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To try and publicize the variety of Gold Open Access article publication options on offer, I’ve decided to create a visualization of the journal data that has previously been collected as part of my survey of ‘Open Access’ publisher licenses’ spreadsheet.

Here is version 0.1 of the ‘Mounce plot’ (much more data still to be added! It’s a work in progress) I may well refine and perhaps add a third axis or variable to the plot in future versions:

UPDATE: version 0.2 of the plot is now available here

 


 

Not all “open access” options provided by publishers actually provide BOAI-compliant Open Access, and this is very important - thus I have used the y-axis in this plot to reflect the level of openness supplied for the fees paid (x-axis). Therefore, the ‘best’ journals providing CC BY BOAI-compliant Open Access for the lowest fees possible appear in the top left of the plot. The ‘worst’ journals providing a far inferior level of openness for a high price appear in the bottom right of the plot. The lowest level of ‘free’ access is provided by journals and societies who provide free access to papers, but seem not to provide them with recognised standard licences such as those from the Creative Commons suite. Ambiguity is arguably the worst and laziest thing a publisher can offer from a re-user / reader POV and thus I score this as the lowest class.

 

Kudos then to Cellular Therapy and Transplantation , Multidisciplinary Digital Publishing Institute , Copernicus PublicationsJournal of Advances in Modeling Earth Systems (an American Geosciences Union journal, ’tis a shame they charge $3500 for other AGU journals!), Standards in Genomics Sciences and others for providing low cost BOAI-compliant immediate Gold Open Access publishing options. [...and what a mouthful that last statement was. It is such a pity that the meaning of 'open access' has been degraded and loosely applied since it was originally (well)defined, that I have to apply so many additional adjectives to describe exactly what I mean.]

I’d be amazed if The Lancet & Cell Press journals (e.g. Cell) published by Elsevier could still get away with the absurdly high APC’s they ask for in 5 years time. I hope all researchers are sensible enough to realise that they can publish their manuscripts in other Open Access venues and have just the same research impact (and avoid these hugely expensive options).

I may well make further posts in future with updated, corrected and further explored and deliberated plots. There’s a lot still to talk about!

 

UPDATES:   I sometimes encounter academics who have never heard of fee waiver schemes before. If you look at this plot as an unfunded academic with no or little institutional funding, you might panic. DON’T : a lot of good Open Access publishers offer ‘fee waiver’ schemes to such academics that really cannot pay the APCs. Examples are PLoS and BMC . You can’t always get your fee waived but it is certainly worth asking if you think your circumstances deserve it.

PMR has noted that I have included some ‘predatory’ Open Access publishers in this plot e.g. the OMICS publishing group. I will just state that by placing publishers on this plot I am not especially endorsing any of them unless otherwise stated. There are of course other important criteria aside from ‘price’ and ‘openness’ in choosing where to submit a manuscript. Choose your venue wisely!

 

Further Reading:

[1] Page, R. 2010 http://iphylo.blogspot.com/2010/12/plant-list-nice-data-shame-it-not-open.html

[2] Murray-Rust, P. 2010 http://blogs.ch.cam.ac.uk/pmr/2010/12/17/why-i-and-you-should-avoid-nc-licences/

[3] Hagedorn, G., Mietchen, D., Morris, R., Agosti, D., Penev, L., Berendsohn, W., & Hobern, D. (2011). Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information ZooKeys, 150 DOI: 10.3897/zookeys.150.2189

[4] Carroll, M. W., Nov. 2011. Why full open access matters. PLoS Biol 9 (11), e1001210+. http://dx.doi.org/10.1371/journal.pbio.1001210

Technical notes:

  • Some journals charge a fee per page thus I have assumed 10 pages per article for my plot
  • Where fees are not listed in USD I have converted them into USD using the current exchange rates.
  • Where the journal permits authors to choose a licence I have assumed authors will choose the better, less restrictive licence option (although sadly, in reality some authors do opt for a more restrictive licence for their work).
  • Some journals offer discounted ‘OA fees’ if they are at a ‘member institution’ or some such. This usually involves additional cost to the member/subscribing institution thus I have used the full ‘non-member’ rate in such instances for a fairer comparison.
  • I only included a couple of BMC journals, just to show the range of prices offered (small: BMC Research Notes, and larger: BMC Biology). They split their prices quite finely between journals so I chose not to overcrowd the CC BY layer with too many BMC journals.
  • When I get time I’ll update WileyOpenAccess to the CC BY top class (they recently changed policy). Sadly, the Wiley OnlineOpen (hybrid) option, which is available to 100 times as many journals,  is still NC-restricted and less open.
  • Don’t see your publisher or Open Access option on the plot? Make your own plot then – the data is all there on the spreadsheet. I don’t doubt that many could make a better job of visualising it than I have done here…

Comments, extra data and/or corrections are welcome as always.  This data was hand-collected, so there may be errors.

Considering I emailed him on a Friday, Darin Croft has done well to reply to my questions about the SVP abstract embargo so soon, on Monday. I don’t always get such swift replies, so that is much appreciated. [Thanks Darin!]

Below is his email in full, as promised (the bits in quotes are my original questions) publicly supplied so the confusion can be cleared-up for all:

> 1.) What would happen if a researcher (and SVP member) deliberately broke
> the embargo and blogged/tweeted/published research that was the basis of
> their own submitted talk abstract (I’m surprised this hasn’t happened
> already tbh, given how early the abstract deadline is – some e-journals have
> very quick turnaround times…)

Our embargo is meant to protect the researchers themselves so that
they have greater control over when and how their research is made
accessible to members of the media. Therefore, our embargo policy does
not apply to a researcher publicizing their own work. This has, in
fact, happened many times already, typically in the scenario you note
(i.e., a researcher’s work is published after the abstract deadline
but before the annual meeting). Based on your question, perhaps this
is something we should clarify to avoid confusion.

> 2.) What would happen if a researcher (and SVP member) broke the embargo and
> blogged or tweeted some or all the of the content of another researcher’s
> talk abstract

This would most likely be referred to the SVP’s Ethics Committee,
which is the standard procedure in the case of possible violations of
the SVP’s Bylaws or policies by a member.

> 3.) If a blogger or journalist *did* write an article or two on the basis of
> the meeting abstract booklet – do you seriously think that could harm the
> chances of VP’ers getting published in one of the glamour mags?

I believe this has actually occurred in the past, though before my
tenure as Chair of the Media Liaison Committee. Regardless, I cannot
speak for what the editors of high profile journals might or might not
do in such an instance. I would suggest you contact them directly. Our
current policy is that the potential risk for researchers does not
outweigh any potential benefit.

I hope that information is useful. Thank you for letting me know
beforehand that you plan to publish these responses.

Cheers,

Darin

————————————————–
[End of email]

So, from that it seems we can at least talk about our own abstracts. I still disagree that the potential ‘risk’ of freely accessible abstracts outweighs the benefits, but I’ll leave it there for now – I’m just happy to let you all know what my talk is about without fear of losing the talk slot!

I thoroughly agree with Darin that they should change the wording of the policy next year to make this clearer, because frankly what is written in the embargo policy currently (as emailed to all conference registrants) clearly contradicts what Darin says here, and I’m not the only one to have been confused and slightly annoyed by this.

I’d also be intrigued to know more about the SVP’s Ethics Committee procedures, Bylaws and rules. Perhaps there is a URL for these somewhere? But I will not pursue that any further now.

That just leaves me to say that my talk for this year’s SVP will be:

EXAMINING CHARACTER CONGRUENCE AND COMPATIBILITY OF VERTEBRATE CLADISTIC DATA – EMPIRICAL APPROACHES APPLIED COMPARATIVELY ACROSS CLADES

by Ross Mounce & Matthew A Wills, University of Bath

Previous phylogenetic work using conventional character partition homogeneity tests has
often revealed significant incongruence between cranial and postcranial character data. We
extend this approach by applying pairwise character compatibility tests across a sample of
more than 60 pseudo-independent vertebrate data sets. We contrast ‘fuzzy’ compatibility,
boildown bootstrap and clique approaches. In particular, we find that the Le Quesne
probability (LQP) has several desirable properties. The LQP is simply the probability that a
randomly permuted character will have incompatibility with other characters in the matrix
as low or lower than that of the original character. Within recent analyses of Sauropod taxa
we find that characters related to neural arches often conflict with dental characters in some
datasets but it is difficult to generalise; we are still exploring possible causative mechanisms
for this. In contrast, other vertebrate groups such as ratites appear to have relatively
little character conflict between morphological characters. Pairwise tests of character
compatibility work well with binary data and ordered multistate characters, but can only give
an indication of ‘potential compatibility’ with unordered multistate characters. Composite
‘higher’ taxa and polymorphic codes are also problematic for existing compatibility
software, typically creating artificial incompatibilities. We recommend that composite taxa
are decomposed into their constituents in order to remove ambiguity for the purpose of these
tests, or else that polymorphic states are treated as missing data.

It’s part review, part defence of an oft ignored method, and part meta-analysis of lots of datasets using congruence methods to look at character compatibility. It forms part of my thesis work on comparing different statistical methods to compare and contrast the utility & congruence of morphological characters in phylogenetic analyses.

Great to be able to talk about my research without worry :)

I just sent this email to Darin Croft (of SVP). I chose to contact him because he recently answered questions about the embargo for EmbargoWatch and it was rather unclear who else I should approach. I did not want to blanket email the whole council.

This is the (entire) email I sent him, from my gmail account:
(I will post his reply as and when I receive it)

Dear Darin,

It’s been noted many times before, by many different researchers – but the SVP meeting abstract embargo just doesn’t make sense to me. I know of no other conference that operates like this, and indeed for most other conferences the abstract booklet (and it’s open, free availability online) is a big promotional aid in getting people interested in the event in the lead-up to it.

I saw you answered some questions on EmbargoWatch recently, so I thought you might be the correct person to contact for my queries on the same subject:

I have blogged my own displeasure with the embargo policy here:
http://rossmounce.co.uk/2012/08/23/the-ridiculous-svp-embargo-is-back-again/

I would like to ask:

1.) What would happen if a researcher (and SVP member) deliberately broke the embargo and blogged/tweeted/published research that was the basis of their own submitted talk abstract (I’m surprised this hasn’t happened already tbh, given how early the abstract deadline is – some e-journals have very quick turnaround times…)

2.) What would happen if a researcher (and SVP member) broke the embargo and blogged or tweeted some or all the of the content of another researcher’s talk abstract

3.) If a blogger or journalist *did* write an article or two on the basis of the meeting abstract booklet – do you seriously think that could harm the chances of VP’ers getting published in one of the glamour mags?

I look forward to hearing from you, and will publish your response in full context with this email on my blog

Best,

Ross



-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-
Ross Mounce
PhD Student & Panton Fellow
Fossils, Phylogeny and Macroevolution Research Group
University of Bath, 4 South Building, Lab 1.07

http://about.me/rossmounce

-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-

Sometimes you just have to laugh…

The year is 2012, we have the internet, we have blogs, and a huge variety of other tools to enable free, efficient and rapid communication of information and yet the Society of Vertebrate Paleontology annual meeting rules still insist that all information within this year’s abstract booklet remain a big secret until the day of the event.

Many others have justly written to complain about this before.

Here’s the 2012 version I just received in my inbox today:

SVP Embargo Policy Regarding Content in the Program and Abstract Book

Unless specified otherwise, coverage of abstracts presented orally at the Annual Meeting is strictly prohibited until the start time of the presentation, and coverage of poster presentations is prohibited until the relevant poster session opens for viewing. As defined here, “œcoverage” includes all types of electronic and print media; this includes blogging, tweeting and other intent to communicate or disseminate results or discussion presented at the SVP Annual Meeting. Content that may be pre-published online in advance of print publication is also subject to the SVP embargo policy.

So I think I can tell you I’m giving a talk there in the ‘Phylogenetic and Comparative Paleobiology — New Approaches to the Study of Vertebrate Macroevolution’ symposium.

But can I tell you what the title of my talk is, or the abstract I submitted (a rather long time ago, which is another bugbear I have with this particular conference)? Well, given the quote above, probably not!

And therein is part of the ridiculousness of the embargo. By submitting a (subsequently accepted) talk & abstract to this conference – I’m banned from communicating about my own research on that subject until I give the talk. Not even a tweet about it.

It also seems to me that they’re preventing their own members from effectively promoting the event with this policy. Wouldn’t it be great if all speakers could blog and tweet: “Hey, I’m giving a talk on new dinosaur XXXX and it’s unusual anatomy (further details of which are in my abstract here) at a meeting in Raleigh, NC. Come along, tickets still available here” Isn’t that 100 times better than “Hey, I’m giving a talk at this conference – I can’t tell you what the title is or the subject, sorry” ?

This policy strikes me as a massive and unjustified own goal. I appreciate some of the science glamour mags don’t take kindly to press reportage of science before it is published in their glossy pages BUT I think we’ve got to remember that science talks & posters are NOT papers, and they should not and are not treated as such. The abstracts for SVP are only minimally peer-reviewed before acceptance and the talk content itself is completely unreviewed. Therefore if a journalist/blogger/tweeter did report on the abstract booklet (and btw, it would take tremendous journalistic spin to make good, interesting copy from most talk abstracts I’ve ever seen – they’re rather short!) they’d be reporting non-peer reviewed discussion, that may or may not be related to unspecified future peer-reviewed publications. So I don’t buy [what I presume is the justification for all this?] the argument that reportage of talk abstracts jeopardises the publication of peer-reviewed papers. The two may be related, but are also very distinct from each other.

I think it’s only a matter of time until this policy changes. SVP have being doing reasonably well with respect to openness recently. They’ve reduced their hybrid Open Access fees, and instituted new editorial policy encouraging data archiving so that data published in their journal is more transparent & re-usable (=better science). But it seems there are still improvements to be made. Will there be an abstract embargo in 2013 I wonder? I for one hope not.

Open Access discussed on the radio

August 20th, 2012 | Posted by rmounce in Open Access - (0 Comments)

[I'm cross posting this from the OKFN version so I can embed the audio of the show in the post]

Last Friday (17/08/12), representing the Open Knowledge Foundation, I had the pleasure of discussing the new Research Councils UK (RCUK) plan for all UK publicly-funded research to be published Open Access, on a special half hour Voice of Russia UK broadcast radio discussion.

I have written about this policy before and am very supportive of it, just as I am with Open Access in academia in general. I personally believe it will aid transparency and equality in research – so that no researcher has an unfair advantage over another through greater/easier access to vital research literature (just one of many worthy benefits arising from Open Access). But there are certainly also vocal opponents to this plan – mostly those with vested interests in keeping the obscene profits of the traditional subscription access publishing system alive (which commonly generate >30% profit margins largely derived from the taxpayer-spending of the world’s research libraries on journal subscriptions). Whilst others express vague and often unspecified “concerns” about Open Access and further still many academics are notably apathetic towards it, or are even proudly agnostic on the issue.

Thus a publicly-broadcast discussion of this new open policy is well warranted.

No secret science
Voice of Russia UK radio Open Access discussion hosted by Daniel Cinna
I won’t say anything about the discussion itself, only that you should listen to it (embedded above; alt link here) if you are at all interested in the future of science, and the benefits of the new RCUK Open Access policy.

The members of the discussion panel included Rita Gardner, the Director of the Royal Geographical Society, noted for her concerns about the potential effects of Open Access on UK Learned Society income and revenue [paywalled link]; Ross Mounce, Panton Fellow promoting open data in science (myself) from the Open Knowledge Foundation; Bjorn Brembs, Professor at the Department of Genetics at the University of Leipzig, noted critic of for-profit publishers and their lack of ‘value-add’ amongst other issues; and Timothy Gowers, the Rouse Ball Professor of Mathematics at Cambridge University, instigator of the popular academic-led boycott of the academic for-profit publisher Elsevier.

The ensuing discussion was ably guided by VoiceofRussia radio presenter Daniel Cinna, and recorded by a backroom team with an impressively professional studio setup (Timothy & Bjorn were joining the debate via phone from abroad almost seemlessly, whilst Rita and I were in the London studio). As noted by Rita off-air, it would have been nice to have had a publisher representative in the discussion to add their unique viewpoint but apparently the VoR production team had asked, but no for-profit publisher they had asked was willing to take part. So one cannot attribute any blame to the VoR team if the discussion panel lacked representational balance.

About Voice of Russia (adapted from their own website):

The Voice of Russia is the world’s oldest international broadcaster and is among the world’s top five radio broadcasters today which include the BBC, the Voice of America, Deutsche Welle and Radio France International. The London-based team produces programs for VoR that bring our listeners a Russian perspective on our two countries and the world. VoR broadcasts to 160 countries in 38 languages using short and medium waves, FM, satellite and the global communications network. In London we are now also available online and via DAB radio. We aim to welcome a new British audience to our 109 million listeners worldwide.

It’s the Olympics now so this work update is a) late and b) short

Nevermind…

As ever progress has been exciting – look what we can extract from some PDFs:

(click to enlarge each) Attribution: The left panel is from Cánovas et al. BMC Evolutionary Biology 2011 11:371 doi:10.1186/1471-2148-11-371

On the left is the original figure, and on the right we have an SVG representation of the data we can extract automatically from this figure. We have the topology, the taxon labels AND the support values 100% correctly interpreted! Obviously we can’t reclaim phylogenetic data with this much precision and recall from all papers. But it’s a promising example, automatically generated – no manual guidance or tweaking needed – just feed it the PDF. [My WordPress server won't let me upload the original SVG copy of this for "security reasons" so the image on the right is a .jpg copy of the original .svg]

 

I should also note this was achieved completely independently of previous image-based tree-extraction softwares like TreeSnatcher Plus, TreeRipper & TreeThief. This is a great example of why it’s very important for editors and publishers to strictly stipulate that diagrams in figures containing data such as this be uploaded and produced in the final PDF version as lossless vector graphics rather than lossy bitmaps such as .png .jpg or .bmp – only vectors keep the fidelity of the underlying data. We note that there are many publishers out there who regularly seem to produce figures in their PDFs that are NOT on the whole very good quality wrt this. Difficult to know whether the authors or the publishers are to blame in each case but either way standards need to be improved.

 

By mining PDFs we can re-extract and re-release far more than just phylogenetic data from the literature – we’re fairly sure we can reliably identify the rough type of figure depicted in PDFs by machine methods using certain diagnostic features such as number & proportion of horizontal and vertical lines.

 

 

Peter Murray-Rust & I now are looking for a collaborator to help us implement machine learning methods to classify scientific figures into discrete categories e.g. bar charts, scatter plots, network diagrams (including phylogenies), pie charts, box & whisker plots etc… in an automated way.

If you’re interested please contact myself or Peter.

That’s all for now.

PS If you’re watching the London 2012 Olympics Volleyball tomorrow morning you may well just see me in the crowd. Managed to snaffle some returned tickets by setting up an alert for new tickets using a combination of www.page2rss.com (to alert me to page changes on the ticket website) and http://ifttt.com/ to email me as soon as the RSS feed gets a new item (updated ticket information). Without this nifty trick I very much doubt I’d have got any tickets.