Last week I had a useful day at The Genome Analysis Centre, discussing the scientific opportunities for the Norwich Research Park and more generally. I also participated in part of a very interesting event on scientific storytelling, and some of the celebrations attendant on this year’s Diamond Jubilee winners of the Queen’s Anniversary Prize for Higher and Further Higher Education, where a welcome number of the winners were from our BBSRC-funded community. We also had a very good meeting with Tim Wheeler and colleagues at the Department for International Development, with whom we already co-fund a number of programmes such as SARID, CIDLID and SCPRID.
Stephen Curry in his recent comments on Open Access (OA) raised some important points relating to OA and the Research Councils, quoting BBSRC as an example (in his opinion) of things not working as well as they should. Anyone who knows me will know that I am a very strong supporter of Open Access and of text and data mining. Indeed, I have blogged quite often about Open Access (and have been known to write scholarly articles such as this and this) on the subject. There is no doubt that significant aspects of my own scientific work would be made much easier if all papers were freely available, and it is straightforward to give examples in areas such as genome-based metabolic network reconstruction, text mining for systems biology, and pulling together disparate literatures and synthesising inductive knowledge in pharmacokinetics, medicine and toxicology.
And it will all happen (note my use of the future tense). So, it is, put simply, coming in the future, but the future is not always easy to get to and this is a case in point. In BBSRC we are very conscious of the need to do more to make OA publication as straightforward as possible for our research community and we are working with the other Research Councils to help make this happen. In doing that it is worth bearing in mind some of the constraints that we face:
- There is genuine pressure – not least from academic institutions – for all the Research Councils to run the same systems, which means having to cater for different and equally strongly held views across the academic community, be they historians, bioscientists or particle physicists (physicists being of course well catered for by arXiv).
- Funding is limited, particularly at the moment, and we must be very clear about how and why public money is spent. It is a zero-sum game, so if more money is channelled into publishing costs then this means that there will be fewer grants.
- Establishing more clearly which published outputs relate to which individual grant or funder is not without its difficulties, as is sorting out which side of dual support has the lead responsibility for meeting OA costs and where the boundary lies
Running a parallel system in which libraries continue to pay subscriptions for ‘closed access’ while funders are also asked to contribute to Gold Open Access publication is not intellectually defensible, and we have to recognise the difficulties of the period of transition to an era of fully Open Access under sensible business models that respect the legitimate aspirations of stakeholders including researchers, public and charity funders, publishers and learned societies. All that said, BBSRC is fully committed to moving ahead as quickly as we can on open access, and things that will help are indeed happening, not least as a result of Hargreaves.
Working cross- Council
- We are closely involved via our ESRC colleagues in Dame Janet Finch’s group on expanding access, which is tackling several of the barriers to access and has good representation from interested parties
- The RCs are rewriting the joint statement and each Council is aiming to tighten up compliance with existing policy where clearly more needs to be done
- Within this we aim to have comparable mandates and comparable sanctions, for example withholding the final payment on an award, withdrawing the eligibility to apply for further Research Council funding from individuals who fail to comply, and accepting only open access publications as part of the track record of delivery of Research Council-funded research
- All Councils have established and introduced systems for comprehensive reporting on publications (among other outputs), through which it will be possible to check compliance levels routinely. The most recent system (the Research Outcomes System, ROS, used by AHRC, BBSRC, EPSRC and ESRC, and shortly to be adopted by NERC) has only recently been made available to grant holders, with the first full round of data collection currently underway. By early in the next financial year the Councils already using ROS should be in a position to check compliance levels systematically.
- As well as checking compliance levels, we will continue to work with our communities to ensure the OA policy remains known and understood by our grant holders. This will involve further specific and targeted communications, to remind grant holders of their obligations, and to reiterate why we consider this to be important.
- BBSRC is one of the funders of UKPMC, which includes a system for authors to deposit their publications, as well as having automatic deposit by some publishers. And we are working through the Funders Group and through other routes to engage publishers in revising their business models. We are not yet in a position, as MRC does, to mandate deposit in UKPMC because our remit is broader than biomedicine. But we do recommend UKPMC as a first choice.
- On the detailed funding side we are aware of the complexity of the system and, as part of the RCUK review of current practices this too will be reviewed. In the meantime we are also very happy to work with individual institutions on how they might build an institutional OA fund, drawing sums per grant from indirect costs as a number of universities have already done.
So I’d say both that we are moving in the right direction and that we know that we have more to do, but it is good to know the interest and support that there is for us to progress more on OA and indeed with the data and text mining that become possible when the data and text themselves become fully and openly available. But it is authors, not Research Councils, who choose where to submit their manuscripts…and some are committing publicly to publish only in OA journals…albeit ironically some Open Access is more Open than others…
Meanwhile, I enjoyed reading a variety of papers, including an excellent one (including some first class data visualisation) on how metagenomics projects can reconstruct full genomes from previously unknown clades, one on channelrhodopsin structure, and one on cellular control exerted more by the dynamics than the structure of RNA. As seen also in the work of Tom McLeish with whom I chatted last week, I think the study of enzyme dynamics will have much to teach us for industrial biotechnology. And for a splendidly whimsical piece of writing, look no further than a judgement of Lord Denning on a cricketing dispute.
- Ananiadou, S., Kell, D. B. & Tsujii, J.-i. (2006). Text Mining and its potential applications in Systems Biology. Trends Biotechnol 24, 571-579
- Ananiadou, S., Pyysalo, S., Tsujii, J.-i. & Kell, D. B. (2010). Event extraction for systems biology by text mining the literature. Trends Biotechnol 28, 381-390
- Attwood, T. K., Kell, D. B., McDermott, P., Marsh, J., Pettifer, S. R. & Thorne, D. (2009). Calling International Rescue: knowledge lost in literature and data landslide! Biochem J. 424, 317-333. Full free text as pdf
- Dethoff, E. A., Chugh, J., Mustoe, A. M. & Al-Hashimi, H. M. (2012). Functional complexity and regulation through RNA dynamics. Nature 482, 322-30
- Dobson, P. D. & Kell, D. B. (2008). Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? Nat Rev Drug Discov 7, 205-220
- Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasić, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B. (2008). A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol. 26, 1155-1160
- Hull, D., Pettifer, S. R. & Kell, D. B. (2008). Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol 4, e1000204. Full free text
- Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L. & Armbrust, E. V. (2012). Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335, 587-90
- Kato, H. E., Zhang, F., Yizhar, O., Ramakrishnan, C., Nishizawa, T., Hirata, K., Ito, J., Aita, Y., Tsukazaki, T., Hayashi, S., Hegemann, P., Maturana, A. D., Ishitani, R., Deisseroth, K. & Nureki, O. (2012). Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482, 369-74
- Kell, D. B. & Oliver, S. G. (2004). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 26, 99-105
- Kell, D. B. (2009). Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Medical Genomics 2, 2. Full free text
- Kell, D. B. (2010). Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples. Arch Toxicol 577, 825-889. Full free text
- Toncrova, H. & McLeish, T. C. B. (2010). Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP. Biophys J 98, 2317-26. Full free text