GigaScience editorial requests regarding software registration and citations

[dhimmel]

From Hans Zauner on 2023-02-20:

Two editorial notes:

1) Please register any new software application in the bio.tools and SciCrunch.org databases to receive RRID (Research Resource Identification Initiative ID) and biotoolsID identifiers, and include these in your manuscript. Computational workflows should be registered in workflowhub.eu and the DOIs cited in the relevant places in the manuscript. These will facilitate tracking, reproducibility and re-use of your tool.

2) If you refer to repositories, software sites or other online data sources (URLs or dois) in the text, please add a numbered reference for the doi/URL to the bibliography and cite it from the main text by reference number, rather than adding the hyperlink directly (exception: if you refer to several sub-directories of the same repo, it's enough to include the main URL once in the bibliography). Please refer to our citation guidelines for details.

[dhimmel]

Running list of metadata entries created for the editorial request:

• https://bio.tools/hetmatpy
• https://scicrunch.org/resolver/RRID:SCR_023409
• https://bio.tools/connectivity-search

[dhimmel]

If you refer to repositories, software sites or other online data sources (URLs or dois) in the text, please add a numbered reference

To make the software repos citeable, we can a CITATION.cff file to the repos. See:

• https://citation-file-format.github.io/
• https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
• https://citation-file-format.github.io/cff-initializer-javascript/#/

I'm personally against citing these repos as opposed to linking them. The CITATION.cff creates a maintenance burden, can grow stale, requires hard decisions about repository authorship, etcetera. But the Gigascience guidelines are pretty clear that they want citations instead of hyperlinks.

[dhimmel]

Update

The resubmission of GIGA-D-23-00005R1 was accepted in principal! Will track any additional requests from the data curation team here as well.

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Dear Casey,

Many thanks for your revised submission to GigaScience. Peer review is now complete and I'm happy to let you know that the manuscript is acceptable for publication, in principle. Before we proceed, our data curators will have another look and they will prepare an archival snapshot of your code for our database GigaDB.

They will contact you shortly with any requests they may have.

Kind regards, Dr Hans Zauner Editor, GigaScience

[dhimmel]

GigaDB entry is live:

Supporting data for “Hetnet connectivity search provides rapid insights into how two biomedical entities are related” Himmelstein S Daniel, Zietz Michael, Rubinetti Vincent, Kloster Kyle, Heil J Benjamin, Alquaddoomi Faisal, Hu Dongbo, Nicholson N David, Hao Yun, Sullivan D Blair, … Greene S Casey GigaScience Database (2023) https://doi.org/gr77bv DOI: 10.5524/102389

Will add a citation in the mansucript, but likely wait to see how GigaSceince does it.

[dhimmel]

Follow up issue:

• https://github.com/greenelab/connectivity-search-manuscript/issues/49