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At Oxford last week Bob Campbell of Wiley said that if anyone wished to text-mine content in Wiley journals all they had to do is ask.

Thank you Bob! This is a formal request from scientists in:

Dear Bob Campbell,
We were at the meeting last week in Oxford on the “Evolution of Scholarship” where you stated that anyone could mine content in Wiley journals for factual information, and re-use and republish it. Cambridge subscribes to many Wiley journals and I and many other scientists wish to mine factual information using machines.

We cannot do this at present as Wiley imposes two barriers:

•  legal restrictions of text-mining through contracts (Wiley has in the past threatened scientists with legal action for extracting facts)
  
• Wiley’s server-side robots which will shut off the University if we attempt to download publications automatically.
  

I would therefore like you (immediately, as we wish to start immediately) to confirm that Wiley will absolutely and for ever allow subscribers, at no additional cost, to mine all content for facts in both back issues and current publications as soon as they appear.

Answeriing “YES” to this question is all that is required. Any other answer, including the request for discussion will be taken as “NO”. Please reply by the end of today (2012-03-07).

I have published a background document (/pmr/2012/03/04/information-mining-and-hargreaves-i-set-out-the-absolute-rights-for-readers-non-negotiable/ ) which also gives a wide range of illustrations of factual information. In places it reads “Elsevier”, please substitute “Wiley”.

Please note that we do not need any help from Wiley in systematically downloading papers. We shall use a delay of 1 second between downloads and we shall not re-publish verbatim the papers we download.

Thank you and I look forward to your immediately reply and agreement.

Note that we want to get started tomorrow! There are lots of projects – today I’ll be working with physicists and putting in place the systems to start immediately Wiley gives the go-ahead. But it will also be useful for bioinformaticians, economists, chemists, and lots more I collaborate with.

This is an account of my last few days, continuing to struggle against Elsevier for the right for academics to use their knowledge in the way that they wish. (Of course it’s not just Elsevier, it’s a large percentage of STM publishers). But Elsevier continues to be at the top of my list. I am going to upset a number of people. But I also hope that some others will see the seriousness of the situation and act.

Very simply, academics, we are in the middle of a titanic struggle for our digital future. There is massive power in the knowledge we create and we don’t recognise it. We are giving it away and asking the publishers to control us with it. The current issue is information mining (“text-mining”).

In previous posts I have recounted how over two-and-a-half years I have tried to get permission from Elsevier to text-mine the journals that Cambridge subscribes to. The subscriptions cost a LOT of money. UCL pays well over a million to Elsevier and I have no doubt that Cambridge does as well. So you might think that having paid for access – note that we don’t OWN the journal, we RENT them. If we stop subscribing we lose the right to back issues.

What? We don’t own the contents of our scientific libraries?

No – we own them as much as we own apps on mobiles or ebooks. We RENT them.

How did this happen? Did universities ask the publishers to change the system? No – the publishers thought it was a good idea (for them) and the universities meekly accepted it. Any shouts of protest? I didn’t hear them. It’s great for the publishers – if you cancel the journal you lose the back numbers.

I remember a meeting run by Cambridge University Library (CUL) about 8 years ago. There were librarians en masse – I think from outside Cambridge as well. I can’t remember the exact title – but something about the challenge from the publishers. There were no publishers there. The whole discussion was about cost. No one was worried that publishers were controlling scholarship.

Except me. I got up and said the issue was who controlled scholarship – us or the publishers. I think one or two people understood what I said – but most were only concerned with cost.

Don’t get me wrong. Cost matters. But if control the market you lose control of the cost. And that’s exactly what has happened. Now I am sure Librarians try hard to reduce costs by bargaining with publishers. But they are trained as librarians , not as salespeople. And the publishers have trampled over the librarians. If you doubt me look at the monster profit margins and the annual rise in costs to libraries. This is because there are 200 universities in the UK and most of them have little experience in the tough world of commerce. Because the publishers salesforce is clever and they know how to negotiate. Yes, there are some apparent victories for libraries but they are sporadic and do not dent the inexorable increase.

But libraries are fixed on costs and fail to protect our other interests. RENTing journals??? Why didn’t we raise a firestorm. But hardly a mention.

And worse. Libraries have acquiesced to contracts which forbid academics to use 21^st Century tools on the scholarly literature. Daniel Lowe in our Centre has extracted 1 million chemical reactions from the patent literature. 1 year’s worth takes a day on an average desktop. It’s a huge enhancement to our scientific literature. It would save chemists repeating reactions that had already been done. Allow them to predict the best solvents. Find the right temperature.

So I asked Elsevier if I could extract reactions from the journals they publisher. (I shall NEVER use the term “*ls*v*er Content” – it’s OUR content – we did the reactions – we published them). It has taken me two and a half years and I still haven’t got a satisfactory answer.

Now Elsevier and other publishers are saying “All you have to do is ask “. Well I’ve asked. I’m portrayed as a grumpy old man and trouble. So be it. But I am fighting for academic rights and I urge those of you who care to fight with me.

The problem is that universities (presumably through their libraries) have meekly signed appalling restrictions in the contracts. If I had known at the time that this was being done I would have gone ballistic. I’d have done what I could to alert universities to the critical danger. But I didn’t know. Massive rights have been signed over. I don’t know for how many years but far too long. If you want to do anything with the literature you need the publishers’ permission.

So now the gory and unedifying details. I’ve blogged about the Oxford meeting and Elsevier’s offer to re-open my concern on textmining (after the facile assertion from Wiley that “all I had to do was ask”).

I reiterate that what I want is control of the information. I want to publish it when and where I want and in whatever quantity. If I decide I want a million molecules from Elsevier I want to be able to do it in a day. I don’t want to have to go through groundhog day for a fifth time. Or go down the same rathole. And get stuck in the same tarpit. Because, readers, that is what I was offered, and because I have seen it all too often I know the symptoms.

Publishers start off by offering to help.

PMR: I don’t want help. I am a world expert in textmining. I have written he software. I can crawl sites responsibly.

Publishers then offer to meet.

PMR: I don’t want to meet the publishers. I want to run my software.

Publishers want to know “what I want to do with textmining”

PMR: Publishers know nothing about my science and don’t need to

This is the opening of the rathole. Step into it and you are lost. The tarpit. Go no further.

I asked Elsevier a very simple question:

“Can I textmine your journals in the way I want to without being sued or cut off?” YES or no.

I have repeated this questions several times. Elsevier have repeatedly failed to answer. They suggested that we get together and meet the Cambridge Librarians. Now I have much respect for the Cambridge Libraries – we have a JISC project on Open Bibliography – but I don’t need their help in parsing chemistry.

But no, Elsevier kept trying to fix up a meeting with the library and them. I know the symptoms and I know the dangers. I have told Elsevier I will publish all their correspondence and recaord all telcons (and I advise you to do the same). So the story starts…

From Alicia Wise, Department of “Universal Access”

Dear Anne, Patricia, [CUL library top management] and Peter [PMR]

We are keen to arrange a teleconference with you all to discuss ways to enable text mining for academics at Cambridge University.  I met Peter for the first time on Wednesday, and he clearly feels very frustrated with Elsevier as he has sought in various ways to obtain text mining services for the last couple of years.  We clearly need to focus on his specific project, but I am hopeful that in parallel we can explore whether there is a broader text mining requirement at Cambridge (I strongly suspect there is) and the best way to empower the library to support this.  By working together we are most likely to find solutions that will scale.

My colleague, Jason Roof, has kindly agreed to set up this teleconference for us. 

With very kind wishes, and looking forward to speaking with you soon –

Alicia

This is the entrance to the rathole. “We clearly need to focus on his specific project”.

PMR: No we don’t. I don’t want Elsevier to have anything to do with my project. They are only relevant because they are actively preventing me doing my research. And “his specific project”. That’s because they are terrified of what I want. I want my rights. I want any subscriber to have access to the literature for whatever purpose. By agreeing to a single project I would fall right down the rathole. I would be bound to go back to Elsevier for every project I wanted to do. My project controlled by Elsevier. Groundhog day for ever.

I didn’t ask for a telcon. I asked for the Elsevier robots to be turned off. A telcon is a waste of my time.

But it might not be a waste of YOUR time. So I told Elsevier I would record the telcon and publish it. So that you would know first hand what a telcon with Elsevier is like. What a rathole looks like

Jason Roof sent out at 0900 times for yesterday. I said I could make it at 1700. I heard nothing from him and the telcon wasn’t run at 1700. I wasted my time. Elsevier said I had to wait till everyone had CONFIRMED. Are you getting the picture? Anyway a few more mails with Elsevier, more fluff about telcons and more avoidance of my question.

So I told them I wasn’t spending any more time on this fruitless process.

You may think I’ve rushed to judgment. After all we have only been communicating for 3 days.

No – we’ve been failing to communicate for 30 months. Every time it starts like this. I waste time, and after a few months I get a different contact in Elsevier. There is no point in going down the rathole.

So what would have happened if I had continued? Would I have got my wish?

Well unbeknownst to me UBC have been negotiating with Elsevier on textmining. Heather Piwowar – who has done great science and who is very well known for her championing of Open data and new metrics wants to text mine Elsevier Content content in Elsevier Journals. Elsevier truned up in force to help – lots of them. And involved the UBC library.

Here’s Heather’s account. It’s very well written. It’s almost like sitting in on the telcon

talking text mining with Elsevier

Is it what we want? Have we reached Nirvana? Or is it a rathole? Heather’s very positive. Am I just a grumpy old man who can’t change his views? YOU decide. I’ll comment tomorrow. But read it first

As I have already blogged I have been asked by Ben Hawes at the UK Intellectual Property Office to respond to the Hargreaves report on “textmining”. I shall be getting help from my OKF colleagues. The issues are, in my mind, simple:

• Legitimate human readers of the literature (“subscribers”) have a right to extract factual information from the literature and have exercised this for 200 years.
• We can now do this with machines, often better than with humans. It’s vastly faster and cheaper. It increases the value of the literature
• The publishers forbid us to do this and put in place legal and technical obstacles on top of normal copyright
• We are now demanding the removal of these obstacles.

This is not a negotiation, it’s a statement of our absolute right. As a corollary it is an integral part of what we pay for human access so there is no reason to make any charge for this.

In essence we shall report to Hargreaves:

• Our position and the justification for it
• Whether the publishers have agreed that these are our rights. I have made them simple because they are simple. Publishers wish to appear “helpful”; this is their chance to show that they are working with us as they continually claim

We shall contact 9 publishers tomorrow through known contacts; this represents our best approach to non-repudiation. Since the publishers have no-formal mechanism for readers to make formal enquiries (in itself Institutionalised unhelpfulness to readers) it will be done through this blog and email. There is enough evidence to show that all publishers will be aware of this request and if they wish to be helpful they can.

Background and clarification

Human abstracters have for centuries abstracted from and commented on the scholarly literature and made the results public without requiring permission from publishers and/or authors. Indeed science is based on being able to do this. In our present request I shall confine the request to “facts” in scientific papers, but the permission I am asserting extends to abstracting papers and to commenting and other activities practised in the paper era. None of this requires new permissions; it is explicitly and implicitly part of current practice. If I read a paper I can write an abstract; I can also critique parts (e.g. reproduce paragraphs and comment in detail on what the authors said. Refusal to allow this is a direct attack on the integrity of science.

I do not have to be the owner of a scientific article to do this. If I borrow a journal from the public library I can sit at home and write abstracts on every paper. I would strongly urge anyone interested in abstraction, commentary, parody, etc. to make representation to Hargreaves – I personally only have time to address the extraction of scientific facts and indexing the literature.

To illustrate “facts” here is the Wikipedia article on aspirin http://en.wikipedia.org/wiki/Aspirin. The article is essentially a collection of facts (as it should be – WP is very strong on removing opinions). The fact that someone reported them in natural language does not stop them being facts. Here are some examples:

• [Aspirin] was first isolated by Arthur Eichengrün, a chemist with the German company Bayer.^[1]
• It has also been established that low doses of aspirin may be given immediately after a heart attack to reduce the risk of another heart attack or of the death of cardiac tissue.^[4][5]
• (the factual synthesis of aspirin from salicylic acid and acetic anhydride)
• Physical data Density 1.40 g/cm³ Melt. point 135 °C (275 °F) Boiling point 140 °C (284 °F) (decomposes) Solubility in water 3 mg/mL (20 °C)

All of these are FACTs. As is:

Synthesis of (+)-η⁵-Cyclopentadienyl(η⁴-(3aS,4S,7aS)-methyl 2,2-dimethyl-3a,7a-dihydrobenzo[d][1,3]dioxole-3a-carboxylate)cobalt(I) 18

Diene 16 (301 mg, 1.43 mmol, 1 equiv) was dissolved in dry, degassed toluene (10 mL) in a side-armed Schlenk that had been purged and refilled with argon three times. The resulting solution was added via cannula to η⁵-cyclopentadienylbis(ethylene)cobalt 17 (258 mg, 1.43 mmol, 1 equiv) and the mixture was stirred for 30 min at room temperature until the evolution of ethylene had ceased. The solvent was removed in vacuo and the solid residue was redissolved in a minimal amount of hexane and left to crystallise at -28°C for 48 h. Complex 18 was isolated as red-orange crystals (124 mg, 26%); m. pt. 118-120°C; [α]_D +42 (c = 1, CH₂Cl₂); ¹H-NMR (300 MHz, C₆D₆, Additional file 2) δ 5.44 (1H, d, J = 5.0 Hz, O-CH-), 5.09-5.04 (2H, m, -CH=CH-CH=CH-), 4.41 (5H, s, Cp-H), 3.53 (3H, s, O-CH₃), 3.14 (1H, dd, J = 5.5, 1.0 Hz,=CH-C-COOCH₃), 2.82 (1H, td, J = 5.0, 2.0 Hz, -O-CH-CH=), 1.42 (3H, s, C-CH₃), 1.28 (3H, s, C-CH₃) ppm; ¹³C-NMR (75 MHz, CDCl₃, Additional file 2) δ 174.9, 113.9, 82.1, 80.8, 79.8, 74.6, 51.6, 48.9, 48.6, 27.1, 25.6 ppm; ν_max (film) 2986, 2937, 1732, 1436, 1370, 1307, 1259, 1229, 1206, 1166, 1109, 1064, 1009, 888, 821, 762 cm^-1; HRMS (+ve ESI-TOF) m/z calcd for (C₁₅H₂₀CoO₄+H)⁺, 335.0688, found 335.0694. Found: C, 57.58; H, 5.76. C₁₅H₂₀CoO₄ requires C, 57.49; H, 5.73%).

Everything in this paragraph is factual – what was done, what was observed, what was measured. And our software can extract 95% of the meaning from this in a few seconds, whereas many final year undergraduates might struggle.

Factual information is frequently contained in graphs, tables, images, speech and video. Therefore “text-mining” is a subset of information-mining and I shall use that term. Indeed our software can understand simple human spoken discourse about chemical reactions and extract the facts.

Alicia Wise from Elsevier wants to know what I want to do with the content. There is no reason why I should have to justify what I do to Elsevier, but here it is:

I want to extract as many facts as I can from the scientific literature and publish them (as CC0) for me and others to do science with, to build new scientific tools and improve the quality of science.

It is my right. There is absolutely no reason why anyone should need to involve the publisher in information-mining. I have legally mined 200,000 scholarly documents without requiring help or permission from the publisher. I strongly urge anyone thinking of information-mining to explore what, if anything they need the publisher for. Scientists should not have to ask permission not should they have to “use the publisher API” and they should never have to pay.

Legitimate publisher concerns about information-mining

There is only one valid reason for liaising with the publisher – the possibility of server overload. This is a negligible problem if done responsibly – for example if one allows a short pause between each download request (I use 1 second, but I’m willing to be informed of best practice.

Non-legitimate
publisher concerns about information-mining

I suspect the following concerns:

• Peter Murray-Rust will steal and publish “our” content. I find this deeply offensive. I have been confronted by publisher robots which, in essence, announce: “You are illegally downloading content; we have cut off the journal supply to the whole University; you will have to justify to a senior member of the university why we should reconnect you”. [I did nothing illegal or anticontractual – these robots act at the slightest trigger].There is no debate. PM-R is guilty until proved innocent. It is demeaning to be confronted by colleagues who accuse you of having their It is publisher HADOPI except it is “1 strike and you are out”. It is publisher institutionalism at its worst. An unbelievable arrogance that the scientific world is out to defraud publishers. And to say “oh, it’s not you but it’s your graduate students” is worse. If there is anything that underpins science it is the need for ethical behaviour and almost all scientists are highly ethical. If unethical behaviour is detected they are severely reprimanded by the community and it may be the end of their career. To accuse scientists of being thieves (even if you accept that sharing copyrighted papers is theft) is inexcusable
• Peter Murray-Rust and his robots will find errors in our papers. I hope that no-one is afraid of this. It is the purpose of science to find errors and our robots are better than humans at finding many types of error. The publishers’ refusal to allow us to validate the literature is damaging science, not enhancing it.
• Peter Murray-Rust will create disruptive technology that will seriously disturb our cosy monopolies. I think this is the real crux. Elsevier forbad me to data-mine chemistry because it threatens their cosy data monopolies. Here’s what they said in 2010-12

  [An Elsevier staff member] have not been able to get a clear story on the Tetrahedron supplementary content mining. There are two opposing views on this (roughly: ScienceDirect is fine with it, and Reaxys is not), and it is not clear what the resolution is. I am very sorry about this, and will keep trying to get a coherent response out of the multifarious monster that is a big company. As soon as I know, you’ll know.
  

  Interpretation. Elsevier run a chemical database where they abstract information from the literature (Reaxys) which probably has a revenue stream of several hundred million USD [ACS do the same (“Chemical Abstracts”, CAS) and estimates are in the range 200-500 million USD]. So to preserve their monopoly they prevent me mining information. Is it a real threat? One chemist against Elsevier? Yes. Because I have many people who think the same way.
  Other walled gardens include bibliography and citations. It’s possible to extract both of these robotically and we have the technology to do this. But Scopus and World of Science will be disrupted by this.

What Elsevier and other publishers should do, and what we should do.

The Elsevier contract states (http://lists.okfn.org/pipermail/open-science/2011-April/000724.html )

The CDL/ Elsevier contract includes [@ “Schedule 1.2(a)

General Terms and Conditions “RESTRICTIONS ON USAGE OF THE LICENSED

PRODUCTS/ INTELLECTUAL PROPERTY RIGHTS” GTC1]

“Subscriber shall not use spider or web-crawling or other software programs,

routines, robots or other mechanized devices to continuously and automatically

search and index any content accessed online under this Agreement. ”

It forbids me to do anything. The answer is simple:

SCRAP THE ANTI-MINING CLAUSE

[Aside: How my University and any other University could meekly sign this without a titanic public fight is beyond me.]

If Elsevier don’t scrap it I’ll urge Universities to take them to court. It’s against natural justice. We’ve paid enough for the subscription – we should be allowed our natural rights to do whatever we want.

Then the robots:

TURN THE ROBOTS OFF

The robots have no benefit to the subscriber and are deeply insulting.

I am prepared to agree that we should be considerate in our crawling. I have been very considerate so far, verbally agreed it with at least two publishers. It’s insulting to suggest that Universities are incapable of writing robots.

That’s it. We demand our rights and will – in one area – agree to abide by a common technical protocol for information mining. There is no other legitimate reason for denying us.

And this applies to ALL toll-access publishers.

Wiley/Blackwell have just launched “Chemistry Open”.

http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292191-1363/

It’s described as a “fully open access” journal.

http://www.wileyopenaccess.com/view/browse.html?journalId=1377333&infoId=1239257

And it costs 2500 EUR to publish one article (in the UK we have to pay VAT, so read 3000 EUR or about 4000 USD.

I’m not going to critique the chemistry (though I’m competent to do so). I’ll critique the model and practice of “Open Access” and what authors and readers get for 4000 USD per article. (I’ll mention that there is some competition – primarily Beilstein J of Org Chem (Organic Chem is a subset of chemistry so only available for some of the articles) http://www.beilstein-journals.org/bjoc/about/aboutJournal.htm which is CC-BY, no author charges, no reader charges. Also Chemistry Central (BMC) http://journal.chemistrycentral.com/ which is CC-BY, 950 EUR (1200 EUR inc VAT). These are (in my expert opinion) highly reputable and equivalent in peer-review to any other chemistry journal. I declare an interested – I am (unpaid) on the editorial board of the sister BMC journal J. Cheminform.

I have provided the key links to Wiley info so you can verify my summary: Here are the instructions for authors

http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292191-1363/homepage/2011_authors.html

• Chemistry Open is CC-NC. This is not compliant with the Budapest definition of Open Access or any other definition I have seen
• The author pays 3000 EUR
• The author assigns copyright to Wiley
• The authors signs a contract restricting their rights in PRE-peer-review material (e.g. they would be debarred from posting in ArXiV)
• The author signs an agreement that every copy of the article will link to the Wiley site and journal article

This is not Open Access, it gives almost no permissions beyond simple self-archiving. The NC clause forbids almost every serious type of re-use without applying to Wiley and probably paying additional charges:

• Cannot translate to a foreign language
• Cannot re-use the diagrams
• Cannot re-use the citations
• Cannot re-use the abstract
• Cannot re-use for text-mining and other information mining

Here’s Wiley’s FAQ for “demystifying” the author-side From Submission to Publication: Demystifying the Process

The most commonly asked question is “why should I submit the manuscript in the journal’s template?”. The answer is a simple one: to

facilitate the peer-review process. In our experience, a manuscript fares better in peer

review when it is well organised and formatted in an easily read manner. Using the template

ensures that our reviewers get a standard manuscript layout with the graphics appearing

in the appropriate place….

PMR: Rubbish. Scientists are used to reviewing from a wide range of sources and they have to get used to the unnecessary practices of publishers. As an example I reviewed a grant proposal last night. It was as complex as a paper and had its own particular set of questions and free text. I *enjoyed* doing it. For publishers to tell the world that only they can organize peer-review is rubbish. We review grants, job applications, software and data, theses, etc. *We* are the ones who know what to do

Of course, if a manuscript is accepted we ask for the production data in a completely different

format, often to the dismay of our authors. There is a method to our madness! When a

manuscript is accepted, revised by the authors and the final version received, the text

undergoes what we term “coding”. This process involves a number of technical steps to

standardise the presentation of units, symbols, non-breaking spaces, table formats and other

style requirements of the journal in both the print and online formats….

PMR: Do I need to spell out why the publishing industry is 20 years adrift and why the production costs are insanely high? It costs 6 USD to process a manuscript on ArXiV and lots of people read them!

Another commonly asked question is “why are figures embedded in Word unusable?” Again,

the answer is simple: quality! When a figure is embedded in Word, a certain amount of

resolution is irreparably lost from the image. While this is acceptable for viewing on screen or

even printing from your office printer, high quality production requires high-resolution

images. For this reason we ask authors to supply the graphics, including the image for the

Table of Contents, as separate files in their original format,

In an Open world authors can make images available in whatever forma they like. I haven’t heard the world complaining that Figshare http://figshare.com/ trashes images and – if it does – I expect Mark Hahnel would create a workaround in a week. An image in Word is processable without destruction – I have worked with Microsoft for 2 years. I suspect that the problem is in the publisher process which generally destroys considerable amounts of information.

With chemical structures and schemes, we ask that authors use our ChemDraw template.

Our copy editors will adjust all images that do not meet our requirements; if a chemical scheme

already meets our standards

Yes, and then Wiley destroys the Chemdraw files. Admittedly almost all publishers do this. Some because they aren’t competent to process them, some because it costs, some because they have downstream walled gardens of chemical information which can sell for hundreds of millions of USD annually (this is true of Elsevier, ACS and Wiley). Open information would be disruptive (I shall recount Elsevier’s correspondence with me elsewhere) . If chemistry journals published these, and the spectra and the crystallography in the form they received them and as supplemental information then the world would immediately gain huge benefit. But in http://onlinelibrary.wiley.com/store/10.1002/open.201100010/asset/supinfo/open_201100010_sm_miscellaneous_information.pdf?v=1&s=d34b9827460dd2e4675043163cdc1cd10d81793a they have reduced the machine-processable Chemdraw files to unreadable PDFs. This is “publisher added value”. Simple stick the Chemdraw files on the web site and *I* will show what can really be done with them. [Note: Wiley have a large market reselling chemical spectra data so they know how to do this technically.]

That’s enough for you to get the idea. Authors can pay 3000 EUR to publish in Chemistry Open. I wonder why anyone would?

I suspect the members of the editorial board – and I know a few – have no idea of what Wiley is imposing on authors and readers. I hope some of them will feel as angry as I do (if they feel 10% of my anger that’s good enough). If this is the “Golden heaven” of OA that we are moving towards I want none of it.

The sad fact is that the OA community doesn’t (yet) care. Gold is not necessarily better than Green or nothing if we still leave publishers in control.

I have been invited by the UK Intellectual Property Office to collect information and produce a reply to the Hargreaves report on copyright reform. The particular area that Ben Hawes (IPO) and I agreed on is “text-mining” [I shall refine this term later]. We are doing this under the aegis of the Open Knowledge Foundation and with the help of their software. However it is not appropriate for the OKF, as a partner in the UK Government Transparency activity, to lobby for change so it will be an ad hoc group of identified individuals (perhaps under the label @ccess). It is probable, however, that the protocols we intend to develop will be part of the OKF activity, perhaps under the “Panton” brand.

Our group will represent that very serious harm is done to science and the use of science by the refusal to allow textmining. We shall be preparing our material completely in the open, coordinated on http://lists.okfn.org/mailman/listinfo/open-access. Anyone can take part in the discussion and interested parties such as publishers are invited.

We shall argue that as from today all publishers know of our activity and have the opportunity to influence what we say. A major problem is that publishers make it extremely difficult for a reader to get a useful reply to any question on rights and practice. I know, however, that staff in all major publishers follow this blog. We shall concentrate on a small subset of high-profile publishers, probably limited to Wiley/Blackwell, Elsevier, Springer, Nature, AAAS (Science), PLoS, BMC and because of my involvement in chemistry ACS and RSC. Those organizations have the opportunity to make their views and practice known on open-access. Any private mails on this subject will be posted to the list.

The publishers argue, from their own surveys, that the scholarly community assert that publishers are extremely helpful over text-mining and agree to a large percentage of requests (data collated by Eefke Smit, STM publishers’ association). Our group asserts the opposite – that publishers have been extremely unhelpful.

We shall also argue that the publishers “institutionally” oppose text-mining. (In the UK we have a phrase, “institutional sexism/racism/ageism, etc.” which identifies practices and attitudes – whether conscious or not – that oppose fundamental rights (http://en.wikipedia.org/wiki/Institutional_racism ). Thus the UK police have been described as “institutionally racist” and I assert that the scholarly publishing industry is “institutionally opposed” to text-mining. [If anyone has a better term please let me know]. The “glass ceiling” is a similar term. This is reflected in the large number of barriers, whether conscious or not, that publishers put in place or leave in place that effectively prevent text-mining. Institutionalism is defined as “the collective failure of an organisation to provide an appropriate and professional service to people” and I assert that the scholarly publishing industry is almost universally guilty of this for its READERS.

I will start by stating an unpleasant but true fact: many people no longer trust the scholarly publishing industry. There have been too many assertions of “we are doing everything we can”, “I’ll get back to you”, “our marketing people will look at the problem” to trust effective action. This is “institutional” – I no longer care whether it’s deliberate or unconscious, the effect is the same.

On Wednesday I talked with Alicia Wise, Elsevier’s Director of “Universal Access”. I put my concerns to her including the unacceptable manner in which Elsevier had treated me and I asserted my rights to text-mine scholarly content. [I intend to formalise these rights in the submission to Hargreaves]. It was an informal, unplanned conversation in the presence of other people and I shall not put words into her mouth. She agreed, I believe, to treat me with professional courtesy and to respond to my points in public. She said she would mail me yesterday (she hasn’t) so I am assuming she will read this blog. I have her email and will email her.

** THIS DISCOURSE NOW INCLUDES THE NINE PUBLISHERS ABOVE AND THE STM PUBLISHERS ASSOCIATION. I SHALL EXPECT THEM TO BE AWARE OF THE DISCOUSRE AND TO PROVIDE CONTACT DETAILS ON THE OPEN-ACCESS LIST **

If a publisher fails to take part in public discourse on text-mining and fails to comment on the principles and protocols we shall create on the list we shall represent them to Hargreaves as “institutionally opposed to text-mining”. If you wish to take part please make your contact details known on the list, not on this blog.

The response to Hargreaves will consist of a number of questions which (generally) require the response “YES” to be seen as helpful to the provision of text-mining. A typical one is:

• “Do you agree that facts and data are uncopyrightable?”

The only answers are YES and “not-YES” (which will be labelled by us as “unhelpful”). The following are examples of “not-YES”:

• Failure to reply
• Additional of conditions (“it depends on…”)
• “I don’t have authority to answer this question”. Sorry – that’s institutionalism. It may not be YOUR personal fault, but it is your organization’s fault
• Promises to “get back to us” – you have two weeks max as we need a week to collate for Hargreaves. That’s a fact. So start preparing now.
• Asserting that OPEN-ACCESS should have approached person X rather than person Y.

Any publisher who is actually well-intentioned towards textmining should be trivially able to answer the questions in half an hour. Any publisher who has to worry about them is probably guilty of institutionalism.

This is the first of several posts. I shall next address our RIGHTS and what “information-mining” covers. I may then give further examples of my and my colleagues experiences of publisher institutionalism.

The list will create protocol will be a draft of acceptable textmining practice by readers, subscribers and publishers.

** PUBLISHERS and STM-PUBLISHERS ** your immediate action should be to register with the OPEN-ACCESS list and make known the identity of the persons who will answer questions for Hargreaves. That can be done today (It’s a working day in most countries).

This is a brief personal account of my recollections of the 2 hours at Oxford discussing the future of scholpub. http://duraspace.org/scientific-evolution-open-science-and-future-publishing . It’s a useful milestone if not a Huxley-Wilberforce confrontation. Please let me know if there are errors,

It was extremely well run by Simon Benjamin ably assisted by Victoria Watson. Simon chaired the session very well making sure that all the key points were covered. There was a packed audience ?300. I don’t think anyone was turned away. I benefited as much from the post-event discussions including with Victor Henning (Mendeley) on the train back.

Hopefully everything has been recorded (though the acoustics at Rhodes House seem variable and I doubt that everything will be picked up – we shall see). The speakers had 6-7 mins each. In simple terms:

• Robert Kiley (Wellcome) Gave an excellent and compelling account of why Openness was essential. Only someone with misaligned motivations could fail to agree with him. He wasn’t challenged. But this was a fairly polite meeting.
• Alicia Wise (Elsevier, Universal Access) and Alison Mitchell (Nature PG) said that the publishers were working hard to create new products for the benefit of everyone (?all subscribers), that they all believed in Open Access, and that if we trust them and let them take us forward everything will be fine. At least that is the essence of the message – there were no facts or announcements that I could discern.
• Robert Winston said that Open Access wasn’t a remedy, that papers were badly written, that it was potential very harmful for the public to have access to medical information and that (I think) there was no need to make a fuss or change anything. Things were OK for him.
• Cameron Neylon dissected the publishing model, showed it to be very seriously wanting and proposed that we should pay publishers only for the added value and that we could choose not to add value if we didn’t want.
• Victor Henning showed how Mendeley was effectively providing the disruptive technology in scholpub, that they already had zillions of PDFs and were going to be doing exciting things. This is very much a space to watch and if I were a publisher I would adjust to the new reality.
• Tim Gowers said that the boycott still existed. He was actively developing new mathematical communities of practice and changing the way that maths was created and communicated. Great stuff.

If anyone disagrees factually let me know.

In the discussion I was invited to ask the first question. Since Robert Kiley had already covered what I was going to ask I said:

• 99% of people, even in rich countries, #scholarlypoor do not have access to the results of public science. This was not challenged.
• That in @ccess we are hearing stories of total dissatisfaction with the current position – anger, frustration, lost opportunities, failure to get medical information.
• Examples of a dinosaur artist who wanted full papers to get the anatomy right. PMR’s doctor who subscribed to BMJ and NICE and couldn’t read the literature (Winston: get another doctor)
• So did the panel feel this was totally unacceptable?

Answer Yes, and errrm, yes, we all want open access.

The Bodleian Library Oxford (one of the three deposit libraries in England – others are BL and Cambridge) was cancelling subscriptions because of price. This sent shocks through the twittersphere.

Yes – Oxford cannot afford to do its job properly.

Text-mining was discussed. The publisher position (e.g. Wiley Blackwell) is that we should ask them for permission. PMR said that we have an absolute right.

*** I WOULD LIKE THE NAME OF THE WILEY REPRESENTATIVE SO I CAN FORMALLY ASK FOR WILEY’S POSITION ***

In the post-discussion I spent a useful time (in the presence of witnesses) talking to Alicia Wise (Elsevier) about my requirements and rights for text-mining. I am not going to put words in her mouth. I am going to formalise my position (next blog) and ask for her formal response within a tight time limit as I shall be collating publisher positions for our response to Hargreaves.

We now have the Twitter tag @ccess! This is fantastic. Thanks to Tyler Neylon for making this happen.

The progress on http://access.okfn.org and http://whoneedsaccess.org is fantastic. On the latter we are getting daily stories from the #scholarlypoor – people who want to read the scholarly literature and cannot. Read them and see how powerful their stories are – people who leave their job feel a great sense of loss and deprivation, and spending thousands of dollars is not an option.

I’m going to Rhodes House Oxford for : Scientific Evolution, Open Science and the future of publishing www.evolutionofscience.org/ This is a great event and I’ve been asked to ask a question. I’ve sent this in – not sure whether the panellists have seen it so I shan’t put it here but it’s about the #scholarlypoor. The tragedy is that the world is deprived of scholarship and we have to put that right. The first step is to recognise it and cement it in our articles of policy – my approach is /pmr/2011/09/30/access-to-scientific-publications-should-be-a-fundamental-right/ .

Then we have to work out how to make it happen. This is where the #scholarlypoor have the power. We – I count myself as part of the #scholarlypoor as the publishers have forbidden me to do the research I want – should mobilise and make our voice heard. If the world trembles when 7000 academics (including me) Boycott Elsevier then how much more the power of the world, feeling the deprivation.

And, yes, unlike the woolliness of most academics this is a hardball fight. The #scholarlypoor have no hIndexes to worry about and their demand is simple (I have been on enough demonstrations to know this by heart!)

• What do we want?
• Access.
• When do we want it?
• Now

If you can remember this simple chant, join us.

I’ve been invited to a very timely meeting in Oxford next week to discuss the future of Scholarship. “Open Science and the Future of Publishing” http://www.evolutionofscience.org/webFlyer.pdf . The question I want to ask is (roughly):

“We the public pay 10 billion USD annually in journal subscription fees [*] and 200 billion USD for research; what value do WE get? And what value do WE lose by closed access?”

[*] throughout this post I use guestimates which are probably off by half an order of magnitude either way (i.e. factor of 3). This is partly because much of the information is secret (and some so secret that you will be sued if you divulge it) and partly because academia and we the public don’t yet care enough to find out. I am also removing CC-BY publications from the argument to avoid having to say “except for CC-BY” all the time. It’s about 5% of the market, if that. So I’d like your help.

I am also working this up for a (unfortunately virtual) presentation I am giving in Poland next month. I am taking my text from Wikipedia: http://en.wikipedia.org/wiki/Value_%28economics%29 (This is 6 years old and not disputed so I take it as more-or-less correct. If anyone can fault this, we shall all benefit)

Let me tackle COST and PRICE first.

The COST to the public purse of scholarly publishing is of the order of 10 billion USD. There are also contributions from industrial subscriptions, and from student fees, and 1% from pay-per-view, but the bulk is from taxpayers. In return for this the public get virtually no value or rights. If you the public, you the government, you the NHS want to read a paper you either have to pay again or walk to St Pancras and read it in the British library premises (you cannot get this online because of publisher restrictions – mad and sad but true. The BL even charges me to read my own CC-BY papers if I’m not at St P.).

This is set by the PRICE of electronic journals. This bears no relation to the COST of production. The cost of production can be very low. It’s USD 7 for ArXiV (not peer-reviewed) and about 100 USD for Acta Cryst E (a very high-quality peer-reviewed data journal). In an efficient organisation it’s inconceivable that the COST of production of a journal article is more than 200 USD. Any higher PRICE comes from the following:

• The ADDED_VALUE that the publishers assert they add
• Inefficiencies (often gross) in the publishing system. (For example almost all author manuscripts are retyped from scratch).
• Profits

Publishers like Nature estimate costs-per-paper at 20,000 USD. That is not related to the cost of production but something else. Perhaps the high rejection rate? The basis of these “costs” is kept highly secret.

The PRICE of pay-per-view articles (about 35 USD for one day’s rent) is the only part with real elasticity http://en.wikipedia.org/wiki/Elasticity_%28economics%29 . The only evidence I have is from my FOI requests to Oxford/Cambridge University presses (they are public organizations, parts of the Universities, so have to reply – if you want publishing facts consider University presses).

CUP:  [http://www.whatdotheyknow.com/request/88390/response/224094/attach/html/2/FOI%202011%20236%20Murray%20Rust%20response%20letter.pdf.html ]

In 2010, 13,646 articles were purchased as PPV. In 2010, the total number of articles for potential purchase via CJO was 680,000.  Revenues from PPV approximated to 1.3% of Journal subscription revenues in 2010. 

OUP [http://www.whatdotheyknow.com/request/85085/response/214837/attach/html/2/Murray%20Rust%20Reply%20OUP%20PPV.pdf.html ]

 In 2010, 37,157 PPV articles were purchased [OUP do not know how many purchasable articles they publish]  PPV represents around 1.5% of total journal subscription income. 
 

I take heart from the consistency of the figures (TWO coincident points!) and surmise that other publishers get 1.5% of their income from Pay-per-view. It’s possible, but unlikely, that the large profits of other publishers comes from Pay-per-view but I and you will doubt that. It’s clear that the price is far too high and it amazes me that publishers still use these levels which were – I assume – set by the cost of paper in interlibrary loans. I’m no economist, but it’s actually stupid to run these prices . If they cut their prices to a fifth – 7USD – and gained 5 times more custom they’d still make the same income, incur no more costs (really!) and gain a great deal of goodwill. And even if they gained no more readers they’d only have lost 1% of their income. But they probably know something about a small subset of customers who have to use this service and they don’t care about everyone else. Which is also inelastic.

If any closed access publisher can give figures here we’d be delighted.

It’s also a serious condemnation of the effort to promote scholarship. Only 2% or all articles are ever purchased each year. I imagine the 680,000 includes historical articles, and if we take this as 50 years, then each modern article is purchased about once each year. Which shows that it’s value to the public is almost zero.

We now need to establish the cost of public (include charity) funded research. I have asked many times without finding authoritative results. So here’s a beer-mat calculation, and allow +- half an order of magnitude. I approach it from these directions:

• Wellcome Trust allow about 2% of a grant to cover publishing. So if scholarly publishing is USD 10 billion, then public research is 500 billion USD
• The income for Cambridge, Stanford, etc is ca 500 million. Assume 1000 research universities in the world (can anyone do better?) and a power law and we get ca USD 200 billion
• The NIH is funded at USD 35 billion. It’s probably the largest, but add in national funders and you are well over USD 100 billion

Let’s use a figure of USD 200 billion (though I am sure it’s higher).

I’m now using VALUE in the sense (from Wikipedia):

Value in the most basic sense can be referred to as “Real Value” or “Actual Value.” This is the measure of worth that is based purely on the utility derived from the consumption of a product or service. Utility derived value allows products or services to be measured on outcome instead of demand or supply theories that have the inherent ability to be manipulated. Illustration: The real value of a book sold to a student who pays $50.00 at the cash register for the text and who earns no additional income from reading the book is essentially zero. However; the real value of the same text purchased in a thrift shop at a price of $0.25 and provides the reader with an insight that allows him or her to earn $100,000.00 in additional income is $100,000.00 or the extended lifetime value earned by the consumer. This is value calculated by actual measurements of ROI instead of production input and or demand vs. supply. No single unit has a fixed value. Value is intrinsically related to the worth derived by the consumer. [Burke(2005)].

And asking “What VALUE do the public get for their 200 billion dollars?”

And

“what extra VALUE would they get if the research was published openly?”

And again, if you have insights let me know.

There’s an arrogant assumption among many academics that scholarly publishing is produced by academics (maybe 1% of the population) to be read only by other academics (1% of the population) and that no-one else matters. After all why would anyone other than a dinosaur scholar be competent to read a paper on dinosaurs. And surely dinosaur papers have no financial benefit to the world.

WRONG – on both counts.

Mike Taylor has done an awesome – truly awesome – job in pulling together our ideas and hope for the @ccess movement – the imperative to make scholarship available for the #scholarlyporr. Those are the people who don’t have access to a University library. And access doesn’t mean driving to a building, filling pout forms and getting a paper copy. It means online access. Immediate and expansive. Because that’s the only form of access that’s now reasonable for scholarly articles [I deliberately omit books].

Mike’s been interviewing the scholarly poor. I’ve done an interview [http://whoneedsaccess.org/2012/02/18/peter-murray-rust-chemistry-researcher/ ]– just because I’m at a rich university doesn’t mean I can use the electronic library as I want to. My research is stalled because the publishers forbid it. Everyone is scholarly poor when it comes to text-, data- and image-mining. But you know all that.

What’s tremendous is the stories that are emerging. And I get the impression from Mike that he’s got a number yet to be published. So here’s someone who passionately wants to read the dinosaur literature. http://whoneedsaccess.org/2012/02/21/craig-dylke-teacher-and-artist/ You’ll need to read it yourself, best beloved, because I can’t show his dinosaur pictures. Here is he teaching, and I’ll give some exceprts below:

CD: I try to help connect the science of palaeontology to a larger audience. Palaeo-art lets me do this in a way that combines my childhood obsession with palaeontology and my love of digital art. I’ve become so interested in the the philosophy, and methodology of palaeo-art that, together with Peter Bond, I co-founded the community blog ART Evolved where we discuss and encourage palaeo-art of all forms.

But why does Craig need the literature?

When you scientifically reconstruct an animal, every detail of its physical appearance is important. For most prehistoric life, the only place to get details about fossilized remains and informed speculation on what that extinct life might have looked is in the scientific literature. From my perspective as an artist rather than a researcher, the most useful part of papers is the diagrams and photographs of the fossils

Craig cares about getting it right. As simple and as important as that.

… there are times when I would love to have it to check “facts” in popular children’s books. The number of factual mistakes in these books is sometimes quite alarming. Being on top of the most recent publications can also lead to good discussion topics for my students: news outlets only report a fraction of new science discoveries.

And the problems?

The fees for subscriptions, or for single papers are simply outrageous. Many of my digital art software packages cost less!

Limited access to scientific literature has also created an interesting problem in palaeo-art. Without access to source material, many artists resort to referencing other artists. Then you get artistic “memes” in which organisms are consistently shown with characteristics that we have no actual evidence for. (Since the art is the closest thing we have to photographs, they gain an implied credibility when repeated enough times). This runs completely counter to my science education goal.

What changes would you like to see?

Frankly that answer is simple. Either researchers only publish in free access journals or the publishers get with the times and open access to their content.

I’d also like to see more journals offer unlimited illustrations for authors. On any given subject PLoS papers are almost always the superior source material for me as an artist, as the authors tend to fill them liberally with photos and diagrams of their specimens. Too often I’ve been disappointed to track down a critical paper on topic from a mainstream journal only to find there are no diagrams or photos, leaving me at square one on my restoration.

As I have already noted, even a fraction of the scholarly literature is valuable. We’re fighting to get it all, but until that time we are trying to get as much as possible together for Craig.

And there’s no money in dinosaurs, is there? Jurassic Park grossed 900M USD. By depriving the creative #scholarlypoor of the literature we are denying them their full potential.

Today we have launched @ccess – a new site, and more importantly a new community – to make scholarly information REALLY LIBRE available. I’ll stress to start with that this means all disciplines and all types of information and means of communication. Because I’m a scientist I’m concentrating on STEM but it covers everything. By LIBRE we ean free to use, re-use, and redistribute for any purpose. It’s covered by the Open Knowledge Definitions and the actual text of the Budapest Declaration on Open Access 10 years ago.

I’ve blogged about this before. Any information is better visible than not, but simply “being on the web” isn’t good enough for many (I’d say most) modern uses. There are 101 reasons why information must be fully LIBRE and why GRATIS is not good enough. There are 10 million paragraphs on chemical reactions I want to read each year and I must use machines to do this. GRATIS does not work for machines. They can’t work out rights or protect me from being sued. And that’s the reality. If I use a scientific paper beyond what I am allowed to do I’ll be sued and the University of Cambridge will be cut off.

The only way to ensure this is to make sure all the information we want is LIBRE. Free to use, re-use, redistribute for any purpose, commercial as well.

Note that the term “Open Access” is operationally meaningless. The term “fully Open Access” is even worse because it is seriously misused. Some publishers offer “fully open access” and give the reader no rights at all.

The problem is that only about 3-5 percent of current scholarly information is LIBRE. It’s actually very difficult to get a figure, because information isn’t generally labelled with its rights. Print a typical scholarly pub and the print will often tell you very little about the rights. It may not even give the actual copyright owner – so you don’t know whether you can copy it and who will sue you. Some “open access” publishers DO label the material – here’s BMC:

All articles are immediately and permanently available online. Unrestricted use, distribution and reproduction in any medium is permitted, provided the article is properly cited. See our open access charter.

But almost all hybrid papers – where you pay substantial money (perhaps 2000 USD) to make the paper “Open Access” – are neither labelled nor LIBRE. Ross Mounce has shown that only 5% of publishers offer LIBRE “open access” – the rest still impose restrictions or severe restrictions on use. And in my simple study of avian malaria in Pubchem only about 3 papers out of 70 were LIBRE at first glance.

So let’s say 5% of the current published scholarly output can be reused without thinking and without worrying. Because that’s the only guide. If you have to think, then it’s effectively not re-usable on a large scale. Machines can’t understand lawyers. And they can’t interpret information this isn’t given.

What can you do with 5%?

More than you might think at first glance. Much more.

Academics often have a narrow mindset that the only reason for publishing a paper is so some other academic can read your paper. That if we don’t have access to the precise paper we cannot do anything. Sometimes that’s true. But sometimes we just need representative material in that area. Let’s say I want to know the conditions for making an ester (a type of chemical) and there are 500,000 esterifications published a year. 5% of that is 25,000 different reports. My machines will certainly find all the mainstream types of reaction. If I want to know how to grow a common cell type, or prepare a specimen, or find the methods using for recognising motifs in genes or … I’ll certainly find enough examples. If I want to find images of mosquitoes, or a graph of the average rainfall in W Africa the LIBRE literature is almost certainly good enough. If I want to analyse the type of language and terms used in malaria articles the LIBRE literature is more than enough. If I want to find which countries the work is done in the LIBRE literature is all I need.

So we need to label and liberate LIBRE scholarship. And then persuade people to label their articles properly. And hopefully to persuade them of the immense value of LIBRE over GRATIS.

So the recent heroes of our effort have been

• Tom Olijhoek and Bart Knols. Here’s Tom’s report in Malaria World http://www.malariaworld.org/blog/how-easy-can-you-find-information-you-need . Malaria is a really good place to start as the concept is well contained and we can find everything through UK/PubMedCentral. They have also helped to create the site http://access.okfn.org/ . That’s a really good place to start
• Mike Taylor, sauropodologist (http://en.wikipedia.org/wiki/Sauropoda ). Mike has campaigned tirelessly and burnt midnight oil to create the site http://whoneedsaccess.org/ which runs in parallel with the @ccess site. He’s collecting interviews, including one from me, on why we need LIBRE @ccess.
• Mark MacGillivray who continues to add fantastic design and power to http://bibsoup.net . Mark’s Bibserver uses faceted search in an incredibly powerful manner. The technical details are completely hidden from the user. The technology can interact with the Semantic Web / Linked Open data and is a great community builder

Anyone can be a member of this effort – you just need passion and energy and a need to provide LIBRE resources. And if you have a story about how and why you need LIBRE material and can’t get it , then highlight it on the mailing list or help populate the questions on the wiki.