Open Access and Fuzzy Access

In reply to my request for lists of Open Molecules

  • Dietrich Rordorf Says:
    May 4th, 2007 at 10:52 am eHave a look at MolBank: http://www.mdpi.org/molbank/
    Molbank (ISSN 1422-8599, CODEN: MOLBAI) is fully open-access and publishes one-compound-per-paper short notes and communications on synthetic compounds and natural products. A MDL Mol file is available for each compound. The journal is fully HTML and downloadable with WGET over http.
    Dietrich

This is a useful start. Yes, there is a MOL file for each compound. And the MOL file format is so primitive that there is no space to add a copyright notice, so we can reasonably regard this as factual data and therefore Open.
However the journal, which describes itself as Open Access includes the statement on each paper:

© 2006 MDPI. All rights reserved.

This is incompatible with the BOAI declaration of Open Access, which states:

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.

The fact that Molecules has required the author to transfer copyright to the journal makes it incompatible with the declaration. I queried this more than once with the editor of Molecules but did not receive a reply. Perhaps Dietrich can help?
On a more technical note. It is actually not easy to download all the molecules from Molecules. AFAICS you have to write a spider which traverses the idiosyncratic HTML for the TOC and then scrape every mol file in every paper. This is a limitation of many sites which think that humans are the only readers than matter.
If Molecules provide:

  • an index of the molecules
  • an agreement that we can download every paper and scrape chemistry from it
  • and reuse the results

then I shall be delighted and I shall publicly praise their endeavour.

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5 Responses to Open Access and Fuzzy Access

  1. baoilleach says:

    I note that according to:
    http://www.mdpi.net/journals.htm
    the MDPI journals claim to adhere to the BOAI. There is clearly some confusion here.

  2. Indeed I had considered MolBank a while back to submit our syntheses but was disappointed with the copyright terms.

  3. Thanks for the comments.
    Firstly, “MolBank” and “Molecules” have been separated since 2001, and are published as separate journals.
    Secondly, the copyright notice for MDPI journals has been “(c) 200x by MDPI (http://www.mdpi.org/). Reproduction is permitted for noncommercial purposes.” since 2000, excepted for the MolBank journal. Actually we forgot to change the copyright statement for this journal, and it is only changed this year (see http://www.mdpi.org/molbank/molbank2007/m522.htm for an example).
    Thirdly, regarding BOAI, the statement says “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.” “Should” is not the same as “must”. Therefore, we believe to adhere to the BOAI.

  4. In reply to Jean-Claude Bradley:
    You may read the “Instructions for Authors” of the MolBank journal at http://www.mdpi.org/molbank/publguid.htm:
    “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 PUBLISHER.”

  5. Dietrich,
    Yes, the issue is that there is requirement to transfer the copyright (unless special arrangements were made).

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