Rough timeline of the
Journal of Cheminformatics.
The linked PDF has linked years
with references.

… read more in the full letter on Zenodo.

A personal note and thank you

I will remain Editor-in-Chief until the end of the year. The journal is doing awesome things and if I get the chance, I will likely continue help the journal become even more open science.

Thanks also to Chris and David for starting the journal. It has been an honor and pleasure to follow their steps. Also a huge thanks to Rajarshi with whom we have been Editor-in-Chief for close to five years now. It has been a great pleasure to work so actively on Open Science. Also thanks to Nina and Barbara to joined me and Rajarshi as associate editor and have helped shape the journal. It is comforting I leave the journal with an excellent team. Also, a big thanks to Samuel and Matthew who have been helping us getting the Open Science things done and the the current and past Editorial Board members for important discussions in the telcons. Finally, a thank you to all the authors and reviewers who have all been working so hard to make the journal a success!

Of course, I also have to show a screenshot of what the annotation actually looks like, so here goes:

Thanks for the authors for adding these annotations!

Data Rich Publishing

Peter had a detailed blog about why he joined the editorial board:

I take this position with some trepidation as I have grave reservations about the current practice of cheminformatics. It suffers from closed data, closed source and closed standards, and thereby generally poor experimental design, poor metrics and almost always irreproducible results and conclusions which are based on subjective opinions.

I strongly agree with this observation, and have discussed my view on this in my thesis (send me an email if you want a copy).

So, what has the journal to say about this (see Instructions to the Author, emphasis mine):

Journal of Cheminformatics recommends, but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so.

Regarding data, they even less revolutionary; recommended figures formats (EPS, PDF, PNG) focus on nice graphics instead of reuse of data. I also note that I cannot upload data in the Open Document Format, or, hey, let’s really push things, in RDF. Well, not according to the Instructions. And surely, I can put the [O|R]DF in the supplementary information, anyway. It would also be nice if I could use Jmol as an applet to enrich the graphics, and improve data reusability of the paper, like the RSC recently started to allow .

Regarding the supplementary information, there is a section on additional files, which, unconveniently are capped at 20MB size. No mention of chemical formats at all, neither any recommendation on semantic formats like CML (I wonder when this was discussed with the Editorial Board, and where Peter was at the time). How am I going to put online my 500 molecular structure CML file now? (Though it’s good to know it is virus scanned ;)

So, why do I vent my concerns about these limitations? I had not blogged about the launch of the journal earlier, because I have not made up my mind about it. On one side, I am happy to see a journal that promotes (scientific) use of papers, and a journal that allows me to keep copyright on the material. However, on the other side, what the current Instructions suggest, the data I could use from the papers is available only in an old-fashion way. That’s a lost opportunity and could have killed competition for sure. Instead, the unique selling point is now restricted to using an open access license. Nature Chemistry, on the other hand, chose data rich publishing as a selling point (though in competition with things done at the RSC).

The other thing I want to mention about the journal is the following. Rajarshi blogged about Bachrach’s paper on Chemistry publication - making the revolution (DOI:10.1186/1758-2946-1-2). Firstly, by adding a link like that for the DOI I just gave, Chemical blogspace can pick it up; we need this later. Secondly, the paper actually suggests that “[b]y publishing lots of data, available for ready re-use by all scientists, we can radically change the way science is communicated and ultimately performed”; this is in strong contrast to what I have seen in the Instructions so far.

Starting the Scientific Communication

Rich replied to Rajarshi about the requirement to log in before someone could make a comment, which he did not like. He suggested alternative ways to prevent SPAM and sorts. The choice for this commenting approach may also originate from having an Open discussion, where everyone takes responsibility for what he says. The use of OpenID, as Rich suggests would only partially address that; on the other hand, setting up a fake email address is quite common in the blogosphere too.

If Rajarshi would have used the DOI to link to the Steven’s paper, as said, Chemical blogspace would have recognized it. Instead, he chose to link directly to the PDF. This is a typical case of hamburgers in action. However, others did when they discussed the first research paper in the journal (DOI:10.1186/1758-2946-1-3). These blogs were picked up by Cb and are listed on this page.

Now, I only need to remind you of Userscripts for the Life Sciences (DOI:10.1186/1471-2105-8-487) that we have the methods to link these comments back to the journal website. The Quotes from Chemical Blogspace and Postgenomic script in particular, does the hard work (needs GreaseMonkey, the script can be downloaded here; see also Noel’s original post). This way, we can read the comments when we visit the papers homepage:

Now, the script has not yet been updated for the new journal (Noel, can you please upload the revision?), so you need to edit the source right now and add http://*.jcheminf.com/* to the list of website the script acts on:

The Obernai meeting strongly suggested chemoinformatics [1], but the start of the open access Journal of Cheminformatics is the killer. I can no longer resist: I’ll follow the wish from my advisory board , and the general trend around the world (except India ).

The journal’s editor-in-chief is David Wild, while Christoph Steinbeck seems to be going to lead the European branch. People seem to like the idea. The journal will clearly be in direct competition for market share with the JCIM, QSAR & Combinatorial Science, and even the open access Chemistry Central Journal. Interesting to see where this is going…