Molbank, published by Molecuar Diversity Preservation International, is one of the oldest of a handful of Open Access journals in chemistry. Although its longevity is a remarkable accomplishment in itself, there is much more to Molbank than meets eye. Just below the surface is a feature so revolutionary, yet simple, that chemistry publishers years from now will wonder why they didn’t implement it sooner.A Molbank article consists of a short monograph on a single compound, or possibly two. This may strike some scientists as a strange way to publish results, and it is unusual. On the other hand, this system offers vast potential to capture useful, but “unpublishable” findings that would otherwise be lost. Back when scientists actually read hardcopy journals, such a system would never have been feasible. Today, with hard drive space measured in terabytes, fiber optics cables crisscrossing the planet, Internet connectivity for almost everyone, and servers that can be had for virtually nothing, this system not only looks perfectly feasible, but preferable in many ways to the status quo.
Here’s the revolutionary part: each article that Molbank publishes is accompanied by a publicly-available, machine-readable file encoding the structure of the article’s subject molecule. That’s it. There’s nothing tricky or high-tech about it. In fact, the practice is about as low-tech as you could imagine. The file format in which structures are encoded, molfile, dates back at least fifteen years, and nearly every piece of chemistry software – both end-user and developer tools – can handle it. What makes Molbank’s practice revolutionary is that not a single chemistry journal, Open Access or subscription-based, currently does this.
Why does the simple inclusion of a publicly-available molfile encoding molecular structures in a paper matter so much? This is where the second two entities of the trinity named in this article’s title come into play: Open Source and Open Data. By providing a mechanism for a computer to decipher the chemistry in a paper, Molbank has opened the door to a host of highly-productive integration activities that nobody outside of Chemical Abstract Service has even been able to contemplate, let alone prepare for.
This article is the first in a series aimed at exploring the wide-open space that Molbank has created. Rather than arguing my point with words, I’ll actually build working demonstrations of what is now easily within reach. At the same time, I’ll document my work on this blog. I’m not sure where all of this will end up, but I do hope to shine some light on a vital, although currently obscure, component of the Open Access debate.
- Copyright of published papers. We will typically insert the following note at the end of the paper: © 200… by MDPI (http://www.mdpi.org). Reproduction is permitted for noncommercial purposes. For alternate arrangements concerning copyright please contact the Editor-in-Chief.
and it has some form of “differential Open Access”:
- Important additional information: All thematic special issues will be fully Open Access with publishing fees paid by authors. Open Access (unlimited access by readers) increases publicity and promotes more frequent citations as indicated by several studies. More information is available at http://www.mdpi.org/oaj-supports.htm.
and from the copyright transfer form:
The copyright to this article is hereby transferred to MDPI, effective if and when the article is accepted for publication.The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, microform, electronic form (offline, online) or any other reproductions of similar nature. In the case of a Work prepared under US Government contract, the US Government may reproduce, royalty-free, all or portions of the Work, for official USGovernment purposes only, if the US government contract so requires.The author warrants that his contribution is original and that he has full power to make this grant. The author signs for and accepts responsibility for releasing this material on behalf of any and all Coauthors.
The undersigned author, as corresponding co-author of the Work, states that all co-authors have been made aware that this manuscript has been submitted to this journal, that they have or will be provided with a (electronic) copy of the manuscript, that they have consented to be co-authors of the manuscript and to transfer the copyright.
The literature that should be freely accessible online is that which scholars give to the world without expectation of payment. Primarily, this category encompasses their peer-reviewed journal articles, but it also includes any unreviewed preprints that they might wish to put online for comment or to alert colleagues to important research findings. There are many degrees and kinds of wider and easier access to this literature. By “open access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.
- BOAI permits commercial re-use; MDPI does not.
- BOAI permits non-exclusivity of copying; MDPI does not
- BOAI permits automatic crawling of data; MDPI gives no explicit permission
- BOAI acknowledges the value of copyright to the authors; MDPI requires the authors to surrender this.
Brief summary of what Open Access means for the reader:
Articles with this logo are immediately and permanently available online. Unrestricted use, distribution and reproduction in any medium is permitted, provided the article is properly cited. See our open access charter.
Anyone is free:
- to copy, distribute, and display the work;
- to make derivative works;
- to make commercial use of the work;
Under the following conditions: Attribution
- the original author must be given credit;
- for any reuse or distribution, it must be made clear to others what the license terms of this work are;
- any of these conditions can be waived if the authors gives permission.
Statutory fair use and other rights are in no way affected by the above.
Without an EXPLICIT machine-readable statement of the sort above “Open Access” is effectively useless for Open Science. Remember that we increasingly want to use machines to trawl sites. If I knew I had permission I would set our robots over the whole of MDPI tomorrow. (I am probably allowed to extract all the molecular files as they are (IMO) “data” unless the grotesque sui generis database restriction applies.
Open Science cannot make effective use of:
- author self-archiving. Much self-archiving – whether on websites or repositories – will not be accompanied by licenses of the sort above.
- journals that do not assign copyright to the authors AND do not explicitly allow crawling of the publishers site AND do not provide machine-readable licenses. How many hybrid journals do that?
I would recommend the use of the phrase
If publishers adopted something like that it would solve my problems. It’s simple. However I guess that an increasing number of publishers are likely to let fuzz and FUD drift around their sites, especially those who have been dragged unwillingly into the “a few authors pay so we are Open Access”. We hear encouraging figures about the growth of Open Access journals….
… but how many of these are explicitly BOAI-compliant?