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Springer (commendably) publishes most of its APC-paid Open Access under CC-BY licences and allows free re-use for any purpose. However some “Open Access” (e.g. Drugs in R&D) is licensed under CC-BY-NC (non-commercial). This excludes, for example, re-use as teaching materials. Anyone wishing to re-use material in lectures will have to pay Springer, even though the author probably wanted it to be freely used. Here is the evidence; I strongly urge Springer to drop all NC licences, as otherwise it harms academics and many other sectors.

Visit RightsLink, enter as an academic…

And it will cost 151 USD (probably VAT on top) to use them in lectures.

Ultimately, of course, this is paid by student fees.

I must apologize to the Royal Society of Chemistry for material in the blog last week (/pmr/2013/07/31/does-the-royal-society-of-chemistry-deliver-on-its-commitments-on-open-access/ ). I failed to give the complete picture by implying that the RSC did not offer CC-BY as a paid option for Open Access. RSC does (http://www.rsc.org/AboutUs/News/PressReleases/2013/RSC-adopts-CC-BY-licence-open-access.asp ), and I should have congratulated them on the change and do so:

RSC adopts CC BY licence for Gold open access papers

07 March 2013

The RSC has announced today that it is making a change to copyright arrangements for open access papers published in RSC journals.

From 1 April 2013, authors will have the option to publish under the Creative Commons Attribution (CC BY) license, when choosing to publish their research via the Gold open access route.

Publishing research articles under the CC BY licence, a requirement by many funding agencies, makes the article available for anyone to copy, distribute, adapt or make commercial use of it, as long as the research is attributed to the author or licensor.

RSC’s Managing Director for Publishing, Dr James Milne said: “The RSC is a strong supporter of sustainable open access and has traditionally offered a relatively liberal licence for Gold open access articles. This move to make research findings published in RSC journals available under the Creative Commons licence continues to show our commitment to enhancing access to chemical sciences research.

“Adopting the CC BY licence also aligns us to the requirements of a number of funding agencies who promote and support Gold open access, including Research Councils UK and the Wellcome Trust. All RSC journals are therefore ‘open access compliant’ for these funding agencies.”

The RSC will also offer authors of Gold OA papers the option to publish under the Creative Commons Attribution Non Commercial (CC BY NC) licence, should they and/or their funders find this more appropriate. 

I believe that the CC-NC option (which I discourage) is priced identically to the CC-BY option and so there is no price pressure to choose the more restrictive licence. I have argued elsewhere /pmr/2013/08/01/why-cc-nc-hurts-authors-hurts-readersreusers-and-only-makes-additional-money-for-publishers/ why I believe this to be harmful.

esare Bellini from EDINA and I are doing a developer challenge, adapting my hack4ac prototype to annotate images with licence information. See /pmr/2013/07/24/making-images-open-can-and-should-be-routine/ for the idea. What we are going to do is:

• Point to a URL of an image (we’ll use Figshare for the demo, but it could be any CC-BY/CC0 image, so BMC, PLoS, etc.
• Upload a licence image (we can customise this for any author)
• Add the licence PIXELS to the image
• Save to file

I shall demo with a local implementation and Cesare is building it on a server.

We take an image, such as in http://figshare.com/articles/Megalodontes_merceti_on_a_flower_Spain_Rivas_Vaciamadrid_/761200:

[Note this is REALLY exciting for Ross Mounce and me working on biodiversity].

We then take a CC licence. Here I’ll use CC-BY:

And then we add this to the image and save locally (truncated…):

This has added the licence INTO the pixels. No-one can remove it (without it being obvious). It’s rendered in print. For ever.

If SpringerImages and their glitch ever “copyrights” it for Springer we can always point to the licence.

The code is trivial. Literally 10 lines of Java (it took me ca 1 hour to find my way around).

Cesare hopes to customize this on a server and we might even have something working that YOU can try by the end of the day.

I’m going through publishers in a semi-systematic way looking to see whether paid Open Access (Author Publishing Charges, APC) gives readers and authors the results they deserve. Look at the preceeding posts for RSC and Elsevier where readers are forbidden to use it for “commercial” and (Elsevier) no derivatives can be made. (PMR: This is a travesty of Open Access and though legal is highly damaging and serves only to preserve publisher control and monopoly.).

By chance Wiley tweeted #openaccess with http://www.wileyopenaccess.com/details/content/12f25e69a17/Institutional–Funder-Accounts.html announcing a number of dealas they have done with (mainly UK) universities so the university pays the APCs not the researcher. Although not perfect (because most of this will be Hybrid-OA which mainly benefits the publisher and only makes sense for megajournals) it’s a useful step. But what does “Open Access” mean?

So I went to a paper and found:

Pretty clear (CC Attribution is abbreviated to CC-BY). Good for Wiley. [I actually knew this, but needed to check the paper had explicit wording.

But some readers may want additional reassurance they can reuse it so I went to “Request Permissions”. This took me to Rightslink.

(Rightslink are primarily a rent collector service and about as cuddly). The “rights” generally refer to the right of the publisher to charge the reader for re-use. For Open Access articles some publishers ensure that you are told that the article can be re-used without charge. But in this case

“Permission to reproduce this content cannot be granted via the RightsLink® service”

The system COULD tell you that it was free and publishers really should do this. [If RSC had got their RightsLink information correct (instead of charging for re-use in theses) I might have been less critical.]. So following back to www.wiley.com and then “Rights and permissions” just takes you round the system indefinitely.

Simply:

If publishers point to Rightslink they have a duty to make sure it gives the correct answer in all cases and also indicates immediately whether something is free of charge and/or confers rights. It’s unacceptable (as the RSC and Elsevier have done) to leave seriously incorrect information on Rightslink.

In the last two posts I have shown examples of how legacy publishers charge additional money for the re-use of CC-NC (“non-commercial”) articles. I have taken examples of the Royal Society of Chemistry and Elsevier, but this is applicable to almost all “closed access” publishers. There’s been quite a lot on Twitter. I have the honour to serve as a member of the Creative Commons (CC) Science Advisory Board so even if I cannot always give a definitive answer I can get one where possible. The area is complex and fuzzy, so here’s a brief introduction:

• “Open access” (OA) is used so widely that it’s operationally meaningless. In particular a reader told that a paper is OA has no definite information about what rights, if any they have.
• CC has created a number of licences which are legal instruments valid in most countries. The following CC-licences may be relevant: CC-BY (attribution required but otherwise full reuse rights); CC-SA (sharealike, reuser have to use the same licence terms – the copyleft approach); CC-NC (Non-commercial), CC-ND (“no derivatives”); CC0 (“public domain” but this may be country-dependent). They can be mixed in many proportions (e.g. CC-BY-NC-ND – forbids any commercial use and forbids derivative works). The use of “under a CC licence” is effectively meaningless in defining “open access” – you have to specify which licence.
• The Budapest Declaration of Open Access (BOAI) defined open access operationally “By “open access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.” This is clear and operationally valid.
• Unfortunately many “OA advocates” have argued and practised that simple visibility somewhere on the Internet is “open access” even though the reader/user has no rights to copy or reuse. This devalues the term so it becomes a political slogan rather than a definition. So a publisher announcing “open access” without a clear legal specification of terms is not providing value to the community. In practice many legacy publishers have a small amount of “open access” whose rights are often extremely unclear. Many publishers do not have a CC licence at all but a series of terms and conditions which are almost always unclear. Writing licences is a specialist business and most hand-crafted attempts will have seriously problems. Moreover they have to be carefully read whereas CC licences are immediately recognisable and do not have to be understood more than once.
• There are a number of people (e.g. Heather Morrison) who argue that CC-NC prevents scholars being exploited. IMO this is completely mistaken and I urge her and others to change their views as the only thing it does is increase the power and revenue of publishers.

A number of publishers have adopted CC-BY as their only Open Access licences. This is to be welcomed. All the mainstream new generation OA publishers (BMC, PLoS, eLife, PeerJ, Ubiquity, etc.) use CC-BY. I argue strongly that any publisher charging authors (APC) should offer only CC-BY. It’s a fair bargain. Authors pay publisher and publisher has no special rights thereafter. As far as I know BMC or PLoS or … has never had any problems of downstream misuse. The paradigms of scholarship and other legal concepts are sufficiently powerful: “passing off”, “fraud”, “plagiarism” are not made worse by CC-BY – in fact the reverse as they can be openly indexed by machines and humans. AFAIK no serious re-use of BMC material (e.g. third parties creating fake journals) has occurred and I am quite sure that BMC would have defended this.

However a number of legacy publishers (traditional subscription publishers with Closed Access) now have APC-supported Open Access. Many of these do not use CC-BY, either writing their own (imperfect) terms or using CC-NC. This blog now deals with CC-NC and the harm it is already doing.

I should applaud many funding bodies (e.g. RCUK) and assessments (e.g. UK’s HEFCE REF) in insisting on CC-BY. In the light of this it is even more worrying that many reputable legacy publishers have developed CC-NC as default or lower-cost option. This is not in response to community desire, but is publisher-led. I shall show now how it hurts authors and readers and serves simply to increase the publishers’ revenue.

First what is “non-commercial”? It’s very poorly defined and hasn’t been tested in court for scholarly publishing AFAIK. It is probably MUCH more restrictive than you think. Non-profits can be commercial – taking student fees is a commercial transaction – the universities increasingly contract to deliver defined products. Before you rush to judgment read:

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information

Gregor Hagedorn 1, Daniel Mietchen 2, Robert A. Morris 3, Donat Agosti 4, Lyubomir Penev 5, Walter G. Berendsohn 6, Donald Hobern 7 ZooKeys 150: 127–149, doi: 10.3897/zookeys.150.2189 http://www.pensoft.net/journals/zookeys/article/2189/

Excerpts:

A major implication from this study is that the definition given in the CC license is ambiguous, since both sides believe that the CC NC license term is “essentially the same as” or compatible with” their definition

Despite a long case history and detailed assessment rules, it is possible that an organization achieves non-profit status in one taxation district, and fails to do so in another. Assessing the non-commercial intent of individual actions in court may be vastly more complicated

So while Richard Kidd of the RSC may think it’s obvious that teaching is non-commercial, I and many others don’t.

However I shall now choose a clearer case of a book author. I’m using the RSC as the example, partly because it’s easy to get the figures and partly because I sincerely hope they will reconsider the use of CC-NC after seeing the harm it does to authors and readers. Lets’ assume I want to re-use an image from an article in a book.

• This is responsible science – often the diagram is the primary means of communicating the science precisely (e.g. points on a graph). The book and science would be poorer without the diagram.
• The diagrams are created by the author (or their software/instruments), not the publisher (a few may redraw the image so they can claim copyright).
• The author wants their work to be read widely and this includes the diagrams.

So let’s assume I am writing a book. This is undoubtedly a commercial activity. I go to the RSC site and ask to reproduce the images in a book

It’s clear – I hope – that I have to consult RightsLink:

This should be absolutely clear:

If I want to re-use 2 OPEN ACCESS APC-paid images from RSC in a book I have to pay nearly 300 USD extra. The author gets no benefit. It is pure profit for RSC and RightsLink.

It’s a serious disadvantage for the author. One likely outcome is that the book author will simply not use image in the book (I know authors who have taken this view). The work might even not be cited. Did the author really understand that the only beneficiary of CC-NC is the RSC?

It’s a serious disadvantage for the book author. They simply won’t use this material.

And CC-NC does nothing to prevent re-use of the ideas in the article as HeatherM suggests – it simply prevents re-use of the image which is bad science.

So science suffers and the only potential gainer is the publisher’s income.

(BTW Rightslink will also charge the same amount for a thesis – don’t take my word, try it.)

So please RSC change to CC-BY. I have no idea why you use it. You can only gain from changing. And I would applaud it (as I have done for other publishers like Springer).

The legacy publishers are not shy of promoting “their” latest articles under the #openaccess twitter tag. Here’s todays from Elsevier. You might think that when an author had paid APCs to publish an article as “Open Access” you’d be allowed to use it for teaching 50 students. But no. I asked for permission – as an academic – to re-use 3 pictures from this article for teaching. And I am to be charged 82 dollars for

Let’s review …

• Bowen and colleagues do some research.
• They draw the diagrams to support the research
• They PAY Elsevier so the whole world can read this

And Elsevier still refuse to allow this to be used for teaching without additional payment.

So what happens?

Either the lecturers break the law and show the pictures to the students. Or they refuse to show the pictures, which is bad education and bad science and immoral.

And no-one except me and a few others get angry. Because after all it’s only taxpayers’ money we are spending anyway.

Nearly a year ago I blogged that the Royal Society of Chemistry was charging ca 100 USD per student for re-use of a 2-page “Open Access” article (/pmr/2012/11/06/royal-society-of-chemistry-will-charge-students-for-re-using-gold-open-access-articles ). The RSC has responded (very slowly) and in June replied to this blog: /pmr/2012/11/06/royal-society-of-chemistry-will-charge-students-for-re-using-gold-open-access-articles/#comment-138142 :

An update, to show we deliver on our commitments:

We’ve fixed the Rights Permissions problem on OA articles. Now also clear licence information on the article, including CC-BY as an option.

e.g. http://doi.org/mt4

So I went back to the article:

Clicked on “Request permissions” and got:

So just the same 100 USD per student. This has been “fixed”? “Delivering on commitments”? Doesn’t look as if the RSC even tried it (it takes 2 minutes to check).

Now I don’t suspect that RSC are deliberately continuing to try to charge people for Open Access articles. But it raises the question of their competence – and probably many other publishers – in assuming that Open Access articles are managed properly. And any errors seem to be in the publishers’ favour.

Today is the first (half) day of Repository Fringe in Edinburgh and we are having Workshops. Chris Gutteridge from Southampton is running one on Consuming Linked Open Data:

RDF & Linked Open Data are terms becoming more common in the repository community, but what are they and why should you care?

Open data is only useful if people are using it! This workshop will give a hyperbole-free introduction to using the technologies. Attendees will learn how to use PHP to consume RDF data and do useful things with it, including doing some stuff with bibliographic data.

This workshop will be run by Christopher Gutteridge, developer of the award winning University of Southampton Open Data Service and more recently founder of data.ac.uk, and Patrick McSweeney, notorious University of Southampton developer.

Requirements: ideally you will bring your own laptop with PHP installed (Apple & many Linux machines will have it installed by default), and a text editor. Don’t panic if you don’t have any PHP programming experience, you are welcome to buddy up with somebody who does.

Well, I like workshops and want to help make them successful so I signed up and the numbers have since trebled.

I must admit that I have no use or linking for PHP. It’s a broken language for Unicode – and I do a lot with Unicode. And it’s possible to write very bad code. But hey ho… So I went to find an installation for Windows and got into one of those chains…

“Cannot find MSCV01.dll”. Search on the web. “You must install Visual Studio C++”. What??? I thought I had seen the last of Visual Studio when Chem4Word finished. So try more search. “You need an Apache server”. You can’t install that without FTP, Fake Email Server, Tomcat, Perl and goodness knows what. So I have installed about 8 things I didn’t want to get something I didn’t want running…

But I am approaching the workshop in a very positive spirit and can now help other attendees install the same stuff…

Ok – what and why is Linked Open Data? It’s described by a mug:

The most important thing is that

THE DATA ARE ON THE WEB

The problem is that most academics don’t put their data on the web. Most academics just let their data decay. Governments are telling them that they must have data management plans. Academics ignore them. This isn’t true in bioscience or crystallography or astronomy. But:

THERE IS NO MATERIALS SCIENCE DATA ON THE WEB.

None.

Not quite true. Wikipedia is doing a great job of systematising data. But they can only do what people make available.

OF THE SEVERAL MILLION CHEMICAL SYNTHESES REPORTED EACH YEAR, HOW MANY ARE OPENLY AVAILABLE?

(Guess).

OK, let’s move to biodiversity. After all the future of our planet – in some part – depends on knowing about species and ecosystems. 10,000+ phylogenetic trees are published each year. How much of that data is on the web? Guess.

Wrong! It’s not zero. It’s 4%!

Linked Open Data is a great idea. I support it.

But you can’t link data when there isn’t any.

Well, like the first telephone, one site by itself is not much use. It’s not Linked Open Data, it’s LINKABLE. To be linkable the data provider has to:

• Understand the data on the site and have a formal description of each bit (“semantics”). It’s no good labelling it “tree” if you don’t know whether it’s a tree preservation order or a phylogenetic tree. You need some formal of vocabulary. (Posh word is “ontology”).
• Give each bit of data a unique identifier. The posh name is “URI”. If you make it unique on your site and combine it with the domain name that’s roughly what a URI is.
• If the chunks of your data have relevance to other chunks of your data you can add links. Then the site is an example of internally linked open data.

But the real value of LINKED comes when others to link to it. And for that you have to:

• Create data that other people want
• Make it easy for them to find it and use it

And that’s very difficult. Because the academic system implicitly tells people not to do this. No reward points. So no-one does it.

Well I and my group did it. We made 200000 computational chemistry calculations available in DSpace. It was too difficult to use. It’s months of wasted work.

We’ve tried again, this time on our own server, with RDF!

No-one want to use it.

We’ve done the same for crystal structures. And now Ross and I are going to do the same for phylogenetic trees.

We are mad. We are hoping that the huge interest in Open Data (data.gov.uk, data.gov, etc) will lead people to start linking data sources. We are hoping that people want phylogenetic trees. We never learn.

The time is coming. At some stage scholars/universities will realise the value of domain repositories. Will they help support them? In the way they have poured money into Institutional Repositories? I doubt it. So the value has to come from funding bodies governments and – I think – foundations like Wikimedia who are years ahead of academia in their thinking.

Anyway today Chris is pointing us to bibliographic data. JISC supported us to create #openbib some years ago and we helped national libraries to Open their metadata and to create a protocol (BibJSON).

See you there at 1400

Ross Mounce @rmounce and Joseph W Brown have been tweeting about the lack of data to support published phylogenetic studies. (Readers of this blog will know that Ross and I start work in October to extract trees from published PDFs – an awful statement of how bad the situation is.)

Very simply, phylogenetic data is key to our understanding of the history, ecology and biodiversity of the planet. If we don’t understand species then we shall lose them, and if we don’t understand how species interact we shall lose ecosystems. Look into the details of pollination and often the loss of one species affects others directly. (Though Darwin was wrong about cats->->-> clover http://triscience.com/Species/Field/the-cats-to-clover-chain/doculite_view ).

Most peer-reviewed phylogenetics is in closed journals (40 USD for a 1 day read). It’s appallingly arrogant to assume that anyone who needs it (academics) can get the info. But worse, almost none of the data are published. Phylogenetic trees are mainly computed using molecular information (DNA of key genes) and are costly. Yet the data are relatively simple. They are well understood (30+ years of sequence / gene repositories) and they are compact (accession numbers are often fine). An uncompressed tree costs perhaps a few Kb and with indexing/compression a complete study could be published in ca 1 Mb. That’s less than the size of many single images!

Here’s what sparked the discussion. http://www.botanyconference.org/engine/search/index.php?func=detail&aid=167 I’ll give it in full, and argue that any reasonably literate person could understand it. I have highlighted some parts

Missing data lead to holes in the tree of life.

The fundamental importance of archiving scientific datasets has received increasing attention over the past several years, and failure to properly archive data can adversely affect study reproducibility. However, in plant systematics (or evolutionary biology) there has been no comprehensive review that examines the deposition practices of the underlying phylogenetic datasets and trees that are the foundation of the discipline. Furthermore, there is little understanding of how the deposition rate of DNA sequence alignments and phylogenetic trees has changed over time. In the process of gathering data to build the first tree of life for all ~1.9 million named species (the Open Tree of Life Project), we sifted through over 7200 peer-reviewed phylogenetic studies published between the years 2000 and 2012. Our survey covered over 100 journals and included publications focusing on green plants, animals, fungi, microbial eukaryotes, bacteria, and archaea. This broad survey included 1243 seed plant publications. Overall, we found that only 17% of examined studies made nucleotide alignment data and/or trees available in an accessible repository such as TreeBASE or Dryad. Within seed plants, only 24% of studies from the past 12 years have been archived. Furthermore, most corresponding authors (54% for seed plants) that we contacted for un-deposited datasets and trees did not respond to our repeated (2) requests for data. Thus, most of the trees and alignments produced during the past several decades is essentially lost forever. The plant systematics community needs to significantly improve data deposition practices to ensure that crucial data (trees, alignments) are archived and thus freely available to other interested scientists. Our results illustrate that voluntary data submission policies have not worked, and dictate the urgent need to adopt new policies requiring public archiving of DNA sequence alignments and trees in a routine manner as is done routinely with raw sequence data. These stark findings should encourage the systematic community as well as journal editorials to adopt data sharing policies that require deposition of alignments and resulting phylogenetic trees in established databases prior to publication.

Very simply (this applies to many subjects):

Many/most authors don’t care about making their science available to the world. The final result of their work is a “scholarly article”, not useful, reusable, verifiable science that can be built on, re-used by policy makers and citizens. The authors do not feel that being publicly funded gives them any obligations to the public. The ivory tower only rewards their work in the torrid market of scholarship, not the wider value to the world.

It has worked in some subjects – sequences/genes, crystal structures, galaxies. Here the disciplines have developed cultures where scientists are expected and then mandated to deposit data. The commonest ways are (a) on publishers’s websites (e.g. crystallography) and (b) in domain repositories (e.g. sequences).

Making phylogenetic data available for each study is technically straightforward. The bytecount is insignificant in today’s world. The standards and protocols (e.g. nexml) exist. The problem is 99% a people problem.

The problem is community. In some cases the learned societies are more concerned to generate income than to service science (Where are the publishers that actually make subscription material available to the world within – say – 6 months of publication?) Many are actually making it more difficult. The last 12 months have confirmed that most legacy publishers are part of the problem, not the solution.

So how, if publishers are antagonistic or indifferent to requiring publication data do we manage it? The Universities are totally vapid today – they have shown no leadership. So the only clear path is funders mandates.

And that will work. I’ve seen the pressure in the US that the NSF mandate on data management has applied and I think it’s starting to work. That’s got to happen everywhere. So my message to funders is:

Mandate the deposition of data at time of publication. And if not, chop 10% off the grant.

That works. It’s a lot of work, but it’s a trivial amount compared with the current loss of data (which I estimate as >> 100 Billion USD per year).

We are going to the Repository Fringe this week and are going to present a PechaKucha. What’s that? It’s 20 slides of 20 seconds each that change automatically. So 400 seconds in all. And the first one has to introduce you and that last says thanks. You can see some past ones at http://www.youtube.com/playlist?list=PL692EDA7EE606D73C.PMR has a slot called “Capturing and Publishing Scientific Data”. He’s asked us [#animalgarden] to create the slides

We’re #animalgarden – we make photocomics about openness. Here’s one we made about #openbibliography. /pmr/2012/09/14/animalgarden-at-digital-research-2012-openbiblio-and-bibsoup-and-okfest/. It won second prize. (We don’t do it for the prizes, we do it because we like making photocomics).

PMR doesn’t think Institutional repositories work for scientific data (or publications). He thinks we need domain repositories (e.g. proteins, galaxies, phylogenetic trees, molecules, crystal structures, materials, etc. So we’re going to present the issues as a photocomic.

We all take different roles

Here’s Chuff (the OKFN Okapi) advocating open data, clean penguin being a hacker, and OWL (geddit?) representing the Semantic Web. We’re thinking about props and roles (PMR hasn’t worked out the story yet).

Back to work … See you at #rfringe13