Heather shows that Open Data increases Citations

If your life is driven by citations, then Heather Piwowar has shown that data openly accessible in papers increases the citations. From her blog:

Piwowar HA, Day RS, Fridsma DB (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3):e308.
doi:10.1371/journal.pone.0000308

I use the DOI to find the paper in PLoS where she and co-authors write:

Background

Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available.

Principal Findings

We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression.

Significance

This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

SIXTY-NINE percent increase in citations because you share your data with the rest of the world! Yes, many scientists don’t like posting their data – why? because someone else might check it – well we have to accept that is part of science. Someone else might be cleverer than us and see patterns in it that we have missed. Again part of science. Someone else might mash it with other datasets and come up with new findings. Of course.
But they have to cite us! So it’s not a bad bargain (if citations are honest). And it makes you feel good. And after all understanding cancer microarrays might help us in developing better therapies.
So well done Heather, and thanks for your blog. We’re glad to see that PLoS publishes bibliometrics so you could get a paper there. I know you haven’t been cited yet, but perhaps PLoS lets you know how many people download your paper. I hope it’s a lot. And maybe even the citation in this blog will prompt someone.
And, while on downloads, wouldn’t it be a good idea if publishers gave us a count of how many downloads of DATA there were? That’s a real metric. And one where Open Data shines. So, publishers – a level playing field for Open Data…

Posted in data, open issues | 2 Comments

Problems with character sets when blogging

This post is primarily to test Feedburner which gripes about strange characters. Some of my material comes from other sites such as the publisher’s web pages that I have been analysing recently. These contain all sort of strange material such as scripts, character entities, etc. and I normally simply cut and paste them. (I can’t easily see any other way). Sometimes the web cruft destroys the post completely, sometimes it spills over into another post following it on a Planet, etc. I don’t know if there is a way of santizing this – e.g. paste into another web page offline and run it through HTMLTidy or something?
While I’m on techie stuff ocacsionally stuff goes into the blog spambin. I skim this very rapidly – ca 300 mails/day and I caught a mail from Egon today and saved it. No idea why it got there.

Posted in Uncategorized | Leave a comment

Do authors want to give publishers a monopoly over their data?

In response to my post Why doesn’t Springer use a CC licence? and Bill Hooker’s reply Egon Willighagen writes:

  1. Egon Says:
    Bill, regarding [1]… I think the following plays a role here. Say the make it CC-BY, and someone extracts the data (the most important bit for chemoinformaticians), set up a database with that, competing with the databases the publisher already provides… so, I would say, it is not just the profit from the article, but also the profit from the data that is at stake. The NC clause would prohibit at least commercial competition.

Egon, I can’t agree with you on this one! Essentially you are saying that when an author publishes in journal X then implicitly they agree to prevent any competition with any of the projects that the publisher of that journal produces.
[NOTE ADDED LATER. EGON HAS CLARIFIED THAT HIS COMMENT WAS ON THE PUBLISHER’S MOTIVATION, NOT WHAT HE [EGON] WOULD LIKE TO SEE – EXCELLENT. AND IT GAVE ME A CHANCE TO AIR THE OPEN DATA THEME AGAIN. SO WE CERTAINLY WISH TO STRIVE FOR CC-BY RATHER THAN CC-NC].
IMO the publishers control far too much information already. We need – in the UK term – a “level playing field”. I have no fundamental objection to commercial databases “won by the sweat of the brow” but I do object to publishers owning scientific data submitted by article authors. I have taken this up with the journal “Molecules” – you can see previous posts on the blog – where the journal forbids commercial re-use of the material in the published papers. The also sell collections of molecules, so any abstraction of molecular information from their journal would compete. Let it be so – they have a head start so if their product is better they should be able to beat the competition. If their product is inferior then they deserve to lose out.
As an example, Wiley have a database of 350,000 spectra (or something like tnat). We’ve had lot’s of fun discussing on the blogosphere how it stands with NMRShifDB (20,000+ molecules). Now if your logic was followed we’d say that no-one should build a commercial database out of spectra published in Wiley journals because it would compete with theirs. My argument is completely opposite – I want all spectra in any journal to be Open and re-useable for any legitimate purpose including commercial. Then anyone can create a database. What they cannot do is claim a monopoly on the individual contents.
And I’m sure that the Blue Obelisk mantra – Open Data, Open Standards, Open Source allows commercial re-use. 🙂

Posted in chemistry, data, open issues, Uncategorized | 2 Comments

"Open Access" – Elsevier, Wiley, RSC

xx
My survey of “open access” in chemistry publishers is part of a larger project which will be revealed shortly. I had not planned to look at closed access publishers but thought it was worth checking what they offered and the last few days of this blog records much of that. I shall summarise shortly.
Peter Suber summarises what I have posted:

In three detailed posts, Peter Murray-Rust documents the access barriers at the hybrid journals from the ACS (Author Choice) and Blackwell (Online Open). These are barriers left in place even after authors or author-sponsors pay for the “open” or “free” access options.

Comment.

  • Peter examined the access barriers at the Springer hybrid journals (Open Choice) on July 8.
  • These are valuable studies, especially when supplemented by clarifying publisher responses (like Jan Velterop’s response to Peter’s post on Springer). When a hybrid program doesn’t claim to offer “open access”, then I don’t criticize it for falling short of the BBB definition of OA, even if I criticize it on other grounds. But some of the hybrid programs do claim to offer OA; and even when they carefully pick new terms and avoid promising OA, their access barriers should be well-documented to help authors, funders, and universities decide whether their fees are worth paying. Journals should clearly describe their access policies –OA or not– and when they don’t, we count on independent investigations like Peter’s.

As always PS identifies the issues and I agree completely with:

“When a hybrid program doesn’t claim to offer “open access”, then I don’t criticize it for falling short of the BBB definition of OA, even if I criticize it on other grounds.

so I did not criciticize the ACS’s Free Access policy per se, but the fact that certain pubklcations were not offered under the conditions that were advertised in the policy – i.e. a paper which was labelled “Free Access” could be accessed in a manner which required or invited the reader to pay to view. The same was true for Springer and Blackwell.
Note that I have not carried out a comprehensive survey of every paper offered as “Open” or “Free” or whatever – partly because some of the publishes make it almost impossible to locate these by this criterion alone.
To continue the survey I have looked at three publishers who offer specialist chemistry journals (i.e.journals labelled as chemistry). I shall not look at publishers who offer multidisciplinary journals (e.g. PNAS) though I would be grateful to know of other journals (e.g. from Nature, Royal Soc, etc.) which are primarily chemistry and which offer Open schemes of some sort.
I have looked at Elsevier, Wiley and RSC. The methodology was to type “Elsevier Open Access” , “RSC hybrid”, (etc.) into Google and see what I got. If the publisher had a clear hybrid offering I would visit it and try to find some papers. Findings:
Elsevier has no hybrid offerings in chemistry (Peter Suber, Open Access News) blogs 6 journals in different subjects. I shall not pursue this further other than to note that they seem to use the term Sponsored Article.
Wiley Announces New Funded Access Service [2006] and uses the term “Funded Access”. The service and list of Journals is here. Some are fully chemical – I have only scanned them very cursorily and found no offerings. I found an example of FA in proteomics and AFAICS the service was adequate – I i.e the abstract announced the paper was free to read and it was. But I only have a sample of one, and I think a number of Wiley journals are society so I don’t expect a consistent approach.
The Royal Society of Chemistry uses the term “Open Science” to describe its pay to read policy. The FAQ seems fairly clear. I skimmed the whole set of TOCs for Chemical Communications in 2007 (28 issues, ca 25 articles per issue = 700 articles). Chem Comm (in which I have published several times) is a flagship journal for rapid communications and might be the sort of place where authors would wish to pay-to-expose. I only skimmed the TOCs for icons and found none relating to Open Science. So I conclude one of the following:

  • There are no Open Science communications in Chem Comm
  • The RSC does not label the TOCs with OS icons

To summarise so far:

  • It is EXTREMELY difficult to find any instances of Hybrid Open Access. The only publisher which helped me find articles was ACS who had a direct pointer to all 27 articles under its Free Access Scheme.
  • The way that publishers lay out their journals and their TOCs is AWFUL. There is no consistency between publishers (well I wouldn’t expect that) but all of them make things very difficult. For example in ACS you do not seem to be able to find all the TOCs for a given journal.
  • The nomenclature for Hybrid Open Access (and presumably in Springer’s case Full Open Access) will confuse the hell out of any normal human. “Online Open”, “Sponsored Access”, “Open Science”, “Free Access”, “Author Choice”, “Open Choice”. What are these meant to mean?? (Andrew Walkingshaw pointed me at APS whose TOC page is simple, honest, does-what-it-says-on-the-tin, and uses the simple phrase “FREE TO READ”. But there again, physics is light years ahead of chemistry as a scholarly discipline.
  • There is very little evidence that any of these publishers want to actively promote anything Open other than noises in press releases. The take up appears to be between 0% and 1% (these are approximations and I would be delighted and surprised if any publisher supplied me with accurate figures.)
  • Where a society journal is published by a major closed access publisher there is even greater confusion. None of my findings are critical of society publishers. Some of them appear to have dual access – one through their own web site and one through the major publisher and the offerings can be different.

Most of the hybrid schemes in chemical journals appear to have been going for about a year. (Some societies have been running this for longer). So to be fair it will take some time for the community to react.
But the simple fact is that after a year less than 1% of chemistry papers which could be published as hybrid open access actually are thus published. There are many reasons but one of them is that the publishers are not working hard enough to make it work. The impression going through all these websites – a depressing experience – is that there is no promotion of the concept, visual signals are awful, web architecture is inconsistent, rubrics are illogcal and fuzzy, there is little good labelling, etc. The immediate impression is that for most of these publishers hybrid open access is an inconvenient political necessity that they must pay lip service to but that they would rather it wasn’t around. Peter Gregory, when at RSC in 2006 described Open Access as “ethically flawed” (my first post on this blog!) and stated:

But the Royal Society of Chemistry’s director of publishing, Peter Gregory, disagrees. ‘We have absolutely no interest shown from our editorial board members, or our authors, for open access publishing,’ he said.

Now PeterG has left RSC (to another large publisher I think?) and I don’t think RSC hold the same views now. However I haven’t found many “open science” publications.
So end-of-term report of the class of 2006 hybrid access publishers we can give the following report:
“Could try harder”

Posted in open issues | Leave a comment

Why doesn't Springer use a CC licence?

In a reply to a post of mine, Jan Velterop of Springer writes, and I comment, I hope, constructively.

  1. Jan Velterop Says:
    July 11th, 2007 at 10:29 am eDear Peter (and Bill), [Bill Hooker]
    JV: The wish to improve findability is a fair one and we are working on that. But I’m afraid I cannot see how a document carrying the publisher’s copyright is by definition restricted in terms of open access. If that were so, carrying the author’s copyright would be just as restrictive.

PMR: we clearly have a major problem in communicating our views here. Copyright is, by default, restrictive. If I have a film copyrighted by Disney I am restricted in what I can do with it. If I have a book by J K Rowling I am restricted as to what I can do with it. If this blog simply said “Copyright P. Murray-Rust” you would be restricted as to what you could do with it. By default the world assumes that IN THE ABSENCE OF ANY OTHER INFORMATION copyright on a scientific article restricts its use. There are recent cases where publishers have taken action against scientists who they believe have broken their copyright.
Scientists and other scholars are trained to observe and honour copyright. There are limits to what we can do with photocopying, multiple copies, etc. We can be audited. We normally have to ask permission.
So I cannot see how you can assert that a document carrying a copyright is not restricted.
Please also note that most scientists do not have the time to spend working their way through complex arguments on copyright. They simply note “this is copyright – I have no other information – therefore I cannot re-use it”.
It is, in fact, precisely because copyright is so ineffective at asserting the rights of the user that publishers have resorted to using licenses (such as CC or GPDL).

  1. JV: The Bethesda Statement says this (and the Berlin Declaration, too, without the ‘copy-’):“The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship[2], as well as the right to make small numbers of printed copies for their personal use.”JV: It says ‘author AND copyright holder’, implicitly recognising that they can be different. Otherwise it would have said ‘author AS copyright holder’. Any copyright holder can attach an open access licence. Indeed, ONLY a copyright holder can do that. Besides, ‘condemning’ any open access articles to a non-OA status because the copyrights are held by someone other than the author is doing great injustice to all those articles that have been made fully open after they were published. That would be a mistake. It seems to me that doing so is indeed declaring nail varnish more important than food, to extend my earlier analogy.

PMR: “Any copyright holder can attach an open access licence”. Exactly. What could be simpler? Yet Springer have failed to do so, and by failing to do so have implied that they do not regard the document as having the same level of open access that other publishers assert by attaching licences.
By default your articles are Open Access (rather than freely viewable) by reason of the complex structure of your web pages. The only argument I can make for the document being open access runs something like this (forgive me if I have missed some part of the trail):

  • Springer have asserted on their publisher site that SOME (not all) of their articles have “full open access”. It goes on to list the conditions which, though not a licence, might be reasonably read as such. So far, so good. (I disagree with the NC phrase – below – but that is a separate argument at present). So with that caveat I would accept (reinforced by your statement on this blog) that Springer intends certain articles are “full open access”.
  • Any particle article – divorced from the web site environment – carries NO INDICATION of the fact that it is “full open access”. It carries the standard copyright applied to all other articles. So if I were shown two Springer articles – one closed access, one full open access – on someone’s web page or in a repository I would have NO idea what rights I had. By default I would assume none.
  • A scientist visiting your site through a DOI (one of the most common ways) is presented with an abstract page which carries the following:
  1. A page about rights (all pertaining to the publisher)
  2. A option to pay for the article (which would presumably be enforceded)
  3. A small black icon called “Open Choice”. This icon gives no indication of its purpose and has no links. While Springer staff and regular vistors might know what “Open Choice” means, the average scientist has no clue. Given we already have “Online Open”, “Free Access”, “Author Choice” from other publishers, some of which are severaly restricted, the author cannot be blamed for regarding the article as closed or partially restricted access. There is no indication that the author has to refer publishers home page to find out what it means
    1. JV: This phrase in the Bethesda Statement: “the right to make small numbers of printed copies for their personal use” clearly limits commercial use. That never seemed to be problematic. Why is it problematic now? Non-commercial is in no way a limiting factor for open access to the on line version. … Jan Velterop

    PMR: I may come back to this later – it seems to be the only reason for preferring NC over BY. It only occurs in one statement – I am sure there was a good reason at the time but it  hasn’t been seen as important by many other OA publishers.
    PMR: The real point – and to me it seems obvious – is that copyright per se is inadequate to indiacte anything other than the denial of an unspecified set of rights. The simple way to tackle this is to add a licence. I do this for my software, PLoS/BMC and many others do it for their papers. If the licence is located IN THE ARTICLE there is no confusion. I see the paper, I know what the rules are. It takes 10 seconds.
    I would have no problem with a “Springer Open Access Licence” – indeed I would encourage it. There are many organization-based licences in Open Source – Mozilla, Apache, Eclipse as well as  the more widely used BSD, GPL, Artistic (which I use). SOAL would solve all the problems (assuming it read as your home page). I’d prefer CC-BY and I suspect the authors would as well. So the simple question is:
    “Why doesn’t Springer simply adopt a CC license and add it to the text of its OA publications?”  I cannot think of any reason.

    Posted in open issues | 6 Comments

    Blackwell also fails to deliver Open Access

    [To verify my assertions in this you will have to be on a machine that does not have institutional access to Blackwell publications. I am doing this from home]
    I am a crystallographer and proud of it. We work very closely with the International Union of Crystallography who have an enlightened appraoch to access to data – more later. They publish many journals, and now use Blackwell publishing to manage these – at least from the masthead. In this post there is no criticism of the International Union for which I have high praise.
    I turn to the contents page of Acta Crystallographica E (reports on crystal structures and the basis of part of our Crystal Eye program). Most are closed access (although the data are open) but some are Open Access denoted by:
    [Open access]
    which when you click on it asserts (you can skip this at first reading):

    open access and Crystallography Journals Online

    This document provides a summary of the open-access policy for electronic editions of journals published for the International Union of Crystallography (IUCr) by Blackwell Munksgaard. The journals are:

    Acta Crystallographica Section A: Foundations of Crystallography, http://journals.iucr.org/a/journalhomepage.html
    […]

    1. Introduction

    […]The Executive Committee of the IUCr have decided that starting in January 2004, authors publishing papers in IUCr journals should be given the opportunity to make their papers open access on Crystallography Journals Online. The policy will be reviewed by the Executive Committee on a regular basis.

    2. Open access and authors

    Authors will be given details of how to make their articles open access at the proof stage. Although a charge is levied for making an article open access, authors unwilling or unable to choose open access are in no way excluded from publishing in IUCr journals as these will contain a mix of both standard and open-access papers.
    The charge for making an article open access is USD 900. […] Open-access articles will be clearly marked in contents pages and search results.
    A paper may be made open access at any time after the proof stage on receipt of the appropriate payment. […]

    3. Open access and subscribers

    IUCr journals will include a mix of both standard subscriber-only papers and open-access papers for the foreseeable future. Funds generated from open-access payments will be used to keep our subscription costs as low as possible. Where an open-access fee has been paid, the article will be available free of charge to subscribers and nonsubscribers.
    For full details of the subscription policy for Crystallography Journals Online, see subscriptionpolicy.html.

    4. Open-access membership

    Institutions may take out open-access membership of Crystallography Journals Online. Researchers from member institutions have the right to publish an unlimited number of open-access articles in IUCr Journals without paying open-access charges. All UK Further Education Institutions are currently members. For a full list of open-access members, click here. If your organisation would like to become a member, please contact support@iucr.org.

    5. Open access and copyright

    Authors will be asked to sign a copyright form for articles as usual. However, for authors who wish to retain the copyright of their articles, the IUCr provides a licence agreement as an alternative to signing a copyright form.
    The existing terms and conditions of use of Crystallography Journals Online remain valid for open-access articles. In particular the IUCr permits ‘fair use’ of the articles but republication or systematic or multiple reproduction of longer passages from Crystallography Journals Online is permitted only under licence.

    6. Other information

    Since the launch of Crystallography Journals Online in 1999, the IUCr has had a policy of providing free access to the full texts of certain types of article (for example, CIF Applications, Prefaces, Editorials, Letters to the Editor, Book and Software Reviews, Crystallographers, Notes and News, Addenda and Errata, and New Commercial Products); this policy will continue. In addition, a number of services including tables of contents, e-mail alerting, and the provision of supplementary material (e.g. CIFs, structure factors and other structural data) are free of charge to both subscribers and nonsubscribers.
    The IUCr has an active policy concerning the long-term preservation and access to publications in its journals. The charge made to authors for open-access publication includes a contribution to the cost of the long-term preservation and access of the publication.


    I take a recent issue:
    which includes:

    [HTML version][PDF version][Article Abstract][CIF][3d view][Structure Factors][Supplementary Material][CIF check Report]  [Open access]
    Acta Cryst. (2007). E63, m1864  [ doi:10.1107/S1600536807027626 ]

    catena-Poly[[[diididocadmium(II)]-[mu]-3,3′,5,5′-tetramethyl-4,4′-bipyrazolyl-[kappa]2N:N‘] methanol solvate]

    D.-Q. Li, L. Hou and S. W. Ng

    Online 13 June 2007

    and click on the HTML or PDF button and get…
    The full text?
    NO.
    A request for
    “Enter username and password for “Crystallography Journals Online/Synergy” at jttp://journals.iucr.org
    User Name:
    Password:
    … so the paper isn’t Open Access in any sense of the term. (BTW Synergy is Blackwell’s trademark or similar and indicates that the problem is likely to be at the Blackwell end).
    Now presumably somebody has paid for this – the author, JISC, The International Union, I don’t know. But whoever it is hasn’t get very good value for their Open Access, have they?
    Some astute readers may have noticed that I have visited 3 major publishers Springer, ACS and Blackwell and in each case found that access to Open Access articles was technically barred in a way that most readers would not be able to circumvent easily. All cases offered the users the chance to pay for the article.
    Perhaps I will let readers draw their own conclusions as to whether the publishing industry is really trying to make Hybrid Open Access a success. If so let’s hear your views

    Posted in open issues | 5 Comments

    SPECTRa – we've been blogged!

    It’s rather gratifying when someone else reports our own work, nn this case Chemistry Central blog. They have picked up our 18-month project with Imperial and this substantial summary saves us the work of creating our own:

    The findings of the SPECTRa project’s final report

    The final report for of the JISC‘s SPECTRa project (Submission, Preservation and Exposure of Chemistry Teaching and Research Data) was recently published. The project was funded by JISC’s Digital Repositories Programme as a joint project between the libraries and chemistry departments of the University of Cambridge and Imperial College London, in collaboration with the eBank UK project. (It is worth noting that a member of our editorial advisory board, Dr Simon Coles of the University of Southampton, was an eBank Project representative for the SPECTRa study).
    The aim… The broad aim of the eighteen month study, which ended in March, was to “address the provision of Open Access to primary chemical research data in molecular and related subjects through institutional repositories”. The project focussed on three areas of chemistry: synthetic organic chemistry, crystallography and computational chemistry.
    Various chemistry data repositories have been launched in recent years, such as the University of Southampton’s eCrystals and Cambridge’s World Wide Molecular Matrix. However, in general “Chemistry as a discipline has been slower than the physical and biomedical sciences to adopt and exploit OA concepts in the handling of experimental data and research publications. Most of the data (analytical, spectral and even crystallographic) associated with peer-reviewed publications from chemistry departments are never communicated to the scientific community. In those limited instances where a publisher does provide a means of accessing primary data to supplement a published paper, the data may then be subject to the publisher’s IPR practices. In most cases the primary data are simply not published…“.
    In light of this, the five key objectives of the SPECTRa study were established as being; to undertake surveys of communities in computational and organic chemistry; to and refine crystallography tools developed by eBank; to develop automated validated and indexing tools specific to computational and synthetic chemistry, and provide interactions with the OAI-compliant DSpace repository platform; to develop chemical metadata functionality based on Dublin Core; and, to disseminate and promote project outcomes to encourage widespread adoption.
    The findings… Surveys of chemists at Imperial College and Cambridge University investigated their current use of computers and the Internet and identified specific data needs. The salient points to emerge from the feedback were: a lot of data is not stored electronically (e.g. lab books, paper copies of spectra); a complex list of data file formats (particularly proprietary binary formats) are being used; there is significant ignorance regarding digital repositories; there is a requirement for restricted access to deposited experimental data.
    In addition, two interesting statistics to come out of the surveys were that “[o]ver half (52%) of the [171] respondents stated they were aware of digital repositories however, but only 9% of respondents are currently using one”, whilst, “[a]bout 50% of the data created by research chemists is still stored in non-digital formats.” Also to emerge from the survey results was the concept of a “golden moment” – a point at which the researcher best understands the process, possesses a comprehensive package of information to describe it, and is motivated to submit it to a data management process.
    Based on interviews with key researchers, distributable software tool development using Open Source code was undertaken to facilitate deposition into a repository. The project has provided tools which allow for the preservation aspects of data reuse. All legacy chemical file formats are converted to the appropriate Chemical Markup Language scheme to enable automatic data validation, metadata creation and long-term preservation needs. Additional tools would however be required to add value to any large-scale data aggregates. The deposition process adopted the concept of an “embargo repository” allowing unpublished or commercially sensitive material, identified through metadata, to be retained in a closed access environment until the data owner approved it for release. The resultant repository architecture envisages a federated framework in which data will first be deposited into an intermediate departmental repository, before possibly later being pushed into a central OA repository.
    The project’s main findings included the following: scientific data repositories are more complex to build and maintain than are those designed primarily for text-based materials; the specific needs of individual scientific disciplines are best met by discipline-specific tools, though this is a resource-intensive process; institutional repository managers need to understand the working practices of researchers in order to develop repository services that meet their requirements; IPR issues relating to the ownership and reuse of scientific data are complex, and would benefit from authoritative guidance based on UK and EU law.
    In conclusion, the report states that “[t]here is no universal ‘shrink-wrapped’ approach which works for every discipline. We have designed a toolkit to address problems which should be applicable in a generic fashion to other institutions with similar research interests… The organisational and technical architecture of institutional repositories may be improved by creating intermediate “departmental” repositories between the researcher and the central institutional repository. Such departmental repositories, designed to meet the needs of specific local communities of researchers, and in particular offering an embargo facility, may be more successful in establishing the degree of confidence, competence and trust that will persuade researchers to deposit data readily.”
    The full report can be viewed here.

    I’ll just add that Jim Downing continues to manage the SPECTRa software and we’d be happy to hear from chemistry departments who are interested in capturing and archiving their crystallographic, computational or spectroscopic data (rather than letting it decay). Of course it’s up to you to implement the system but the tools work and Jim is looking at very lightweight repositories (DSpace is not well desgined for scientific data – nor are any of the others. Watch Jim’s jackrabbit …)

    Posted in chemistry, data, open issues | 1 Comment

    Voyages into publisher copyright – End of course exam

    In the last 4 posts we have seen several varieties of Open Access (or Free Access) (or Hidden Access) or Fuzzy Access. Now it’s time to see how well you have been following these tutorials. So we have picked yet another major publisher – Blackwell – and we are going to show you the web pages and leave you to work out what the access is and what the labelling on the web pages is. Here is the first publisher web page:

    Blackwell Publishing’s Position on Open Access

    Open Access is an important development in scholarly communications which aims to deliver unrestricted access to academic research to all those who seek it. Blackwell Publishing has been proactive in the debate: monitoring the evolving issues, contributing to government and industry evaluation initiatives, and advising the 665 societies and 800+ journal editors with whom we work.
    At Blackwell our primary goal is to facilitate the dissemination of research through the licensing of access to institutions and individual customers whilst continuing to provide a return to the societies for whom we publish. We will support Open Access models which ensure that viable high quality society publishing continues to flourish.
    Following is a summary of the ways in which Blackwell Publishing and the societies with whom we publish are responding to the calls for Open Access publishing:

    1. Self-archiving – Our copyright assignment policy allows authors to self-archive their final version of their article on personal websites or institutional repositories.
    2. Author pays – We are offering a new service called Online Open which gives authors the choice to pay a publication fee in order for their article to be openly accessible to all.
    3. Free back files – Several journals offer free access to content after a set time period, or to certain types of material such as review articles.
    4. Developing world access We offer free or low cost access to libraries in the poorest countries through our participation in the HINARI, AGORA, OARE, INASP and related initiatives.

    In this post we’ll concentrate on 2 (author pays). Note that the article is described as “openly accessible”. Blackwell “support Open Access models… ” and respond to “the calls for Open Access publishing…”. So is “Online Open” one of them. Read this very carefully because that’s your first question (BTW employees of Blackwell are eligible for this competition):

    About Online Open

    Online Open offers authors who wish to publish their research in a Blackwell journal the opportunity to ensure that their article is immediately made freely available for all to access online.
    This pay-to-publish option is an important part of Blackwell’s response to the calls for open access and our commitment to viable high quality publishing on behalf of societies.

    Authors pay-to-publish

    Authors of accepted peer-reviewed articles may choose to pay a fee in order for their published article to be made freely accessible to all via our online journals platform, Blackwell Synergy.
    Authors are required to download the OnlineOpen Form from the individual journal’s website or by clicking a link in the Instructions for Authors.
    For 2007, the Online Open fee is fixed at US$2600, 1950 Euros or £1300 (plus VAT where applicable). Any additional standard publication charges will also apply, such as for color images or supplementary datasets.
    The publication fee is charged on acceptance of the article and should be paid within 30 days by credit card by the author or other funding agency. Payment must be received in full for the article to be published Online Open.
    In addition to publication online via Blackwell Synergy, authors of Online Open articles are permitted to post the final, published PDF of their article on a website, institutional repository or other free public server, immediately on publication. Blackwell Publishing will also deposit the final text of relevant Online Open articles on publication with PubMedCentral (PMC) in addition to any mirror of PMC (such as UKPMC).

    Articles are published as normal

    All Online Open articles are treated in the same way as any other article. They go through the journal’s standard peer-review process and will be accepted or rejected based on their own merit.
    The accepted articles are prepared for publication in the usual manner and are posted online on Blackwell Synergy with the full range of features associated with that journal. The articles are archived for perpetuity and are registered at relevant Abstracting and Indexing Services and at CrossRef.

    Readers have full access

    The only difference for the reader is that they can access all Online Open articles without restriction, something that may not be available for subscription-based articles.
    Online Open articles are identified on Blackwell Synergy as being freely available for all. They are also included in the print edition of journals with an indicator which shows that the article is available for free online.

    Impact on subscription prices

    During the first six months of each year we undertake our annual pricing review for the following year. One of the key factors we take into account in setting subscription prices is any increase in the amount of material we expect to publish in the journal in the following year.
    We will continue to use this information in setting pricing but only take into account material published under the traditional publishing model. Any articles published under the Online Open model are excluded from this calculation.

    Note to authors funded by the Wellcome Trust

    The Online Open service is approved by the Wellcome Trust and mentioned in its information for authors as such.

    […]

    OK – you’ve read this. so
    QUESTION 1 (20 marks)
    “Is Online Open compatible with the full BBB declaration of Open Access? (see Peter Suber, Bill Hooker and Klaus Graf for precise definitions. If it’s not compatible, what is the difference?”
    OK – you’ve finished the question. Did you find the answer from the rubric above? No? Well neither did I. Readers can “access all articles without restriction”. Let’s guess that means full Open Access and that they won’t send the lawyers. Probably a bare pass mark.
    What you forgot is that the Second Law of Publisher Obfuscation means that you cannot find the information where you expected but in a completely different place. Where you SHOULD have looked for information about Online Open is “Author Self-Archiving”. Obvious, when you see the answer. Now read this very carefully:

    Blackwell Publishing and Author Self-archiving

    Blackwell Publishing recognizes the importance of the Open Access debate for scholarly communications and its aim to deliver unrestricted access to academic research to all those who seek it. As the world’s leading society publisher, Blackwell has a responsibility to ensure that viable high quality society publishing continues to flourish. As well as making an active contribution to the OA debate, we have also made a public commitment to support Open Access models which contribute to this goal. This now includes allowing the author to retain the copyright of their Article while granting Blackwell exclusive rights to publish it. The author may also self-archive their final version of the Article on personal websites or institutional repositories, while providing a link to the definitive published version for users to refer to.
    All Blackwell Publishing Journals
    Author rights prior to acceptance:
    Provided they acknowledge that the Article has been submitted for publication in the journal from the relevant society and Blackwell Publishing, authors may:

    • share print or electronic copies of the Article with colleagues;
    • post an electronic version of the Article on their personal website, their employer’s website/repository and on free public servers in their subject area.

    Standard Blackwell Publishing Journals
    Author rights after acceptance:
    The following author rights apply to all Blackwell journals, apart from Online Open articles (see below).
    Provided they give appropriate acknowledgment to the journal, the relevant society and Blackwell Publishing, and give the full bibliographic reference for the Article when it is published, authors may:

    • share print or electronic copies of their version of the Article with colleagues (not the final published version);
      use all or part of the Article in other publications;
    • use the Article for educational or research purposes;
    • post their version of the Article on their personal website, their employer’s website/repository and on free public servers in their subject area after the embargo period stipulated by the journal has been passed (note that the embargo period will vary by journal, e.g. 6 months or 12 months, and that some journals do not have any embargo on self-archiving at all – see note below).
    • When posting on the web, authors must give full bibliographic details plus a link to the published version of the Article as follows: ‘The definitive version is available at www.blackwell-synergy.com ‘.


    Additional points to note:

    • Many journals, though not all, have an embargo period before which posting Articles on the web or in institutional or subject-based repositories is restricted. This is in order to provide extra protection to the subscriptions base of the journal. This embargo period is clearly stipulated on copyright agreements and in the terms and conditions relating to the use of PDF offprints.
    • Authors cannot reproduce the Article for commercial purposes (commercial purposes = ‘for monetary gain on [their] own account or on that of a third party, or for indirect financial gain by a commercial entity’). However, this does not affect an author’s rights to receive a royalty or other payment for works of scholarship.

    Guidelines for Librarians/Institutional Repository Managers
    Librarians who are managing their institution’s repository should approach the authors within their institutions directly, rather than the publisher. The authors of Articles which are published in Blackwell journals will be able to provide their final version of their Articles for posting and can confirm the embargo period on posting the Article on the web. The institutional repository record should include full bibliographic details and provide a link so that users can make reference to the final published version of the Article.
    Online Open Articles
    The following author rights apply to all Online Open articles.
    Provided they give appropriate acknowledgment to the journal, the relevant society and Blackwell Publishing, and give the full bibliographic reference for the Article when it is published, authors may:

    • share print or electronic copies of the Article with colleagues;
    • use all or part of the Article and abstract in personal compilations or other scholarly publications of their own work (and may receive a royalty or other payment for such work);
    • use the Article within their employer’s institution or company for educational or research purposes, including use in course packs;
    • post the final PDF of the Article on their own personal website, on their employer’s website/repository and on free public servers in their subject area. Blackwell Publishing will deposit the full-text of their Article on publication with PubMed Central (PMC) in addition to any mirror of PMC (e.g. UKPMC). Electronic versions of the accepted Article must include a link to the published version of the Article together with the following text: ‘For full bibliographic citation, please refer to the version available at www.blackwell-synergy.com ‘.

    Third parties will be entitled to re-use of the Article, in whole or in part, in accordance with the conditions outlined in the Creative Commons Deed, Attribution 2.5 Non-Commercial (further details from www.creativecommons.org), which allows Open Access dissemination of your work, but does not permit commercial exploitation or the creation of derivative works without your permission. Please address any queries to journalsrights@oxon.blackwellpublishing.com

    Third parties (readers) have CC-BY-NC rights, and these can be MORE than the author has!
    QUESTION 2 (20 marks): What rubric (license, copyright) will an Online Open article (and its context, TOC, abstract) carry? (HINT: find an Online Open article – if you can and read it).
    OK – done?
    What did you find?
    Well I found everything! Copyright journal, copyright authors. Copyright nobody. To be fair Blackwell manages society journals. Let’s end on one of happier ones I found:

    Temporal and mechanistic dissociation of ATP and adenosine release during ischaemia in the mammalian hippocampus1

    1Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

    and in the paper (PDF) itself:
    OnlineOpen: This article is available free online at www.blackwell-synergy.com
    Copyright The Authors
    Journal Compilation Copyright 2007 International Society for Neurochemistry,
    So, Other journals take note – it CAN be done! All it requires is a few words at the technical editing stage. That won’t be too painful, will it.

    Posted in open issues | 1 Comment

    Voyages into publisher copyright – Less than full Open Access and less than Free

    Continuing our exploration of Open Access – let’s stick with chemistry (after all I don’t know about anything else). Last year the American Chemical Society (ACS) announced:

    ACS Offers Open-Access Option To Authors

    Sophie Rovner

    In October [2006], American Chemical Society journal authors will have the option of paying to immediately provide free online access to their articles on the society’s website. Authors will also be able to post electronic copies of their sponsored articles on personal websites and institutional repositories. Fees for the program will range from $1,000 to $3,000 per paper, depending on whether the author is an ACS member or is affiliated with an institution that subscribes to ACS journals.
    The new ACS AuthorChoice option “underscores the society’s willingness to experiment with innovative models to broaden access to highly valued, peer-reviewed research” while upholding editorial standards, says Brian D. Crawford, senior vice president responsible for the journal publishing program of ACS, which also publishes C&EN. “The fee was established in light of the society’s actual costs incurred in the peer review and publication of an article.”

    My analysis here is not with whether this is a good or bad thing or whether the fee is reasonable (I have views but I’ll keep quiet today) but whether it is clear what is going on. From the official page:

    American Chemical Society Announces New ACS AuthorChoice Open Access Option

    FOR IMMEDIATE RELEASE: Released 8/14/06
    The American Chemical Society’s Publications Division is pleased to announce an important new publishing option in support of the Society’s journal authors who wish or need to sponsor open access to their published research articles. The ACS AuthorChoice option establishes a fee-based mechanism for individual authors or their research funding agencies to sponsor the open availability of their articles on the Web at the time of online publication. Under this new policy, to be implemented later this Fall, the ACS as copyright holder will enable unrestricted Web access to a contributing author’s publication from the Society’s website, in exchange for a fixed payment from the sponsoring author. ACS AuthorChoice will also enable such authors to post electronic copies of published articles on their own personal websites and institutional repositories for non-commercial scholarly purposes.
    The base fee for the ACS AuthorChoice option will be set at $3,000 during 2006-2007, with significant discounts applied for contributing authors who are members of the American Chemical Society and/or who are affiliated with an ACS subscribing institution. The fee structure will be as follows:
    […fees snipped…]
    The ACS AuthorChoice option will be extended to authors only after peer-review and editorial acceptance of their articles for publication, so as to ensure complete separation between scientific editorial decision-making and economic considerations. Upon an author’s payment to sponsor the ACS AuthorChoice option, the ACS will make the article freely available upon Web publication.

    It is IMMEDIATELY CLEAR WHAT IS GOING ON. The Society will make your article available on its web site and also allow you to post your own artcle on yours for a fee of USD 1000 to USD 3000. The ACS retains copyright and – presumably by defualt – all other rights. They offer “unrestricted access” to the author’s web site. So one cheer for clarity.
    So what does it look like:

    An Exciting New Option for Authors…

    ACS AuthorChoice facilitates unrestricted web access to your published ACS article—at the time of publication—for a one–time fixed payment, provided by you or your funding agency. Contributing authors who are ACS members and/or are affiliated with an ACS subscribing institution receive significant discounts. This policy also allows you to post copies of published articles on your personal website and institutional repositories for non–commercial scholarly purposes.
    As a part of the ACS Cycle of Excellence, we are committed to providing the highest level of support for our authors. ACS AuthorChoice is one of many unique benefits offered to authors who contribute to ACS journals along with the ACS Paragon Plus System, Citation manager Functionality, and ACS Articles on Request to name a few.
    More About the ACS AuthorChoice Option

    “Those of you who read my Editorials know that I have been urging the American Chemical Society to address the open access issue. The Board of Directors recently adopted a new policy called Author Choice, which enables authors to pay to have their articles completely open access from day one… I think it is such a good deal that I have taken advantage of it myself. An article that I published in the October, 2006 issue of Chemical Research in Toxicology is the first fully open access article published in ANY American Chemical Society journal.”

    Lawrence J. Marnett Editor–in–Chief,
    Chemical Research in Toxicology
    Mary Geddes Stahlman
    Professor of Cancer Research
    Vanderbilt University School of Medicine

    Another cheer for the large logo which is instantly obvious (and is contained in all graphical abstracts). Also the phrase “Free Access” is extremely clear and obviously different from “Open Access”. So, in terms of CLARITY the ACS has done well – far better than Springer.
    What about the papers themselves? Well again the ACS has done better than Springer – it gives a list of all the currently available Open articles ACS AuthorChoice Articles Currently Available which I visited. There are 27 in total from all journalsl (the ACS has 37 journals) and the scheme has only been going a year. So here’s the first research article:

    The Structure of Testis Angiotensin-Converting Enzyme in Complex with the C Domain-Specific Inhibitor RXPA380
    Hazel R. Corradi, Itai Chitapi, B. Trevor Sewell, Dimitris Georgiadis, Vincent Dive, Edward D. Sturrock, and K. Ravi Acharya
    Biochemistry; 2007; 46(18) pp 5473 – 5478; (Article) DOI:
    10.1021/bi700275e

    (I hope I am not breaking copyright by posting this beautiful picture – I’ll plead fair use.) So what’s it about? I visit the ABSTRACT:

    [Journal Home Page] [Search the Journals] [Table of Contents] [PDF version of this article] [Download to Citation Manager] [Purchase Article]
    Biochemistry, 46 (18), 5473 -5478, 2007. 10.1021/bi700275e S0006-2960(70)00275-1
    Web Release Date: April 18, 2007
    Copyright © 2007 American Chemical SocietyThe Structure of Testis Angiotensin-Converting Enzyme in Complex with the C Domain-Specific Inhibitor RXPA380
    Hazel R. Corradi, Itai Chitapi, B. Trevor Sewell, Dimitris Georgiadis, Vincent Dive, Edward D. Sturrock,* and K. Ravi Acharya*
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom, Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa, and CEA, iBiTecS, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Gif sur Yvette, F-91191, France
    Received February 8, 2007
    Revised Manuscript Received March 19, 2007
    Abstract:
    Angiotensin I-converting enzyme (ACE) […snip…] the design of truly domain-specific pharmacophores.


    [Full text in html]
    [Full text in pdf]

    NOTE : NO MENTION OF OPEN ANYTHING OR FREE ANYTHING. So minus one cheer.
    OK – I expected the abstract and the paper to be copyright, but I can still READ it… (clicks [Full text in html] … and gets:

    Authorization Required

    You have requested content from ACS Publications that requires authorization or purchase.
    <!–Shibboleth Users Click Here
    –>

    Subscribers Log In Here

    User ID:
    Password:
     

    Retrieve Purchased Articles

    Enter your Order Number:

    • The Structure of Testis Angiotensin-Converting Enzyme in Complex with the C Domain-Specific Inhibitor RXPA380
      Hazel R. Corradi, Itai Chitapi, B. Trevor Sewell, Dimitris Georgiadis, Vincent Dive, Edward D. Sturrock, and K. Ravi Acharya
      Biochemistry, 2007, 46, (18), pp 5473–5478.

    Important Notes

    1. You may already be a subscriber. Please check with your company or institution before purchasing an article.
    2. This server uses session-based cookies for controlling access to secure documents/services. No personal or confidential information is stored in the cookie, and the cookie is deleted when you quit your browser.
    3. The Web Editions of the ACS journals require a separate subscription from the print subscription for online access. Read more about how to subscribe to ACS publications.

    If you have questions or require assistance, please contact the ACS Publications Help Desk at (800) 227-9919 (toll-free in USA/Canada) or (202) 872-4357. The Help Desk operates from 7:30 a.m. until 6 p.m. (Eastern Time).

    var SA_ID=”acspix;acspix”; WHAT’S GOING ON? I thought this was a free article? Let’s return to the abstract. No, there is a purchase button. So although this is a “free paper” it is impossible to read it without paying.
    So we remove all cheers. The ACS has said the paper is free but it isn’t. (At least I can’t purchase the article because I am too stupid to understand their shpooing cart system. I can’t believe anyone actually pays for articles.)
    OH DEAR.
    What’s actually going on is that the paper is free but ONLY if you go through the TOC. Does that matter? YES!! because if you resolve a DOI you go straight to the abstract and there is NO INDICATION THAT THE PAPER IS FREE. It would be very easy for someone coming that way to think it was a pay-per-view article. How many of you would go to the TOC to check for Free Access (after all the chance of any ACS article being Free is statistically about 0.1%).
    What do I say? This is exactly the same problem that occurred with Springer – a free article for which the author was offered a purchase option. I’ll choose my words very carefully so as not to upset anyone out there.
    Is it just possible that the ACS has slipped by a fraction of a percentage point from being “committed to providing the highest level of support for our authors.”? I am sure it will find all readers who have mistakenly paid for a free article and send them 50 free accesses to itto send to their friends. And I am sure that its web staff will tackle the enormously challenging task of rerouting 54 URLs so that any visitors to the site will thank authors that they now have “unrestricted web access to your published ACS article”.
    Because they don’t at the moment.

    Posted in open issues | 2 Comments

    Voyages into publisher copyright – Full Open Access.

    Some readers may wonder why I am spending energy and words on Open Access to publishers’ sites when I can simply read the papers they have listed as OA. Surely that’s all that matters?
    Well, no. I’m a scientist and I want to developed data-driven science – the idea that there is a huge amount of data out there that is telling us about the natural world, the human world and our technology. Much of this data is semi- or un-structured but we are developing tools to overcome this. We believe that there is a huge amount of undiscovered science out there and that machines can help us liberate it. After all we have shown (with Indiana University) that our software can read 500,000 Pubmed abstracts in a day. Why can’t we do the same for full chemistry papers.
    Very simple. We can’t get access to them, and if we do we are in danger of being cut off or worse. (I don’t know what “worse” is, but we’ve been cut off and I don’t want to find out.). Many publishers make it EXTREMELY difficult to access the data in their publications. My current blogging is an attempt to find out whether this is deliberate and if not, to suggest ways forward.
    The major problem is legal access rights. As Peter Suber says, many people are not prepared to break copyright – I try to be one of them. If I see a copyright on a paper – unaccompanied by a license or other guide – then by default there is very little that I know I can do with it.  If I copy it onto my web site, use it for teaching, put pictures from it is a book the chances are I will have the lawyers after me. So copyright, by itself, is a MAJOR deterrent.
    Copyright is also complex. It varies from country to country and is rimged around with fuzzy concepts like fair use which – in essence – say: here are some rough ideas of what things you are allowed to do but we can’t tell your how often, how much and you could anyway be taken to court. If so you might be able to use “fair use” as a defence.
    Now some publishers want us to re-use their material. Here is a typical example from Biomed Central website :

    BioMed Central is an independent publishing house committed to providing immediate open access to peer-reviewed biomedical research
    All original research articles published by BioMed Central are made freely and permanently accessible online immediately upon publication. BioMed Central views open access to research as essential in order to ensure the rapid and efficient communication of research findings.

    and

    All research articles published by BioMed Central may be freely accessed, re-used and re-distributed
    Authors publishing with BioMed Central retain the copyright to their work, licensing it under the Creative Commons Attribution License. This license allows articles to be freely downloaded from the BioMed Central website, and also allows articles to be re-used and re-distributed without restriction, as long as the original work is correctly cited [more information].

    The important thing about this is that it is INSTANTLY CLEAR WHAT IS GOING ON.  That is what I am banging on about at the moment. It takes me 10 seconds to understand the BMC website. I have not yet – sorry – understood the Springer policy after half an hour or more.
    But suppose I find a paper from and I didn’t know it was published by BMC. I’d be afraid of violating copyright. Does the paper help? Yes!:

    © 2007 Spjuth et al; licensee BioMed Central Ltd.
    This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
    which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    What could be simpler than that? nothing… it is INSTANTLY CLEAR WHAT IS GOING ON.
    And I could have picked many other publishers such as PLoS, Beilstein Journal of Organic Chemistry and so on. They all use Creative Commons or similar licenses.
    So the practice for “full open access” is simple:

    • announce the policy on the journal masthead
    • announce the policy in the TOC by each Open Access article
    • put appropriate copyright notices (i.e. NOT the publisher, but the authors) in the paper and accompany them by a clear statement of the terms of re-use. This is most easily done by a simple inclusion of a well-known and understood license. The publisher might, if they wish, create their own license with the same intent but different words, but why bother?

    So my concern with Springer – and this is the last mention in this post – is that the only mention of Open Access is in the publishers’ web page and they retain copyright of the paper. Jan, why don’t you simply use CC as illustrated here. That would save a lot of angst and make friends.
    … now we’ll move onto not quite so open …

    Posted in open issues | 3 Comments