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Saturday, September 13, 2014

CDK 1.5.8, Zenodo, GitHub, and DOIs

Screenshot from John blog post.
John released CDK 1.5.8, which has a few nice goodies, like a new renderer. The full changelog is available. Interesting aspect of this release is, that it uses one ZENODO to make the release citable with a DOI. And that is relevant because it simplifies (making it a lot cheaper!) to track the impact of it, e.g. with #altmetrics. And that matters too, because no one really has a clue on how to decide which scientist is better than another, and which scientist should and should not get funding. Where we know peer review of literature is severely limited, we happily accept it to determine career future.

Anyways, so, we have a DOI now for a CDK release. So, everything using the CDK in research can cite this specific CDK release in their papers with this DOI. Of course, most publishers still don't support providing reference lists as a list of DOIs and often do not show the DOI there, but all this is a step forward. John listed the DOI with a nicely ZENODO-provided icon in the release post.

If you follow the DOI you go to the ZENODO website (they effectively act as a publishing platform). It is this page that I want to continue talking about, and in particular about the list of authors. The webpage provides two alternatives. The first is the most prominent one if you visit the page first:


This looks pretty good, I think. It seems to have picked up a list of authors, and looking at the list, not from the standard AUTHORS file, but from the commit messages. However, that is unsuited for the CDK, with a repository history in CVS, via SVN, to Git, but only the latter show up. The list seems sorted by the amount of contributions, but note that Christoph is missing. His work predates the Git era.

The second list of "authors" is given in the bottom right of the page, as "Cite As":


This suggestion is different, though it seems reasonable to assume the et al. (missing dot) refers to the rest of the authors of the first list. In the BibTeX export the full author list shows up again, supporting that idea.

Correct citation?
This makes me wonder: whom are the authors of this release? Clearly, this version includes code from all authors in some sort of way. Code from some original authors may have been long replaced with newer code. And we noted the problem of missing authors, because of the right version control history.

An alternative is to consider this release as a product of those people who have contributed patches since the previous release. In fact, this is something we noted as important in the past and now always report when making a release. For the 1.5.8 release that list looks like:


That is, this approach basically takes an accepted approach in publishing: papers describing updates of running projects involve only the people that contributed to that released work.

Therefore, I think the proper citation for this CDK 1.5.8 release should be:
    John May, Egon Willighagen, Mark Vine, Oliver Stücker, Andy Howlett, Mark Williamson, Sambit Gaan, Alison Choy (2014). cdk: CDK Release 1.5.8. ZENODO. 10.5281/zenodo.11681
Also note the correct spelling of the author names, though one can argue that they should have correctly spelled their names in the Git commit messages. Here are some challenges for GitHub in adopting the ORCID, I guess.

The question is, however, how do we get ZENODO to do this they way we want it to do? I think the above citation makes much more sense, but others may have good reasons why the current practice is better. What should ZENODO pick up to get the author provenance from?