Show me the data!
Header

This morning, a PhD student asked me if I could get access to copy of:
“Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses” by Jeremy M Brown and Robert C Thomson which was first published online (ahead of print) on 20th December 2016. DOI: http://dx.doi.org/10.1093/sysbio/syw101

The student urgently needs access to this work because it relates very closely to some of his research and he has a manuscript in the final stages of preparation doing something similar or related to this work.

As of 23-01-2017, this paper is seemingly completely missing from OUP’s new website (they appear to have migrated all journals to this base URL now: https://academic.oup.com ) and they have failed to put in place any redirect links that resolve to where this article is, if it is online at all. This paper may have been missing/offline/unavailable since January 13th 2017 – remember it has not appeared in print yet, thus it is only electronically available.

Old links to it that used to work include:
http://dx.doi.org/10.1093/sysbio/syw101
http://sysbio.oxfordjournals.org/content/early/2016/11/14/sysbio.syw101.abstract

The society itself knows this article exists, it tweeted about it:

A third-party website also acknowledges the existence of this article:
http://www.pubpdf.com/pub/28003531/Bayes-factors-unmask-highly-variable-information-content-bias-and-extreme-influence-in-phylogenomic-

Sci Hub preserves access to paid-for scholarly content, when the original publisher fails to do so

Interestingly, Stian Håklev alerted me to the fact that the full text of this otherwise missing paper is available via Sci Hub https://twitter.com/houshuang/status/823478936030052352

Direct Sci Hub link to this paper here: http://dx.doi.org.sci-hub.cc/10.1093/sysbio/syw101

It is deeply ironic that my only available access to an article that my library (and thousands of other libraries and personal subscribers around the world!) has paid a publisher to make available is at a so-called “pirate library” like Sci-Hub. Why do we pay large sums to legacy publishers for incompetent service provision, whilst our libraries pay nothing to competent, low-cost archival services like Sci-Hub? “Lots of copies keeps things safe” as they say.

Final questions…

HOW MANY OTHER PUBLISHED PAPERS ARE NOW “MISSING” (NOT AVAILABLE ONLINE) AT JOURNALS PUBLISHED BY OXFORD UNIVERSITY PRESS? IT STRIKES ME THAT THIS PROBABLY ISN’T AN ISOLATED CASE – IT SEEMS THAT OUP HAVE NOT USED ROBUST AUTOMATED PROCESSES TO MIGRATE CONTENT AND CREATE APPROPRIATE REDIRECT LINKS.

BUT EVIDENCE OF ABSENCE IS HARD. WE HAVE ONE ROBUSTLY EVIDENCED CASE HERE BUT THERE ARE PROBABLY MORE.

PLEASE HELP FIND MISSING ARTICLES SO WE CAN ASSESS THE TRUE SCALE OF THE LOSS OF SERVICE HERE.

LIBRARIES AND INSTITUTIONS AROUND THE WORLD PAY SUBSCRIPTIONS TO HAVE ELECTRONIC ACCESS TO THIS CONTENT. THIS IS CLEARLY A SIGNIFICANT BREACH OF SERVICE. WILL OUP BE MADE TO PAY COMPENSATION FOR THIS PROFESSIONAL INCOMPETENCE?

This week I chose the papers for the Brockington Lab ‘journal club’ here at the Department of Plant Sciences, University of Cambridge (I prefer to call it the ‘weekly research round-up’ though, because good content has nothing-to-do with journals per se!).

We rotate the choice of papers between each lab member every week. Sometimes the focus is betalain or cuticle research, but every 3rd week the focus is on broad-interest research.

The three papers I picked this week are all super-interesting and have a common theme: open research!

1.) Islam et al. (2016). Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae bioRxiv DOI: 10.1101/059832

2.) Erin C McKiernan, Philip E Bourne, Titus Brown, Stuart Buck, Amye Kenall, Jennifer Lin, Damon McDougall, Brian A Nosek, Karthik Ram, Courtney K Soderberg, Jeffrey R Spies, Kaitlin Thaney, Andrew Updegrove, Kara H Woo, & Tal Yarkoni (2016). How open science helps researchers succeed eLife DOI: 10.7554/eLife.16800

3.) Eklund, A., Nichols, T. E., and Knutsson, H. (2016) Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates. PNAS DOI: 10.1073/pnas.1602413113

 

Paper 1

Paper 1 by Islam et al. is what we spent the most time discussing. The Open Wheat Blast project came to my attention a few months ago via Nature News. It’s really good to see such a globally-involved multi-author collaboration where all the authors have ORCIDs, posting a preprint before the journal submission AND making all the data openly available as it happens. I won’t say too much but we did have some questions over the science of the paper — was it really necessary to do full scale transcriptomics/genomics to identify the possible origin of the pathogen? We’re not experts in plant disease but could less expensive, more targeted nucleotide sequencing approaches have given the same phylogenetic results?

Paper 1 was also made available online at a preprint server which gave me an excellent opportunity to explain what a preprint server was to the group. I even tried to give an account of possible ‘negatives’ of preprinting: the only one I could think of was embarrassment if the work was demonstrably incorrect or obviously messy/unfinished (but who would actually do that?).

It was also fun to read and analyze a paper in it’s unformatted state. This is what a paper looks like at submission before the imposition of a 2-column layout, journal branding, logos and other crap.

 

Paper 2

screenshot of the 'How open science helps researchers succeed' paper

 

 

 

 

 

 

 

 

 

 

 

 

 

It was my delight to see ‘How open science helps researchers succeed’ get published in eLife the week before the research round-up meeting: perfect timing! We didn’t get much time to discuss it but I hope our group read it. It’s a really solid review of how open research practices can help the individuals doing open science, not just ‘sacrificially’ helping others, as people sometimes tend to cynically interpret it. I was tempted to also suggest the recent opinion paper ‘How publishing in open access journals threatens science and what we can do about it‘ but it’s such a poor quality paper with so many glaring factual errors (there’s an excellent post-publication review on Publons) I didn’t even bother to send it round the group.

Paper 3

Again we didn’t get time to discuss this in detail but I was really pleased that Caroline our visiting undergraduate from Oberlin College had read about this one even prior to me selecting it for our weekly round-up. It’s had a heck of a lot of media coverage (deservedly!), and we hope to talk about it in depth at one of the next OpenCon Cambridge meetups — there’s been some useful discussion of it over on the OpenConCam mailing list. You might think it weird to suggest a neuroscience fMRI paper in a plant sciences group – but the relevance isn’t about the study system. It’s the fundamental need for data archiving, and statistical rigour that are demonstrably important here and it’s a lesson for all disciplines not just neurosciences.

 

In about seven weeks time it’ll be my turn again to choose the papers. It’ll be hard to top those three papers for awesomeness though! Well done to all the authors for the great work.

There are a lot of really interesting works being published over at Research Ideas and Outcomes (RIO).  If you aren’t already following the updates you can do so via RSS, Twitter, or via email (scroll to the bottom for sign-up).

In this post I’m going to discuss why Chad Hammond’s contribution is so remarkable and why it could represent an exciting model for a more transparent and more immediate future of scholarly communications.

Version1

 

 

 

 

 

 

So, what’s special?

Well, to state the obvious first: it’s a grant proposal, not a research article. RIO Journal has published quite a lot of research proposals now, it’s becoming a real strength of the journal. But that’s not the really interesting thing about it. The really cool thing is that Chad published this grant proposal with RIO before it was submitted it to the funder (Canadian Institutes of Health Research) for evaluation.

You’ll see the publication date of Version 1 of the work is 24th March 2016. Pleasingly, after publication in RIO Chad’s proposal was evaluated by CIHR and awarded research funding. Chad received news of this in late April:

…and the story gets even better from here because thanks to RIO’s unique technology called ARPHA, Chad was able to re-import his published article back into editing mode, to update the proposal to acknowledge that it had been funded:

This proposal was submitted to and received funding from the annual Canadian Institutes of Health Research (CIHR) competition for postdoctoral fellowships.

The updated proposal was then checked by the editorial team and republished as an updated version of the original proposal: Version 2, making-use of CrossMark technology to formally link the two versions and to make sure readers are always made aware if a newer version of the work exists. Chad’s updated proposal now has a little ‘Funded’ button appended to it (see below), to indicate that this proposal has been successfully funded. We hope to see many more such successfully funded proposals published at RIO.

Title and metadata

 

 

With permission given, Chad was also able to supply some of the reviewer comments passed to him from CIHR reviewers as supplementary data to the updated Version 2 proposal. These will undoubtedly provide invaluable insight into reviewing processes for many.

Finally, for funders and publishing-tech geeks: you should really take note of the lovely machine-readable XML-formatted version of Chad’s proposal. Pensoft has machine-readable XML output as standard, not just PDF and HTML. Funding agencies around the world would do well to think closely about the value of having XML-formatted machine-readable grant proposal submissions. There’s serious value to this and I think it’s something we’ll see more of in the future. Pensoft is actively looking to work with funders to develop further these ideas and approaches for genuinely adding-value to scholarly communications.
RIO is truly an innovative journal don’t you think?
:)

References

version 1:
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

version 2:
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: e9115. doi: 10.3897/rio.2.e9115

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.