As a service manager, my first impulse is always to give people what they want. My primary objective is to keep the customer happy (yes, I’m afraid even in Libraries these days we have started to call our users ­customers). To keep information-hungry researchers happy is simple: just provide access to everything, everywhere. The only snag is that I also have to stay within a budget, so I have to make choices about what access to purchase. Most of my budget is spent purchasing journals, so journal selection is always a major concern. I try to keep to a steady state, maintaining the same range of journals with only small tweaks (individual additions and deletions), but there are periodic hiccups (cancellations at times of budget crisis).

I was interested to see in a recent report that “Publishing companies, especially the large and commercial ones, are launching journals at a higher rate than in 2005”. New journals are the best way for a publisher to attract new subscriptions, so it’s not surprising that new launches are increasing. The report, from the Association of Learned and Professional Society Publishers (ALPSP), also found that publishers are closing more titles.

Requests from library users for new journals are a mixed blessing. On the one hand, it’s very useful to know what people want to read. On the other hand, I can’t satisfy all requests as the budget will not stretch that far. How do I decide when a subscription is justified? I look at the brand (Nature Publishing and Cell Press titles usually go to the top of the list), and at the topic of the journal (not interested in Nature Geoscience here but translational medicine is a hot topic). If the journal is not completely new then I do some data analysis (counting up how many times NIMR authors have published in it, cited it, asked the Library for articles from it). Finally I look at who is asking for it (a lone postdoc voice or a group of PIs?).

When Science STKE changed to Science Signalling and started to publish primary research articles, then I got messages from three heads of division plus another two PIs telling me they must have access, and I knew that I must add the title to our deal with the publishers, AAAS.

When another senior scientist forwarded an email from the editor of two journals he was connected with, I took less notice. The email begged him to recommend his librarian to start subscriptions to the two titles, but he later sheepishly admitted “I am not quite sure why I agreed to be on the editorial board – but so far this is the first thing they have asked me to do”. My analysis showed there had been no previous interest in the titles and I decided to do nothing further.

A couple of lone voices asked for two other titles. Both were in core subject areas for NIMR, but had not been heavily requested or cited by NIMR authors. I put them in the category of “nice to have, not essential”, so the result is no action. One of the titles may be part of a “big deal” later on, which is the other complicating factor in choosing whether to subscribe.

Occasionally I will take the initiative myself. When the Company of Biologists (CoB) announced their new journal Disease Models & Mechanisms I knew the topic was one we had to be interested in. Translational research is being pushed by the government and all biomedical research funders so this title, aiming to publish “across the entire spectrum of disease research, including basic, translational, and clinical research” looks unmissable. The range of topics in the first two issues seemed a good match for NIMR interests and CoB have a good track record in producing high-quality journals. (As an aside, I see fellow blogger Heather has just published there). After a bit of consultation I agreed to try a subscription for a year or two. However, just like buses, two translational journals have come along at the same time.

We also have EMBO Molecular Medicine due to start in 2009, with a very similar set of aims and impressive-looking editorial board. The good news is that they are offering free access to all content for the first two years of publication, so I can delay making the decision to part with any money just yet.

I went to the JISC Collections Annual General Meeting today. They are the people who procure and negotiate licences for electronic content (electronic journals, search tools like Web of Science and Scopus, and e-books) for UK Higher Education, Research Councils and various bits of lower education. The formal part of the AGM was no more or less dull than these things usually are, but then they laid on an interesting quartet of speakers to talk about text mining. At first glance there may seem to be little connection between procurement and text mining, but it soon became clear that there is an important link. If text mining is to be successful then some new thinking about electronic resource licences is needed.

Liam Earney from JISC Collections briefly introduced text mining, defining it as gathering up big chunks of literature and performing computations on it to learn something new. Cliff Lynch has written that text mining opens up

entirely new ways to think about the scholarly literature (and the underlying evidence that supports scholarship) as an active, computationally enabled representation of knowledge that lives, grows and interacts with its contributors rather than as a passive archive or record.

But there are barriers to text mining – publishers (in general) do not make it easy for their material to be gathered in this way. As Cliff Lynch wrote:

As the scholarly literature moves to digital form, [how can we] move beyond a system that just replicates all of our assumptions that this literature is only read, and read only by human beings, one article at a time? What is needed to allow the application of computational technologies to extract new knowledge, correlations and hypotheses from collections of scholarly literature?

The indefatigable Peter Murray-Rust explained the problems to us very clearly. He started by outlining an appalling story in today’s Guardian about Ordnance Survey and their very restrictive approach to use of their mapping data, then retold a couple of other well-known stories about scientific publishers being overzealous in protecting their rights. This happens despite the main scientific publishers’ organisations having agreed that data in research articles should wherever possible be made freely accessible to other scholars. In reality this is not happening and would-be text miners cannot gain access to the journal source material they need. Peter stated forcefully that ejournal licences should be amended in order to allow text mining. The team from JISC Collections were sympathetic to his request and agreed it was something that must be worked on.

Peter also mentioned two of his projects – Crystaleye , that trawls for and aggregates crystallographic data from selected journals and TheOREm – a system for creating semantic theses.

Sophia Ananiadou, from the National Centre for Text Mining (NaCTeM ) gave an excellent overview of text mining, and its potential for helping to deal with information overload and information overlook (I like that term). She described a process of information retrieval, entity extraction, mining and pattern-finding, finally visualisation. NaCTeM have built a range of tools and services with strange names like TerMine, KLEIO, MEDIE and FACTA (all available from their website) and are looking forward to applying these to UK PubMedCentral.

Richard Kidd, from the Royal Society of Chemistry, described the impressive Project Prospect that has brought semantic enrichment to the RSC journals. He also referred to the Sciborg project – another Peter Murray-Rust project – that the RSC are collaborating with.

Finally Alastair Dunning, from the JISC Digitisation Prgramme, described how text mining is providing new ways to look at the results of digitisation efforts. His main example concerned English newsbooks from the mid-17th century.

All in all, this mini-conference nicely complemented the Open Knowledge Foundation workshop I blogged about earlier , highlighting the link between open knowledge and new knowledge generation.

I’m not sure whether presentations are more like curries or sponge cakes. A curry is usually better if you prepare it in advance and leave it to mature for a day or two. A sponge is nicest when it is fresh. There are of course limits. If you leave the curry for too long there is a danger that several days later you will find it mouldering in a corner of the fridge, quite inedible. On the other hand, if you try to eat a sponge just as it has left the oven it will tend to fall apart.

Well, I have one week left to prepare a talk on “Data for biomolecular sciences” and I really don’t want to fall apart. I’ve given the talk a subtitle “a quick skirmish” as it is intended as a high-level (i.e. superficial) overview. I think it is impossible to do more than that in just 50 minutes. The audience is fellow librarians, people wanting to support information-seekers unfamiliar with these tools. I have done similar talks before but not the last was in 2003 and I am a bit rusty. Back then I borrowed a fair bit from the User’s guide to the human genome published in Nature Genetics around that time. Sadly this has not been updated since September 2003 and I’m not sure how good a guide it is now. The excellent Current Protocols in Bioinformatics helps, as do training materials at NCBI and EBI.

A number of sites of course demand to be mentioned – EBI, NCBI, Uniprot, OMIM, PDB and possibly KEGG. Trying to choose what to show on the bigger sites is hard. I’ve heard praise for other sites such as WikiGenes, WikiProteins and IHOP. Jenny Rohn’s post on gene names gave some useful clues to practical utility.

I’d be grateful for more guidance from your good selves:

1. What are your essential everyday resources for biomolecular data?
2. What are the typical questions you need to answer (and is the 2003 Nature Genetics guide still useful)?
3. Can you recommend any more tutorials / guides?

Thanks!

Following Martin Fenner’s lead , and telling you a little more about this blog, this is my martinmeme.

1. What is your blog about?

Usually it is about things that I encounter in the course of my work as a Librarian. Or to put it another way, it contains impertinent reflections about science, scientists and their behaviours as they relate to knowledge, information or libraries. Sometimes it is about libraries or librarianship issues with just a tenuous science connection, sometimes I dare to delve into the world of data, sometimes I cross over into the world of PEST (Public Engagement in Science & Technology). I may also sortie into the wider world of science policy, but only if I can see a clear run ahead of me and a safe escape route. I hope to include one or two historical reflections, but they have not surfaced yet.

2. What will you never write about?

I will not write about things I have learnt in confidence. I will not write about things that I really don’t understand, though I will sometimes write about things that I understand only a little. I will not eschew a personal slant but I don’t intend Frank Norman to be the blog’s main topic.

3. Have you ever considered leaving science?

I have never joined, in the strict sense. I consider myself to be around science rather than in science. I see Martin Fenner has clarified this question, explaining that he defines science in the broader sense, so perhaps I am in science after all and so the answer is “yes”.

4. What would you do instead?

I have been tempted sometimes to do my own thing and set up as an independent information consultant, but never made the move.

5. What do you think will science blogging be like in 5 years?

It will either be very similar to how it is now, or completely different. I think that services like Natureblogs may change how (and how many) people use science blogs, but it’s too early to judge yet. I suspect that the power of blog platforms (can I call them publishers?) will grow, as bloggers see benefits in being part of a particular blog empire. If the number of science bloggers grows say by 100-fold or 1000-fold then the science blogosphere will be a very different place.

6. What is the most extraordinary thing that happened to you because of blogging?

Still waiting.

7. Did you write a blog post or comment you later regretted?

No. I am very cautious by nature. I start many more comments than I finally post.

8. When did you first learn about science blogging?

I think 2006 was when I first really looked into it. We started a Library blog about that time.

9. What do your colleagues at work say about your blogging?

Nothing as yet.

10a.: How the heck do you have time to blog and do research at the same time?

Time is a problem. I’ve not yet got into a regular sustainable pattern of blogging. It is usually a weekend or evening activity.

10b. Extra credit: are you able to write an entry to your blog that takes the form of a poem about your research?

Chasing butterflies is easier than
Grasping the truth of information use.
A bigger net and faster feet
Will not catch a scientist’s fleeting thought.
To know my job I have to know your mind
But you never have time to tell me.

I recently attended a workshop on open scientific resources organised by the Open Knowledge Foundation (OKF). The OKF blog has some Notes from the meeting, but I present a few of my own reflections on the day here.

The definition of open data was new to me. Providing free access via a web interface does not constitute openness. To be open a data resource must require no payment and no logon; it must allow redistribution and must allow the full dataset to be downloaded without barriers. This may seem like a tough definition of “open” but the point is to make it as easy as possible for data to be used and reused. There was quite a bit of discussion about licence conditions and the way that these can interfere with data use. Some prefer the use of “community norms”, i.e. non-legal mechanisms (one person suggested a curse!). Crucially, scientists wanting to make data available should also make their intentions about rights to use clear. Uncertainty over rights to use a dataset creates a barrier to use of the dataset. The Open Knowledge Definition has more information on all this.

Practical ways to help achieve openness were also discussed: guidelines for making data open / opening up data; advocacy for open data; expanding the work of editors and curators.

It was interesting to see possible solutions emerge from the discussion, though it was clear that much has already been done by the Open Knowledge Foundation and other players (e.g. the Science Commons). The OKF’s Comprehensive Knowledge Archive Network is a repository of datasets that are open, according to the above definition. This is a good base for further action – such as a proposed “unlocking service” that helps people to request a dataset to be made open. It was also proposed to create a simple recipe for making a dataset open.

Advocacy is needed in order to embed openness in scientific culture. There is a need to educate students, particularly at post-graduate level, and to engage with both research funders and publishers. Publishers will not want to take too much of a lead in this but should be happy to help enforce community norms once those are settled. But the need for advocacy also extends to the software industry and instrument makers – if their products output data in non-open formats that will create problems for those wanting to reuse that data.

There is a need for better recognition of the work of data packagers, data curators, and others who work with data. This to some extent echoes the points made in the recent JISC report that I blogged about previously. It was suggested that there is a need for data packagers, akin to the open source software packagers such as Debian. I wasn’t convinced by this, but time will tell. OKF hope to recruit more people to help curate and expand the CKAN registry.

Cameron also mentioned the concept of the fully supported paper and gave a number of examples of steps to achieving this. Cameron’s Science in the Open blog is a good source of more reading on this.

It was a highly interactive workshop – essentially a free discussion with just a few nudges in direction provided by the organisers, Jonathan Gray and Rufus Pollock. The presence of open science gurus such as Cameron Neylon and Peter Murray-Rust and Tim Hubbard from the Sanger Centre ensured a core of scientific data expertise. Also present were one or two scientists and researchers, a publisher, a data archive manager and a couple of other librarians besides myself.

The British Library have published their strategy for the next three years. The document is admirably well-designed, clear and, at 16 pages, concise. It sets out the Library’s purpose and aims then summarises various “catalysts for change” and elaborating seven strategic priorities. Key objectives for each priority are delineated.

The British Library (BL) is concerned with the whole realm of knowledge but they do pay particular attention to science. They are developing a content strategy for Science, Technology and Medicine researchers and they are committed to focus more on the particular characteristics and needs of researchers according to discipline. They show awareness of current research fashion in their intention to develop an interdisciplinary focus. Nature Network readers will not be surprised to learn that the BL will support and sustain cross-disciplinary research by building virtual research communities.

The document is largely free of management-speak, though I was not too sure about change is gradually transforming traditional scholarly dependency on the physical library as a major source for meeting research needs into a complex network of options, with varying levels of accessibility, authoritativeness and depth. It started well but then gets a little vague. The rest of the Catalysts for Change section is a good overview of current currents. Here are some excerpts as a stream of consciousness:

Growth in multidisciplinary research … More large-scale scientific research through international collaborations … Research impact measurements… More research in Russia, China and India… Evidence-based research for policy making…Researchers want everything to be available on the web immediately, permanently and preferably free of charge…Large quantities of research data in digital form – should be preserved and publicly available…Demand for images and sounds in digital form…Growing demand among all users for information services to be consistent with the Internet experience…Many lack essential search skills and are far from fully information literate or Intellectual Property literate…Growth of Open Access…More born digital and e-only…Consolidation in STM publishers…Internet search industry is growing fast…e-book use is growing…The web is revolutionising the way researchers work…the roles of publisher, library, aggregator and author are converging.

The seven priorities and some of the action points are:

1. Capture extensively and store UK digital publications (more e-deposit)
2. Connect our users with content (better searching of BL catalogues, with web 2 stuff. Look at digitisation and textmining as alternatives to traditional cataloguing. Work with JISC more)
3. Transform access and preservation for newspaper collection
4. Support UK research with innovative services and
   integrated processes (work towards providing an e-infrastructure to support UK research; UKPMC; work with Research Councils on interdisciplinary themes; test the Research Information Centre; develop service models for shared library services to corporate libraries)
5. Build our digital infrastructure (Continue to build our digital library system for storing
   and preserving many kinds of e-materials; Enable long-term preservation of digital items)
6. Develop storage and preservation for the physical collection
7. Develop as an organisation (ensure staff have the right skills to deliver the objectives)

On the same day that I saw the BL strategy document I also saw an announcement from the Department for Business, Enterprise & Regulatory Reform (BERR), or what used to be the DTI. This concerned an action plan to secure the UK’s place at the forefront of innovation, investment and quality in the digital and communications industries that the Minister, Lord Carter, is to develop by Spring 2009. The plan will bring together extensive expert analysis to develop a strategy for a fully digital Britain. The title ‘Digital Britain’ doesn’t inspire me – it sounds so 1990s.

The plan will also look at issues such as Internet user security and safety and a workable approach to promoting content standards. And it mentions Universal access to high quality, public service content through appropriate mechanisms for a converged digital age and work to deliver a digital copyright framework. These all sound like areas of interest to the British Library too, and I note that although BERR does not directly control the BL it does provide some funding to the BL. I wonder if the BL will get a mention in this action plan?

It’s only rarely that I attend a scientific seminar. Plunging into a dense jungle of cryptic terminology and unfamiliar concepts in the hope of seeing light at the end of the tunnel (to mix my metaphors) can be unproductive and often results in slumber. I make the effort from time to time as it seems such a waste not to hear some of the eminent speakers who come to talk at Mill Hill. I try to choose those that have more general appeal, e.g. Andrew Brown talking about J.D. Bernal, or our own Doug Young talking about mycobacterial research, or those given by high-profile speakers such as V.S. Ramachandran on neurology and human nature. I don’t always choose well and can find myself after 15 minutes struggling to make any connection with the subject matter and wishing I were back in the Library.

Today I thought it would be wise and possibly worthwhile to attend a lecture by our future Director, Jim Smith. It seemed like a historic occasion and I have a keen sense of history so I went along. Although it turned out to be fairly hard-core developmental biology (well, from my point of view) Jim had clearly worked hard to beat a path of comprehension through the jungle. After a brief introduction to mesoderm induction he proceeded in gentle steps before showing a scary slide of signalling pathways. As usual there came a point when a few moments of inattention caused me to drop into a deep pothole of unknowing, but I managed to clamber back out quite quickly.

It was good to hear a little bit of science history – all the way back to 1984 – and to discover that ChIP on Chip is not some kind of incestuous chip butty but a fiendishly clever assay technique. The best part was the question session. It’s good to hear questions from immunologists, structural biologists, mathematical biologists with an evolutionary bent, and of course developmental biologists. It reminds of the advantages of a richly multidisciplinary institute like NIMR.

I haven’t been to very many rock concerts. It therefore came as rather a surprise to find myself at the Oasis concert in The Roundhouse last night, the final gig in the BBC Electric Proms . It was even more of a surprise that I was on stage, performing alongside Noel and Liam and the rest of the band. Well, I say “alongside” but actually I and the rest of the Crouch End Festival Chorus (CEFC ) were placed somewhat to the back of the stage. If you have good eyesight you can just spot me a few times on the BBC video . I’m the one in the middle row with the orange shirt and the shiny head. [Note – video only available for 7 days. It’s about an hour long. The last 5 minutes is the best].

I have to say that the Roundhouse looked magnificent. I kept wondering if I had somehow strayed into the Large Hadron Collider.

The music was rather different from Bach, Stravinsky, Elgar or Adams, CEFC’s usual territory. It was certainly outside my immediate comfort zone. The volume level was the most obvious difference. At times it was almost at the level that causes pain, but also created a physical exhilaration. The method of sound projection we used was also rather different from our usual technique. Instead of drawing ourselves up, summoning all the strength in our diaphragm muscles and resonating in all cavities with as much force as we could, we each had a personal microphone headset and had to trust in the sound mixing desk to ensure we could be heard at all. We could barely hear ourselves let alone our neighbour. Interestingly, the band said they said they were playing more quietly than they ever have before!

It was an exhilarating and memorable experience. Outside my comfort zone, but probably also outside the band’s comfort zone if truth be told. We and they learned something new about music, and shared our skills and experience to create something that neither could have managed alone.

I am a great believer in treading outside my comfort zone. This blog is living evidence of that – it can be scary to release a post into the NN community. I think that data curation is also outside my comfort zone, but it has a strange fascination perhaps because of that. Can I , and fellow librarians, find a means of projecting a librarian’s voice and perspective into the high volume rock and roll of data creators and data scientists? It depends whether they are ready to listen to our quieter voices, or find a means to feed us into the mix. And it depends on librarians’ readiness to walk onto that scary stage and start performing.

I was interested to see a report issued by the JISC last week entitled Skills, Role & Career Structure of Data Scientists & Curators: Assessment of Current Practice & Future Needs. Written by Alma Swan and Sheridan Brown from Key Perspectives, well known for their work on Open Access and Publishing, it makes recommendations on “the role and career development of data scientists and the associated supply of specialist data curation skills to the research community”.

What are data scientists? Are they scientists who look after data? Or IT people who look after data? Or other people who look after data? Do all data scientists do the same kind of “looking after”? Do we know exactly what they do? Do we care?

I do care, though I certainly don’t know the answers to these questions. The report goes some way to providing answers, defining four varieties of data person: Data Creator, Data Scientist, Data Manager, Data Librarian. I guess these represent points along a continuum, with the focus gradually changing from “making the data do something” at one end to “ensuring the data survives” at the other end.

I was intrigued by the suggestion that research funders should require at least one member of the project team to be nominated as the project’s data scientist. I wonder how popular that will be? However, my main interest is of course in the contribution that libraries and librarians may or not have to play in this field.

I can see similarities between some work that librarians do and this new field of data curation. I’ve been wondering about data for some years. As a librarian I tried to engage with biological databanks just as sources of information, making users aware of what was available and helping them to make use of the resources. That worked for a bit, until the resources became so numerous and complex that I could not provide any meaningful assistance. Then a few years later the question “who should look after data?” came up. Well, libraries “look after” stuff, so should we also look after data? Three years ago I went along to the first Digital Curation Conference to ask the question but didn’t really get an answer and I am still not clear. I certainly wouldn’t feel ready to put on a data librarian hat any time soon. It seems I am not alone – there are apparently only five data librarians in the whole of the UK.

The report is quite encouraging, saying:

The role of the library in data-intensive research is important and a strategic repositioning of the library with respect to research support is now appropriate. We see three main potential roles for the library: increasing data-awareness amongst researchers; providing archiving and preservation services for data within the institution through institutional repositories; and developing a new professional strand of practice in the form of data librarianship.

That seems reasonable to me, bearing in mind that the data librarians would be working within a framework of data scientists and data managers. I’d be interested to hear what the data scientists and data managers think. Do you need a new breed of data librarian?

As is the way with such reports, it also sets out a series of further studies that need to be completed:

• A description of the role played by data scientists and the value of the contribution they make to research
• Examples of data science careers
• The development of a set of practices that represent good practice in data science

For those interested, there is also a workshop next month on Roles and Responsibilities for Effective Data Management, organised by the Research Data Management Forum. It’s not related directly to this report.

I crave a few seconds out of your life to read this post. It is the second account on NN of the launch of the second phase of Nature’s Second Life presence. Joanna Scott has posted an official account and explanation. In essence, the Second Nature islands have become part of a larger SL offering from NPG’s parent company Macmillan publishers, called The Elucian Islands . This new site provides space not just for scientific stuff but the whole range of knowledge and scholarship. It will be interesting to see how it develops.

Accounts of the launch have been posted by Jon Reed on his Publishing Talk blog and by others else where .

Nature laid on a good spread of champagne and canapes, plus a couple of speakers, introduced by Timo Hannay.

Timo revealed that the first speaker had inspired him several years before. Eddy Shah had been a pupil at the same school that Timo attended somewhat later and he came back to give an inspirational speech to the boys, including the young Timo.

It’s interesting to note this link between Eddy Shah , the man who transformed British newspaper publishing by introducing new technology, and Timo Hannay, who oversees new developments at Nature and is synonymous with new technology in science publishing.

Eddy Shah is a newspaper entrepreneur and technology enthusiast turned writer. His forthcoming thriller Second World is based on Second Life. He explained that it had been written 13 years earlier but rejected by publishers as being too far ahead of its time. Now the world has caught up and his book will be released as a mainstream thriller.

Mr Shah has the passion of a technology geek. When he talks about Second Life and the amazing virtual reality worlds that are just around the corner he has a glint in his eye. He clearly believes wholeheartedly that great things will come from virtual reality very soon. I couldn’t decide if he’s right or just possessed.

The second speaker was Anthony Steed, a Reader in Virtual Environments and Computer Graphics at UCL. His research concerns immersive reality environments and mixed reality systems. He showed a number of ways that they are exploring virtual environments. One picture was of a life-size screen with a man standing in front of it looking at an image of another man on the screen. That second man was stood in front of a similar screen looking at an image of the first man, and they were conversing. This system lets them use and see the full gamut of body language. It gave me a funny turn as I’d just been reading Haruki Murakami’s novel After Dark) . Some scenes in that book take place in a room with a TV screen that is showing another room and there seems to be some connection between these two rooms:

We want to check out the interior of that other room directly, with our own eyes… And so we decide to transport ourselves to the other side of the screen. It’s not that difficult once we make up our mind. All we have to do is separate from the flesh, leave all substance behind, and allow ourselves to become a conceptual point of view devoid of mass. With that accomplished, we can pass through any wall, leap over any abyss … We let ourselves become a pure single point and pass through the TV screen separating the two worlds.

Seeing Dr Steed’s system made Murakami’s scene seem almost realistic. Furthermore, in the corner of the room at Nature where the meeting took place was a screen showing a Second Life room full of avatars listening to the talks. I came away thinking that this SL stuff is getting closer to our world after all. Clearly Nature think so, given their continued investment. I wonder how long it will be before Nature publishes its first paper that can only be fully appreciated inside Second Life?