Pub2Arc 0.0.3

Pub2Arc

Quick tool to create ARC-starters from publications.

Dependencies

• DrBiber: BibTex parsing
• ARCtrl: ARC creation

Usage and Input options

The tool works with three types of user input

1. --bibtexpath: A BibTex file (exported from a bibliography manager) with one or more publications
2. --doi: A single DOI
3. --doilistpath: A text file with one DOI per line

USAGE: pub2arc [--help] [--bibtexpath <path>] [--doilistpath <path>] [--doi <path>] [--arccollectiondir <path>] [--addreadme]

OPTIONS:

    --bibtexpath, -b <path>
                          file path to a BibTex file with one or more publication references
    --doilistpath, -dl <path>
                          file path to text file with one or more DOIs (one per line)
    --doi, -d <path>      a single DOI
    --arccollectiondir, -o <path>
                          directory path to collect the created ARCs
    --addreadme, -r       whether to add a default README.md to the ARC
    --help, -h            display this list of options.

Design

This tool helps to quickly generate a new ARC based on a publication. It takes the publication details (e.g. title and authors) to create generic ARCs with those details added to the investigation level. The use-case could be during data stewardship of a specific lab or group to show-case what their publications could look like in an ARC.

Theoretically this could quickly be done for long lists of publications. However, the real work follows when trying to sensibly divide the publication (chapters) into studies and assays, trying to add the respective data, metadata, protocols and raw datasets to meaningful locations in the ARC.

1 DOI = 1 ARC

Theoretically one ARC can result in or combine multiple publications. However, to keep things simple for this helper tool, this is not intended here. It would need more sophisticated user input, e.g. to determine who of the publication authors of the multiple publications should (not) be added to the list of Investigation (or study) contacts.