Pub2Arc 0.0.5

pub2arc

Tool to create ARC-scaffolds from publications.

• Design
  • One DOI or BibTex entry = One ARC
• Installation
• Usage and Input options
  • Example
  • Detailed usage instruction
  • Recommendation
• Dependencies

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 suitable locations in the ARC.

One DOI or BibTex entry = One 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.

Installation

The tool is released via nuget.

1. Install .NET 8.0
2. Run dotnet tool install --global Pub2Arc

💡 You can de-install (e.g. before installing a new version) via dotnet tool uninstall --global Pub2Arc

Usage and Input options

The tool works with three types of user input

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

Example

The following example

pub2arc --doi 10.1093/hr/uhae313

creates a single ARC folder called Ziegler-2024, with Ziegler being the first author's last name and 2024 the year of publication.

Detailed usage instruction

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.

Recommendation

Especially for larger lists of publications, the BibTex option (--bibtexpath or -b) is recommended over the DOI option (--doilistpath or -dl), since (i) the crossref API is called for every DOI and they might limit the number of allowed transactions and (ii) especially if titles or author names contain special characters, these may be curated in reference files.

Dependencies

• DrBiber: BibTex parsing
• ARCtrl: ARC creation