Consider adding prominent, formal citation mechanism

[seandavi]

https://support.bioconductor.org/p/9162963/

Possibilities:

• Put citation output on the README or in a chapter
• Publish to zenodo or data dryad to get a DOI and use that
• We COULD mint a bioconductor DOI.

[lgeistlinger]

When referring to the OSCA book including individual sub-books please cite the OSCA paper:

Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. Nat Methods 17, 137-145 (2020). https://doi.org/10.1038/s41592-019-0654-x

[PeteHaitch]

I've got mixed (selfish) feelings about just citing the OSCA paper because few of the authors on the OSCA paper have been involved in the maintenance of the book.

[lgeistlinger]

It's a good point.

There is an unfortunate practice that software maintenance and other valuable contributions to software are not receiving proper credit - at least for software associated with a peer-reviewed journal article.

Starting with the Bioconductor project itself - which is typically cited using the 2004 and/or the 2015 paper, not including in the citation some of the core team members that have maintained and developed key pieces of the infrastructure since then (and also not the many members of the community that contribute to the project in a voluntary or honorary capacity). There are also many examples of Bioconductor packages with maintainer changes after the companion paper has been published, see eg @alanocallaghan's scater package or my PathNet and safe packages.

That said, citing the OSCA paper and the corresponding subbook sounds reasonable given the maintenance effort that is put into keeping the book operational within the ecosystem. The main concern with getting into the practice of citing individual subbooks is that funding bodies have the tendency to measure impact of software projects by looking at citation counts of peer-reviewed journal articles. It is therefore in the interest of the project that the OSCA paper gets cited every time some component of the OSCA book is used.

[LTLA]

I don't have a good solution for the general issue of recognition but I would be happy to list all current OSCA maintainers as authors of the scrapbook that aims to replace OSCA.basic and parts of OSCA.advanced.

[LTLA]

FYI Bioconductor/Contributions#4074