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Just a quick update to let you know how the new Research Ideas and Outcomes (RIO) journal is going. You may remember I wrote a blog post here explaining my enthusiasm for this new journal. I’m delighted to say it is exceeding my expectations.

After announcing the launch with coverage in Science (AAAS) News, Nature News, and Times Higher Education amongst others, RIO has now published many interesting and highly novel outputs.

My choice of the word ‘outputs’ rather than ‘articles’ is very deliberate. RIO is a sophisticated platform that publishes more than just articles. Central to the ethos of the journal is that academia should publish entire research cycles, not just traditional research articles. So in our first 24 published outputs there is impressive diversity on show. Below is a breakdown of these published outputs by type:

One Editorial

  • Mietchen D, Mounce R, Penev L (2015) Publishing the research process. Research Ideas and Outcomes 1: e7547. doi: 10.3897/rio.1.e7547

Ten Grant Proposals

  • Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal. Research Ideas and Outcomes 2: e8424.doi: 10.3897/rio.2.e8424
  • Susi T (2015) Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG). Research Ideas and Outcomes 1: e7479. doi: 10.3897/rio.1.e7479
  • Simms S, Jones S, Ashley K, Ribeiro M, Chodacki J, Abrams S, Strong M (2016) Roadmap: A Research Data Management Advisory Platform. Research Ideas and Outcomes 2: e8649. doi: 10.3897/rio.2.e8649
  • Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, Rafes K, Germain C, Dunning A, Pintscher L, Kinzler D (2015) Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes 1: e7573. doi: 10.3897/rio.1.e7573
  • Wagner S (2015) Continuous and Focused Developer Feedback on Software Quality (CoFoDeF) . Research Ideas and Outcomes 1: e7576.doi: 10.3897/rio.1.e7576
  • Hartgerink C, George S (2015) Problematic trial detection in ClinicalTrials.gov. Research Ideas and Outcomes 1: e7462. doi: 10.3897/rio.1.e7462
  • Hammond C (2016) Widening the circle of care: An arts-based, participatory dialogue with stakeholders on cancer care for First Nations, Inuit,and Métis peoples in Ontario, Canada. Research Ideas and Outcomes 2: e8615. doi: 10.3897/rio.2.e8615
  • Tóth J (2016) Tools of Persuasion in Visual Advertisements at Maltese Sites of Cultural Tourism: A Social Science Analysis. Research Ideas and Outcomes 2: e8726. doi: 10.3897/rio.2.e8726
  • Wojnarski M, Hanken Kurtz D (2016) Paperity Central: An Open Catalog of All Scholarly Literature. Research Ideas and Outcomes 2: e8462.doi: 10.3897/rio.2.e8462
  • Koureas D, Hardisty A, Vos R, Agosti D, Arvanitidis C, Bogatencov P, Buttigieg P, de Jong Y, Horvath F, Gkoutos G, Groom Q, Kliment T, Kõljalg U, Manakos I, Marcer A, Marhold K, Morse D, Mergen P, Penev L, Pettersson L, Svenning J, van de Putte A, Smith V (2016) Unifying European Biodiversity Informatics (BioUnify). Research Ideas and Outcomes 2: e7787.doi: 10.3897/rio.2.e7787

One PhD Project Plan

  • Senderov V, Penev L (2016) The Open Biodiversity Knowledge Management System in Scholarly Publishing. Research Ideas and Outcomes 2: e7757.doi: 10.3897/rio.2.e7757

Two Data Management Plans

  • Fisher J, Nading A (2016) A Political Ecology of Value: A Cohort-Based Ethnography of the Environmental Turn in Nicaraguan Urban Social Policy. Research Ideas and Outcomes 2: e8720. doi: 10.3897/rio.2.e8720
  • Pannell J (2016) Data Management Plan for PhD Thesis “Climatic Limitation of Alien Weeds in New Zealand: Enhancing Species Distribution Models with Field Data”. Research Ideas and Outcomes 2: e8664. doi: 10.3897/rio.2.e8664

Four Research Ideas

  • Gordon R (2016) Partial synchronization of the colonial diatom Bacillaria “paradoxa”. Research Ideas and Outcomes 2: e7869. doi: 10.3897/rio.2.e7869
  • Vyshedskiy A, Dunn R (2015) Mental synthesis involves the synchronization of independent neuronal ensembles. Research Ideas and Outcomes 1: e7642.doi: 10.3897/rio.1.e7642
  • Zou Y (2015) Determining the direction of a gamma-ray burst’s jet in its host galaxy. Research Ideas and Outcomes 1: e7506. doi: 10.3897/rio.1.e7506
  • Page R (2016) Towards a biodiversity knowledge graph. Research Ideas and Outcomes 2: e8767. doi: 10.3897/rio.2.e8767

One Methods article

  • Abdullah N (2016) Vertical-Horizontal Regulated Soilless Farming via Advanced Hydroponics for Domestic Food Production in Doha, Qatar. Research Ideas and Outcomes 2: e8134. doi: 10.3897/rio.2.e8134

One Research article

  • Chen R, Shen T, Tsai K, Hu C (2016) Pericardial window operation for malignant pericardial effusion may have worse outcomes for lung cancer than the other cancers. Research Ideas and Outcomes 2: e8758.doi: 10.3897/rio.2.e8758

Three Workshop Reports

  • Wetzel F, Hoffmann A, Häuser C, Vohland K (2016) 1st EU BON Stakeholder Roundtable (Brussels, Belgium): Biodiversity and Requirements for Policy. Research Ideas and Outcomes 2: e8600. doi: 10.3897/rio.2.e8600
  • Vohland K, Häuser C, Regan E, Hoffmann A, Wetzel F (2016) 2nd EU BON Stakeholder Roundtable (Berlin, Germany): How can a European biodiversity network support citizen science? Research Ideas and Outcomes 2: e8616.doi: 10.3897/rio.2.e8616
  • Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. doi: 10.3897/rio.2.e8622

One Project Report

  • Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L (2016) Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes 2: e8458. doi: 10.3897/rio.2.e8458

Sustainable Development Goals

Sustainable Development Goals (SDGs)

Another feature of RIO is that all articles are labelled with their relevant Sustainable Development Goals. Interestingly, RIO has attracted 13 outputs which relate to SDG number 9: ‘Industry, Innovation and Infrastructure’. I take this as a great compliment to the journal – I infer from this that authors interested in true innovation and scholarly infrastructure are clearly attracted to this journal.

Openly Published Data Management Plans (DMPs)

I pushed hard to make sure Data Management Plans were included as their own distinct output type in RIO, so I’m really glad to see two exemplar DMPs being published, as well as the Roadmap research proposal which also relates to DMPs. A lot of US and UK researchers see funder-imposed DMPs as a bureaucratic checkbox exercise of little value to them. I hope that by being able to publish a DMP, researchers will see the point-of-it a little more – the documents will suddenly have value and meaning beyond the grant proposal process because other people can and will read them.

We have more DMPs in the pipeline too, so keep watching!

If you want to keep up to date with everything that gets published at RIO; follow the RSS feed, the journal Twitter feed, or the Facebook group. You can also read more blog posts about RIO at the official RIO Journal blog.

 

TL;DR summary: ESA data papers should be free to read but Wiley (ESA’s new publishing ‘partner’) just charged me $45.60 yesterday to access one of them. They have done this kind of ‘accidental’ profit-generation before, as have other big publishers.

John Wiley & Sons (whom I will refer to as ‘Wiley’ from now on) is not a very competent company when it comes to providing free or open access to research. Don’t take my word for that. Ask the Wellcome Trust: over 50% of articles that they had paid to be open access with Wiley were not compliant with their open access policy. I have also had my problems with Wiley: I caught them selling access to thousands of articles that should have been free to access this time last year. They also paywalled an article I wrote which should have been free to access.

Despite all this, and the detailed letter I sent to the Ecological Society of America (ESA) back in 2013 during their open access consultation process, the ESA decided to switch to publishing with Wiley: a profit-driven company who’s goals conflict with the goals of the society. I was very disappointed with this decision.

 

Now that the switch is complete there are some problems readily apparent. Wiley are selling some bits of ESA journal content for $45.60 (inc. tax) a time that ESA did not previously charge readers to access. I discovered this yesterday on Twitter thanks to Jaime Ashander & Stephanie Peacock. So I made a test purchase to see if Wiley really were charging for access to this free content (they were!). Below are tweets documenting this:

 

Amusingly, the first time I tried to buy access to the article, my bank blocked the transaction thinking it was a suspicious payment to a scammy company! Only after I confirmed with my bank was I actually allowed to purchase access to the data paper – it really IS hard to access research that is paywalled, even when you have the money to pay for it!

ESA have acknowledged the problem on Twitter and will see if I can get a refund on Monday:

Discussion

There is more than meets the eye to this case.

Data papers are still a fairly new concept to most. Thus I honestly didn’t know what I’d be getting from behind the paywall when I paid for access – I did expect more than just the abstract. It would not surprise me if others could also make this mistaken assumption (we are wearily used to abstracts hiding much longer papers behind paywalls).

Charging the authors of ESA data papers $250 with the excuse that this is for “long-term hosting and maintenance” is absurd and unjustifiable. At the very most it should be $120 which is what Dryad charges, with a reminder that Figshare and Zenodo continue to sustainably archive data for free. Charging each and every reader outside the paywall in addition to this $45 to read the abstract of an ESA data paper in PDF format is just ridiculous.

The cost of single-article purchases has now more than DOUBLED since ESA moved to Wiley. Below is a screencap I took from the old ESA publishing platform. ESA articles were paywalled for just $20 and that allowed 30-day access. Now with Wiley, the exact same content is available to me for $45.60 (inc. UK tax) and I only have a 24-hour permitted-access period. This price-hike and narrow access window are utterly absurd and unjustified. Is it any wonder everyone uses SciHub these days?

Does this help raise the awareness of ecological science?

The old paywall was half the price and gave 30-days access, not just 24 hours!

 

 

 

 

 

I’m also frightened that ESA had no idea this was going-on. This is exactly what happens when you give all your content to an unscrupulous oligopoly publisher like Wiley to sell on your behalf. It seems to me that many academic societies are receiving big fat cheques every year from their commercial publishing ‘partners’ and are completely ignoring where from and how this money was generated. It’s well known that the academic publishing oligopoly is siphoning huge margins of money away from research. Why are academic societies so willingly complicit in this racket? It seems to me as if it is a sadly common approach to deal with this impropriety by turning a blind eye: “Take the money, don’t ask questions!” As long as society members benefit (at the expense of the rest of the world), anything goes.

Some final questions…

  1. Does ESA know how much Wiley is charging libraries around the world for subscriptions to ESA’s journals?
  2. Does ESA actually know anything of the real cost of production and publishing services that Wiley provides – not the price Wiley says it costs (inc. unhealthy profit margin) but the actual cost?
  3. How many readers like me (‘the scholarly poor’) outside the paywall has Wiley charged for access to ESA data papers that should have been free to access?
  4. Given Wiley’s lack of transparency, can we trust them when they report back how many others have also bought access to these ESA data papers that should have been free?

Update 2016/04/09: Thankfully, I did eventually get a refund for this article purchase on 2016/04/08, although I still appear to have lost out due to currency conversion issues with my bank:

wiley-refund 

 

 

This has done the rounds on Twitter a lot recently, and justifiably-so but just in case you haven’t seen it yet…
I thought I’d quickly blog about this excellent graph published on a FrontiersIn blog late last year (source/credit: http://blog.frontiersin.org/2015/12/21/4782/ )
Source, Credit, Kudos, and Copyright: Pascal Rocha da Silva, originally posted here.

Source, Credit, Kudos, and Copyright: Pascal Rocha da Silva. Originally posted here.

With data from 570 different journals, it appears to demonstrate that rejection rate (the percentage of papers submitted, but NOT accepted for publication at a journal) has no apparent correlation with journal impact factor.

 

Why is this significant?

 

Well, a lot of people seem to think that ‘selectivity’ is good for research. That somehow by rejecting lots of perfectly valid papers submitted to a journal, it somehow ensures increased ‘quality’ (citations?) of the papers that are eventually accepted for publication at a journal. The fact is, high rejection rates in practice indicate that a lot of good research papers are being rejected just to satisfy an unjustified fetish for arbitrary and crude pre-publication filtering. This is important evidence for advocates of the ‘publish first, filter post-publication’ philosophy; as put into practice by journals such as F1000Research and Research Ideas and Outcomes.

 

Release early, release often?

 

Rejecting perfectly good/sound research causes delays in the dissemination of knowledge – rejected manuscripts have to be reformatted, resubmitted and re-reviewed elsewhere at great cost. The overwhelming majority of initially rejected manuscripts get published somewhere else, eventually. So why bother rejecting them in the first place, if all it does is waste time and effort?

Please show your friends the graph if they haven’t already seen it. I think data like this could change a lot of people’s minds…

Further Reading:

Similar findings have been reported before with smaller samples:
Schultz, D. M. 2010. Rejection rates for journals publishing in the atmospheric sciences. Bull. Amer. Meteor. Soc. 91:231-243 DOI: 10.1175/2009bams2908.1

I’ve written 29 blog posts this year! Still time for one more…

This work relates to my new postdoc at the University of Cambridge in Sam Brockington’s group.

I’ve been closely examining IUCN RedList data for plant taxa and found some rather odd things.

Out of the 100 or so plant species that the IUCN RedList asserts as ‘extinct’, at least 16 of them are growing alive and well somewhere in the world at the moment.

For some species even Wikipedia notes the conflict between reality and the ‘official’ IUCN assessment e.g. for Rauvolfia nukuhivensis.

Here are the 16 plant species that I think are incorrectly assessed as ‘extinct’ right now by the IUCN RedList:

Astragalus nitidiflorus, Cnidoscolus fragrans, Cynometra beddomei, Dipterocarpus cinereus, Dracaena umbraculifera, Madhuca insignis, Melicope cruciata, Ochrosia brownii, Ochrosia fatuhivensis, Ochrosia tahitensis, Pausinystalia brachythyrsum, Pouteria stenophylla, Rauvolfia nukuhivensis, Wendlandia angustifolia, Wikstroemia skottsbergiana, Wikstroemia villosa

Additionally to the 16 above, with less certainty, I also think the Hawaiian taxa Delissea kauaiensis and Delissea niihauensis might have some individuals still alive according to this Department of Land and Natural Resources ‘Fact Sheet’ from 2013.

 

Why not harness the wisdom of the crowds and/or semi-automated text mining?

 

It’s remarkable that the IUCN RedList still lists some of these as ‘extinct’ when there are easily findable peer-reviewed articles reporting the rediscovery and hence extant status of these taxa. To their credit, many are listed as “needs updating” but still, if there are important updates to statuses why not just go in and make the change(s) to correct the record?   The IUCN RedList page listing Wendlandia angustifolia as ‘extinct’ is possibly the worst example – it was reported as rediscovered back in the year 2000, more than a decade ago! The IUCN has had 15 years to update their incorrect assertion of ‘extinct’ for this taxon!

I can’t possibly go through the literature and check all other IUCN-listed plant taxa myself but this does seem like a great opportunity for ContentMine tools to help the IUCN RedList stay on top of the latest updates about IUCN RedListed taxa. See ‘Daily updates on IUCN Red List species‘ for more on that idea.

 

Below I list sources of information relating to the 16 species that I think are definitely NOT extinct, despite being listed as such on the IUCN RedList.

Wahyu, Y., Wihermanto, N., Risna, R. A., and Ashton, P. S. 2013. Rediscovery of the supposedly extinct Dipterocarpus cinereus. Oryx 47:324.

Martínez-Sánchez, J. J., Segura, F., Aguado, M., Franco, J. A., and Vicente, M. J. 2011. Life history and demographic features of Astragalus nitidiflorus, a critically endangered species. Flora – Morphology, Distribution, Functional Ecology of Plants 206:423-432.

Lorence, D. and Butaud, J.-F. 2011. A reassessment of Marquesan Ochrosia and Rauvolfia (Apocynaceae) with two new combinations. PhytoKeys 4:95+

Viswanathan MB, Harrison Premkumar E, Ramesh N. 2000. Rediscovery of Wendlandia angustifolia Wight ex Hook.f. (Rubiaceae), from Tamil Nadu, a species presumed extinct. J. Bombay Nat. Hist. Soc. 97. (2): 311-313

Oppenheimer, H. 2011. New Hawaiian plant records for 2009 Records of the Hawaii Biological Survey for 2009–2010. Bishop Museum Occasional Papers 110: 5–10 [notes the rediscovery of Wikstroemia villosa]

Shenoy et al. 2014. Extended distribution of Madhuca insignis (Radlk.) H. J. Lam. (Sapotaceae) – A Critically Endangered species in Shimoga District of Karnataka. ZOO’s PRINT  Volume XXIX, Number 6

Sudhi, K. S. 2012. Rediscovered tree still ‘extinct’ on IUCN Red List. The Hindu. [Cynometra beddomeii]

Missouri Botanical Garden 2012. Umbrella Draceana. [Dracaena umbraculifera might be extinct in the wild, but it is still successfully grown in many botanical gardens!]