Wesabe's Open Data

Because Glyn Moody commented on my blog I visited his and found another concern about Open Data:

Monday, September 3, 2007

Should “open source” include open data?

[From Matt Asay .. general manager of the Americas and vice president of business development at Alfresco, who has nearly a decade of operational experience with commercial open source and regularly speaks and publishes on open-source business strategy. He is a member of the CNET Blog Network. ]I just read Glyn Moody’s post on the importance of open data and, increasingly, open source, in science. Good science requires good data – data available to any who want to replicate another’s results and ensure that true science is going on, not pseudo-science.
Marry that to Tim O’Reilly’s insistence that data, not code, is the new lock-in (and cross that with my own declaration that Microsoft’s new platform for lock-in is Sharepoint, not Office), and you end up with what I think is an implicit, urgent need in open source today:
The need to ensure data remains free/open.
I’m not speaking for the Open Source Initiative here, but to me this makes it critical to add open data provisions to the Open Source Definition. Why? Because open source that locks down one’s data is not all that open, in the grand scheme of things.
As some others have suggested, I, too, believe that Wesabe’s Open Data Bill of Rights is a good start. It requires:
  • You can export and/or delete your data from Wesabe whenever you want;
  • Your data is your data, not ours. Our job is to help you understand and act on your data;
  • We’ll keep all of your data online and accessible for as long as you have an account. No “archive access” charges;
  • Any data you want us to keep private, we will.
  • If a question comes up not covered by these rights, we will answer it remembering that your data belongs to you.
Simple and yet powerful. It means, essentially, that getting one’s data/content out of Wesabe is as easy as putting it in. This is obviously good for the customer, and maybe makes monetizing user data more difficult than it otherwise would be. Too bad.
Open data should be an inalienable right that customers should expect from their vendors, whether the product is consumer-focused financial services (as Wesabe is) or enterprise-level content management software (as Sharepoint is).
Is there any downside to expanding the Open Source Definition to include data rights? Or should that be an entirely different body that approves data policies, separate from the OSI?
PMR: Yet another example of a community realising it needs Open Data (see WP). I hope that groups like this will help to expand – or constrain the definitions and usage of “Open Data”. When I launched the WP page and the SPARC Open Data list I was thinking primarily in terms of scholarship, but it’s clear that we also need to manage many other sorts of data.
I’m personally convinced we need a separate approach from Open Source – there are many issues that it cannot cover easily. That is, for example, why I support the Open Knowledge Foundation (WP) and use their “Open Data” logo on some of our output – others use Creative Commons. Neither is ideal but a great deal better than nothing.
In the example above there is a fairly close idea of customerclients, whereas in science there is much more likely to be researcherscientists – almost the inverse relationship.
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Miss PRISM has a rat up her pants

Alma Swan is one of the most insightful scholar/researcher/facilitator/commentators in the scholarly communication arena and I am delighted to be collaborating with her (on an Open Data project). Her writing is always careful and attractive to read. I’d tried to cut some out for brevity, but can’t…


I know that I am late in writing about the launch of PRISM, the coalition of publishers and, well, publishers, that purports to represent ‘research integrity’. I hope I don’t sound too new age if I say I was exploring my reactions to their opening salvo. I know a lot of bloggers and journalists have had a field day doling out ridicule, and others have patiently demolished PRISM’s arguments point by point (once again), and yet others have given vent to outrage. I’ve decided that primarily I just feel very sad and, secondarily, disappointed.

Why? Because of the level of dishonesty and distortion in PRISM’s language, primarily, and because of further evidence that the partners in this ‘coalition’ are just not doing what I had hoped they would eventually do, which is to see clearly and act well. […]

Until PRISM, it still seemed that these companies, if not exactly the most popular kids on the block, at least maintained some absolute integrity. They do what such businesses are meant to do – they maximise their profits, they operate within the law, they look after their employees. I speak from the perspective of one who, along with the rest of the staff of Pergamon Press (and other companies under the Maxwell Communications Corporation umbrella), once had to digest the news that many years’ pension contributions did not, anymore, reside safely in our pension scheme, did not reside anywhere in fact, but had been spent by our erstwhile employer to prop up his failing businesses. By that time, though, we had all become employees of Elsevier Science which announced – gratifyingly swiftly – that Elsevier would restore the shortfall for us all. The company was under no obligation whatsoever to do this, but it did, with no hesitation. That’s really honourable.

PMR: It is very important to give credit where it is due. Companies are not intrinsically immoral – they are made up of people. But large companies cannot easily integrate the morals of their components

Many people argue for Open Access on the grounds that publishers make too much profit, but that is skating on very thin ice. There are very good reasons for Open Access but this isn’t one of them. Most of those who argue that way live in capitalist societies and implicitly accept that the profit motive drives their country’s economy, local small businesses and personal effort (outside the public sector). And for those in the public sector who may consider themselves above all this, it would be rare for their own personal financial situation not to be tangled up with the fortunes of companies such as the big scholarly publishers. The custodian of the other large chunk of my own pension contributions is the Universities Superannuation Scheme in the UK, which of course holds Reed Elsevier shares in its equities portfolio. Anyone who has worked for any length of time at a British university has this kind of stake in Elsevier. And since Reed Elsevier is also listed on the NYSE, this probably holds true for US public sector employees as well. Elsevier’s profits, then, are going to help fund all our old ages. What a cosy thought.

But aside from this extreme example of self-interest, commercial businesses have a profit motive and that’s that. They are just doing their job. And yes, I know all the arguments about how this particular market doesn’t work properly, but we can’t expect businesses operating in it to come over all soppy and turn themselves into public services.

PMR: Yes. There is a real need for new business services in this market. There is no shortage of legitimate ways to make lots of money.

That, however, is exactly what they appear to be trying to do in this PRISM blurbage. And they are not only portraying themselves as mediators and curators of the integrity of research (and they know full well that the term ‘research integrity’ already has a very specific, community-embedded usage) but as custodians of the moral high ground. Their language is carefully contrived to tell untruths in the most plausible way. Phrases like ‘surrender to the government’ do sound risible, I know, and my first reaction was to giggle, but the more I read, the more incredulity settled upon me. The PRISM publishers (it is not clear who exactly they are but the list of members of the sponsoring body, the AAP, is long and includes the big commercial publishers, scholarly societies and university presses) are conflating peer review, governmental influence in the form of legislation that all publicly-funded research results should be freely available (spectacularly termed ‘censorship’ at one point: hey, don’t hold back, PRISM publishers), creator copyright, and preservation all into one argument, which is essentially that without the current scholarly publishing ‘free market’ [sic: their terminology] the whole shebang would implode. They know very well that it won’t, that peer review continues as usual under an Open Access model, and that there is no question of censorship by government. There is even an attempt to equate Open Access with ‘junk science’. Dishonourable conduct, ladies and gentlemen.

PMR: The core of the problem.

Should we be surprised, after the Dezenhall/pitbull revelations? Frankly, yes. Seeing what advice such a person would come up with was a legitimate tactic, worth exploring, and par for the course in the world of big business. Wherever there are lots of dollars to be made, play gets tough. There is, though, a difference between playing tough and playing dirty. Dirty this is, and that’s one reason why I’m sad about it all.

Pat Schroeder, quoted on the PRISM website says: “We want to share as much scientific and medical information as possible with the entire world. That’s why we got into this business in the first place.” No, ma’am. Your business works by restricting access to the information you have in your grasp. As long as that is your business model, you can’t claim the opposite. You got into the business to do what such businesses are expected to do, which is to make money. There is nothing shameful in that, but there is in telling porkies.

PMR: and again.

I said I was both sad and disappointed. The reason I am disappointed is that in their focus on obstructing Open Access the PRISM publishers are playing the wrong game. They are busy tying string round their ankles in case the Open Access rat runs up their pants, while ignoring the bull elephant that has stomped into the room. Open Access to research articles is going to happen, but it is surely not the most significant issue for scholarly publishers. Other things are going on that mean a much more fundamental change to what the PRISM publishers term ‘the whole scholarly communication process’. Along with a raft of threats, those things offer up a whole host of opportunities for publishers who are uniquely placed to solve the problems that will roll along with the changes, all the way along the value chain. I’d really like publishers to look a bit more strategically at the course of events and use their business skills to capitalise on them, providing for the research community the new services it will need over the next decades. A few, and two big publishing names in particular, are already doing so. Let’s hope others follow. There are a lot of moving targets, to be sure, and that invokes nervousness. At such times, one nervous twitch can mean shooting yourself in the foot (viz PRISM). Better to put the gun down and do something constructive. Many pensions could benefit.

PMR: As an (ex-)experimental scientist I make the analogy with scientific suppliers of instruments, chemicals, genekits, software, etc. These markets generally work well. There is competition, niche products, etc. Most scientists appreciate the ease of buying a kit that does something that used to take days. They pay what the market will bear. They buy image plates to measure diffraction and solve crystal structures.
What they expert the manufacturers to do is tell the truth. What are the compounds in this pack? What is the angular limit of this instrument? etc. Lying – or hype – lasts for only a short time – the market will determine the reality. And in the era of the Internet it takes only minutes to debunk a product.
The supreme irony is that the PRISMoids’ primary products are quality and integrity. And this is precisely what they are destroying before our eyes. They claim to be the guardians of quality – better than amateurs or governments. But one look at their Open Access products shows shoddiness, don’t-care, incompetence. And this now permeates their thinking. They rely on monopoly and restrictive practices – incredibly risky because when (not if) this bubble bursts they are left with nothing.
Leaving idealism aside and to echo Alma’s theme, PRISM is simply really awful business practice which is destroying their market.

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CrystalEye: a crystallographic knowledge base looking for collaborators

Egon Willighagen asks about collaboratin on Nick Day’s CrystalEye knowledgebase.  I reproduce his post – note that CrystalEye should be able to provide many examples to increase the size of data sets – and then discuss some of the advantages of using CrystalEye over conventional closed databases.

Automatic Classification of thousands of Crystal Structures

Clustering and classification of crystal structures is hot. Parkin hit the front cover of CrystEngComm with a story on Comparing entire crystal structures: structural genetic fingerprinting (DOI:10.1039/b704177b). Now, the story itself, while rather interesting and well written, has three major flaws:

  1. the data set it way too small
  2. the proposed proof-of-concept is not novel at all
  3. they do not cite me

Well, the latter sounds a bit boohoo, and it is 🙂 (BTW, I do like this paper.)
The propose the work as proof-of-concept, but use a very artificial data set of only 12 crystal structures (benzene and eleven polycyclic aromatic hydrocarbons, like naphtalene, anthracene, phenanthrene, triphenylene, pyrene, perylene, and coronene). While such a small set does make a nice example where you can still list all similarities (0.5*N*(N-1)), it is really too artificial.
Now, you may wonder if I am in the position to criticize this shortcoming, but I think I am. As part of my PhD work, I analyzed this problem myself, and published two years ago the paper Method for the computational comparison of crystal structures (DOI:10.1107/S0108768104028344). Apparently, Parkin was not aware of this publication and did not cite it. I should have went to a crystallography conference with a poster, and advertise my work more. In this paper, I analyzed a data set with 48 crystal structures, manually validated by visual inspection, resulting in having to compare 1128! crystal structure pairs. Took me two full weeks behind a Silicon Graphics. Yes, I really understand why the took only 12 structures 🙂
However, there is more prior art. While my approach was based on a new radial distibution function-based whole crystal structure descriptor, my supervisor (Ron) used the more common powder diffraction pattern and showed in Representing Structural Databases in a Self-Organising Map (DOI:10.1107/S0108768105020331) it to be a good enough descriptor for clustering of thousands of crystal structures using a self-organizing map (SOM).
Last week, my second paper in crystallography appeared: Supervised Self-Organizing Maps in Crystal Property and Structure Prediction (DOI:10.1021/cg060872y). In this paper, we show how supervised SOMs (see DOI:10.1016/j.chemolab.2006.02.003) can be used for supervised classification and even for property prediction. Note that these supervised SOMs are truely
Finally, another advantage of this last work: the code is open source. The code for the unsupervised SOMs is available as R package: kohonen; and for powder diffraction patterns: wccsom. Details can be found in this R News issue. The first package is not actually limited to crystal structures, and can be used for any clustering problem. However, the articles mentioned here make use of simulated diffraction patters, and I am not sure there are open source tools to generate those.
BTW, I would still be interested in teaming up with CrystalEye in one way or another, and couple these data analysis methods to live streams of new crystal structures. Nick, let me know if you are interesting in idea exchange.
Getting back to Parkin’s paper, I do like the work. Hirshfield surfaces are an interesting tool to visualize packing characteristics, and using them to describe a crystal structure sounds like an interesting idea indeed. I just hope that the method properly scales.

PMR: We would be delighted to see if CrystalEye can be used to help. A word of warning – Nick starts writing up at the end of this month and so the amount of effort is limited. However it would be great to be able to run – or re-run your study.
We see CrystalEye as part of the next generation of crystallographic knowledgebases. It already abstracts all current crystallography unless the publishers (Elsevier, Springer, Wiley in particular) prevent us doing this. It has several novel advantages over conventional compilations.

  • It is free/Open to use in all senses
  • it integrates inorganic and organic papers
  • The complete experimental data (CIF) is available
  • there are links back to the original publications
  • it is available in RDF
  • all new strucures, and parts of structures, are available in RSS feeds
  • it integrates the Crystallographic Open Database and identifies duplicates
  • All data is available in XML-CML
  • The chemistry has been automatically extracted and analysed giving a complete set of bond orders, charges where possible and chemical structure
  • The structure can be decomposed into moieties (individual disjoint molecules or ions)
  • each has a Jmol display with links to bond lengths, angles and torsions
  • There will (soon) be complete histograms of all bond lengths with hyperlinks to all entries
  • The major crystallography sources of “error” – disorder, constrained refinement, etc. are automatically identified.

Joe Townsend has developed a protocol whereby he can – with 99% accuracy – reliably identify those structures which have errors in coordinates less than 0.01 Angstrom. This is good enough for almost all modern crystal and chemical structure analysis. It means that chemical deductions can be reliably drawn from such structures without worrying that you are merely analysing experimental errors.
We have an automatic program of computing these strucures by QM programs – GAMESS and MOPAC. These will initially identify any structures where computation and experiment disagree. In practice almost all the disagreements (for organic molecules) have been due to experiment, meaning that calculation is an effecfive means of checking the validity of structures.
There is a large, tested, library of crystallographic software (CIF2CML and JUMBO) which deals with symmetry, geometry, bonding etc. This makes it easy to ask and answer many questions rapidly with small Java programs. Moreover CrystalEye has been translted to RDF so that the full power of the semantic web can be brought into play.
There are at least two funded collaborations just starting which will use CrystalEye and we have several offers of contributions from individuals and organisation (e.g. of theses).  Please let us have ideas.

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The right to roam and the right to read – should we use civil disobedience

I have spent a splendid week in Scotland to celebrate 40 years of the University of Stirling where I was one of the first staff. Before the celebrations we spent 4 days in the mountains in which there is now an official Right to roam. This contrasts strongly with the lack of a right to read.
Shortly after I moved to Stirling I went to climb Ben Vorlich by a footpath marked as public by the Scottish Rights of Way Society. Half way up I was met by a gamekeepr with a gun who threw me off the land – my rights were less powerful than possession of the land and the gun. Now, by contrast, I found well managed access – the landowners have a “Hillphones” system where you can ring to find out where stalking is taking place and which alternative routes are open. There are welcome notices explaining the purpose and methods of the farm and its land, and offering a code of conduct of mutual value.
How did this change come about? By a change of heart of landowners? In part, certainly – as communication becomes universal we listen to more arguments and appreciate different points of view. But also through legislation. Driven by the vision of our parliamentarians? Not really. Driven much more by a major act of civil disobedience, the Mass trespass of Kinder Scout. From WP:

[Kinder Scout] is a popular hiking location and the Pennine Way crosses Kinder Scout and the moors to the North. This has resulted in the erosion of the underlying peat, prompting work by Derbyshire County Council and the Peak District National Park to repair it. The plateau was also the target of the mass trespass of Kinder Scout in 1932, which resulted in a UK-wide rethink of access to public footpaths. From the National Park’s inception, a large area of the high moorland north of Edale was designated as ‘Open Country‘. Eventually, in 2003, the “right to roam” on uncultivated land was enshrined into law, and this area of open country has been significantly extended.

and:

The mass trespass of Kinder Scout was a notable act of willful trespass by ramblers. It was undertaken at Kinder Scout, in the Peak District of England, on 24 April 1932, to highlight weaknesses in English law of the time. This denied walkers in England or Wales access to areas of open country, and to public footpaths which, in previous ages (and today), formed public rights of way. Political and conservation activist Benny Rothman was one of the principal leaders.
A commemorative plaque now marks the start of the trespass at Bowden Bridge quarry near Hayfield (which is now a popular area for ramblers). This was unveiled in April 1982 by an aged Benny Rothman during a rally to mark the 50th anniversary. The trespass proceeded via William Clough to the plateau of Kinder Scout, where there were violent scuffles with gamekeepers. The ramblers were able to reach their destination and meet with another group. On the return, five ramblers were arrested, with another detained earlier. Trespass was not, and still is not, a criminal offence in any part of Britain, but some would receive jail sentences of two to six months for offences relating to violence against the keepers.
The mass trespass had a far-reaching impact, some of which is still playing out today. Eventually, changes in the law would allow all citizens access to public footpaths, regardless of whether they crossed private land. This culminated in the Countryside and Rights of Way Act 2000, which legislates a limited right to roam over scheduled access land (see Open Country).

PMR: The land rights of the nineteenth century are similar to our current copyright laws. These latter are complex, counterproductive and generate widespread. frustration and hostility. For example when I talk with a librarian colleague they tell me that I cannot photocopy an 85 year-old scientific paper because it might violate copyright. The British LIbrary appears to have a universal system where it is easier to copyright everything rather than tackle the copyright problem head-on. I never use Internlibrary Loans because of their stupidity in the Internet age, but an ex-colleague at Stirling told me she had just got an electronic ILL. She could only read it once – after that it would self-destruct – mission impossible.
Will librarians try to help us break this cycle of impotence rather than kowtowing to it. If not I suspect that coordinated or uncoordinated civil disobedience will become widespread. I’d prefer it to be coordinated.
And please, please, don’t wait 70 years until the law is changed.

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Blogs are Weapons

From BoraZ:

Blogs are Weapons

Sunlight is the best disinfectant. And many bloggers’ eyes and typing fingers bring a lot of sunlight to whatever anyone is trying hide. This makes bloggers dangerous to many entrenched and powerful interests.
Not that bloggers are Martians, recent arrivals on this planet, to be treated as a ‘special interest’ group. Bloggers are people. And the Web gives people the ability to say what they think, to report what they see, to fact-check the PR outfits, to use their own individual expertise to parse others’ arguments and, yes, to point fingers at the guilty.
And in many countries around the world, this is well understood. And acted upon. Harshly.
Here in the USA, some efforts have appeared here and there to place bloggers under some tougher laws, but that did not fly here. Op-eds against bloggers appear with some regularity, with the only result that the author has his/her reputation stained forever (google: Skube; google: PRISM; for just the two most recent examples of the power of blogs to uncover the truth, make it available to millions forever, and in the process make everyone know who the bad guys are).
Bloggers elsewhere have a much tougher time. As in “much, much tougher time”. Just read this post by Mo.
Web is global. If a blogger somewhere gets imprisoned and tortured for telling the truth to the power, we need to speak up in defense and shame the entire country for it. It worked on Libya (google: Tripoli Six). It should work on others as well.
Remember: bloggers are people. And for the first time in history, people have a voice that can be transmitted to the entire planet in a matter of minutes. This is an immense power. We need to use it to do good.

PMR: I have been forced – reluctantly – to use military terms such as “battle” when discussing the blogosphere’s reaction to PRISM. It is a case of asymmetric warfare. We conduct our campaign by collating facts, analysing arguments and publicising them. We also use blogs as a means of gathering support and coordinating it. The blogs are part of our command-and-control.
But the PRISMoids do not fight on this battlefield. So far it is unclear where they will choose to fight, but it appears to be the golfcourse, Washington clubs, the The Corridors of Power and other places where lobbying takes place. By default blogs are largely ineffective here. So while they are one of our weapons, they are not sufficient.
Perhaps we have to consider – however reluctantly – Civil disobedience.

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OUP wants me to pay for my own Open Access article

I have been dismayed (previous post: “Open Access”) at the lack of commitment to OA by mainstream (primarily toll-access (TA)) publishers and have described this as a “systemic failure” of the industry. Here is another unacceptable lack of clarity and commitment from an Open Access journal from a major publisher. I had been investigating OUP’s site for another reason (PRISM: Open Letter to Oxford University Press) and since I had published with them thought I would have a look at papers I had written (“I” and “my” include co-authors). This is what I found (screenshot):
oup.PNG
The electronic article is accompanied by a sidebar with “request permissions”. I followed this and the result is shown above. The journal wishes to charge me 48 USD to:

  • USE MY OWN ARTICLE
  • ON WHICH I HOLD COPYRIGHT
  • FOR NON-COMMERCIAL PURPOSES (TEACHING)

The journal is therefore

  • SELLING MY INTELLECTUAL PROPERTY
  • WITHOUT MY PERMISSION
  • AGAINST THE TERMS OF THE LICENCE (NO COMMERCIAL USE)

I am lost for words…
… the only charitable conclusion I can draw is that the publisher ritually attaches the awful Rightslink page to every article automatically and that this is a genuine mistake. I have found such “genuine mistakes” with other publishers in their hybrid journals (i.e. where only some of the papers are OA, the majority being toll-access TA). But this is a fully OA journal – all papers are OA – I assume CC-NC. There is no excuse for including the Rightslink page on ANY OA paper, let alone every one on a journal.
If this is – as I desperately hope – a genuine mistake then my criticism might seem harsh. But it is actually part of the systemic failure of the industry to promote Open Access. And I hope that OUP can and will clarify and rectify the position. If, however, it is deliberate and that the publisher actually intends to charge readers and users for Open Access articles I shall reserve comment.
This is not a trivial point. The normal reader of a journal who wishes to re-use material has to navigate copyright constraints and restrictions on an all-too-frequent basis. Such a reader, especially if they were relatively unaware of Open Access could easily pay the journal for “permission to use an Open Access article for teaching”. (Note that other charges are higher – to include my own article in a book I write would cost nearly 350 USD).
It is all indicative of an industry that simply isn’t trying hard enough.
RECOMMENDATION:
OPEN ACCESS ARTICLES ON PUBLISHERS’ WEB PAGES SHOULD NEVER BE ACCOMPANIED BY RIGHTSLINK OR OTHER PERMISSION MATERIAL. INSTEAD THE PUBLISHER SHOULD PRO-ACTIVELY POINT OUT THE NATURE OF OA AND ENSURE THAT THE READER AND RE-USER IS FULLY AWARE OF THEIR RIGHTS.
After all, the author has paid for this…

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"Open Access" reported in Information World Review

Tracey Caldwell of Information World Review has reported on the discussion in this blog  about  (hybrid) Open Access as  follows:
Scientific data should be freely available for re-use and OA policies need clarity

[…] Peter Murray-Rust has blasted publishers for “a systemic failure to embrace open access”. He warns that anyone who purchases author-pays Open Access content may end up paying a lot of money for something not labelled as Open Access.
In an emotive posting on his blog he resigned from one journal after finding that Springer had retained the copyright after authors had paid $3000 to make their papers Open Access.
“I am a scientist who believes that there is a major advance taking place with data driven science, using data as a primary route to understanding. I believe all scientific data should be published openly, relying on the BOAI declaration which implies that any data associated with open access should be openly and freely used without any permission,” he told IWR.
Murray-Rust was researching publishers to see to what extent they were enabling and encouraging the re-use of scientific data. When he looked at publishers with author pays business models he was shocked to find how imprecisely their open access policies were worded and the lack of clarity about data.
“I had assumed Open Access meant the author would retain copyright and Open Access would be enabled by the journals adding licences such as Creative Commons,” he says.
Jan Velterop, Springer senior director of Open Access, said, “I disagree with Murray -Rust that the Open Access is not clear. If it is open, it is open and that is clear. There are flaws in the way that is presented and we are addressing that technically. If it is a new article that is Open Access the author’s name will be on the copyright line. If it is retrospective, Springer’s name will be on the copyright line as it was before, as we don’t want to change the printed record.”
He added, “We have made some changes as a result of this as we will refer to the Creative Commons licence used in the article itself.”
Velterop does not have high hopes of the publishing community working together to create a consistent and proactive Open Access policy: “It is difficult as these things need co-ordination and the publishing industry is analogous to the scientific community in that it is fairly anarchic.”
Murray-Rust asked all the publishers to respond to his concerns but by press time only Springer and Libertas Academica had done so. “It is difficult to escape the conclusion that that the publishers do not have their hearts in this process and want to keep their options open,” said Murray-Rust.

PMR: Thank you Tracey for a balanced piece (my quotes were given over the phone). You are right, I was emotive, as the issue took me by surprise at the time and now I have got used to the realisation that this is a much bigger problem than I thought. It is, indeed, systemic in the publishing industry. And I think that JanV makes an accurate assessment when he says he does not have high hopes of the industry creating a “consistent and proactive Open Access policy”.
I should make it clear that I have no criticism of those publishers who espouse OA completely. BMC, PLoS  and Beilstein Journal of Organic Chemistry are examples of this. Libertas Academica had an unclear public stance, but when I highlighted this to them they immediately responded positively and enthusiastically to clarify their practice and adopt Creative Commons licenses.
But this last expression is unacceptable. We – authors/funders – are paying the industry a lot of money (per article) for Open Access. If one of the leaders of OA admits that the industry is not in a position to produce a quality product the position is intolerable. The toll-access (TA) publishers make a great deal of play about how the enhance the quality in a way that no-one else can – reviewing, copy-editing, etc. – but it seems they are not even trying to make OA work.
It is not acceptable to use the excuse of anarchy to excuse incompetence. The TA publishers have had no problem in installing RightsLink – a tool whose purpose is to take money from readers and users – it seems to be a pretty uniformly used tool. Nor are they unable to use DOIs, or the services of CrossRef to link their papers. So I don’t buy the arguments that Open Access cannot be provided on a simple uniform platform. BMC and PLoS have no problem in making all their offerings available as full Creative Commons CC-BY. They don’t even need to coordinate on this – CC provides everything they need. The problem only comes (as I shall show in the next post) when they try to add non-OA or non-CC refinements to their products or simply fail to add them when they should.
If indeed this is the position, I think we shall see a fracture in the industry. Fully committed OA publishers – those whose journals are completely or almost completely OA – will have no technical or organisational difficulty making OA work. They may be competitors in some areas, but they will make sure OA is properly and uniformly implemented. The PRISM community – currently unclear – will find it very difficult to include any OA in their offerings. The middle will include publishers who have partial OA – either through hybrids (journals with some OA and some non-OA papers) , or with a small proportion of their journals completely OA (e.g. Nature has just one such). This middle group is likely to do OA incompletely and poorly unless special care is taken (see next post). This is because the overall heart of the publisher is still in TA. This “systemic failure” will permeate the whole infrastructure of the publisher who will regard it as a chore rather than a growing point.
On to an example of  such a problem…

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PRISM: Open Letter to Oxford University Press

Open Letter to Henry Reece, Chief Executive Oxford University Press
Dear Henry Reece,
I am writing as an individual member of Oxford University (MA, DPhil) and also as an author of Open Access articles in OUP journals. I am heavily engaged in developing new approaches to scientific scholarly publishing and am writing to ask about OUP’s involvement with the recently launched PRISM initiative from the AAP (http://www.prismcoalition.org/). This initiative is an
undisguised coalition to discredit Open Access publishing and its launch a
few days ago has generated universal dismay and anger in many quarters
including several outside mainstream publishing. The press release was
reported in full by Peter Suber on his Open Access News blog
(http://feeds.feedburner.com/~r/earlham/dGCQ/~3/147374721/2007_08_19_fosblogarchive.html)
where he has objectively answered and dismissed the basis of PRISM and its
methods. PRISM describes all Open Access publishing as “junk science”, presumably including the papers with yourselves which I have co-authored (http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D515, http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/23/4315, etc.). There is much more from PRISM which is both deliberately factually incorrect and
misleading and I cannot see how a reputable scholarly organisation such as
OUP could be associated with it. Indeed at least one similar publisher
(Rockefeller University Press
http://feeds.feedburner.com/~r/earlham/dGCQ/~3/150207794/2007_08_26_fosblogarchive.html)
writes:
“I am writing to request that a disclaimer be placed on the PRISM website
indicating that the views presented on the site do not necessarily reflect
those of all members of the AAP. We at the Rockefeller University Press
strongly disagree with the spin that has been placed on the issue of open
access by PRISM.” [rest of letter omitted here]
The PRISM site is so incoherent and so removed from good publishing practice that it is almost impossible to extract any clear message except:
“PRISM sees all Open Access publishers as a threat to be destroyed by whatever means are most expedient”.
Peter Suber writes on his Open Access blog
(http://www.earlham.edu/~peters/fos/2007_08_26_fosblogarchive.html#3366666992239868540):
“I suspect that AAP/PSP did not consult its members before launching PRISM. But in any case the members should know that the launch of PRISM tarnishes them, alienates authors, readers, and referees, and, if successful, will only harm science by entrenching rather than removing access barriers to the results of publicly-funded research.”
– a clear analysis which publishers should take very seriously.
The purpose of my letter is simply to request factual information from OUP
about its involvement with PRISM and any support for its “aims”. Since PRISM itself has not reacted to any of the recent comment it is unclear whether PRISM is de facto composed of all the members of the AAP or whether it uses their unsought goodwill to reinforce the apparent strength of the PRISM organization.
This mail is an Open Letter (posted on my blog, http://wwmm.ch.cam.ac.uk/blogs/murrayrust) and I would intend to publish
your reply in toto and unedited since your position (and those of similar
publishers) is of great public interest). If there is anything you would
not wish to be published, please indicate. Alternatively you may leave a
comment on the blog itself. (My blog itself, though strongly advocating
Open Access and particularly Open Data, attempts to be fair and accurate).
Thanks in advance
Peter Murray-Rust
[NOTE AFTERWARDS: I have tried to send a copy of this by mail to oxfordjournals.org but so far the mail has bounced, so I would be grateful if any reader could forward it.]

Posted in open issues | 1 Comment

PRISM: Open Letter to Cambridge University Press

I have sent the following letter to the Chief Executive of Cambridge University Press requesting factual information about the involvement of CUP in PRISM, and have asked that I can publish the reply on this blog
Open Letter to Stephen Bourne, Chief Executive Cambridge University Press
Dear Stephen Bourne,
I am writing as an individual member of staff in the University (heavily
engaged in developing new approaches to scientific scholarly publishing) to
ask about CUP’s involvement with the recently launched PRISM initiative
from the AAP (http://www.prismcoalition.org/). This initiative is an
undisguised coalition to discredit Open Access publishing and its launch a
few days ago has generated universal dismay and anger in many quarters
including several outside mainstream publishing. The press release was
reported in full by Peter Suber on his Open Access News blog
(http://feeds.feedburner.com/~r/earlham/dGCQ/~3/147374721/2007_08_19_fosblogarchive.html)
where he has objectively answered and dismissed the basis of PRISM and its
methods. As an example of the language of PRISM it implies that publishing
in Open Access journals (as I do on occasions) is “junk science”. There is
much more from PRISM which is both deliberately factually incorrect and
misleading and I cannot see how a reputable scholarly organisation such as
CUP could be associated with it. Indeed at least one similar publisher
(Rockefeller University Press
http://feeds.feedburner.com/~r/earlham/dGCQ/~3/150207794/2007_08_26_fosblogarchive.html)
writes:
“I am writing to request that a disclaimer be placed on the PRISM website
indicating that the views presented on the site do not necessarily reflect
those of all members of the AAP. We at the Rockefeller University Press
strongly disagree with the spin that has been placed on the issue of open
access by PRISM.” [rest of letter omitted here]
The purpose of my letter is simply to request factual information from CUP
about its involvement with PRISM. Since PRISM itself has not reacted to any
of the recent comment I can simply speculate that not all members of the
AAP (perhaps including yourselves) were consulted before PRISM made its
press release and new site. In particular it is unclear whether PRISM is de
facto composed of all the members of the AAP or whether it uses their
unsought goodwill to reinforce the apparent strength of the PRISM
organization.
This mail is an Open Letter (posted on my blog,
http://wwmm.ch.cam.ac.uk/blogs/murrayrust) and I would intend to publish
your reply in toto and unedited since your position (and those of similar
publishers) is of great public interest). If there is anything you would
not wish to be published, please indicate. Alternatively you may leave a
comment on the blog itself. (My blog itself, though strongly advocating
Open Access and particularly Open Data, attempts to be fair and accurate).
Thanks in advance
Peter Murray-Rust
Posted in open issues | 2 Comments

PRISM: should I worry?

The last week has seen a spate of immediate reaction to the newly formed PRISM – the (American?) publishers’ lobby to destroy non-commercial open access.  There is so much (germane) comment that there is no need for me to duplicate it, so I try to add a new aspect here – should I care?
Here are Peter Suber’s (almost daily) collections of rebuttals of PRISM’s position, “facts” and “logic”. If you are starting from scratch read these from PeterS:

PMR: So far there does not appear to be any response from PRISM. I am assuming that PeterS would immediately post any information whether firsthand or from another blog. So I’ll assume there hasn’t been any – and I don’t expect any.
PMR: Here are the two posts which I found closest to interpreting the motivation and strategy of PRISM, which are critical if we are to work out how to react.
[1]From John Dupuis at Confessions of a Science Librarian:
  • …I would like to talk a little about the makeup of The Executive Council of the Professional & Scholarly Publishing Division [which launched PRISM].

  • Who are the members of this Committee? Sure, the usual suspects, representatives of the major commercial publishers such as a bunch from Elsevier, John Wiley & Sons, McGraw Hill, Wolters Kluwer Health, Springer Science + Business Media, SAGE Publications, ISI Thomson Scientific….Given that they are for-profit companies, however, it’s not surprising that they would act to protect their profits….Thank god, you’re thinking, that the list above does not include any representatives from scholarly or professional societies. Surely they must understand the importance of free and open access to information, something which can surely only benefit their members, scholarship and society as a whole. Sadly, the Exec Committee also includes members from the IEEE (2, including the chair of the journals committee), American Chemical Society (2, including the chair), American Society of Clinical Oncology, New England Journal of Medicine, Columbia University Press, MIT Press, American Academy of Pediatrics, American Institute of Physics and University of Chicago Press. Unfortunately, scholarly societies see OA as a threat to the income from their publishing programs, which is used to finance all the other membership programs that they have like conferences and continuing education. It’s really unfortunate that they can’t see past these concerns to what the true interest of their members is: for their research to have as high an impact as possible and, as a byproduct of that impact, to benefit scholarship in their discipline and, hopefully, society as a whole as much as possible….

[2] John Blossom, PRISM Promotes the Interests of Scientific Publishers: Is it Better to Lobby or to Change? ContentBlogger, August 29, 2007. Excerpt:

Wired Science has the most in-your-face coverage of the formation of PRISM, an advocacy group formed by scholarly publishers to stem the legislative movement towards free access to government-funded scholarly research. This in and of itself is not a surprise, but Wired claims that the site is an example of astroturf advocacy, meaning an organization that tries to position itself as a grass-roots movement when in fact it is created by others wanting to appear to have grass roots support. PRISM is the creation of the Association of American Publishers, so one assumes that the roots of this organization are more likely to grow in the yards of scholarly publishers than the scientists providing the research….
The primary problem with PRISM is that it seems to be advocating on a range of issues which, while valid in their own right, are more about fear, uncertainty and doubt – those familiar sales tools – than the real issues at hand….
[The claim that OA will undermine peer review] seems to be somewhat disingenuous, in that there may be alternative methods for supporting effective peer review that have not been explored by scientific publishers. Certainly a government-mandated publishing of research for free that doesn’t take into account how that research is produced has the potential to be an unfunded mandate that could place an undue burden on scientific publishers. This is a real issue, but the answers to the issue may not lie with the government itself – they may lie with addressing how the peer review process is funded in general….
Surely politics should stay out of science, but there’s no indication at this time that the government would have the ability to influence the peer review process politically through these proposed [OA] mandates any more than it does today….
If the purpose of PRISM is to convince legislators that there is an advocacy group that supports the publishers’ goals then my sense is that they are going to fail. The site is not very convincing and lacks information about its supporters or any input from them that would influence people into thinking that there is a broad base of support for PRISM’s views. PRISM does raise some important issues that need to be addressed in the rush to make access to government-funded research public, especially in how to support the peer review process realistically in an era in which public access to research is becoming a given. But the broader outlines of the solutions to many of these problems would seem to lie in how the scholarly publishing community has resisted changes in publishing technologies that disrupt their traditional business models.
With some added focus and some sponsorship of honest debate between government research sponsors, scientists and publishers PRISM may yet serve a positive and constructive purpose as an advocacy group. But if PRISM remains little more than an “astroturf” organization that defends the commercial interests of publishers then it’s not likely to gain the needed respect from any of the parties that it needs to influence in this debate. Publishers in general are reluctant to engage their markets in a more conversational manner, but if scholarly publishers can position PRISM as a tool to build an honest conversation about the future of commercial and non-commercial scholarly publishing then they may be able to make some headway. At the moment I wouldn’t bet on that happening, but you never know.

PMR: The first thing to understand, especially for non-Americans such as me, is that this is in large part an American activity. Agreed that there are several large mulitnational publishers who are not strictly American, but in general it’s highly US-centric.
This type of activity is not new and for those of us who tackled the issues with Pubchem will have seen rhetoric such as  from Rudy Baum: C&EN [Amer. Chem. Soc.]: Editor’s Page – Socialized Science [2004]

National Institutes of Health director Elias A. Zerhouni seems hell-bent on imposing an “open access” model of publishing on researchers receiving NIH grants. His action will inflict long-term damage on the communication of scientific results and on maintenance of the archive of scientific knowledge.
More important, Zerhouni’s action is the opening salvo in the open-access movement’s unstated, but clearly evident, goal of placing responsibility for the entire scientific enterprise in the federal government’s hand. Open access, in fact, equates with socialized science.
Late on Friday, Sept. 3, NIH posted its proposed new policy on its website, setting in motion a 60-day public comment period (C&EN, Sept. 13, page 7). Under the policy, once manuscripts describing research supported by NIH have been peer reviewed and accepted for publication, they would have to be submitted to PubMed Central, NIH’s free archive of biomedical research. The manuscripts would be posted on the site six months after journal publication.
Many observers believe that, if the NIH policy takes effect, other funding agencies will quickly follow suit. In short order, all research supported by the federal government would be posted on government websites six months after publication. This is unlikely to satisfy open-access advocates, who will continue to push for immediate posting of the research.
I find it incredible that a Republican Administration would institute a policy that will have the long-term effect of shifting responsibility for communicating scientific research and maintaining the archive of science, technology, and medical (STM) literature from the private sector to the federal government. It’s especially hard to understand because access to the STM literature is more open today than it ever has been: Anyone can do a search of the literature and obtain papers that interest them, so long as they are willing to pay a reasonable fee for access to the material.
What is important to realize is that a subscription to an STM journal is no longer what people used to think of as a subscription; in fact, it is an access fee to a database maintained by the publisher. Sure, many libraries still receive weekly or monthly copies of journals printed on paper and bound as part of their subscription. Those paper copies of journals are becoming artifacts of a publishing world that is fast receding into the past. What matters is the database of articles in electronic form.
[…]
Which is, I suspect, the outcome desired by open-access advocates. Their unspoken crusade is to socialize all aspects of science, putting the federal government in charge of funding science, communicating science, and maintaining the archive of scientific knowledge. If that sounds like a good idea to you, then NIH’s open-access policy should suit you just fine.

I have not posted this in full as it’s copyright, but I have given the weblink and I am sure its author would wish as many people as possible to read it. I suspect it will echo the thoughts and motivations of the other PRISMites. It is significant that the terminology used here “private sector”, “socialized science”, “putting the federal government in charge” closely echoes the PRISM language.
So what is PRISM’s purpose? I suspect it is primarily to lobby the political process in the US to put pressure on the NIH to withdraw or moderate its support for Open Access. (I cannot envisage they are going to convince the Wellcome Trust to stop funding “junk science” by engaging in Socratic debate. Indeed I don’t think PRISM care anything for the scientific community except as a source of revenue. ) What they intend to do is use their junk facts and arguments to convince congressmen and governors in the US to support their cause.
Should I care? Yes, because we cannot afford to lose any battles. This will be hard fought and probably dirty and it may not be easy to see when and where the lobbying is. See this newsreport about a Governor overstepping the line. If, as we managed in the Pubchem struggle for Open Data, we are able to convince the US politicians that Open Access is for the benefit of us all then we make the next step easier. And if we lose it gets harder. OA is a series of skirmishes.
So by all means demolish their arguments and provide our own. But also keep a very close watch.
In conclusion I see no need for any non-American publishers to take the slightest involvement in PRISM. It is so clearly a US political lobbying organisation without other substance that a mid-rank, especially society, publisher would have nothing to gain and considerable reputation to lose. I very much hope that the people I know in the publishing industry will try to dissuade their organizations to steer clear.
Unfortunately I now have the feeling that battle lines have been drawn. I had hoped there might be a gentle evolution (if far too slow) towards more modern approaches. Now I think we see a fracture line.

Posted in open issues, Uncategorized | 2 Comments