• Trading knowledge by Frank Norman

    Observations on scientific information, from a librarian's perspective

    • Science in the city

      Sunday, 21 Jun 2009

      Following on from my Parks theme yesterday, I had a lovely stroll in the park today. I think it just about qualifies as a park, but it’s a long thin one, based around a small stream.

      Jesmond Dene is just to the edge of the city. Which city? Well, this is its cathedral:

      The city has a nice line in public scupture:

      and

      It has a famous old Literary and Scientific Institution (forgot to take a photo) and a good few scientific and technical figures such as these two:

      You might see a clue to its sister city across the water in this photo of the famous art gallery:

      shown here again with some more icons of the city:

      That bridge in the background should be the clincher. See it again here:

      Hmm, I was going to ask you to guess where I was but after checking the post in preview I realise I have given the game away completely in one of the photos and I don’t have time to re-edit. I’ll have to be more devious next time.

    • The beauty of parks

      Saturday, 20 Jun 2009

      There is a lovely essay on Parks in the Guardian today. I say Parks rather than parks as the author takes a very strict line on what is or isn’t a Park, proposing five criteria that must e met in order to qualify (large trees, random planting, undulations, scale, and a gate or portal). William Boyd, the essay’s author, was one of eight writers commissioned by London’s Royal Parks to write a story set in a London Royal Park; one writer for each of the 8 parks.

      In his Guardian piece Boyd ranges widely, discussing fiction set in parks, Orson Welles, plane tree, Rio de Janeiro, Queen Victoria, pyschogeography, cemeteries, zoos, Wittgenstein, and sex, though not all at once. Is what he says about plane trees correct? He says that the London plane tree is

      a hybrid derived from the Platanus orientalis and the Platanus occidentalis. This hybrid sheds its bark, a fact that is believed to make it more resistant to the city’s polluting toxins,

      A good friend of mine is a great lover of parks – a complete nut about parks in fact. He made me realise that I love them too – a walk (or run) in a beautiful oark can have a wonderfully calming effect. I also like the dissonance you find in city parks between the urban setting and the rural appearance. Walking through St James Park in London, Central Park in New York, or Lumpini Park in Bangkok you can see the city around you but it is not touching you.

      If you love parks read Boyd’s essay. I think I may need to look the 8 stories too in due course.

      P.S.

      Forgot to say. Boyd also discusses the distinction between town and country writers. This made me wonder if there is a similar split between town and country scientists?

      Is the science done at Cold Spring Harbor, Hinxton or Keyworth any different from that done in South Kensington, Toronto or Manchester?

    • Man dating - love it or hate it

      Friday, 05 Jun 2009

      Dating seems a bit old-fashioned these days, but mandating is becoming more and more popular, though it has to be admitted that there plenty of people who do not love it.

      I went to an interesting event on Friday called Research in the open: How mandates work in practice. It was organised by the RIN (Research Information Network) and the RSP (Repositories Support Project) and provided a good overview of trends in open access policies and research. Open access mandates are part of the research environment now, though one speaker preferred to call them “requirements” as that has a softer ring to it.

      I was impressed by the amount of work that the Wellcome Trust have done, outlined by Robert Kiley, in helping their funded authors to comply with the Wellcome mandate. Firstly of course they have taken the lead in establishing UK PubMedCentral as a repository for biomedical research. They have taken a generous approach to providing open access fees, though mysteriously excepting their own Sanger Institute from this provision. They have also put much effort into smoothing the process by negotiating with publishers, and ensuring that open access options are available for most journals that their funded research might get published in. Despite all this effort they are still seeing only about 35% compliance. Other funders should take note – if you are not prepared to do the leg work with publishers and do not provide the funds to pay OA fees where necessary then you should not expect high compliance.

      I do know of one institute that has achieved closer to 60% compliance with their funder’s mandate. That has been achieved again by hard work, this time by the institute’s librarian. Later in the day Bill Hubbard, manager of the SHERPA project, pointed out that all the UK research-intensive universities (members of the Russell Group or the 1994 group) now have an institutional repository. The people managing these repositories are ideally placed, he suggested, to work with research funders to improve compliance. He suggested that funders should provide repository managers with information about grant-holders in their institution for a start. I agree there is a gap that needs to be bridged between research funders and institutional library or repository managers. One of my problems with UKPMC is its lack of any institutional perspective, so it is not easy to view all authors from your institution or all papers from your institution. Robert Kiley mentioned that UKPMC and the National Library of Medicine (the original begetters of PubMedCentral) are working to tag papers with institutional metadata, so that’s a start. This will help institutional repositories to harvest relevant papers from UKPMC. Bill Hubbard did suggest that perhaps UKPMC should instead harvest papers from institutional repositories, but that didn’t go down well.

      We also heard that publishers actions can improve mandate compliance, Elsevier introduced an improved workflow for author submissions and have seen increased take-up of their author-pays option. It’s not really surprising that if you make it easier for authors to understand what to do then they will do it.

      It would of course be lovely if all publishers had the same policy but that is not a realistic hope. 92% of publishers have an Open Access policy but they vary widely. In particular, re-use rights need to be clear and explicit – they are the key to UKPMC text-mining plans for instance. Wellcome are working with Nature Publishing Group to define a model for rights and it is hoped that this will be quickly adopted by other publishers.

      On the subject of complexity, Bill Hubbard’s presentation had a lovely slide (number 18) showing the bewildering variety of options facing an author trying to comply with a funder’s mandate.

      The RIN report on paying open access fees was referred to by various speakers and there were requests for more case studies to be published along the lines of the Nottingham University case study in that report. Wellcome suspect that, in multi-funded papers, they are currently picking up an unfairly high proportion of costs simply because they have provided funds that are easier to tap into. Wellcome hope this will change. Astrid Wissenburg, from ESRC and RCUK, noted that Research Councils are public bodies and therefore have to follow public accounting rules. They cannot therefore be as flexible as Wellcome in providing funds for OA. Several members of the audience agreed that this is a problem badly in need of a solution.

      Astrid also gave a summary of the recent RCUK report on open access. RCUK is planning to support open access by extending support for publishing in open access journals including pay-to-publish and by building on mandates to deposit research papers. One questioner noted that the report found that researchers were not well-informed about open access, and wondered why RCUK was bothering if researchers were not bothered. Astrid stated that RCUK has responsibility for ensuring adequate research infrastructure and saw a duty to push the debate on open access. She also noted that the report had found an awareness gap, not a lack of interest. Indeed, senior research staff were very supportive of open access. It was interesting that although the day was in general good-humoured there were still undercurrents of antagonism between the pro- and anti- open access parties.

      There were reports from a couple of interesting research projects. One, the EU-funded PEER project is looking at the impact of self-archiving on publishing and research. So much of recent discussion of Open Access has focused on the author-pays route it will be interesting to see the results of PEER, looking at what it calls stage eprints. The project will start producing preliminary reports in autumn 2009 but will its final results are not due until 2011, with a conference due in summer 2011. The Houghton report on Economic Implications of Alternative Scholarly Publishing Models was described by Charles Oppenheim, one of the co-authors. The economic model had 2300 costed activities and 550 basic data items, but it was not possible to find reliable costings for all these activities. There has therefore been trenchant criticism of the report from publisher groups. I rather suspect that the criticism would have been less trenchant if the report had not drawn conclusions widely seen as favouring open access.

      The final part of the day focused on Higher Education. Paul Ayris set out the rationale for UCL’s open access policy (recently announced) – it is a way to achieve UCL’s objectives of “developing and disseminating original knowledge to benefit the world”. Paul Hubbard from HEFCE talked about the Research Excellence Framework. He noted that sharing is an integral feature of research and that shared findings are more likely to built on and applied. Finally Bill Hubbard talked about change and, as noted above, encouraged research funders and repository managers to work more closely to support research authors.

      Another summary by Chris Keene has a clearer account of the day – I just focused on what interested me.

      I took away from the day a sense that mandates are here to stay but they are not sufficient on their own. Funders, institutional managers, librarians, repository managers, publishers – all must work together to help make it as easy as possible for researchers to comply with mandates. JISC, RIN, RSP, RCUK, the EU all have roles to play in producing guidelines and research.

    • Chemistry - feel the love

      Wednesday, 27 May 2009

      My first love in science was chemistry. It was the usual story of an inspiring and eccentric teacher who stoked my interest and got me hooked on transformations, equations and the periodic table. OK, so the bangs, colours and smells helped a bit. My interest lasted until sometime during my chemistry degree course, then unfortunately waned dramatically. After graduating, my interest did pick up a bit but I realised by then that chemistry and me were destined just to be good friends. My relationship with chemistry (and indeed with science) was not going to be an intimate one, with hanky-panky and rumpy-pumpy, but a skittering, lightweight interest. More of a light hydrogen bond than a deep triple-bonded affair.

      I found my way therefore into libraries and started working as a librarian in a pharmaceutical R&D Information department. It seemed to me then (early 1980s) that the most interesting stuff going on was always in chemistry – substructure searches, connection tables and the like. I didn’t get to do any of that but had to content myself with looking after the printed research tools.

      Chemists have always been big information users and Chemical Abstracts was the king of indexes, taking up more shelf space than anything else in my library at that time. The arrival of the quinquennial Chem Abs collected index was always a big deal – we could throw away ten sets of individual volume indexes and replace them by one giant set of indexes. Eventually though pressure on space was such that we could not accommodate the printed Chem Abs and had to make the switch to microfilm. We had a cunning machine that let you type in the number of the abstract you wanted to view and then the microfilm reader automatically wound the film to about the right place on the spool. It was high-tech for those times but now it seems gloriously retro.

      I’m sure many chemists and chemical information specialists will, like me, have shed a tear when they saw this announcement from Chemical Abstracts Service (CAS):

      Effective January 1, 2010, Chemical Abstracts™ and other print products (with the exception of the CA SELECTS™ products) will no longer be available in print.

      Actually I am surprised it has taken this long. Cumulated Index Medicus (the print more-or-less equivalent of PubMed), for example, ceased print publication in 2004. With various online versions of Chemical Abstracts and the wonderful SciFinder interface, the printed volumes are pretty much redundant.

      I nearly broke wind in surprise when I recently read another headline – CAS Launches Free Online Database. Could it be that CAS, after bitterly resisting the US NLM’s work in making PubChem available for free, had undergone a conversion to free data? Were they going to make their database of 44 million chemical substances freely available? Reading further I found my answer:

      [CAS] officially launched Common Chemistry, a free online database containing information on 7,800 chemicals of widespread and general interest as well as all 118 elements from the periodic table … the substances in Common Chemistry were selected because they had been cited 1,000 or more times in CAS databases

      Not quite 44 million, but I suppose 8,000 is a start.

      For now though the PubChem service looks like a better bet, with over 19 million unique structures. It is really a chemical database for biologists though, lacking the physico-chemical properties that chemists may need but offering information mainly on substances with biological activity. PubChem has close links with ChemSpider, another free chemical database with about 21 million substances. ChemSpider was also the result of a recent press release as it has been acquired by the Royal Chemical Society, “to fulfil its strategic objective of disseminating knowledge to the chemical community and advancing the chemical sciences”. The press release says that “ChemSpider is the richest single source of structure-based chemistry information” and it’s good to see that it is in good hands. One can’t help reflecting on the difference between the UK’s learned society for chemists – helping to develop a free chemical database service – and the USA’s equivalent, the American Chemical Society who own CAS.

      Chemistry seems to be everywhere these days. The UK Chemical Database Service (CDS) at Daresbury is again fighting for its life, in the face of a review by EPSRC. CDS have set up an online petition. CDS is a “national facility dedicated to the provision of centralised chemical information for the UK academic community”. It offers crystallographic data, spectroscopy data and synthetic organic chemistry databases. The petition asks users to affirm that they see a need for a UK national chemical database service.

      I also received an email (funnily enough I just received a second copy of it) asking for my input “to help shape the future of chemistry database solutions. The global market research firm mmr is currently conducting a short survey about chemistry database solutions, and you are invited to participate.

      I didn’t at first spot the “market research firm” bit. The survey is ostensibly about SciFinder, CrossFire and Reaxys. Perhaps I’m too cynical but in reality the survey looks to me like a marketing puff for Reaxys, Elsevier’s new chemistry database, sorry I mean “workflow solution for chemists”. I thought I was shaping the future of chemistry databases, but in reality I’m just shaping the future of Elsevier’s profits. Oh well, ’twas ever thus.

    • Required reading

      Thursday, 07 May 2009

      Earlier this year Heather drew attention to Vivian Siegel’s editorials on supporting outreach efforts and on authorship and acknowledgement. I’m ashamed to say I did not see Heather’s post at the time but am pleased to find it now as I recently had the pleasure of meeting Vivian Siegel, and hearing her give an excellent talk entitled “How to get published (in a high profile journal)”.

      Vivian is editor of a new journal, DMM: Disease Models & Mechanisms, published by the estimable Company of Biologists, and was previously chief editor at Cell and then executive director and one of the launch editors of PLoS Biology. So she does know something about high profile journals and about editing. Currently she is Director of the Center for Science Communication at Vanderbilt University. The Center aims “to help authors of basic biomedical research publish better papers in better journals, and to help potential editors gain experience and improve their skills”. One example is the Vanderbilt editors’ club, described in an article in DMM. This is a group of post-doctoral fellows and graduate students that offers editing services, free of charge, to Vanderbilt faculty and trainees.

      Anyway, it seems to me that her editorials in DMM are becoming required reading. Thus far she has written on:

      All of these are available for free at present.

      In short, if you are interested in scientific publishing and scientific communication then get along to DMM and have a read.

      Oh, and if you want to know how to get published etc, these were her five bullet points:

      • Do important work
      • Write well (be sure to use presubmission enquiries and a covering letter)
      • Write strategically, for the reviewers
      • Make the editor your advocate
      • Understand the decision
    • Subscriptions and open access fees

      Thursday, 07 May 2009

      Paying for open access has been on my mind recently. All those “open choice”, “author choice”, “open option”, “open article”, “online open”, “open science” and other similar schemes (why does each publisher have to have a different name for the same thing?!?), they create a need for someone to pay a fee in order to get their article published. Richard has already commented on this , highlighting the RIN’s recent report on the topic.

      My preoccupation has been occasioned partly by discussions with our procurement people yesterday about how we purchase journals (in preparation for the RCUK Shared Services Centre). The possible impact of open access on journal subscriptions occasioned a lengthy detour to explain what OA was and what the strategic implications were for procurement. That moved us into high-level RCUK strategy on research outputs, which is the terrain of the RCUK Research Outputs Group, who recently issued their own report .

      When I returned to my office I found a flyer from the Portland Press with news of its new open access journal ASN Neuro . I was perplexed briefly as it mentioned an “Institutional Membership rate of $630”. Sounds like a subscription, but it’s not – the journal is Open Access so it can’t be. No, this membership gives you a $210 discount off the publication charge for any papers that your institution’s authors may publish.

      Other publishers have similar things – OUP’s Nucleic Acids Research has morphed its online subscription into an institutional membership that confers discounts on publication charges. Some, such as PNAS give a discount on publication fees to any institution with an institutional site licence.

      The Portland Press flyer also mentioned their new Opt2Pay (cute name) scheme, also with a tie-in to subscriptions.

      And of course BioMedCentral have had an Institutional membership scheme for some time. In its early years this did not look very attractive as we were publishing little with BMC journals, and the membership charge was relatively high. I think they have modified the scheme, with more options, now and I really must look at it again. PLoS also had an institutional membership scheme, but it required quite a strong commitment. I really need to check it out again.

      I can see that the link between subscriptions and OA fees is going to give me a few headaches when I try to figure out what journals we can afford for next year.

    • Changed relations

      Monday, 04 May 2009

      Bora wrote recently about various aspects of power and how “online” has changed the balance of power in different ways. I want to talk about how the advent of e-journals has changed the power of publishers and other players in the journal market.

      There has for some time been a trend towards fewer personal subscriptions to scientific journals. Writing in 2001 Carol Tenopir said the average number of personal subscriptions per scientist has roughly halved over 20 years, This has probably been accelerated by electronic journals. If your institution provides desktop electronic access to your favourite journals then you have less incentive to retain a personal subscription. Even the weeklies like Nature and Science and popular titles like _Cell were affected by this trend. Each of those publishers thought long and hard about how to introduce a site licence scheme that provided stable levels of total subscription income. When they first introduced their new business models I think it came as a shock to most libraries; we had to pay a premium rate to make up for all those lost personal subscriptions. Publishers realised then that they needed to improve relations with librarians, who were now becoming their principal customers. They developed new websites and information packs aimed at us, enlarged their sales teams and many also established library advisory committees to gather feedback.

      I’ve had the honour of attending some NPG Library Committee meetings, and found them very interesting – a chance to learn both about NPG and about other librarians’ experiences. Of course we can’t expect publishers simply to listen to our views and immediately act on them, but they do take note of what we say and they also explain their thinking to us, to help us appreciate their side. I didn’t attend this year’s meeting, which took place a couple of weeks ago, but I understand that the economic situation figured in the discussions.

      A propos of that, librarian Cristina Pikas has drawn attention on her blog to a statement from ICOLC about the economic crisis. ICOLC is the International Coalition of Library Consortia – a kind of meta-consortium. Their statement seeks to persuade publishers to be gentle with us when it comes to setting prices for 2010. Cristina highlighted one statement we can do without costly new interfaces and features. Now is not the time for new products. That does make sense to me, though work on improving standards compliance is an important exception.

      So, ejournals have enhanced the relationship between libraries and publishers, and perhaps lessened the relationship with direct subscribers. Ejournals have also shaken up the journal supply chain. Traditionally libraries have used a serials agent, like a specialised bookseller, to buy journals. That means we just deal with the agent and they handle the payments to all the different publishers. But as ejournal deals have become ever more complex, so we have had to increase our direct negotiations with publishers. I think most librarians still value the role of agents, but publishers push us more and more to deal direct. One large publisher recently informed me that my request, to switch from print+electronic to electronic-only subscriptions, must be given to them directly as they did not accept such instructions from agents. It didn’t help on that occasion that the publisher and agent used quite different terminology for what I had thought was a simple instruction. Anyway, I had to go and lie down for a bit to lower my blood pressure after that particular exchange!

      All this increased dialogue between librarians and publishers makes life interesting. I have no doubt that online will keep on changing the balance of power between different players in scholarly communication.

    • Big publishing, big deals, big relief

      Monday, 20 Apr 2009

      I heaved a sigh of relief today. My last journal subscription wrinkle of 2009 has finally been ironed out. It’s a pretty big wrinkle (the big deal of one of the big four publishers) and needed a mighty iron to smooth it down but now, only four months late, we have access to that big deal. I won’t mention the publisher, but I expect any academic librarian will guess who I am talking about.

      They are the new behemoth on the block – the product of a merger a couple of years ago. This is the first year that they have fully merged their operations, and it has been a very painful process. The first step was merging the two electronic platforms, meaning the URLs for half the journals needed to change. But that was simple compared to merging the two commercial operations. Two different sets of customer records, two different ways of calculating prices for their big deal, two different sets of staff. All these had to be battered into submission carefully molded into a single operation. I feel for the staff of the publisher, who have had an enormous job to sort out all of the complications.

      In the past we used to sort out journal renewals in September and October, and perhaps up to November for any tricky issues, plus odd problems that might come to light in January. These days we often are still at it until February.

      Sorting out the details of a big deal is always time-consuming and fiddly. In this case it didn’t help that I went away on holiday just days after I received the initial offer from this publisher. But then it didn’t help that the offer, for calendar year 2009, only arrived a week before Christmas 2008. It was never going to be settled in time for 1ate Jan 2009. One highly confusing spreadsheet and a few phone calls later, I began to understand how the deal might work and I started the tricky job of explaining to the other libraries in my group how it might work for them. Four more spreadsheets later and I-don’t-know-how-many more emails and phone calls, and I was ready for the last step – explaining it all over again to the person who has to sign the contract. That happened last week and this morning the access is fully operational.

      I am comforted that fellow librarians across the country, and indeed across the world, have all been experiencing similar frustrations with this deal – it’s good to know that you don’t suffer alone.

      In the light of this, the April Fool’s day joke about publishing mergers was quite scary. Imagine a merger on this scale – we would probably still be sorting out the details in September!

    • Remix - copyright again

      Monday, 20 Apr 2009

      I wrote previously about copyright, and the way that entertainment is influencing science. If you are interested in that topic, then look up a review in this week’s Science of Laurence Lessig’s book Remix:

      an engaging read about how the Internet affects our cultural production system and the policy implications of these effects.

      Copyright law has not kept up with technical change and the consequent cultural change:

      our current approach to copyright developed at a time when quotation from recorded music and audiovisual works was only available to commercial entities, and thus it was designed to regulate such entities… [but it is now]… governing the day-to-day cultural practices of millions of amateurs who are the foundation of Internet culture

      The review draws attention to why this is all relevant to science:

      concerns he raises about excessive property rights getting in the way of creative uses of existing materials apply as well to data and the technical and legal constraints on sharing them, to research tools and patents constraining their application, to materials and material transfer agreements that can impede their employment across institutions and labs, and to open access publishing.

      and also points out that:

      Lessig weaves his tapestry from many stories about human cooperation…Two or three of these touch on efforts to harness decentralized contributors to scientific projects

      Rereading this post, I note that it consists mostly of quotes from that book review, which bears out the importance of quotation, borrowing and remixing.

    • Brief summaries on Nature online contents page

      Thursday, 09 Apr 2009

      I thought I was going mad this morning as I browsed the online contents page of today’s Nature issue. When I got to the sections for Articles and Letters, the entries looked longer than usual, due to the inclusion of a two or sentence summary for each item.

      I checked earlier issues and could not see these summaries, so it looks like a new development, though I haven’t seen any announcement about it.

      I think it is a good idea – making browsing more informed – but some readers may dislike it as it is of course less compact than before.

      It is surprising that many online tables of contents look so much like their print counterparts. Elsevier have a cunning thing that lets you preview the abstract on the contents page, but that’s all that springs to mind without going and checking other publishers.

      So, what do you think of the new contents page?

      I am also curious to know what drove NPG to make the change?


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