One of the consequences of the flood of text and data increasingly available digitally is the need for effective means for summarising and visualising their content. One simple metric is based on the frequency of words (or indeed tags, such as those done collaboratively – a folksonomy), and a widely used visualisation device (a simple one based on tags is also used as a search device in these blog pages) is the word cloud or Wordle, in which frequency is encoded by the font size of a word. More sophisticated versions are based on text mining, and recognise phrases and terms rather than single words alone. The picture below summarises all of the blogs that I have done to date. This multiword term cloud was kindly produced by the JISC-supported National Centre for Text Mining (NaCTeM), using (a) NaCTeM’s TerMine term extraction web service, and (b) IBM’s Word Cloud Generator (WCG) which latter is in fact the same technology underlying Wordle.
A similar production of my recent review on the role of unliganded iron in degenerative diseases leads to the following:
A couple of recent papers also implicate iron dysregulation in prion diseases, a novel and exciting twist with high explanatory power regarding the mechanisms of neurodegeneration subsequent to the conformational changes of the prion protein.
On the text mining front, we have just published a paper in which we describe open access software for assisting the automation of the extraction of enzyme kinetic parameters for the yeast metabolic network. This will assist considerably the next stage of development (its parametrisation) of the principled community-based metabolic network that we described last year (and have subsequently extended).
Last week I visited Japan for several days, first to join the celebration of the 20th anniversary of the Human Frontier Science Programme, attended by one-time Prime Minister Yasuhiro Nakasone who had originally proposed it. Here we also enjoyed a lecture from Nobelist Peter Agre on aquaporins and related water/glycerol channels. It was of particular interest to hear about how these were discovered in the first place, and how poorly permeable are biological membranes even to such tiny molecules in the absence of carriers or channels. This is even more true of pharmaceutical drugs!
Other visits included the Japan Society for the Promotion of Science (JSPS), the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the research arm of the Ministry of Agriculture, Forestry and Fisheries, the Japan Science and Technology Agency (JSTA). We also visited the National Institute for Genetics in Mishima, home of the DNA Data Bank of Japan (DDBJ, somewhat equivalent to elements of the EBI), and the administrative headquarters of the RIKEN where we were briefed on the upcoming 10 petaflops supercomputer (to be built by 2012 in Kobe). JSTA is about to enjoy a £2 billion stimulus package. Overall a very interesting visit, and we anticipate further collaborations in a number of areas such as systems biology and distributed bioinformatics. I also take the view that environmentally benign types of fish farming involving non-carnivorous fish are going to be an important food source in the future; as island nations, the UK and Japan – whose healthy diet is especially rich in fish – are well placed to lead scientifically. The week ended with a very useful discussion with Marion Guillou, President of the French National Institute for Agricultural Research (INRA), with whom we have enjoyed many collaborations in the past and with whom we anticipate considerable further interactions in the future as we develop the global Food Security agenda via our consultation document.
In an earlier blog, I mentioned the importance of understanding bee biology, where we have recently announced a collaborative funding programme, and it is of interest that the genome of Nosema ceranae has just been sequenced and annotated.
Finally, it was just announced that the Department of Innovation, Universities and Skills will merge with the Department of Business, Enterprise and Regulatory Reform to create a new Department of Business, Innovation and Skills. Importantly, the two parts of the dual-support system covering higher education and research will remain together, providing considerable opportunities for synergy as we go forward.
- Cornman, R.S., Chen, Y.P.. Schatz, M.C., Street, C., Zhao, Y., Desany, B., Egholm, M., Hutchison, S., Pettis, J.S., Lipkin, W.I. & Evans, J. D. (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens 5, e1000466
- 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
- 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
- Singh, A., Mohan, M. L., Isaac, A. O., Luo, X., Petrak, J., Vyoral, D. & Singh, N. (2009). Prion protein modulates cellular iron uptake: a novel function with implications for prion disease pathogenesis. PLoS ONE 4, e4468. Free full text
- Singh, A., Isaac, A. O., Luo, X., Mohan, M. L., Cohen, M. L., Chen, F., Kong, Q., Bartz, J. & Singh, N. (2009). Abnormal brain iron homeostasis in human and animal prion disorders. PLoS Pathog 5, e1000336. Free full text
- Spasić, I., Simeonidis, E., Messiha, H. L., Paton, N. W. & Kell, D. B. (2009). KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics 25, 1404-1411