petermr's blog

I have been non-systematically looking at “open access” from major publishers, mainly initiated from their marketing with the #openaccess tag on Twitter. {I have a serious criticism of University libraries that they are not monitoring #openaccess compliance and that it’s left to a few individuals to highlight problems. The issues I highlight should have been identified by them, not me. I can only produce anecdotal evidence.] The sort of questions I ask myself and try to report are:

• What does the publisher offer as “open access”? This can vary from CC-BY (PLoS, BMC, eLife, etc. and Springer , Wiley) to “copyright the publisher, all rights reserved”.
• It’s the offering labelled as Open Access? On the masthead? On the paper?
• What are the re-use rights? In particular are particular groups charged additionally (I use the Rightslink service – normally a “Request Permissions” on the masthead).
• Are there obvious inequities for author or reader, re-user?

It can be very difficult to search for Open Access articles from a publisher. It should be trivial, but isn’t.

So I got the following tweet today:

(You can follow this trail). This is the authors (not the publisher) advertising their paper. Nothing wrong with that except that when everyone does it the tag will be flooded (if it isn’t already). So I follow it to http://pubs.acs.org/doi/full/10.1021/cb400425t and get:

There is nothing saying this is “Open Access” to someone unfamiliar with ACS publications. The paper is © ACS so belongs-to-them. In fact the “ACS Author Choice” is a form of Open Access.

This post now covers what “Author Choice” means in detail. [BTW the ACS+RightsLink does allow the re-use of this article for teaching and dissertation without charge. Try it]

Let’s click ACS Author Choice: nothing happens – it’s not a link.

This is seriously unsatisfactory. If authors/funders have paid for Open Access it should be honoured on the page and on the manuscript. I’ve challenged the ACS on this 6 years ago (/pmr/2007/06/23/author-choice-in-chemistry-at-acs-and-elsewhere/ ), they’ve done nothing, so they are consciously making it obscure that this is an OA paper. I have to Google for ACS Author Choice (it’s easier than trying to navigate the journal pages) to get http://pubs.acs.org/userimages/ContentEditor/1218220609981/authorchoice_form.pdf and http://pubs.acs.org/page/policy/authorchoice/index.html . It costs 3000 USD unless you are a member of ACS or their scheme.

Option A: Standard ACS AuthorChoice

This AuthorChoice Open Access option is best for authors who choose to publish articles under the terms of a license from ACS that allows others the right to use the final published article (the Version of Record) in a variety of ways, including the creation of derivative works such as translations, for noncommercial purposes.
Note: When transferring copyright to the ACS under this option, you still retain all the permissions granted to you under the terms of your Journal Publishing Agreement with the Society.

• Pricing and license information (Option A)
  

Option B: ACS AuthorChoice via the Creative Commons CC-BY-NC-ND License

This AuthorChoice Open Access option is offered for authors who prefer or must publish articles under the terms of a Creative Commons license that allows others the right to use the final published article (the Version of Record) only for non-commercial purposes, but not to modify or alter the published work. You also retain all the permissions granted to you under the terms of your Journal Publishing Agreement with ACS.

• Pricing and license information (Option B)
  

Option C: ACS AuthorChoice via the Creative Commons CC-BY License

This AuthorChoice Open Access option is typically for authors who are required by their funding sponsors to publish articles under the terms of a Creative Commons license that allows others the right to use the final published article (the Version of Record) for commercial as well as non-commercial purposes and to modify the published work. You also retain all the permissions granted to you under the terms of your Journal Publishing Agreement with ACS.

• Pricing and license information (Option C)
  

Note: Effective April 1, 2013, authors receiving funding from the Wellcome Trust and Research Councils UK (RCUK) are directed by their funding agency to publish using the CC-BY license.

As far as I can see there is no price differential between these (but this whole linkset is messy and complex to navigate).

Which option applies to the current document?

I have no idea. I assume it is the first because there is no mention of a licence. This isn’t good enough. If we look at the PDF there is not even any mention this is an “Author Choice” article let alone Open Access (of any sort). Follow http://pubs.acs.org/doi/pdf/10.1021/cb400425t . All you get is “Copyright American Chemical Society”.

It is not acceptable for a reputable publisher not to label its products clearly. The authors and their funders have paid for openness and clarity.

But I also criticize the University libraries strongly. It’s their job to manage copyright and licensing. They’ve done virtually nothing to make things clearer. And, worst of all, they haven’t challenged the publishers. Rather they simply take whatever the publishers offer and enforce it. (Prove me wrong with public examples, please).

As many publishers (including closed access ones) have shown, the simplest solution is simply to publish as CC-BY. It’s simple, it’s honest. It’s universally understood. Here we have the implication that CC-BY is a nuisance introduced by Wellcome and RCUK and wouldn’t we all be better off with CC-NC?

We wouldn’t. But the ACS would be significantly better off. Because they can control the Open Access material they receive and generate a third or even fourth income stream from it by controlling redistribution and re-use in the commercial sector (whatever that is).

Shortly after blogging about Crowdcrafting (/pmr/2013/08/09/crowdsourcing-at-crowdcrafting-were-doing-antimatter-research-2/ ) there’s a new application , just to show you the variety. See http://crowdcrafting.org/app/RuralGeolocator/ :

Rural Geolocator is an application for geo-referencing houses on satellite images.

The current batch of tasks is focused on Rusinga Island, an island in Lake Victoria, Western Kenya. Rusing Island is the location of the SolarMal project, which studies the potential of innovative mosquito trapping technologies for malaria control.

The geo-locations of the houses will be used to inform the project logistics and analysis of the SolarMal project.

Rural Geolocator was developed by the Public Health Computing group at the Swiss Tropical and Public Health Institute in Basel with support from Daniel Lombraña González at the Citizen Cyberscience Center.

The task is very simple – you get a satellite image and have to indicate the houses. Here’s my latest (I have marked ten in the brown box and I think there are 3 more.

It’s simple and provides an occasional useful diversion.

There’s a hashtag #openaccess which I follow. It started by marking useful comments and resources in “open access” but is increasingly being used by (mainly commercial legacy) publishers to promote their offerings in this area. Nothing wrong with that, though it gets congested. So from time to time I follow these to see what the publisher means by OA and what their practices are. Her’s one today:

Elsevier Surgery @ELSSurgery

Publish #openaccess in “The American Journal of #Surgery” – ow.ly/nKie6

Which points to http://www.elsevier.com/journals/the-american-journal-of-surgery/0002-9610/open-access-options. This is APC-paid access, remember.

I’m selecting the options that authors are offered:

User Rights
All articles published Open Access will be immediately and permanently free for everyone to read and download. We offer authors a choice of user licenses, which define the permitted reuse of articles (see http://www.elsevier.com/openaccesslicenses). We are continuously working with our author communities to select the best choice of license options, currently being defined for this journal as follows:
• Creative Commons Attribution-Non Commercial-ShareAlike (CC BY-NC-SA)
• Creative Commons Attribution-NonCommercial-NoDerivs (CC-BY-NC-ND)
• And if you need to comply with your funding body policy you can apply for the CC-BY license after your manuscript is accepted for publication.

Read the bullet points carefully and ask whether they are objective. What Elsevier is saying is that they have “author communities” and that by some form of process (? Is it open) these communities and Elsevier have agreed that CC-NC options are “the best choice”.

I remain to be convinced of the objectiveness of this process. Elsevier have had a default CC-NC for some time (it benefits them as they have effectively a monopoly right of re-use). When funders started to insist on CC-BY, Elsevier had to comply.

But the options above suggest that Elsevier and their authors know best and that these funders have made life difficult by introducing an option which you have to choose if you have to choose but we’ll all rather not, wouldn’t we.

Other publishers have been straightforward. Springer and Wiley are CC-BY only.

Elsevier should to change to CC-BY only as the simple honest straightforward option that makes OA easy for everyone instead of muddying the waters yet again.

Roderic Page @rdmpage tweets:

Why the outrage at people repackaging #oa papers and charging for them? : http://evoldir.tumblr.com/post/58035947020/other-unanticipated-reuse-of-open-access-papers
Don’t like it? Do it better and cheaper!

I fully agree with him and analyse in more detail: The original post included:

Dear Colleagues,

I’ve recently discovered that some commercial publishers are re-editing articles from open-access journals and publishing them as multi-author books, without the authors’ knowledge (example here).  Although most authors I’ve spoken with find this objectionable it’s quite legal, since open-access articles are usually published under Creative Commons attribution-only (CC-BY) licenses.  

Before pressing for any changes I’d like to get a broad survey of researchers’ opinions on this, so I’ve prepared a short (3 question) survey.  Here’s the link:&n bsp;http://svy.mk/1cs8M2v. Please feel free to pass this survey link on to other researchers or scientific email lists.

p.s.  If you’d like more information I’ve also discussed this issue on my blog: 

• http://bit.ly/1630196; 
  
• http://bit.ly/1cs8OHA; 
  
• http://bit.ly/16303xz;
  
• http://bit.ly/1cs8M2x.
  

Dr. Rosemary J. Redfield     redfield@interchange.ubc.ca     Professor, Dept. of Zoology    Univ. of British Columbia                              

In the blog posts above RJR highlights the commercial republishing of CC-BY Open articles. Links 1,3,4 relate to “Apple Academic Press ” [about whom I know nothing]. From the second link above:

But, as the previous post and a related post describe, the CC-BY license creates new problems for authors, because some for-profit publishers have begun aggregating CC-BY papers into high-priced edited books without the authors’ knowledge.  The authors I’ve discussed this with are quite upset.  They trusted the journals to offer licensing arrangements that were in the authors’ best interests, but now they feel that they have relinquished control of their scientific reputations.  (Note that these weren’t predatory publishers, but PLOS One and BioMed Central.)

Most of the discussions of open access licenses haven’t considered the exploitation of these licenses by for-profit publishers, probably because this niche opened only very recently, once open-access papers became widely available.  I and others discovered this problem by accident.  I don’t know how widespread it is, but I expect it will only grow.  (I’d like to do a survey of its prevalence, but I can’t figure out any way to distinguish between such repackaged books and traditional multi-author volumes without having to contact individual authors – any suggestions?)

So far, open access publishing has been presented as both a public and a private good.  Science benefits from barrier-free dissemination and reuse, and authors benefit from wider readership. The only cost under discussion has been the transfer of publication expenses from the reader to the authors or their institution.  Opposition has come mainly from the publishers of subscription-access journals whose profits are threatened. – See more at: http://rrresearch.fieldofscience.com/2013/07/informing-authors-of-real-consequences.html#sthash.o8MF7RGb.dpuf

Anyone who writes Free/Open Source software knows about re-use and resale and has accepted it as a public good (for about 20 years). I write OSS and I have had companies take my software, repackage and resell it. I am perfectly happy about this. My only concern is that I am attributed. I have seen “reputable” companies in cheminformatics bundle software and claim they wrote it and I have attempted to highlight the inequity and illegality of this. But as long as they acknowledge me that’s fine and they can charge what they like.

And it means my software gets used! Which is what I want.

Note that is a non-rivalrous activity. *I* can still sell my software if I want and so can anyone else. The critical problem is monopoly, not an increased market.

Assuming Apple Academic Press do a reasonable job of acknowledging authors and the book is technically competent what’s the problem? The authors get MORE readers which is surely what they want? The problem for RJR and her authors who object seems to be “profit envy”. “Why should AAP make money out of my work?”

I ask “why not?” If it produces something valuable (at least measured by people buying the book) it adds to common value. If the price is too high people won’t buy it. And remember we’he had over 100 years of commercial organizations abstracting the scientific literature and reselling it.

One reason why AAP think they have a market is that journals are such a poor way of aggregating information. The time is overdue for secondary derived products, in this case aggregation. It’s one of the main virtues of CC-BY that we can aggregate, filter, reformat and compute the literature. CC-NC prevents this.

I suspect that products like AAP’s reaggregation will have a short shelf life and short market. The real market will be one that uses modern technologies and ideas to add massive value to the literature. And when this new generation of derivatives arrives (and I hope my Open Software will be involved) then we shall make conventional closed journals obsolete.

[Test] Yesterday was the annual puntcon and about 30 people, geeks and non-geeks turned up. It’s always exciting to meet new people in Cambridge. There’s so much going on that we miss most of it. One of my acquaintances is intending to move back to Cambridge for exactly this reason.

This post also tests if I can upload images – WordPress has been giving problems. So if there is no image, or duplicate posts, that’s why

I got the following advertising tweet today:

Elsevier Energy @EnergyJournals Read recent papers published Open Access in Elsevier Energy journals ow.ly/nMNAe
#OpenAccess
#OA
#energy

I follow the hashtag #openaccess and now many publishers are using this to promote their open access. So I thought I would follow this and see what sort of open access this is. The landing page (http://www.elsevier.com/physical-sciences/energy/open-access-articles) says:

Elsevier offers the option for authors to sponsor access to individual articles through hundreds of individual journals and via arrangements with funding bodies. These options enable authors to decide how their articles are published and to comply with the requirements of institutions, governments and funding bodies.

Sponsored articles are freely available to all readers. Click here for more information.

We are delighted to bring you a selection of the sponsored articles published in Elsevier’s Energy Journals to date:

and started on the table of contents listed on the “open access page” and found these are behind a paywall.

          
A new control strategy for hybrid fuel cell-battery power systems with improved efficiency
International Journal of Hydrogen Energy, Volume 37, Issue 17, September 2012, Pages 13141–13146
Chung-Hsing Chao, Jenn-Jong Shieh

PMR: costs 31.50 USD
           
Enhanced photo-hydrogen production of Rhodopseudomonas faecalis RLD-53 by EDTA addition
International Journal of Hydrogen Energy, Volume 37, Issue 10, May 2012, Pages 8277–8281
Hong-Yu Ren, Bing-Feng Liu, Jie Ding, Jun Nan, Guo-Jun Xie, Lei Zhao, Ming-Guang Chen, Nan-Qi Ren

PMR: costs 31.50 USD

Carbon–ceramic supported bimetallic Pt–Ni nanoparticles as an electrocatalyst for oxidation of formic acid
International Journal of Hydrogen Energy, Volume 36, Issue 16, August 2011, Pages 9581–9590
Biuck Habibi, Nasrin Delnavaz

PMR: costs 31.50 USD

… and I stopped there (and no, I haven’t been through every link and picked

Now I expect it’s an error. But part of Elsevier’s and other publishers arguments is that they claim to add professional quality to publishing and that academics and the world should pay for this. And this was a promotion. Elsevier are saying “look we are doing Open Access”. And they can’t even get a list of ca. 50 titles correct.

My guess is that they don’t have a proper system internally for deciding what is “open access”. Last time I asked them for a list of open access articles they said they couldn’t find it. My guess also is that they use “open access” in several different ways so they can’t create consistent metadata. If they labelled articles as CC-BY – as they should – then this is an easy thing to label. But I have no idea what the actual status of these articles is.

So Elsevier please do Open Access competently. Use CC-BY only, and put it in your metadata. And use it.

The “non-commercial” licence CC-BY-NC option for “open access” is often promoted (e.g. by Heather Morrison) as a means to restrict inappropriate use of the article. It is suggested that NC will prevent pharmaceutical companies from using the information in the article. This is misguided – all that copyright does it to restrict the copying of the article – the information in it can be re-used without permission

I have often argued against CC-NC as a useful tool, partly because “commercial” is very poorly defined, and partly because in practice it does not address authors’ moral rights (which are (implicitly) the primary concerns of proponents). To paraphrase: “we, the authors, do not want the following groups of people to use the article” or “we do not want the article to be used for the following purposes”. However worthy these arguments might be (and they don’t appeal to me and many others) they are unworkable in practice. The FLOSS software community threw out the Non-Commercial option many years ago and no conformant FLOSS licence has such a code (no discrimination against people or fields of endeavour). In practice the only effect of CC-NC is to generate more revenue for publishers (not authors).

I’m prompted to this analysis by a mail I got from a scientist (who I shan’t identify) who had used a CC-NC licence because s/he thought it would prevent re-use. There was no price differential between CC-BY and CC-BY-NC so it was purely a question of moral rights and re-use. They argued that they did not want pharma companies to re-use data, especially images such as micrographs, in their advertising material.

In practice what would happen? An irresponsible re-user would simple re-use the image – perhaps with attribution. What would the author do? Contact the publisher? The author retained copyright so the publisher has no interest. I doubt they would help. So the author has to pursue the re-user themselves. If I were the re-user I would argue the micrographs were facts and an integral part of the factual information. It would depend on the skill of the lawyers (and the domain – this could be fair-use in US) but my guess would be that the re-use would not held in breach of copyright.

What would a responsible re-user do? They’d use the Right-and-Permissions link which normally goes straight to RightsLink. This organization appears to be solely concerned with protecting the rights of publishers to receive income. The normal outcome is “how much do I have to pay” – and I have shown some examples. There is nothing about authors moral rights. In some cases, admittedly, the re-user is directed back to the publisher (not the author) and the publisher then replies as to whether rights are granted and if so how much. I haven’t done this, so it’s possible that moral rights may be included but normally I suspect it is purely about publisher, NOT author, income. [I’d be grateful for any publisher information about nuances of operation.]

But in summary I argue:

CC-NC as operated by publishers only serves to increase the revenue of publishers or to increase the publisher’s control over re-use of the information (e.g. new derivative works).

So, authors, please use CC-BY for “open access”. And if you are offered the “cheaper” option of CC-BY-NC or similar at a cheaper price, highlight the unacceptability of this.

[Note: my correspondent mailed back and said as a result of my points they wouldn’t be using CC-NC in future.]

[Wordpress is playing up so some images may be missing]

I am a strong believer in Crowdcrafting (volunteer “crowdsourcing” ay http://crowdcrafting.org):

CrowdCrafting is a free, open-source crowd-sourcing and micro-tasking platform powered by the PyBossa software. This platform enables people to create and run projects that utilise online assistance in performing tasks that require human cognition such as image classification, transcription, geocoding and more. CrowdCrafting is there to help researchers, civic hackers and developers to create projects where anyone around the world with some time, interest and an internet connection can contribute.

CrowdCrafting is different to existing efforts:

• It’s a 100%% open-source
  
• Unlike, say, “mechanical turk” style projects, CrowdCrafting is not designed to handle payment or money — it is designed to support volunteer-driven projects.
  
• It’s designed as a platform and framework for developing deploying crowd-sourcing and microtasking apps rather than being a crowd-sourcing application itself. Individual crowd-sourcing apps are written as simple snippets of Javascript and HTML which are then deployed on the server. This way one can easily develop custom apps while using the platform to store your data, manage users, and handle workflow.
  

It’s the brainchild of Daniel Lombraña González
and uses the OKFN’s PyBossa (http://dev.pybossa.com/ ) softwareand supported by Citizen Cyberscience Centre . Crowdcrafting is not a single app or activity, it’s a framework that can be used for anyone to mount and run their crowdsourcing app. Daniel presented at OKFN about 2 months ago and among the projects were:

• Do Yellowhammers (Emberiza Citrinella) have different dialects in UK and New Zealand?
• Can we measure gender ratios in science from photographs on Flickr?
• How does human time scale with graph isomorphism?
• Which areas in cities are public parks?

I’m interested in using crowdcrafting in the biodiversity project that Ross Mounce, Matt Wills and I are starting in October – to extract phylogenetic trees and species from the literature. We aren’t quite sure what the details will be, but it may be creating a checked corpus, or disambiguating.

So I need practice and experience and so I was delighted to see a new project launched on antimatter http://crowdcrafting.org/app/antimatter/ . The simple goal, I believe, it to verify that antimatter has normal gravitational mass – i.e. that a proton and antiproton will attract each other gravitationally. (I won’t speculate more as I’m intending to find out in the project itself, and I’ll report back.). The way this is done is to capture annihilation tracks (I think in emulsion), and find out where they originated (“the vertex”). The tracks are faint and humans are better at recognising them than machines (I can believe this, having written image recognition software).

See http://home.web.cern.ch/about/updates/2013/08/join-dots-measure-antimatter for an introduction

Crowdcrafting is not Mechanical Turk. The participants are part of a community and may bring complementary skills. Some could be retired scientists like me, mathematicians developing financial software, web site designers, UI experts, neuroscientists looking at brain sections, electrical engineers, and even fully-paid-up HE physicists who want to be involved. Many will be students, the scientists of the future. And many will be taxpaying citizens who are interested in what their funding goes towards. Some will have social skills in developing online communities – the list is endless. It’s really exciting.

So for me the most important thing is to develop a sense of community. They/we are being asked to contribute time and in return they must have reward. This can range from a leaderboard, to a deeper understanding of the science, and even to discovering new effects (this has happened repeatedly in other projects). So here’s a rough set of what I think are important.

• There should be a clear community infrastructure
• We should know what the overall goal is
• We should know how our contribution will help
• We should understand what we are actually doing and be able to help refine it
• There should be regular updates – stats are critical, but also summaries of more general progress. And measures of how far we have come and how far to go.

So I suggested that we should have a communal discussion group and DanielLG set this up. I posted some initial thoughts and questions and you can see these here https://groups.google.com/forum/#!forum/cern-antimatter-crowdcrafting . I’ve already got useful answers from Michael Doser (who runs the project) who writes:

first of all, thank [everyone] for your interest! As an avid follower of galaxyzoo and related projects, I have been thinking about how to open high energy physics research to public involvement in a similar manner. With the AEgIS experiment, we may have a first possibility, but I am sure that we will find more. AEgIS is built around the attempt to measure the gravitational interaction between matter and antimatter using antihydrogen atoms. [… lots more]

And I was about to blog about the projects and … But 5 minutes ago I got this incredible mail from Daniel:

Today all the available tasks have been analyzed by the volunteers. Amazing. Yesterday we had a huge [s]pike in the answers, and today all the data have been analyzed.
Michael and his team now have to download the results, study them, and if they have more data add it to the system 🙂
Meanwhile you can check the stats of the project. They are really impressive!

Cheers and thanks for your contributions,

Daniel

The stats show this:

• Every dot on the map represents someone who understands Crowdcrafting and will be getting ideas! They are all scientists because they have all participated in science! And the roll of honour:
• 

This is massive. 100+ users join in 1 day and completely finish the tasks. I think it’s taken Michael by surprise. It has certainly surprised me and it’s massively exciting. Here’s the results (they are updated in real-time and actually rotate). 4 of the tracks are from me!

On Tuesday I went to an OKFN data evening in London (5 min from Kings Cross, so easy). They are occasions to meet new people and new ideas. On Tuesday we heard from David Carroll and Joseph McArthur medical/pharmacology undergraduates who are ANGRY. They are ANGRY because they frequently encounter paywalls that stop them reading the medical literature. Unlike most #openaccess advocates they are reaching outside the academic system. They’ve had a big impact already and some of their activities are detailed on their blog (oabutton.wordpress.com) – and they’ve made a lot of contacts and goodwill including PLOS-Cameron Neylon and SPARC-Alma Swan (who have provide funding). There isn’t a home page yet (I have urged them to do so) so I’ll quote from a recnt mail, and then from Cameron’s article (http://cameronneylon.net/blog/guest-post-the-open-access-button/ )

“Every day people hit thousands of paywalls and are denied access to the research they need. Our button will capture these moments and display them in an innovative and provoking way to change the broken scholarly publishing system. The button also try to get you access to those papers. Incentivising use in order to create real change.” (David/Joseph)

Imagine a browser-based tool which allowed you to track every time someone was denied access to a paper? Better yet, imagine if that tool told gave you basic information about where in the world they were or their profession and why they were looking.  Integrating this into one place would create a real time, worldwide, interactive picture of the problem. The integration of social media would allow us to make this problem visible to the world. Lastly, imagine if the tool actually helped the person gain access to the paper they’d been denied access too in the first place. Incentivising use and opening the barriers to knowledge combined can make this really powerful.

That’s what we’re imagining. We’re calling it the Open Access button. Every paywall met is an isolated incident; it’s time we capture those individual moments of injustice and frustration to turn them into positive change.

So here’s the problem paywall (left, costs 31.5 USD for a day’s read) and the button (right). You report to the world that you’ve hit a paywall. That is now logged as a restriction of the flow of scientific information – effectively only rich universities can read this paper (and they are not yet feeling angry enough to change the system urgently).

So the button allows you, the potential reader of the article – who might be a patient, or a charity donor, or a politician, or … to record that you are angry. And, positively, to find copies of the paper that you can get immediately and without payment. After all this only has to be done once – the button would also point you to a free source.

Yes, there are free copies of many papers. It’s generally called “Green OA”. It’s a mess, because universities haven’t created an index, because some copies aren’t in university repositories, and because it’s very patchy. Some authors proactively make GreenOA available, most don’t. Some Universities are proactive, most aren’t. So the OA_Button tells the #scholarly poor where they can find a copy.

In reality most papers won’t be freely available because many publishers don’t promote Green OA and many are actively against it. After the Finch report some publishers increased the embargo period from 0 to 1 or even 2 years. This means the paper is technically “OA” but you can’t actually read it for another year or two – by which time the research will be out of date. So the effect of the OA_Button will be to highlight the scale of the problem, and to shock all involved into getting immediate visibility for all articles.

They’ll plot the results by country. Here’s a snippet of their map.

Note that they are not advocating illegal practices (though it’s very unclear what is legal and what isn’t).

I’m hoping this will engender a wave of anger in the #scholarlypoor, those who don’t have access to the literature and who are often regarded as irrelevant by academia. Repositories are mainly built for the benefit of academics or in response to government mandates, not to provide information to the wider world. (I’d be glad to hear of evidence to the contrary, #scholarlypoor who regularly used repositories to find information).

David and Joseph have a large number of technical problems to solve. But their biggest challenge is getting YOU, especially outside academia, involved.

HTH.

[Readable by non-chemists].

Chembark is a well-known and highly respected chemical blogger. He and others keep the community on its toes in many ways, but often in revealing sloppy or even fraudulent practices. His latest post reveals unacceptable practice in publishing chemical experiments http://blog.chembark.com/2013/08/06/a-disturbing-note-in-a-recent-si-file/ “A disturbing Note in a Recent S[upplemental] I[nformation] File”. Supplemental (or Supporting) Information is the data (or usually a small part of the data) collected in the experiment and which is used to judge whether the authors have made the compound(s) they say they have. Chemists make a compound, purify it, collect spectral data and also analyse the elements in it (Elemental Analysis – how much Carbon, Nitrogen, Hydrogen – we can’t do Oxygen). Chembark’s commenters are split as to whether EA is useful but all agree it is required. (I am in favour of it – it may show that the wrong metal has been used – spectra won’t do this).

Here’s the paragraph from the SI. Even if you don’t understand chemistry you can see it’s the name of a compound (13), a recipe and some data.

This is very formulaic, indeed so formulaic that machines can understand it and 10 years ago 3 summer students and I developed a tool (OSCAR) which could read the numbers. It’s available as FLOSS and available to any publisher who wants to check data. I doubt that many do. (By contrast the crystallographers must submit and validate data before it is published. The current problem, which we’ll get to could never have happened in crystallography.

Here’s the problem – it occurs in the same file (http://pubs.acs.org/doi/suppl/10.1021/om4000067/suppl_file/om4000067_si_002.pdf ): Read it to the end

[Pt2(II)((M,SS,SS)-p-tolyl-binaso)2(μ-Cl)2][BF4]2 (14): A vial was charged with 100mg

(0.126 mmol) 5a and 24mg (0.126 mmol) AgBF4. 2ml CH2Cl2 was added, the vial was

covered and the reaction was left stirring in the dark for 2 hours. After this time, the

reaction was filtered over celite to remove AgCl. Solvent was then removed to leave a

yellow residue in the vial, the remaining clear, yellow solution was concentrated to a

volume of about 1ml, and diethyl ether was added in a dropwise manner to the stirred

solution to precipitate a yellow solid. The vial was centrifuged so the supernatant solvent

could be decanted off by Pasteur pipette. The yellow solid was washed twice more with

ether and the dried completely under high vacuum to give 99mg (93% yield) of product.

Emma, please insert NMR data here! where are they? and for this compound, just make

up an elemental analysis…

So this compound does NOT have any data. You’ve probably spotted the problem, but let’s show that a machine can also spot it. We run it through ChemicalTagger (developed by Lezan Hawizy in our group). ChemicalTagger (you can try this at home) reads a chunk of text and understands the semantic of chemical recipes. Everything coloured makes chemical sense included interpreting compounds and quantities:

The last sentence leaps out as non-chemical! Now I’m not judging the authors (Chembark and his readers will investigate). But it should never have happened. If the file had been a data file, instead of a PDF software would have detected this before it was submitted. This is not a new idea, I have been beating my head against chemists and their publishers for ten years. They are completely uninterested in publishing semantic data.

It’s actually easier to publish semantic data than this PDF. If they published properly errors of this sort could not occur – a data referee would have picked this up. The spectra are all digital – they could be zipped up. But instead they are printed out and copied (see the splodges? That’s not experimental noise, probably coffee or JPEG destruction):

So until chemistry wakes up and manages its data they will consistently get chemistry whose supporting data is questionable. And that means questionable science.