O'Really?

July 15, 2010

How many journal articles have been published (ever)?

Fifty Million and Fifty Billion by ZeroOne

According to some estimates, there are fifty million articles in existence as of 2010. Picture of a fifty million dollar note by ZeroOne on Flickr.

Earlier this year, the scientific journal PLoS ONE published their 10,000th article. Ten thousand articles is a lot of papers especially when you consider that PLoS ONE only started publishing four short years ago in 2006. But scientists have been publishing in journals for at least 350 years [1] so it might make you wonder, how many articles have been published in scientific and learned journals since time began?

If we look at PubMed Central, a full-text archive of journals freely available to all – PubMedCentral currently holds over 1.7 million articles. But these articles are only a tiny fraction of the total literature – since a lot of the rest is locked up behind publishers paywalls and is inaccessible to many people. (more…)

July 7, 2010

Top ten excuses for World Cup football failures (with citations)

NASA Blue Marble 2007 West by NASA Goddard Photo and Video, on FlickrFootball fever grips the globe as we reach the final stages of the 2010 FIFA World Cup in South Africa. Alongside the traditional game where one winning team takes all, leaving 31 losing teams to go home earlier than expected, there is another competition running in parallel. Which losing team can come up with the best excuses for formidable football failure? All manner of feeble and pathetic excuses are offered, but many aren’t backed up with proper citations of peer-reviewed research published in scientific journals. So let’s set the balance straight. Here are the top ten excuses for world cup losers (with citations), using some help from sports scientists [1] and the wikipedian protester demanding that a citation is needed: (more…)

June 22, 2010

Impact Factor Boxing 2010

Golden Gloves Prelim Bouts by Kate Gardiner[This post is part of an ongoing series about impact factors. See this post for the latest impact factors published in 2012.]

Roll up, roll up, ladies and gentlemen, Impact Factor Boxing is here again. As with last year (2009), the metrics used in this combat sport are already a year out of date. But this doesn’t stop many people from writing about impact factors and it’s been an interesting year [1] for the metrics used by many to judge the relative value of scientific work. The Public Library of Science (PLoS) launched their article level metrics within the last year following the example of BioMedCentral’s “most viewed” articles feature. Next to these new style metrics, the traditional impact factors live on, despite their limitations. Critics like Harold Varmus have recently pointed out that (quote):

“The impact factor is a completely flawed metric and it’s a source of a lot of unhappiness in the scientific community. Evaluating someone’s scientific productivity by looking at the number of papers they published in journals with impact factors over a certain level is poisonous to the system. A couple of folks are acting as gatekeepers to the distribution of information, and this is a very bad system. It really slows progress by keeping ideas and experiments out of the public domain until reviewers have been satisfied and authors are allowed to get their paper into the journal that they feel will advance their career.”

To be fair though, it’s not the metric that is flawed, more the way it is used (and abused) – a subject covered in much detail in a special issue of Nature at http://nature.com/metrics [2,3,4,5]. It’s much harder than it should be to get hold of these metrics, so I’ve reproduced some data below (fair use? I don’t know I am not a lawyer…) to minimise the considerable frustrations of using Journal Citation Reports (JCR).

Love them, loathe them, use them, abuse them, ignore them or obsess over them … here’s a small selection of the 7347 journals that are tracked in JCR  ordered by increasing impact.

Journal Title 2009 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™  Score Article Influence™ Score
RSC Integrative Biology 34 0.596 57 0.00000
Communications of the ACM 13853 2.346 3.050 0.350 177 >10.0 0.01411 0.866
IEEE Intelligent Systems 2214 3.144 3.594 0.333 33 6.5 0.00447 0.763
Journal of Web Semantics 651 3.412 0.107 28 4.6 0.00222
BMC Bionformatics 10850 3.428 4.108 0.581 651 3.4 0.07335 1.516
Journal of Molecular Biology 69710 3.871 4.303 0.993 916 9.2 0.21679 2.051
Journal of Chemical Information and Modeling 8973 3.882 3.631 0.695 266 5.9 0.01943 0.772
Journal of the American Medical Informatics Association (JAMIA) 4183 3.974 5.199 0.705 105 5.7 0.01366 1.585
PLoS ONE 20466 4.351 4.383 0.582 4263 1.7 0.16373 1.918
OUP Bioinformatics 36932 4.926 6.271 0.733 677 5.2 0.16661 2.370
Biochemical Journal 50632 5.155 4.365 1.262 455 >10.0 0.10896 1.787
BMC Biology 1152 5.636 0.702 84 2.7 0.00997
PLoS Computational Biology 4674 5.759 6.429 0.786 365 2.5 0.04369 3.080
Genome Biology 12688 6.626 7.593 1.075 186 4.8 0.08005 3.586
Trends in Biotechnology 8118 6.909 8.588 1.407 81 6.4 0.02402 2.665
Briefings in Bioinformatics 2898 7.329 16.146 1.109 55 5.3 0.01928 5.887
Nucleic Acids Research 95799 7.479 7.279 1.635 1070 6.5 0.37108 2.963
PNAS 451386 9.432 10.312 1.805 3765 7.6 1.68111 4.857
PLoS Biology 15699 12.916 14.798 2.692 195 3.5 0.17630 8.623
Nature Biotechnology 31564 29.495 27.620 5.408 103 5.7 0.14503 11.803
Science 444643 29.747 31.052 6.531 897 8.8 1.52580 16.570
Cell 153972 31.152 32.628 6.825 359 8.7 0.70117 20.150
Nature 483039 34.480 32.906 8.209 866 8.9 1.74951 18.054
New England Journal of Medicine 216752 47.050 51.410 14.557 352 7.5 0.67401 19.870

Maybe next year Thomson Reuters, who publish this data, could start attaching large government health warnings (like on cigarette packets) and long disclaimers to this data? WARNING: Abusing these figures can seriously damage your Science – you have been warned!

References

  1. Rizkallah, J., & Sin, D. (2010). Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor, Eigenfactor, and Article Influence Scores PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010204
  2. Abbott, A., Cyranoski, D., Jones, N., Maher, B., Schiermeier, Q., & Van Noorden, R. (2010). Metrics: Do metrics matter? Nature, 465 (7300), 860-862 DOI: 10.1038/465860a
  3. Van Noorden, R. (2010). Metrics: A profusion of measures Nature, 465 (7300), 864-866 DOI: 10.1038/465864a
  4. Braun, T., Osterloh, M., West, J., Rohn, J., Pendlebury, D., Bergstrom, C., & Frey, B. (2010). How to improve the use of metrics Nature, 465 (7300), 870-872 DOI: 10.1038/465870a
  5. Lane, J. (2010). Let’s make science metrics more scientific Nature, 464 (7288), 488-489 DOI: 10.1038/464488a

[Creative Commons licensed picture of Golden Gloves Prelim Bouts by Kate Gardiner ]

June 9, 2010

World Cup Chemistry: How heavy is the FIFA trophy?

Have you ever wondered how heavy all that Gold and Malachite is in the FIFA World Cup Trophy is?

Professor Martyn Poliakoff from the Chemistry department at the University of Nottingham and his partner in crime Brady Haran over at the fantastic Periodic Table of Videos explain:

Which just leaves one question, who will be lifting it this year? Lúcio? Cristiano Ronaldo? Philipp Lahm? Fabio Cannavaro?  Denis Caniza? Steven Gerrard? Giovanni van Bronckhorst? Iker Casillas? Diego Lugano? John Mensah? Javier Mascherano or A.N.Other?

June 3, 2010

The smell of baking and toasting bread: Entity of the Month

Filed under: ChEBI — Duncan Hull @ 7:47 am
Tags: , , , ,

ToastRelease 69 of Chemical Entities of Biological Interest (ChEBI) is now available, with 584,456 total entities, of which 21,369 are fully annotated to three star level. This months Entity of the Month is the smell of bread (baked and toasted), or more precisely 6-acetyl-2,3,4,5-tetrahydropyridine. The text below is reproduced from the ChEBI website where data is available under a Creative Commons license.

Chemistry, like most other fields of human endeavour, has a tremendous capacity for both good and evil. However, arguably one of the best and most delightful reactions in chemistry is the Maillard reaction.

It occurs when amino acids are heated together with sugar and is therefore a prominent reaction when baking bread or brewing beer: many of the reaction products provide the characteristic flavours of these foods, which we all enjoy so much.While the chemical structures and identities of most of the products of this form of “non-enzymatic browning” are only poorly characterised or unknown, our Entity of the Month 6-acetyl-2,3,4,5-tetrahydropyridine (CHEBI:59533) is an exception. It is a well known aromatic compound, which is responsible for the flavour of white bread, popcorn and tortillas and has an extremely low odour threshold, between 0.02 and 0.06 ng l–1[1]. It exists in a tautomeric equilibrium with 6-acetyl-1,2,3,4-tetrahydropyridine, the two forms usually occurring in foods in a 1:2 ratio.

The compound can be synthesized in a simple three-step procedure. In a first step, BOC-protected 2-piperidone is treated with 1-ethoxy-1-lithioethene in a bid to build up the acetyl side-chain. This results in ring opening and the formation of a linear ketone which, after treatment with toluene-p-sulfonic acid, reforms the heterocycle in the form of an ene-carbamate. Treatment of the latter with potassium hydroxide yields the final product [1].

The Maillard Reaction is named after Louis Camille Maillard, a precocious French physiologist, who first described it in the 1910s. Maillard is also known for his contributions towards the diagnosis of kidney disorders.

The image top right shows freshly toasted bread – and the brown colour (the Maillard reaction is a method for non-enzymatic browning) is indicative of the reaction having taken place and is taken from the Wellcome Trust Image Collection

References

  1. Harrison, T., & Dake, G. (2005). An Expeditious, High-Yielding Construction of the Food Aroma Compounds 6-Acetyl-1,2,3,4-tetrahydropyridine and 2-Acetyl-1-pyrroline The Journal of Organic Chemistry, 70 (26), 10872-10874 DOI: 10.1021/jo051940a

May 31, 2010

Martin Rees on Science and the Citizen

This years Reith Lectures by Martin Rees are being broadcast on BBC Radio 4 during June. An important theme in the lectures this year is scientists relationship with society. Rees argues that science is part of our culture, crucial for dealing with pressing international issues like population growth, food security and energy development. He also argues that science is not just for scientists, everyone has have a feel for it, not just the specialists. Here is the blurb from the first lecture: “Science and the Citizen”

“In the first of this year’s Reith Lectures, entitled Scientific Horizons, Martin Rees, President of the Royal Society, Master of Trinity College and Astronomer Royal, explores the challenges facing science in the 21st century. We are increasingly turning to government and the media to explain the risks we face. But in the wake of public confusion over issues like climate change, the swine ‘flu vaccine and, more recently, Iceland’s volcanic ash cloud, Martin Rees calls on scientists to come forward and play a greater role in helping us understand the science that affects us all.”

Lectures are available below and via the iPlayer.

Lecture Topic File Play in Browser
1/4: The Scientific Citizen Who should we should trust to explain the risks we face? mp3
2/4: Surviving the Century Does science have the answers to help us save our planet? mp3
3/4: What We Will Never Know What are the limits of Scientific knowledge? mp3
4/4: The Runaway World How can countries stay scientifically competitive? mp3

[Creative Commons licensed picture of Martin Rees above by The Reith Lectures on Flickr, see also introductory clip on the lectures.]

May 28, 2010

The University of Twitter, UK: A Quick Survey

Twitter icon for a fluid app by Miha  FilejMany people are still trying to work out exactly what twitter is good for [1] but with more than 100 million users worldwide making around 50 million tweets per day, the website is clearly popular with those who like to communicate via short “sound bites” of 140 characters or less.

Communication is an important part of what Universities are all about, so how many UK universities are on twitter? Knowing this could help us assess the use of the latest web technology in research where adoption has been rather limited so far, especially in Science  [2]. Rather than survey all the @UniversitiesUK, for a quick overview, let’s pick the twenty Russell Group Universities. According to their website, the Russell Group:

“represents the 20 leading UK universities which are committed to maintaining the very best research, an outstanding teaching and learning experience and unrivalled links with business and the public sector.”

So they are exactly the kind of places you would expect to be embracing and experimenting with new technology. The table below shows which of these institutions are on twitter:

@RussellGroup University @Twitter?
University of Birmingham @unibirmingham
University of Bristol @bristoluni
University of Cambridge @cambridge_uni
Cardiff University @cardiffuni
University of Edinburgh @uniofedinburgh
University of Glasgow @glasgowuni
Imperial College London @imperialcollege
King’s College London None as of May 2010*
University of Leeds @universityleeds
University of Liverpool @liverpoolfirst
London School of Economics None as of May 2010*
University of Manchester None as of May 2010*
Newcastle University None as of May 2010*
University of Nottingham @uniofnottingham
University of Oxford @uniofoxford
Queen’s University Belfast @queensubelfast
University of Sheffield @sheffielduni
University of Southampton @southamptonnews
University College London @uclnews
University of Warwick @warwickuni

There are plenty of important UK universities (@1994group, @UniAlliance@million_plus etc) excluded from this quick-and-dirty survey but it gives us an idea of what is going on. As of May 2010, 16 out of 20 Russell Group Universities are on twitter – perhaps this is another reason to love Higher Education because it is full of twittering twits?

But the last words on the United Kingdom of Twitter should go to the @number10gov Prime Minister David Cameron who has enlightening views on twitter including this quote below:

“We complain about the sound bite culture [3] but if you think about it and go back in history sound bites have always been used. Do to others as you would be done by, that is a fantastic sound bite … If you can’t convey what you’re trying to convey in a few short sentences you’ve got a problem and you have a particular problem in the media age. You have to work at communicating something complicated in a simple way or you’re not going to take people with you.”

References

  1. Haewoon Kwak, Changhyun Lee, Hosung Park, & Sue Moon (2010). What is Twitter, a social network or a news media? WWW ’10: Proceedings of the 19th international conference on World Wide Web, New York, NY, USA, 591-600 DOI: 10.1145/1772690.1772751
  2. Amy Maxmen (2010). Science Networking Gets Serious Cell, 141 (3), 387-389 DOI: 10.1016/j.cell.2010.04.019
  3. David Slayden and Rita Kirk Whillock (1998). Soundbite Culture: The Death of Discourse in a Wired World. Sage Publications, Inc. ISBN:0761908722

* These Universities had no central account that I could find in May 2010 but some have departmental accounts like  @kingsbiomed, @kingsmedicine, @lsepublicevents, @lse_recruitment, @mcrmuseum and @manunicareers etc which are not counted here because they don’t represent the whole University in question. The University of Manchester has an account @UoMRSSFeed but it isn’t official and hasn’t been updated recently. Dear beloved Alma mater, sort it out!

[Creative commons licensed picture of Twitter icon for a fluid app via Miha Filej.]

May 27, 2010

The 2nd ChEBI workshop: Call for Participation

The NanoPutians:  Synthesis of Anthropomorphic MoleculesThe second Chemical Entities of Biological Interest (ChEBI) workshop will be held at the European Bioinformatics Institute (EBI) in Hinxton, Cambridgeshire, UK on the 23rd and 24th June 2010. The full provisional schedule (including registration page) for this workshop is now available. Speakers at the workshop include:

There will also be several discussion sessions on the future evolution of the ChEBI project. Training will be provided including using ChEBI for research purposes and submitting your chemicals to ChEBI for annotation. We (the ChEBI team) hope to welcome you to Hinxton in June.

References

  1. Image of The NanoPutians taken from: Chanteau, S., & Tour, J. (2003). Synthesis of Anthropomorphic Molecules: The NanoPutians The Journal of Organic Chemistry, 68 (23), 8750-8766 DOI: 10.1021/jo0349227

May 21, 2010

myExperiment: The Videos

myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole Goble at the Universities of Southampton and Manchester in the UK.

Last year, JISC made some professional videos describing the project. Needless to say, the videos were much more fun to make than the accompanying papers [1,2,3] and a probably more informative too. The best way of linking the research papers to the videos on youtube is to blog about them, so here they are. The first video (below) talks about the project generally:

The second video (below) discusses the data used in tackling African trypanosomiasis (sleeping sickness) in cattle.

The videos include interviews with Carole Goble, Dave De Roure, Paul Fisher, Andy Brass and yours truly.

References

  1. David De Roure, Carole Goble, & Robert Stevens (2007). Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows IEEE International Conference on e-Science and Grid Computing, 603-610 DOI: 10.1109/E-SCIENCE.2007.29
  2. David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman (2008). myExperiment: Defining the Social Virtual Research Environment IEEE Fourth International Conference on eScience, 2008. eScience ’08., 182-189 DOI: 10.1109/eScience.2008.86
  3. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., & De Roure, D. (2010). myExperiment: a repository and social network for the sharing of bioinformatics workflows Nucleic Acids Research DOI: 10.1093/nar/gkq429

May 6, 2010

Mephedrone: Entity of the Month

Overdosed by Elad R, on FlickrRelease 68 of Chemical Entities of Biological Interest (ChEBI) is now available, with 549,319 total entities, of which 21,075 are fully annotated. This month’s entity of the month is Mephedrone, a substance which has been in the news headlines lately and as wikipedia points out is “not to be confused with Methedrine, Methedrone, Methadone, or Methylone“. Don’t you just love chemical names?! Text below reproduced from the ChEBI website:

“Mephedrone (CHEBI:59331) is a synthetic central nervous system stimulant and entactogen drug chemically related to cathinone, the psychoactive alkaloid present in the khat plant (Catha edulis, family Celastraceae).

It can be synthesised from 4-methylpropiophenone by an initial bromination at the β-carbon followed by replacement of the bromine by a methylamino group derived from methylamine hydrochloride. Although it was probably not available until 2007, by 2009 mephedrone had become the fourth most popular street drug in the UK, behind cannabis, cocaine and ecstasy. Little is currently known regarding its pharmacology or toxicology, although one recent report suggests the likelihood that it stimulates the release of, and then inhibits the reuptake of, monoamine neurotransmitters [1].

Although already listed as a prohibited substance in many countries, in others it has varying degrees of legality (notably the USA where it is currently unscheduled under the Controlled Substances Act). In the UK, a decision by the Home Secretary to classify mephedrone as illegal caused the resignation of two members of the Advisory Council on the Misuse of Drugs (ACMD) which has led in turn to a general questioning of UK drugs policy. Mephedrone finally became classified as a Class B drug in the UK on April 16, 2010 – prior to this time it was often sold openly under the guise of a ‘plant food’ (although having no known use as such).”

References

  1. Winstock, A., Marsden, J., & Mitcheson, L. (2010). What should be done about mephedrone? BMJ, 340:c1605 DOI: 10.1136/bmj.c1605

[Creative Commons licensed picture ‘Overdosed’ by Elad Rahmin on flickr]

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