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


  1. Anonymous5:39 pm

    Most of these seem like good ideas. Some of them are to some extent already reflected in:,, and
    Using LIBRE or for review externally could also be a useful idea. In general, I think we should be moving towards an open review system where reviews can be stored and displayed across different platforms using open interfaces and standards.

  2. Anonymous4:25 pm

    Nice idea!
    I have had exactly the same idea some time ago! But, I am afraid that the name will not be confusing with the 'famous' elitist, journals, Science and Nature!
    I am ready to participate! But I think this would need some investment!

  3. Ready to participate? If only you signed with your name!

    1. Anonymous9:38 am

      And Villavelius is your name? ;)

    2. You haven't read the post, have you? I always sign with my real name. Villavelius is the latinized version of my last name.

  4. Jan,

    The JONAS ideas seem to have been realised since a year through a novel authoring, peer-review, publishing and dissemination workflow exemplified by the Biodiversity Data Journal ( (BDJ). BDJ is a successful proof of concept with growth of over 300 % in the last quarter of 2014. Now BDJ welcomes other science disciplines to follow. Happy to discuss.

    1. This seems a good initiative, and I hope it takes off. The key to the JONAS concept, however, is that the publisher stays out of arranging the peer review process altogether, and leaves that strictly to the science community, whereas the publisher concentrates on the technical aspects of publishing, so often done sorely inadequately.

  5. Really nice ideas! I like it.

  6. Anonymous10:00 am

    Dear Jan,
    These are very good ideas. Have you noticed the new platform that has launched recently and seems to support at least some of these principles well. I find particularly their approach to peer evaluation of articles very interesting.