Wednesday, October 08, 2014

Journals of Nature and Science

Joe Esposito's recent post on the Scholarly Kitchen prompted me to post the following proposal, which I have discussed with various people, but which has no takers yet. But who knows what the future holds...

I called the proposed system JONAS (for 'Journals Of Nature And Science' – working title, obviously). It is, I think, a new approach to open access publication of peer-reviewed scientific literature. If it isn't I've missed something (entirely possible).

JONAS is about establishing a publishing system that addresses:
  • Open access,
  • Fair and efficient peer review, 
  • Cost of publishing
  • Speed of publishing
  • Publication of negative/null results

Open Access — The JONAS publishing system focuses on the superb technical publication, in various formats/versions, of peer-reviewed articles for optimal machine and human readability and re-use.

Fair and efficient peer review — Anonymous peer review has problems around issues of transparency, fairness, thoroughness, speed, publisher-bias, specious requests for further experiments or data, and possibly more. JONAS is a system using signed, pre-publication peer review, arranged by the author(s) (many publishers ask authors who to invite to review their papers anyway), and merely verified by the publisher (peer review by endorsement). Reviews would be open, published with the article that’s endorsed, non-anonymous, under the rules that peer-endorsers must be active researchers, and not be, or for at least five years have been, at the same institution as, or a co-author of, any of the authors. Such a peer-review-by-endorsement system is likely to be at least as good as, and quite probably better than, the currently widespread ‘black box’ of anonymous peer review. As reviews/endorsements would be signed and non-anonymous, there is very little danger of sub-standard articles being published (not worse than is currently the case anyway), as endorsers/reviewers would not want to put their reputations at risk. The review process between authors and endorsers is likely to be iterative, resulting in improvements on the original manuscripts. “Author-arranged” may perhaps include peer review being arranged on behalf of the authors by services specifically set up for that purpose, as long as the reviewers are not anonymous and conform to the JONAS rules. The LIBRE service is one example (currently in prototype).

Cost of publishing — A system like this can be very cost-effective for authors. The technical costs of proper publishing are but a fraction of the cost usually quoted for organizing and arranging peer review. First indication is that an amount in the order of £100-150 per article can be sustainable, given sufficient uptake. Tiered charges should be considered depending on the state of the manuscript when submitted. If the manuscript needs very little work to bring it up to proper publishing standards, or if the author doesn’t want or need those services, the cost could be very low indeed.

Speed of publishing — Since the peer-review-by-endorsement process has already taken place before the article arrives at the publisher, publication can ensue within days, even hours, depending on the state of the manuscript.

Requirements for manuscripts: ORCIDs for authors and reviewers/endorsers; inclusion of (permanent links to) datasets used, underlying data for graphs, a section “details for replicability and reproducibility” with clear and unambiguous identification of materials used, including reagents, software and other non-standard tools and equipment.
Input: Properly endorsed articles to be accepted in the form of Word, Pages, (LA)TEX, XML, HTML, Markdown, and Excel or CSV for data, and high-resolution image files (where possible scalable vector graphics) attached to emails or via a simple upload site.

Output: Articles would be published as XML, HTML, PDF, ODF and ePub formats, as much as possible semantically enriched and aesthetically formatted, plus Excel/CSV for data (tables extractable and rendered in Excel from PDFs with the software to do that, Utopia Documents, freely supplied).

Commenting and post-publication review (signed comments and reviews only) would be encouraged for all articles, links to comments to be provided with each article. Comments may be made on different sites, and would be linked to, if that is the case. Anonymous comments would be ignored.

Access Licences: CC-BY or CC0 — DOIs for the articles, and where appropriate for individual elements within articles, would be assigned/arranged by JONAS.

The core of the JONAS system would effectively be to have OA journals with a low-cost structure, with superb and highly optimized technical quality of the published articles. The principal difference with other OA journals would be the pre-arranged open peer review ("peer-review-by-endorsement"), organised by the authors themselves, according to a set of rules that ensures a reasonable level of assurance against reviewer bias (because of its openness and non-anonymity, actually more assurance than is provided in the usual anonymous peer review as widely practiced). Since arranging peer review is one of the major costs of any publisher (mostly staff costs), leaving that part of the publishing process in the hands of researchers and the academic community can make a great difference to the cost of publication. So far, efforts to reduce the cost of publishing have been concentrated on technical issues. Changing the mechanism (emphatically not the principle) of peer review offers much greater scope for cost reduction.

What JONAS' job would be is to take such peer-endorsed articles and make them into professionally published and complete (including data and metadata) documents, adhering to all the technical, presentational and unique identifier standards, in a number of formats, linked and linkable to databases and other relevant information, human- and machine-readable and suitable for widespread usage, for text- and data-mining, for structured analysis (incl. semantic analysis) and further knowledge discovery, and, crucially, for long-term preservation in repositories and archives of any kind.

An added service could be that manuscripts submitted in advance of peer-endorsement having been procured, would be placed, ‘as is’, on JonasPrePubs, a ‘preprint’ server, at no cost. This could help to secure priority (as a kind of 'prophylactic' against high-jacking of ideas – which would never happen in science, of course, but better to be safe than sorry, right?).

The JONAS publishing system would also be superbly suited to scientific societies and other groupings that wish to have their own journal. Such a journal could be fully integrated in the JONAS system, provided the manuscripts are submitted fully peer-endorsed or peer-reviewed (whether or not arranged by the author(s) or the scientific society in question). The charges per manuscript for individual authors and for societies wishing to publish their journals in the JONAS system would be the same, I imagine.

The JONAS methodology could, of course, be implemented on various publishing platforms.

Jan Velterop

Monday, September 08, 2014

Does 'Open Access' include reuse?

At the end of 2001, a number of people (me included) came together in Budapest and set out to give the emerging notion that research results, particularly those obtained with public funds, should be available and usable by anybody, anywhere. There wasn’t an agreed term for that notion – ‘free online scholarship’ (FOS) and ‘free access’ were some of the terms relatively frequently used – and in Budapest we settled on the term ‘open access’. The meeting in Budapest resulted in the Budapest Open Access Initiative (BOAI) and in the declaration issued a few months later, we explained what we meant by ‘open access’ of the scholarly peer reviewed research 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.

While this definition has a flaw – there is no mention of immediacy in it – it clearly does include the right to reuse.

So why has there be a recantation of one of the original signatories of the BOAI definition (perhaps more than one, but that I don’t know, and I doubt it)? And why has the BOAI definition been watered down, even adulterated, by some other people. ‘Free access’, ‘gratis access’, ‘public access’, etc. all disregard reuse, a crucial element of the notion of ‘open access’ and of its BOAI definition (as well as of the Bethesda and Berlin Statements on OA – 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.”). The Creative Commons Attribution licence (CC-BY) best captures the intention of these definitions.

What are the motives of those who don’t like CC-BY and the reuse element of the BOAI/Bethesda/Berlin definitions and do what they can to water it all down to access without reuse?

Are these some?
  • Expediency – giving up difficult to reach ideals for potentially easier to reach, though sub-optimal, goals;
  • Appeasement – giving in to established powers and processes;
  • Putting career advancement above the advancement of science;
  • General contrarianism.
Quite possibly a combination of these, and more. Let’s have an open dialogue, including as John Wilbanks suggested, “about the ways publishers are exploiting green to undermine OA.

Comments welcome.

Jan Velterop

Thursday, September 04, 2014

Achieving True Open Access Ain’t Easy

In December of 2001, a number of people who wanted to increase the efficacy and usefulness of scholarly communication, particularly research results published in the peer-reviewed journal literature, came together in Budapest. Quickly, a consensus emerged as to what that would mean:
Peer-reviewed journal articles should be freely available 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.

We called it “Open Access”, and in February of 2002 the Budapest Open Access Initiative (BOAI) statement was published. It is fair to say that we (I was one of them) probably underestimated the difficulty of reaching the goal we set ourselves. It was – and still is – very difficult.

Shortly after, in December of 2002, the CC-BY (Creative Commons Attribution) licence was publicly released, which captured the letter and spirit of the BOAI notion of Open Access very well. For a while, Open Access and CC-BY were, to all intents and purposes, synonymous.

Apart from stating a goal, we also came up with two strategies to achieve it (later called ‘green’ and ‘gold’, respectively):
  • Self-archiving, by the author(s), in open electronic archives or repositories, manuscript versions of articles (to be) published in traditional subscription journals – later called the ‘green’ road;
  • Publishing ‘born-open-access’ articles in journals set up to provide open access to the formally published version at the point of publication – later called the ‘gold’ road.

The strategies were straightforward, it seemed. That proved to be an illusion. Strategy one, self-archiving (‘green’), was based on the idea that authors’ manuscripts, even after they had been peer-reviewed and accepted by subscription journals, were covered by the authors’ copyright and therefore they could do with them what they wanted, including posting the manuscripts in open repositories. Of course, that was correct, up until the moment that authors were transferring the copyright to any of their articles to the publishers. Yet, many publishers (reluctantly) allowed this practice, as they had allowed it for a long time already in areas such as physics, where a long-standing habit of preprint publication existed ( that didn’t appear to harm their subscriptions, and the conviction that the open repository landscape would be chaotic, deposit as well as access cumbersome, and repositories would contain all manner of content with all manner of access restrictions mixed in with open access material, providing an incentive for institutional and corporate users of the journals to stick with their subscriptions. That situation has changed very little. Although it has gradually become easier to find a freely accessible version of many an article, subscription levels have, on the whole, held up. And freely accessible ‘green’ articles are often not covered by a CC-BY licence and thus not freely reusable in the way the BOAI intended. When copyright has been transferred to the publisher, the author cannot subsequently attach a CC-BY licence to the version deposited in an open repository. Were that possible, and habitually done, ‘green’ might be true Open Access. As it is, ‘green’ articles are free to read (gratis access), but rarely free to reuse.

But also strategy two didn’t turn out to be straightforward. The thought was that the only difficulty to overcome was the necessary cost. Some journals are being kept afloat by subsidies, and many funding agencies allow ‘article processing charges’ (APCs) to be paid out of grants, within reason. So seemingly the cost hurdle could largely be taken, except for unfunded, impecunious authors, to whom many journals offer APC waivers. Open Access, i.e. articles published with a CC-BY licence, would result. That straightforwardness proved an illusion, too. The term Open Access is not an officially standardized one, and various publishers have started to call articles Open Access even though restrictions apply that go beyond CC-BY, such as non-commercial clauses (NC). Yet they nonetheless require author-side payment of APCs. Some even require ‘basic’ APCs for restricted access, and APC top-ups for true Open Access CC-BY licences. NC clauses potentially give the publisher the opportunity to exclusively exploit the article further (e.g. reprints) and realize more income than just the APC. I say ‘potentially’, because the sale of reprints is a commercial activity, forbidden by NC, unless copyright has been transferred to the publisher (in which case commercial exploitation is the publisher’s right) or there is an exclusive licence in place whereby the author-copyright-holder gives the publisher the right to do so. An NC clause means, in countries like Germany for instance, that the article in question cannot be used for educational purposes unless explicit permission is obtained, which makes the hurdle, in those circumstances, practically identical to the “all rights reserved” of plain copyright. The upshot is that ‘gold’ is also not always Open Access in the way the BOAI intended.

Since Open Access has become an ambiguous term, you cannot trust the label to mean what you think it does, and certainly not that it allows you to reuse the article. Only CC-BY does that (and CC-zero, which does away with attribution as well – suitable and appropriate for data).

Where do we go from here?

FFAR, I would hope. For data, the concept of FAIR is being proposed (Findable, Accessible, Interoperable, and Reusable). For journal literature, ‘interoperable’ may not be a useful notion, so I’d like to modify the idea to Findable, Freely Accessible and Reusable.

How? Well, ‘gold’ publication with CC-BY is a good way to achieve it, but there remains the hurdle of APCs. The International Council for Science, ICSU, has recently issued a report, in which they advocate the following goals for Open Access:
  • free of financial barriers for any researcher to contribute to;
  • free of financial barriers for any user to access immediately on publication; 
  • made available without restriction on reuse for any purpose, subject to proper attribution;
  • quality-assured and published in a timely manner; and
  • archived and made available in perpetuity.

1 and 2 mean that the cost of 4 and 5 need to be carried by other parties than the user or author. For authors funded by agencies who support Open Access and are willing to bear the APC costs, there is no barrier, but of course, not every author is.

There is no easy way out of this. But it’s not impossible, in principle. However, ingrained deep conservatism of the scholarly community, and particularly scholarly officialdom, is in the way. (You’d think that ‘pushing the envelope’ is endemic to science, but in reality it is applied to knowledge, not to communicating that knowledge). Imagine the following scenario:
  • The authors arrange for peers they trust to review their articles, and openly endorse their article as worthy of publication;
  • Authors publish their article, properly formatted (I’m sure services would spring up for those who’d rather not do that themselves) and accompanied by the open endorsements on one of the many free (blog) platforms available, under a CC-BY licence.

Of course, permanency and archiving in perpetuity is not guaranteed, but that used to be the responsibility of libraries in the print era, and they might wish to take that responsibility again for electronic literature. Central repositories like arXiv, bioRχiv, PubMedCentral, etc. could do that, too.

I’m sure someone could come up with modifications to this scenario that would make it more practicable, technically robust, and such. But the main hurdle to take is academic officialdom, in particular the Impact Factor counters, who would have to accept this kind of publication for career and funding purposes.

Achieving true Open Access ain’t easy. So much is clear.

Jan Velterop

Friday, March 21, 2014

Proposed open access symbol

I have proposed a new Unicode symbol to denote true open access, for instance applied to scholarly literature, in a similar way in which © and ® denote copyright and registered trademarks respectively. The proposed symbol is an encircled lower case letter a, in particular in a font where the a has a 'tail', as in a font like Arial and Times, for instance, (a), and not as in a font like Century Gothic (without the 'tail' as it were).

My proposal should be on the Unicode discussion list (, and I am soliciting support, and input from technically-minded as well as legally-minded open access supporters.

This is the symbol I have in mind:

Jan Velterop