The - could be translated as NULL as the R language would consider this entry empty.
The unknown string could be translated as a proper NA because knowledge is non available.

Compute and visualize overall statistics for the catalog of interactions

On the Shiny App (#4), the front page should show:

• the current number of interactions in the catalog
• the biomes represented
• the fraction of intra- and inter-kingdom that is currently documented

Set up a builder that ask questions to quickly format the line for a new entry in the catalog

Using a set of boxes to ticks, entries to select, the new entry could be properly encoded following the framework.
The interaction name can be deduced from the two strains names and suggested with updateTextBox. The interaction number should be deduced from the existing table.

In the end, the builder will provide first a csv line to be pasted either online on Github or in any editor, into the csv file of the catalog, to be in the end submitted as a pull request.

Display the references of the catalog with a proper bibliography format

The detailed entry in #7 has only the doi whereas a bibliography formatting should be preferred. The package rcrossref could be suitable.

Perhaps a correspondence list of doi towards biblio. format could be built to prevent needless queries to crossref for doi already known. This of course should be re-run for each new contribution

Trigger a new PR from the builder in the Shiny App

A serious improvement from the builder of new entry (#9) would be to trigger a PR directly from the Shiny app. I am not sure if it is possible but worth a try!

Perhaps starting with this: https://github.com/actions/starter-workflows

doi not from peer-reviewed articles but from experiments registered with Zenodo et al.

Consider the possibility to use doi not from peer-reviewed articles but from experiments registered with zenodo for new catalog entry. This could add flexibility for ongoing work without sacrificing traceability with ORCID and affiliations.

The API of rcrossref (#8) does also work with zenodo doi.

Document how to contribute to the catalog

with PR by adding a line to the formatted catalog

Use Github Actions to fetch the bibliography format of the references

for any new contributions in a PR. This is related to #8

Propose conditional downloads of the catalog

Downloading of the catalog could be tailored to:

• include/exclude new entries apart from the original catalog
• include/exclude NCBI TaxID as additional columns (#16)