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 (http://blogs.ch.cam.ac.uk/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: http://blogs.ch.cam.ac.uk/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?

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. http://blogs.ch.cam.ac.uk/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

We are currently processing the applications for our Panton Fellowships (sponsored by CCIA – http://en.wikipedia.org/wiki/Computer_%26_Communications_Industry_Association to whom many thanks). On Thursday Michelle Brook and I worked on this in C4CC – the OKFN’s London hangout:

Firstly many thanks to everyone who applied (and those who spread the word). Obviously we won’t give any personal details at this stage. This year we expanded the eligibility to “Europe” and we’ve had applications from north east south west which is very gratifying.

It’s a pleasure and privilege to read the applications (and I’ve read them thoroughly). People are doing exciting things and having exciting ideas. We appreciate the time you’ve put in.

The Panton Advisory Board (which does the analysis and selection) includes Tim Hubbard, Cameron Neylon, Rufus Pollock, John Wilbanks and myself and is serviced by Michelle. The remit of the Fellowships is broad – it should be based on the ideas of Panton (Open Science Data) and should further those aims, but we looking for applicants to come up with new ideas – and we aren’t afraid of risk. It’s important that the Fellows engage with a community and aim to make an impact but we don’t constrain how. Although it’s absolutely not required it’s gratifying to see applicants who have already come up with ideas and tried them.

It’s very difficult to judge people from a CV and a paper proposal so after an initial selection we ask a short list of applicants to prepare a short video or similar as a complementary way of showing themselves and their ideas. This isn’t judged on technical quality but how the person and idea come over (i.e. you don’t have to hire a specialist! – phones and PCs have reasonable cameras. ) If you can’t read the detail, then it shouldn’t be there!

And I wouldn’t ask anyone to do something I wouldn’t. Two years ago I applied for a Shuttleworth Foundation fellowship which required a 4.5 minute video. The timing caught me in the wilds of Washington State (PNNL) without a video camera. I re-used some existing footage and got enormous help from Jenny Molloy. She used the services in Oxford Computing Services – each night she would edit the latest version and send it to me (9 hours out of phase). So there was only one turnround a day – I would make some written comments and we might have a short Skype. I think it actually turned out quite well.

When I got back I found I had been selected for the next stage and had to make a different video. I couldn’t impose on Jenny, so I found out how to do it on a PC. And it was nowhere near as difficult as I thought. I used “Windows Live Movie Maker” as an editor (which came bundled with the machine). I’m not promoting this product but it worked for me in a rush. I could shoot and edit and release as WMV files (these cannot be read everywhere and I have since moved to using the FLOSS Handbrake for converting to better more compact more universal formats such as MP4).

I didn’t get a Fellowship, but the experience was really valuable. It sharpened by ideas and my technology hugely. Most competitive grant applications are unsuccessful – this is due to competition and not necessarily because they are flawed. So if you are a current Panton applicant and aren’t selected don’t regard your application as necessarily bad. And perhaps look for somewhere different to apply to with a (possibly modified) proposal.

With tools such as Doodle, Googledocs and Skype it’s easy to get synchronous and asynchronous communication over a few days. At least 2 and possibly more Board members are out of the country so we have to aim for restricted hours for Skype – but we’ve done this before and it’s universal in OKFN activities.

Thanks again to all applicants.