Requesting Permissions for Re-use of Copyrighted Material.

Now I am not normally one to rant, at least not on a blog, but today I encountered something that makes me just mad…..and I mean hopping mad.

I have just finished writing a review paper on poly(2-oxazolines)…a class of polymers close to my heart. As it is a review paper, I have included some figures, which were taken from the original research papers forming part of the review. Given that these were not my figures and that I respect and honour the copyright of other authors who have worked hard to produce high-quality and illustrative figures for their publications and the copyright of publishers who have been assigned those rights by an author, I went off to request permissions for re-use of copyrighted material from the relevant publishers. The review was based on about 150 papers, and I had taken figures from a few of them…ACS, RSC…no problem. Their procedures are all more or less automated and relatively pain free, although time consuming. And then, well then I came to Elsevier……

Elsevier has outsourced their copyright clearance procedure to a company called the Copyright Clearance Centre (I have included the link for your edification), which, on its website claims to “help to advance education, innovation and the free flow of information.” So far so good. Following Elsevier’s instruction, the first thing I have to do to obtain permission, is to go and find the resource I took the figure from on ScienceDirect. So off I go and locate the relevant journal (Talanta) and citation on Science Direct. Next, the website instructs me to find the abstract of the paper and to press the “Request Permissions” button.

Pressing this button launches a pop-up window which asks me what I want to do and I make my selections:

I am somewhat curious as to why it asks me which currency area I am currently in, but decide to ignore it for the moment. Having made my choices, I hit the “continue” button. I am then asked to set up an account as I have never used rights link before. Ok, getting tedious, but I hit the button to set up an account (note: none of this is necessary with the other publishers). I am now taken to a page where the anger really sets in: they are asking me how I want to pay.

How I want to pay?? All I want is to request permission for reuse of one small figure. I do not want to pay anything – my institution is subscribing to the journal for me. Why on earth would you want to lump requests for re-use of copyrighted material together with a business process that may be appropriate for the purchase of pay-per-view access? If I do not want to have pay-per-view access, why do I need to hand over payment details? However, the dropdown menu only gives me the opportunity to choose between a credit card payment and an invoice.

Hmmm…..on I go and fill in my details hoping that the “payment” thing is just going to go away down the line. But no such luck and sure enough, on the next screen I am being asked for my credit card details IN ORDER TO BE ABLE TO SET UP AN ACCOUNT to request re-use permissions.

At this stage, I broke off the procedure. I understand that it might be convenient for the “Copyright Clearance Centre” to set up an account for me in such a way, that if I ever wanted to purchase a journal article from one of their customers, they have all the necessary information. IT IS NOT CONVENIENT FOR ME. All I want is permission to re-use a figure in a paper. I do not think that I should have to hand over my credit card details for this and I refuse to do so.

So what is the consequence of this? I am not prepared to set up a Rightslink account with the Copyright Clearance Centre under these circumstances. Therefore I cannot obtain permission to reproduce the figure I wanted and therefore I cannot use the figure in my paper. Furthermore, there is the personal inconvenience: I now have to throw the figure out of the manuscript and to renumber all of my figures in the text. This will cost me at least half an hour.

More significantly though, this has a negative impact on scientific dissemination. On the grand scale of things, it is only a tiny thing, but in effect this has stopped me from re-using a figure created by other scientists, which, I am sure, have a vested interest in their research being talked about, evaluated and disseminated. That is part of a scientist’s core business. The Copyright Clearance Centre has neither helped to advance education and innovation, nor indeed the flow of information, but rather has impeded it. And Elsevier is indirectly guilty: they have not done their best for their authors by helping to disseminate their science, but are collaborating with an organisation which actually puts people off reusing science. They have allowed requests for re-use of material to be lumped into the same procedure used for the purchase of pay-per-view articles. At best that is thoughtless and very poor customer service.

Now as I say, I don’t like to rant, but this kind of thoughtlessness makes me mad.

Sources of Polymer Information

I am currently working on a paper, trying to outline our informatics strategy for the polymer science and in particular for the polymer pharmaceuticals community. As part of the paper, I am reviewing sources of polymer information and their accessibility in terms of open access. And, it will come as no surprise, that the situation is depressing.

So what are the sources of polymer information? Well, there are mainly three: papers, theses and data compilations. Let’s look at these in turn.

Papers. Well, Peter continues to blog about this extensively. Papers are copyrighted by the publisher – all rights reserved. Open Access publishing is practically not done in the polmer science: papers submitted to the standard canon of polymer journals (including supplementary information where available) are fully copyrighted by the publisher. There is a tiny spark of light: e-polymers. Here’s a journal description copied from the e-Polymers website:

e-Polymers is a peer-reviewed internet journal under the auspices of the European Polymer Federation (EPF). In the area of polymer science and engineering, it makes novel scientific and technological results available both in academia and industry, and basically free of charge.

Furthermore, e-Polymers is a forum dedicated to the free and fast exchange of information. Therefore, it will comprise

• original publications on basic polymer science and engineering,
• reviews on trends in science and technology, in academia and industry,
• reports on educational topics,
• information about joint programmes, e.g. of the EU,
• job advertisements and appointments of new chairs etc.,
• business reports (abstracts),
• commercial links and advertisements.

Thus, e-Polymers is the answer to the strange situation that many institutions cannot afford to subscribe to journals which – at the same time – they strongly support by submission of high-quality papers, refereeing etc.”

So far so good. Or not, as the matter may be. When first reading this, one could get the impression, that words and phrases such as “free” and “e-Polymers is the answer to the strange situation that many institutions cannot afford to subscribe to journals which – at the same time – they strongly support by submission of high-quality papers, refereeing etc.” would point to an open access publication or at least to the spirit of open culture. However, this is not so. Upon closer inspection of the author instructions one finds, that upon acceptance of a paper submitted to e-Polymers, the author transfers all copyright to the journal. The journal is therefore merely free to view (which is a first step) but NOT open access according to the Budapest Open Access Initiative Declaration. When digging around the website further, one finds even more obstacles: the journal is a priori only free to view for participating institutions and their members. Non-members can gain free access, though this has to be requested via an institutional library. So it is free to view with obstacles, which removes us even further from true open access. Nevertheless, the European Polymer Federation seems to have correctly diagnosed the problem in scientific publishing at the moment and has taken a baby step to address the issue of access. This is encouraging and maybe can be built on to move to full open access in the future.

Theses. The problems associated with theses in the polymer science field are the same as those encountered for theses in general: availability/accessibility and a clear licence. Although the situation is improving, a significant number of institutions only require the submission of one or several paper copies of a doctoral thesis. As such, of course, the contents of the thesis is lost in terms of machine processing and information extraction. But even when available in an institutional repository, there is usually a lack of a clear licence or the contents are again copyrighted by the institution itself and therefore cannot be freely accessed and used in terms of the Budapest Open Access defintion.

Data Compilations. A number of compilations for polymer data exist, which are in extensive use by scientists. The most important ones are the Polymer Handbook (Eds. Brandrup, Immergut), The Wiley Database of Polymer Properties, Polymers – A Property Database and the PoLyInfo database. Let’s look at these in turn:

The Polymer Handbook. Published by Wiley. Non-digital, contents copyrighted and all rights reserved by Wiley, commercial.

The Wiley Database of Polymer Properties. Published by Wiley and essentially a HTML version of the Polymer Handbook. Digital, subscription basis, log-in required, contents copyrighted and all rights reserved by Wiley, commercial.

Polymers – A Property Database. Published by Taylor and Francis. Digital, subscription basis, log-in required, contents copyrighted and all rights reserved by Taylor and Francis, commercial.

PoLyInfo Database. Developed by the National Institute for Materials Science of Japan. Digital, log-in required, contents copyrighted and all rights reserved by NIMS, non-commercial, free to view.

So overall, the situation is even worse than for small molecule chemistry, where open access resources are starting to make a real impact and which is increasingly liberating chemistry data (see, for example, PubChem, CrystalEye). At the moment, there is nothing even remotely comparable for polymers.

So, how could we change the situation? Clearly, there needs to be a multipronged approach:

Community building: There are a number of existing or emerging polymer communities, which might be open to the idea of open data – a collaboration with just one of them could be enough to act as a demonstrator and maybe is catalytic.

Continued advocacy: Open Culture advocates are getting increasingly vocal and efforts such as those of Peter, Peter Suber, the Creative and Science Commons, the Open Knowledge Foundation (Rufus Pollock) and many many others are invaluable. Education must be part of this: where students are not already aware, they ought to be confronted with the idea as undergraduates: nowhere more so than in chemistry.

Continued technology development: The more I understand about the technologies that we are currently developing and that are already changing the face of the internet, the more I am convinced that these technologies in themselves will force a radical change in the business model that is driving scientific publishing. The current one is becoming increasingly untenable and the aggressive behaviour currently shown by some publishers only indicates an attempt to defend a dying business.

Continued pressure from funding bodies: Funding bodies need to be convinced to “vote with their wallets” and require researchers to deposit manuscripts and data in OA archives/repositories as a condition of funding. The Wellcome Trust is exemplary in this context.

Maybe in this way, we will be able to remove the enclosure, that is currently choking “the intangible commons of the mind”^[1] that currently impedes scientific progress.

[1] Willinsky, J., The Access Principle – The Case for Open Access to Research and Scholarship, MIT Press, Cambridge, Massachusetts, (2006) and references therein. (Available under CC licence from MIT Press webpage)

The Cambridge Polymer Builder.

The first “proof of concept” product of the Cambridge Polymer Informatics Group is up on the web. It is a demo application of a polymer builder, which uses Chemical Markup Language, Polymer Markup Language and Jumbo to build various types of polymers.

The polymers are constructed from small fragments, such as CH, CH2, CO etc. groups with the associated connection table defined in CML. Polymer Markup Language (PML) then contains a set of instructions in terms of how these fragments are “glued” together, how torsions (in 3D representations) are dealt with etc and it can also deal with distributions (of torsional angles just as much as molecular weights) and probabilities (e.g. for random compolymerizations etc.). (More details in a forthcoming paper).
The polymer builder subsequently takes the fragments and the relating PML document as an input to enumerate a full connection table for a macromolecule in CML. (We have not implemented ensemble building in this demonstrator).

Right now we can build most structural motives, such as homopolymers, block- and random copolymers, dendrimers and branched systems. In this demonstrator, we have not currently implemented bump checking and a number of other controls, but we are working on them as I write. The demonstrator app is available as a webservice here. Please go out and take it for a spin. And, by the way, we are grateful for feedback….so let me have your thoughts and comments via the comments function on the blog.

A harmless drudge…..

An awful lot of our work in polymer informatics is concerned with the development of ontologies, taxonomies and dictionaries, all of which aim to define the terms we are using for the benefit of fellow humans but also machines.

In doing so, we are of course part of a long tradition – and one of the most important exponents of this tradition in the UK is Samuel Johnson. I have just finished watching a documentary on the BBC on Johnson’s life and also the trials and tribulations he had to go through when working on the dictionary.

The issues are much the same as those we encounter today: agreeing on the definition of a term (in our polymer work, a favourite and recurring example is IUPAC’s definition of a macromolecule as “a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass” or the fact that IUPAC regards “macromolecule” and “polymer molecule” as synonymous terms, but then goes on to define a polymer as “a substance composed of macromolecules”. In the former example, is thatr really a definition that could satisfy a rigorous scientist? And in the latter case, given the individual definitions of the terms “macromolecule” and “polymer”,..does it make sense to speak of “polymer molecules” in the first place?), the form a dictionary should take and, of course, ensuring that the dictionary is used (i.e. accepted) by a community of people.

It is amusing, then, to see how Johnson himself defines a person engaging in this activity – a lexicographer – and thus by, extension, defines the modern (computational) ontologist:

Lexicographer: A writer of dictionaries; a harmless drudge[...]

Position in Polymer Informatics Available.

A position in polymer informatics has become available in our group. It is a post-doc position for up to 16 months (limit of tenure applies). The holder of the post will help to deepen and expand our capability in text mining polymer (related) information. A complete job description and the official application instructions can be found here. The closing date is 6 July 2007.

Polymer Informatics Lecture

A while ago, I gave a lecture about our beginning polymer informatics work here at the Unilever Centre. We videoed it and have now permission to put it online from our sponsors, so here it is:

Thanks to Jim Downing and Dr Andrew Walkingshaw who were behind he camera.

The talk covers our vision for polymer informatics, namely being able to solve the “inverse structure-property relationship problem” and to develop technologies which allow the rapid development of design-rules for polymers.

Subsequently, there is a discussion of what, at the moment, is preventing us from achieving that ambition. The nature of current polymer information systems is discussed together with a brief discussion of the quality of polymer data.
The talk then goes on to introduce the notion of the semantic web and illustrates how semantic web technologies can be used to address some of the problems that were previously discussed. As a part of this, a markup language for polymers and a polymer ontology are briefly discussed.

The lecture also showcases a polymer builder which makes use of the markup language, together with an example of reasoning over the polymer ontology.

You can download the talk to your iPod directly from the Google Website (clicking on the little Google Video Icon on the bottom right of the player will take you straight there).

Pierre-Gilles de Gennes

Pierre-Gilles de Gennes

In a now not so recent post I talked about the polymer reptation model and Pierre-Gilles de Gennes.

Well, last Friday, de Gennes died at the age of 74 and science lost a great man and a polymath. The New York Times has just published an obituary of the man. Please go and read it when you have a chance.

Photolabile Dendrimers…

…which are in many ways conceptually similar to Shabat’s self-immmolative dendrimers were published by Kevwitch and McGrath in the recent issue of New J. Chem. (DOI: 10.1039/b617289j). These dendrimers contain o-nitrophenyl linkers in the core, which allow the controlled degradation of the material:

The photolabile core can be prepared from piperonal in a relatively straightforward way. As was the case for the self-immolative dendrimers, a trigger event – in this case irradiation – leads to the fragmentation of the dendrimer. In this case, the dendrons detach from the core – no complete unraveling of the architecture occurs.

An elegant synthesis…

…of core-shell brush copolymers has just been reported by Wooley et al. (Macromolecules, 40, 2289 (2007)).<img id="image48"

The exo-norbonene-functionalized raft agent was prepared by esterification of the corresponding alcohol with an acid functionalized raft agent (87 % yield). This was followed by the one pot ROMP and RAFT procedures. The ring-opening metathesis procedure was carried out using a Grubbs catalyst in CH₂Cl₂ to give a poly(norbonene) derivative with an M_n of 40.6 kDa and a PDI of 1.24.

The RAFT polymerization was then carried out using styrene and maleic acid anhydride as co-monomers and AIBN as the initiator (50 deg C reaction temperature). The comonomer pair was chosen due to their low reactivity ratios, which allows the one-pot preparation of statistical polymers of the type poly(styrene-stat-maleic anhydride)-block-poly(styrene). ¹H NMR suggested quantitative conversion of the maleic anhydride after 16 h, but only 8.2 % for styrene. The reaction was allowed to continue for another 16.5 hours and quenched after 12. 8 % styrene conversion to give the desired core-shell brush copolymer (M_n=1200 kDa, PDI = 1.32).

Publishing Volumes

I am currently in the process of preparing a publication on the development of an upper ontology for polymers, that I have been working on for some time. As part of the publication I am arguing that the increasing volume of scientific publication really requires a new information model for chemical and polymer information. To support this with some numbers, I hit SciFinder and did a search on how many journal articles in SciFinder’s database contain either the word “chemistry” or polymers. Here is the graph:

Can you really read from this that the publication volume has doubled over approximately 16 years? In which case….wow….highest highest time we came up with new ways of publishing and mining chemical information.