petermr's blog

I have been concerned about the membership of PRISM and, specifically, UK and other European publishers who might be associated, perhaps incorrectly, with the initiative. I hadn’t got around to writing to Nature Publishing Group (who have been an enthusiastic and vauable sponsor and collaborator in our work). Now Timo Hannay has volunteered Nature’s non-involvement with PRISM. This is a long and valuable post and I shall return to some of the other issues later:

PRISM: Publishers’ and Researchers’ Intensifying Sense of Mistrust

For anyone who’s interested here is Nature Publishing Group’s (NPG’s) take on PRISM: Although Nature America is a member of the AAP, we are not involved in PRISM and we have not been consulted about it. NPG has supported self-archiving in various ways (from submitting manuscripts to PubMed Central on behalf of our authors to establishing Nature Precedings), and our policies are already compliant with the proposed NIH mandate.Those are facts. What follows is just my personal opinion.

PRISM has understandably provoked a great deal of anger among those scientists who care about how the fruits of research are communicated. (In this sense, PRISM has achieved the exact opposite of dog-whistle politics: the only people to sit up and take notice have been those who were outraged by it. Nice work, guys.) My main emotion, however, is closer to bewilderment. Do PRISM’s proponents (whoever they are) really think that their approach will do anyone, including themselves, any good? It’s tempting to suggest that they are out of touch (e.g., with the ways in which technology is changing science and scientific communication), but it’s equally possible that I’m out of touch (e.g., with Beltway politics), so I guess all I can conclude is that they inhabit a different universe to the one I’m in. Time, perhaps, to move on and get back to work.Except that PRISM — and the reaction to it — is having one particularly insidious consequence.The things that I find most ill advised about PRISM are the needless belligerence of the message, the crude them-and-us stance, and the distortion of complex issues into unrecognisable caricatures. I wouldn’t mind so much if the issues themselves were inconsequential, but they’re not. Questions about how scientific communication should be funded, and what roles government should or should not play, are central to scientific progress. If we can’t discuss these in a well-informed, grown-up way then science itself will suffer.
It therefore troubled me that the initial counterattacks on PRISM were themselves often lacking in nuance and discrimination. Given the high emotion generated, this was understandable, but that’s not the same as saying it was correct or helpful. The most general error has been to lump all publishers together in declaring them “evil”, “afraid”, “money-grabbing”, and so on. True, PRISM seems to have come out of the AAP, which is a publishing industry body, but right from the beginning (when I also didn’t have a clue what was going on) it was fairly clear to anyone who cared to make the distinction that PRISM was not the same as the AAP.
To treat the industry as one amorphous lump is a continuation of the kind of misunderstanding that leads people to group together “Nature, Science and Cell” when making comments about scientific publishing. This is a pet hate of mine. If you’re wondering where to send your red-hot molecular biology paper then it’s OK to talk about those three journals in the same breath. But if you’re talking about publishing then you’d better think again: there are hardly three more different organisations on the face of the earth than NPG, the AAAS and Elsevier (the three publishers in question).

[… second half to be discussed later …]

PMR: This is very valuable. I shan’t debate it – except to note that a major part of the problem – and confusion – is the complete lack of coherent communication from any, some, or all of the publishing community. Timo’s is only the second/third substantial contribution from any “main” publisher. All others have remained silent. Given that the prime business of publishers is communication it is enormously difficult to get any coherent response. I shall return to this later, but many of the emotions that arise on this list is because publishers simply ignore the issues.
This blog tries to be fair. Yes, I was upset by PRISM, but I hope I kept fairly cool. But in defence of the blogosphere the PRISM message “open access [equals] junk science” – is a simple factually incorrect insult. If PRISM had conducted a debate – of any sort – the emotions could have been avoided. For example – a hypothetical dialogue:

• PRISM: Open access leads to worse science.
• OA-advocate: Please give me evidence…
• PRISM: A study by X showed that there were proportionally more retractions in OA papers than TA
• OA: But Y refuted this…
• PRISM: But Z showed that Y’s data were too limited

This is the sort of debate I would hope to see the scholarly community indulging in. But PRISM – and almost all publishers (except Nature, OUP, RUP and ColdSpring) are not communicating.

So far I have had replies from Antony Williams of Chemspider and Steve Bachrach. These are thoughtfull and I’ll comment here:

1. Antony Williams Says:
   September 10th, 2007 at 3:50 am eI have commented in a recent blog post about your comments regarding copyrighted data extracted from Wiley articles and resold as a spectral collection. http://www.chemspider.com/blog/?p=126Bottom line…I don’t think there is an issue…all data are probably licensed/purchased from appropriate sources. Now, the issue is whether it is appropriate for an organization/individual to extract and compile literature data and commercialize. MANY organizations do this so I think it is appropriate.

PMR: I’ll reply to the main body later, but the argument that “MANY organizations do something, so it’s appropriate” is invalid. Many organizations take my Open Access article, and resell it, some with their own copyright. This is immoral and illegal and increased number makes it worse, not better.
Much of what Antony writes deserves comment:

ChemGate, eMolecules and Discussions About Copyright

Posted by: Antony Williams in UncategorizedCopyright©2007 Antony Williams
Peter Murray-Rust has initiated a very LIVELY conversation about Wiley’s Chemgate rollout in collaboration with eMolecules. …
In that blog Peter posed an interesting question – “Now, Wiley publish a lot of chemistry. And they accompany this with supplemental info – data which they copyright. Do you think if I ask them nicely they will let me aggregate this non-copyrightable data in the same way as we have done for CrystalEye? Please, Wiley, let me know. ”
This is a very interesting opening for a discussion that has concerned me for a while. Specifically, many companies are aggregators of published data which is then commercialized. Most groups who build databases extract from the literature – whether these are databases of PhysChem properties, assigned NMR shifts, toxicology data etc these are commonly extracted from the literature. This has been going on for decades. if the data are copyrighted within the article then is this permissible? The data on NMRShiftDB may exist within articles and be online…permissible? The data on QSAR World are from the literature..permissible? If there are copyright issues with extracting single measured data points (e.g solubility, pKa, logP values) from the literature or even NMR assignments then the number of potential lawsuits is enormous. I don’t believe it’s possible.

PMR: This is a fair summary of the C20 situation. Many organizations extract and aggregate data. Some simply list it, some comment on it, some select or create the “best” (critical) values. All this is highly worthy. And it’s also reasonable that they should be rewarded for their effort.
But they shouldn’t use this to monopolize the use of the data – later.

What would happen now if someone chose to post a structure and a “value” extracted from a paper to the submission system on ChemSpider? Illegal?
Peter then posted a little more asking a direct question about copyrighting. He commented:
“This is an offer to Wiley (or eMolecules) to explain why they feel they are legally and morally allowed to copyright data and resell it. This blog is developing a tradition of offering publishers a chance to put their view in a highly public forum, so I would be grateful of a reply. ”
also “I realise that not all entries in ChemGate come from Wiley journals – some are private contributions, and presumably some are abstracted from competitor journals. But I would be amazed if there were not entries corresponding to Wiley journals.”
I am not aware of the details regarding the spectral collections on ChemGate in terms of copyright so I did a search online and found that the original ChemGate was probably served up by Specinfo technologies and listed the databases on there under their own branding. I believe this is a revenue sharing model with the generators of the data – there is lots of detail online regarding the providers of the data so I won’t bore you with it – however, I don’t believe any of it is extracted from Wiley publications which is what I believe Peter is pointing to. Is there any evidence that any of the data are extracted from Wiley publications? MORE comments below after the list..
[potential suppliers of info snipped…]
I believe that Wolfgang Robien’s spectral collection has likely been added to the list above (but it might actually already be a subset of the Wiley collection and licensed from Robien directly. Peter has already commented recently about NMR data and predictions directly in relation to NMRShiftDB discussions. This discussion is different since I believe this is about a spectral curve collection OR spectra reconstructed from assigned data.
My best judgment is that the data on ChemGate are likely all appropriately copyrighted. Why do I say this? If you visit ChemGate online at http://chemgate.emolecules.com/ you will see the list of NMR nuclei is : 1H, 13C, 11B, 15N, 17O, 19F , 29Si, 31P. if you visit the Modgraph site then you will see the following statement:

PMR: I have no problem about the database creator and owner owning the collection. I do have problems about copyrighting each individual spectrum since I believe that spectra are data – and therefore not copyrightable. IOW if I use a spectrum from one of these collections the copyright issue is not whether I have the right to reproduce (and potentially resell) the spectrum, but whether I am allowed to extract a certain percentage from the collection.

“The main NMRPredict program is supplied with 131,569 C13 records abstracted from the literature by Professor Robien and co-workers at the University of Vienna over the past 25 years. Three optional additional database available are:
[numbers deleted]
If you compare the nuclei in the list above, and the list on ChemGate, as well as look at the bolded statements, then I judge that ChemGate is serving up the Wiley copyrighted collections (licensed or purchased from their collaborators) rather than serving up any copyrighted data from their articles. So, I think Peter can relax about that.

PMR: It may well be that this is currently true – though I’d like to have definitive statements from the parties involved. But there is no guarantee that this won’t happen in the future and every likelihood that it will. The journals – which now increasingly require authors to publish spectra (rightly) should not immediately feed them back into the publishers databases where they are resold to the authors.

However, based on the comments made on ModGraph’s site and bolded above there may be an issue about copyrights. “In the next few years a dramatic expansion of the databases behind NMRPredict can be expected. The journals selected will cover mainly heterocyclic and medicial chemistry in order to give reliable predictions for candidates for drug discovery (Lipinski’s “Rule of Five”). ” It is unlikely that assigned spectra will be extracted only from Wiley publications despite their special relationship .
I DO NOT believe that there is an issue with extracting assigned spectral data and associated structures from any publications. If there is an issue with this I am very interested in having a publisher declaring that here since I know there are parties reading this blog that do exactly that for their business!

PMR: There are grey areas here. If I sit down (or contract out to wage slaves) to transcribe data manually (with quill pen and parchment) and then type it up again then I think no publisher has an issue. If I read the spectrum electronically and put it in a database then I am liable to be pursued by the publisher for breach of rights. So we have the absurb situation that the only way we can get data is to transcribe it by hand. And each user has to do this. What a laughing stock chemistry is to the IT community.

I will be contacting Wiley this week with the request to index the structures and links back to ChemGate here on ChemSpider. Having been involved with creating spectral databases over the years I believe that the pricing for access to over 700,000 spectra is actually very good. Academic prices are likely lower than those listed online.

PMR: 35,000 USD per year is prohibitive. Even if we could afford it we wouldn’t be able to do anything useful other than look at the spectra because the rights would forbid us to redictribute enhanced data.

Question for all… we are presently accepting both spectra and, shortly, structures and associated data onto ChemSpider. Question for the readers – what is the preferred Creative Commons license you would like to see attributed to the user uploaded data?

PMR: The only one that makes sense is CC-BY. Attribute the author and protect their rights. Allow anyone to re-use the data for whatever purpose including commercial. Unfortunately this doesn’t prevent the aggregation and claims to ownership. So, for example, if I publish 100,000 data and an organization integrates it into its own collection it can claim ownership to the collection. That may make it very difficult for the original author to make sure their rights are fully protected.
I think you for this genuine offer to explore this. I would suggest you contact John Willbanks at Science Commons to see if they have suggestions

Peter commented on his post “I had offered eMolecules 250 000 MOPAC calculations as Open Data.” Peter, we’d welcome the opportunity to host your data for everyone.

1. Collections of data have also been granted copyright protection, for better or worse we can argue. But current US law, and I believe also in the EU, protects collections that are not obvious. So for example, a directory of phone numbers of London residents is not protected. However curated spectral data, where choices have been made to check for accuracy, meta data added, etc. are protected. Without these protections, publishers, so they argue, would have little incentive to create new databases.
2. PMR: I am familiar with publisher arguments. My arguments are that they are (a) suspect (b) detrimental to chemistry
3. I was greatly disappointed when the supreme court extended the copyright duration to 70 years. There is great value in the public domain, and the decay of this resource is deplorable. At the same time, copyright does allow for the creator of new materials to be compensated for her work, and that is worth protecting too.
4. Steven Bachrach

An open letter to the British Library Board about lack of Open Access and restrictions on out-of-copyright works
Dear Andy Stephens BSc (Head of Corporate Planning and Secretariat, The British Library) andy.stephens@bl.uk
I am a chemist at the University of Cambridge with a major research interest in eScience – the UK term for the combination of scientific research and scholarship with the new opportunities and power of the Grid and cyberinfrastructure. The UK, through the DTI and others, has spent many hundreds of millions of pounds and I am funded in this area by EPSRC, DTI, comapnies such as Unilever and also by JISC (the Joint Infrastructure Systems Committee). Earlier this year, for example, I was invited to a joint international JISC/NSF meeting on “data-driven science” to discuss the future of cyberinfrastructure over the next 8 years. At that meeting a central theme was the universal availability of digital information without physical, semantic, financial or legal barriers.
In chemistry much of the primary scientific information first appears in peer-reviewed publications in a form unsatisfactory for eScholarship. The primary barriers are business/legal in that publishers assert ownership over the content and the piecewise requirement to negotiate licences and other permissions. In practice, therefore, the material is limited to non-copyrightable material (data or out-of-copyright) or to Open Access publications where the licence asserts the right of the user (human or robot) to use the material without permission.
I was therefore dismayed to find recently that the British Library not only fails to recognise and promote access to this uncopyrightable or Open material, but also adds additional financial and legal restrictions on access (see http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=571 and http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=543 and several other posts). In summary the BL (a) charges for Open Access articles and (b) puts draconian restrictions on access to and redissemination of material long out of copyright. I do not know how widespread this is, but I surmise that there is a blanket restriction on effective access that applies to all content. If true, this means that the British Library, which is involved in digital research (http://www.bl.uk/about/strategic/digiresenv.html) and understands the potential is, paradoxically, a major barrier to eScience.
eScience is at the stage where it needs large amounts of semantic high-quality electronic content with zero-access barriers. Traditional operation of copyright and permissions stands in the way and I would ask the BL to take a national and international lead in tackling this problem rather than amplifying it.
[NOTE: Peter Suber, the leading Open Access commentator and expert has said publicly that he was not able to understand the BL’s position on payment and access permissions for Open Access journals – and presumably for out-of-copyright material as well]

I am now gobsmacked. Earlier I have recounted (OUP wants me to pay for my own Open Access article) how I was expected to pay for access to my [*] own Open Access paper both through the actual publisher and an aggregator. (These organizations have admitted that this was inappropariate and are changing their technology to support free Open Access as opposed to charging for it). However, arising from concerns about access to out-of-copyright material through the British Library, I raised this here and Peter Suber commented (More access barriers at the BL document delivery service) that the British Library charge for Open Access material.

PS Comment. See the BL response when the PLoS Director of Publishing, Mark Patterson, asked why the BL was charging for copies of PLoS articles, which are all OA. At first I thought the BL was saying, in effect, that it doesn’t have the resources to see whether an article is under an open license (or in the public domain). But it’s more complicated than that, and the more I re-read it, the less I understand it. In the case of PLoS articles, the BL charges a copyright fee set by UKCLA and passes the fee on to UKCLA, keeping nothing for itself. But it doesn’t explain why UKCLA believes that PLoS articles should carry copyright fees

PMR: If Peter Suber can’t understand it, then no-one can. So any futire answer will have to be in simpler language
Well, perhaps that was a mistake and the have put it right. So I thought I would see what they have done with my article. This is told in pictures. I search for electronic journals and find:

“Most of the collections are only available from the St. Pancras Reading Rooms, owing to licensing restrictions, and cannot be accessed offsite. Some collections are freely available on the World Wide Web.”
What on earth is happening here? To view an electronic journal you have to visit the British Library in London? I am lost for words… how can this be part of the UK’s effort in eScience where we have developed tools that can access knowledge across the world’s continents. Perhaps it’s an error, so I search for the OUP issue and find:

So if I want to use an electronic journal I have to travel to the British Library at St Pancras??
Maybe they have another service…
Yes: British Library Direct – search and order journal articles online
and here is my paper:

They are both Open Access. I go for the first which is an Open Access Journal , i.e. all articles are OA so any software swicth can simply be put on the journal. I find:

So I have to pay 20.65 GBP (*1.175 for VAT) => 24 GBP. We have paid the publisher to make this article freely available to the whole world. This is so they do not have to ask permission, do not have to pay, can re-use the material for any non-commercial purpose, etc. So firstly the British Library appears to be breaking the terms of our licence – they are charging for something we authors have paid for to be free.
I am going to write to the BL to ask what is going on. And if I don’t get an answer I can understand I’ll take it to a knowledgeable Member of Parliament. There is a lot of interest in Open Access to funded information among some politicians.
In simple terms this is destroying eScience. eScience is only possible with zero-barrier to access. ZERO. This is worse than the cases I have had before because this is the National Library in the UK. I have, on occasions, parised the BL. But here it is saying that it is more important to put barriers in place than to enable freedom of access.
This culture permeates the library community in Britain. They are terrified of breaking copyright. Even when there isn’t any. I can’t get Open theses because they can’t reach (dead) copyright holders. I can’t get papers written pre 1900 because we can’t get definitive copyright clearance.
I know the BL is a government-funded institution and can’t break laws, but it really should be pushing for the cobwebs to be swept away, not locking the door and letting more grow.
=================================================================
[*] This is a multi-author paper but I am using the singular as I have not discussed this issue with the other authors.