MS2DECIDE article data

Data related to the MS2DECIDE article.

Here is the procedure to generate all our tables and figures which appear in the article (and more).

1. Prepare a work directory

   • mkdir Reproducibility

   • cd Reproducibility

2. Clone this repository

   • git clone -recurse-submodules https://github.com/MejriY/MS2DECIDE_article_data/

   • cd MS2DECIDE_article_data/Extractor/

   • Note that this also gives you a copy of the MS2DECIDE repository at a specific commit (the one used for the article), which ensures exact reproducibility.

3. Install hatch, required for preparing the right python environment

4. Set up the environment and run a shell in it

   • hatch shell

5. Install the local MS2DECIDE clone

   • pip install MS2DECIDE/ (it says: “Successfully installed ms2decide-0.0.1”)

6. Run the scripts

   • clean

   • manuf-geninput

   • manuf-isdb, type isdb/ for the directory where the ISDB database will be downloaded (takes a few minutes)

   • manuf-gensummary

   • manuf-genarticle

   • pleio-isdb, type isdb/ (takes a few minutes)

   • pleio-gensummary (takes a few minutes)

   • pleio-genarticle

   • pleiok-transform

   • pleiok-genarticle

These commands modify the Reproducibility/MS2DECIDE_article_data/Extractor/Generated/ and the Reproducibility/Article/Generated/ directories. After running them all, you will have there data to inspect our results (see in particular Reproducibility/MS2DECIDE_article_data//Extractor/Generated/Manufactured case/4 - Tables/Compounds joined.tsv and Reproducibility/MS2DECIDE_article_data/Extractor/Generated/Pleiocarpa case/7 - Tables/Compounds joined.tsv) and the data that we used to generate the tables and figures in the article.