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Besides Nature Chemistry , another journal was launched last week (see\nhere and\nhere): the\nJournal of Cheminformatics. First of all, congratulations to Chris\nand David for their efforts! While the journal only published one research paper yet, it already found\nits place on\nChemical blogspace. I have two things I want to blog about: data rich publishing, and\nstarting the scientific communication.
\n\nPeter had a detailed blog about why he joined the editorial board:
\n\n\n\n\nI take this position with some trepidation as I have grave reservations about the current practice of cheminformatics.\nIt suffers from closed data, closed source and closed standards, and thereby generally poor experimental design, poor\nmetrics and almost always irreproducible results and conclusions which are based on subjective opinions.
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I strongly agree with this observation, and have discussed my view on this in\nmy thesis (send me an email if you\nwant a copy).
\n\nSo, what has the journal to say about this (see Instructions to the Author,\nemphasis mine):
\n\n\n\n\nJournal of Cheminformatics recommends, but does not require, that the source code of the software should be made\navailable under a suitable open-source license that will entitle other researchers to further develop and extend\nthe software if they wish to do so.
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Regarding data, they even less revolutionary; recommended figures formats (EPS, PDF, PNG) focus on nice graphics instead\nof reuse of data. I also note that I cannot upload data in the Open Document Format,\nor, hey, let’s really push things, in RDF. Well, not according to\nthe Instructions. And surely, I can put the [O|R]DF in the supplementary information, anyway. It would also be nice if I could\nuse Jmol as an applet to enrich the graphics, and improve data reusability of the paper, like the\nRSC recently started to allow .
\n\nRegarding the supplementary information, there is a section on additional files, which, unconveniently are capped at\n20MB size. No mention of chemical formats at all, neither any recommendation on semantic formats like\nCML (I wonder when this was discussed with the Editorial Board,\nand where Peter was at the time). How am I going to put online my 500 molecular structure CML file now? (Though it’s good\nto know it is virus scanned ;)
\n\nSo, why do I vent my concerns about these limitations? I had not blogged about the launch of the journal earlier, because\nI have not made up my mind about it. On one side, I am happy to see a journal that promotes (scientific) use of papers,\nand a journal that allows me to keep copyright on the material. However, on the other side, what the current Instructions\nsuggest, the data I could use from the papers is available only in an old-fashion way. That’s a lost opportunity and could\nhave killed competition for sure. Instead, the unique selling point is now restricted to using an\nopen access license. Nature Chemistry, on the other hand, chose\ndata rich publishing as a selling point (though in competition with things done at the RSC).
\n\nThe other thing I want to mention about the journal is the following. Rajarshi blogged about\nBachrach’s paper on Chemistry publication - making the revolution\n(DOI:10.1186/1758-2946-1-2). Firstly, by adding a link like that for the\nDOI I just gave, Chemical blogspace can pick it up; we need this later. Secondly, the paper actually suggests that\n“[b]y publishing lots of data, available for ready re-use by all scientists, we can radically change the way science\nis communicated and ultimately performed”; this is in strong contrast to what I have seen in the Instructions so far.
\n\nRich replied to Rajarshi about the requirement\nto log in before someone could make a comment, which he did not like. He suggested alternative ways to prevent SPAM\nand sorts. The choice for this commenting approach may also originate from having an Open discussion, where everyone\ntakes responsibility for what he says. The use of OpenID, as Rich suggests would only partially address that; on the\nother hand, setting up a fake email address is quite common in the blogosphere too.
\n\nIf Rajarshi would have used the DOI to link to the Steven’s paper, as said, Chemical blogspace would have recognized\nit. Instead, he chose to link directly to the PDF. This is a typical case of hamburgers in action. However, others\ndid when they discussed the first research paper in the journal (DOI:10.1186/1758-2946-1-3).\nThese blogs were picked up by Cb and are listed on this page.
\n\nNow, I only need to remind you of Userscripts for the Life Sciences (DOI:10.1186/1471-2105-8-487)\nthat we have the methods to link these comments back to the journal website. The Quotes from Chemical Blogspace and Postgenomic\nscript in particular, does the hard work (needs GreaseMonkey, the script can be downloaded here; see also\nNoel’s original post). This way,\nwe can read the comments when we visit the papers homepage:
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Now, the script has not yet been updated for the new journal (Noel, can you please upload the revision?), so you need\nto edit the source right now and add http://*.jcheminf.com/* to the list of website the script acts on:
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