O'Really?

September 1, 2010

How many unique papers are there in Mendeley?

Filed under: data mining,publishing — Duncan @ 10:17 am
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Lex Macho Inc. by Dan DeChiaro on Flickr, How many people in this picture?Mendeley is a handy piece of desktop and web software for managing and sharing research papers [1]. This popular tool has been getting a lot of attention lately, and with some impressive statistics it’s not difficult to see why. At the time of writing Mendeley claims to have over 36 million papers, added by just under half a million users working at more than 10,000 research institutions around the world. That’s impressive considering the startup company behind it have only been going for a few years. The major established commercial players in the field of bibliographic databases (WoK and Scopus) currently have around 40 million documents, so if Mendeley continues to grow at this rate, they’ll be more popular than Jesus (and Elsevier and Thomson) before you can say “bibliography”. But to get a real handle on how big Mendeley is we need to know how many of those 36 million documents are unique because if there are lots of duplicated documents then it will affect the overall head count.

An obvious place to start looking for duplicates is a personal bibliography, but  I’m not a regular user of Mendeley. However, I do have a collection of stuff on citeulike. Thankfully users of citeulike can synchronise data with their mendeley accounts, to save re-entering publications (again).  So I pulled my data from citeulike, entered my citeulike username into the importer and Bingo! I’m a Mendeley user – nice and easy. Looking closely at some of the papers, its easy to spot quite a few duplicates that are not unique, and this problem hinges on the thorny issue of identity. Any given paper be can be identified in different ways and these need to be resolved. For example, all the identifiers below use different ways to identify the same paper:

  1. http://pubmed.gov/18974831 (PubMed)
  2. http://dx.doi.org/10.1371/journal.pcbi.1000204 (DOI)
  3. http://ukpmc.ac.uk/articlerender.cgi?tool=EBI&pubmedid=18974831 (UK PMC)
  4. http://www.ploscompbiol.org/article/info:doi:10.1371/journal.pcbi.1000204 (PLoS)
  5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2568856 (US PMC)

Part of what all reference management software does is resolve multiple identities to the same thing. Database people call this normalisation – and it can be tricky to do with web data. In citeulike for example, all of these different id’s are ultimately recognised and normalised to the same unique thing: citeulike.org/article/3467077 which has been saved by 297 users. Citeulike, which currently stands at just over 4 million articles is doing a reasonable job of detecting and merging duplicates although it’s not perfect – it’s a hard problem. How does Mendeley compare on the same problem?

If you search Mendeley for the same example paper, you currently get at least seven different results that are not recognised as the same thing:

  1. defrosting-digital-library-bibliographic-tools-next-generation-web-240/ (saved by 99 users)
  2. defrosting-digital-library-bibliographic-tools-next-generation-web-252/ (saved by 123 users)
  3. defrosting-the-digital-library-bibliographic-tools-for-the-next-generation-web/ (saved by 399 users)
  4. defrosting-the-digital-library-a-survey-of-bibliographic-tools-for-the-next-generation-web/ (saved by 1 user)
  5. sr-kell-db-defrosting-the-digital-library-bibliographic-tools-for-the-next-generation-web/ (saved by 93 users)
  6. a-framework-for-scientific-knowledge-generation/ (ignore misleading title, saved by 93 users. Same as above? Might be)
  7. tropical-forest-fragmentation-and-the-local-extinction/ (ignore misleading title, saved by 7 users )

This particular paper may be an extreme case, but this kind of redundant duplication is certainly not uncommon. A quick search of some other papers reveals many have at least one duplicate in Mendeley – which means there is room for improvement. But popular papers like Error bars in experimental biology (saved by 894 users), don’t seem to have any duplicates at all – maybe that’s why they appear to be so popular?

So how many unique papers are there in Mendeley? It depends on how many duplicates there are, and that’s quite difficult to calculate accurately. Some papers have zero duplicates, others have as many as seven. So Mendeley might have as little as ~20 million unique documents or it have as many as ~30 million, who knows? But it’s probably not as much as 36 million. Well, at least not just yet anyway…

References

  1. Victor Henning, & Jan Reichelt (2008). Mendeley – A Last.fm For Research? IEEE Fourth International Conference on eScience, 327-328 DOI: 10.1109/eScience.2008.128

[The duplicitous Lex Macho Inc. by Dan DeChiaro on Flickr, see extra commentary on this post over at friendfeed.]

July 27, 2010

Twenty million papers in PubMed: a triumph or a tragedy?

Filed under: data mining,publishing,web — Duncan @ 3:37 pm
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pubmed.govA quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it is?

PubMed triumphs

Let’s start with the reasons to celebrate the triumphantly relentless growth of PubMed. Crack open the champagne!

  • A central index freely available globally: Many biomedical scientists probably take PubMed for granted, but try to imagine biology and medicine without it – we would struggle to find anything. Unlike other bibliographic indexes (Scopus and ISI WOK etc), PubMed is freely available to anyone, anywhere with an internet connection – it is an essential scientific service that many depend on every day to do their research.
  • Twenty million citations: That’s a lot of data and it’s growing at a rate of about one paper per minute (on average). This kind of big data can lead to big discoveries, bigger data could mean bigger discoveries – hopefully. Data can be unreasonably effective [1] so the more the merrier.
  • More than a billion searches in 2009: That’s an average of 3.5 million searches per day or 40 searches per second and around 767 million of these queries were done interactively by users on the web …
  • Entrez Utilities: … the other 514 million of those 1.3 billion searches were executed programmatically by machines rather than people. None of this web-enabled goodness would be possible without the reliable and successful Entrez Utilities services – which allow the data to be easily re-used by other software. Lots of useful applications have been built this way.
  • A treasure trove of weird and wonderful things: A quick browse through NCBI Rolling On the Floor Laughing (ROFL) reveals all manner of strange reports indexed by PubMed (alongside the regular serious stuff).

PubMed tragedies

But there are also some reasons to commiserate the tragically relentless growth of PubMed. Pass round the anti-depressants…

  • PubMed is too big and full of noise: Theodore Sturgeon’s law states that 90% of everything is rubbish. If correct, this means around 18 million records in PubMed are worthless junk. But that won’t stop them cluttering up the database and your search results making it harder to find what you want when you need it. Many of the papers indexed by PubMed are “salami-sliced” by publication-hungry scientists into the least publishable unit and are of little or no actual scientific value. It can be difficult (or impossible) to find what you need in PubMed. Cameron Neylon calls this discovery deficit, but however you describe it, finding the information you need in PubMed can be frustratingly difficult – despite the redesigns. There is so much in PubMed it is impossible to keep up.
  • PubMed is too small: Some people argue that an overly conservative indexing and editorial policy prevents PubMed from including lots of biomedically relevant literature that is published in physics, chemistry, mathematics, engineering and computer science journals. Currently much of this data is excluded from the database. Actually, what we really need is PubSCIENCE (covering non-medical sciences) but that idea got tragically axed back in 2002.
  • Identity crisis, ambiguous authors: one of the most useful ways to navigate the mountain of information that is PubMed is not to search by journal(s) or by keyword(s) but to search by author(s). Authors like Barack Obama are easy to find (because of their unique name) but poor John Smith (and many others like him) are much harder to find. A recent study has estimated that almost two thirds of authors in PubMed have ambiguous names [2] – where their last name and first initial is shared with one or more separate authors. Another recent study has shown that search by author is one of the three most frequent types of searches on PubMed [3] but unfortunately the precision and recall of these searches is typically poor due to ambiguous authors. This isn’t just a problem for PubMed, but scientific publishing generally. Hopefully ORCID (or something like it) will solve that problem one day…
  • Identity crisis, missing document identifiers: There are over forty million unique document ID’s in the form of DOI’s. They are a useful way to uniquely identify papers on the Web and link directly to their full content wherever they were originally published. But you might have trouble using DOIs in PubMed. Sometimes DOI’s get left out of records (see some random examples here) altogether. When they are included, they can get buried and are not very accessible. For example this record has a DOI but you won’t find it anywhere in the default page served by PubMed, which means you can’t easily click through to the full text of the article which the DOI would take you to. What this means is, PubMed is not as well integrated with other databases as it could and should be.
  • Mostly abstracts only: PubMed has 20 million freely available abstracts rather than 20 million full text papers. Imagine how the rate of scientific discovery and invention might increase (and the cost might decrease) if it was PubMed Central that had 20 million citations instead of just PubMed. Alas, PubMed Central is currently closer to the 2 million mark than the 20 million mark, but it is growing rapidly thanks to deposition mandates and open access publishing.
  • Ranking results: by default PubMed ranks search results by date – but if Google did the same, very few people would bother use it. Ranking results by relevance, by using an algorithm more like PageRank, would be much more useful to many users as demonstrated by Pierre Lindenbaum.
  • Text mining and ontologies: We’ve still a long way to go before fully exploiting the possibilities offered by text-mining and ontologies to allow PubMed users to semantically search and browse the data. MeSH is just the beginning but that’s another story…

20 million PubMed papers can't be wrongSo should we celebrate or commiserate passing the 20 million mark in PubMed®? The triumphs far outweigh the tragedies, many of which are either beyond the control of PubMed or can be sorted out (hint hint: anyone from NCBI reading this?). PubMed is a substantial fourteen years of work which continues to have significant benefits for many scientists around the world. There is plenty of room for improvement, but it’s hard to imagine Life® without PubMed®.

The complete catalogue of PubMed triumphs and tragedies is much longer than the above list, so if you think I missed any important ones, please leave a comment below.

References

  1. Alon Halevy, Peter Norvig, & Fernando Pereira (2009). The Unreasonable Effectiveness of Data IEEE Intelligent Systems, 24 (2), 8-12 DOI: 10.1109/MIS.2009.36
  2. Vetle Torvik & Neil Smalheiser (2009). Author Name Disambiguation in MEDLINE. ACM transactions on knowledge discovery from data, 3 (3) PMID: 20072710
  3. Rezarta Islamaj Dogan, G. Craig Murray, Aurelie Neveol and Zhiyong Lu (2009). Understanding PubMed user search behavior through log analysis. Database : the journal of biological databases and curation, 2009 PMID: 20157491

* These statistics were correct at the time of writing in July 2010 but will rapidly change over time. See more commentary on this piece over at friendfeed.

July 26, 2010

Please Sir, I want some more Science!

Filed under: communication,publishing — Duncan @ 5:27 pm
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Science Online London 2010 (soloconf)Science Online London (#solo10 September 3-4, 2010) is an annual gathering of people interested in the use of web technologies for scientific collaboration and communication.  The organisers at Mendeley, Nature Network and The British Library continue to do a great job of hosting this important gathering, now in its third year:

I’ve been the last two years (2008 and 2009), and it has been worth attending because of the mix speakers, delegates and topics covered. This year includes talks from:

See the impressive full programme here. Reading through the speaker list I wondered, where are all the scientists at science online this year? At the time of writing this, 12 of the 13 speakers are politicians, publishers or journalists with scientist Peter Murray-Rust the odd man out. I’ve nothing against politicians, publishers or journalists but it would be great to have a more balanced event this year. The UK is full of high-profile scientists with blogs who would probably jump at the opportunity to speak at this event. So:

Or as the skeptical Sid Rodrigues said “this looks like fun, needs more nerds though“…

[See more discussion of this post over at friendfeed.]

July 15, 2010

How many journal articles have been published (ever)?

Filed under: Science,publishing,search — Duncan @ 8:14 am
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Alexandria Library Interior by Mindy McAdams on FlickrEarlier 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.

PubMed, a freely available index of biomedical abstracts published by the National Center for Biotechnology Information has a collection of more than 19 million citations.  Nineteen million is hard to comprehend but around one paper per minute* is added to this database (on average) and this is an easier number to understand. But even this enormous database excludes large swathes of published articles in Physics, Mathematics, Chemistry, Engineering and Computer Science not deemed “worthy” of indexing by the United States National Library of Medicine. Neither does it include all the humanities publications - PubMed is not the world ®.

Next up, Scopus, a subscription-only database of journals covers a wider range of literature than PubMed and currently claims to have indexed over 40 million records. A rival of Scopus, ISI Web of Knowledge (WOK), claims to be a similar size with 40 millon items. But again like PubMed, Scopus and WOK are not the world. Google Scholar which is currently trying to take over the world, indexes all this data too, but they don’t say how big their index is [2].

Finally, Arif Jinha at the University of Ottawa has recently estimated that the number of journal articles published since time began is about 50 million [3]. This estimate is based on what has been published since 1665 when the journal Philosophical Transactions of the Royal Society first started. The 50 million article estimate has recently been published in Learned Publishing [3]. It’s debateable how accurate the estimate is, since its actually quite tricky to work out, but  50 million is still a big number to get your head around. Perhaps its easier to think of 50 million papers like this:

So how many journal articles have been published (ever)? It depends on what you mean by “journal”, “article”, “published” and “ever” – and these terms are taking on new meanings since the invention of the Web. But for the definitions used in [3] an estimate of 50 million seems reasonable, plus or minus a few million.

[update: see commentary on this article via bit.ly. Please note these stats were correct at the time of writing but will obviously change over time.]

References

  1. Henry Oldenburg (1665). Epistle Dedicatory Philosophical Transactions of the Royal Society of London, 1 (1-22) DOI: 10.1098/rstl.1665.0001
  2. Peter Jacsó (2010). Metadata mega mess in Google Scholar Online Information Review, 34 (1), 175-191 DOI: 10.1108/14684521011024191
  3. Arif Jinha (2010). Article 50 million: an estimate of the number of scholarly articles in existence Learned Publishing, 23 (3), 258-263 DOI: 10.1087/20100308 free pre-print available from author here

[Creative Commons licensed picture of the interior of the Bibliotheca Alexandrina by Mindy McAdams on Flickr]

* One paper per minute is based on 679,858 papers per year in 2009 / 365 days / 24 hours / 60 minutes = 1.29 papers per minute. The PubMed database isn’t updated that frequently, but if it was, there would be 1.29 papers added per minute according to MEDLINE statistics.

July 7, 2010

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

Filed under: football — Duncan @ 8:30 am
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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:

  • Blame it on the players: They are over-paid, under-achieving prima donnas who are too reliant on so-called superstars [2] who fail to deliver the goods under pressure, due to a lack of teamwork [3] and excess of testosterone [4]. They didn’t score that crucial first goal [5] and were never likely to snatch victory from the jaws of defeat.
  • Blame it on the boss: The manager/coach can’t motivate the players and is useless at managing people. All teams are dysfunctional [6] but the manager is the main reason that the players didn’t function as a successful team. Sack the manager now!
  • Blame it on the ball: The Jabulani ball is too unpredictable for players to pass/score with and keepers to save. The complicated aerodynamics [7] of the ball are the reason our team crashed out early.
  • Blame it on the fans: There were too many / not enough fans who didn’t support their team – instead they made a dreadful noise with those deafening vuvuzelas [8]. How can the players concentrate with that terrible cacophony?
  • Blame it on the women: The absence/presence of Wives and Girlfriends (WaGs) from the training camp was detrimental to player performance [citation needed]. Has anyone done any controlled experiments on this?!
  • Blame it on the funding: Our nation spends too much / not enough money on grassroots / club / national football [citation needed].
  • Blame it on the referee: The referee and the linesmen are visually-impaired, incompetent, stupid, biassed [9], recipients of large bribes and enjoy frequent self-abuse etc [citation needed].
  • Blame it on geography: The altitude, [10] latitude, longitude and climate were to blame – these adverse conditions ultimately impaired athletic performance on the field.
  • Blame it on psychology: It’s only a game isn’t it? What is all the fuss about [11]? We expected too much of our players, they are after all, only human and fallible. Our national ego was massively over-inflated [12] and just waiting for the inevitable deflation.
  • Blame it on FIFA: The Fédération Internationale de Football Association has allegedly been corrupted by the power and wealth they have accumulated [citation needed]. How can they continue to ignore demands for goal-line technology [13] and other video enhancements that would clearly improve the game?

So which teams have offered the best excuses for losing so far? Italy, France, Brazil, Portugal, Argentina and England are currently leading the table and (at the time of writing) will soon be joined by all but one of Germany, Spain and The Netherlands. All of this just goes to prove the Jimmy Cliff hypothesis, that the harder they come, the harder they fall (one and all) and makes for most of the entertainment at the competition.

If you can provide any of the citations needed for the above, please leave a comment below with the details. But wherever you are from, whoever you support, enjoy what is left of the 2010 FIFA World Cup – no excuses.

[update: A spanish translation of this post is available at Las diez excusas via perogrullo.com]

References

  1. Travis, K. (2010). Scoring a Career in Sports Science Science DOI: 10.1126/science.caredit.a1000067
  2. Lucifora, C., & Simmons, R. (2003). Superstar Effects in Sport: Evidence From Italian Soccer Journal Of Sports Economics, 4 (1), 35-55 DOI: 10.1177/1527002502239657
  3. Duch, J., Waitzman, J., & Amaral, L. (2010). Quantifying the Performance of Individual Players in a Team Activity PLoS ONE, 5 (6) DOI: 10.1371/journal.pone.0010937
  4. Zak, P., Kurzban, R., Ahmadi, S., Swerdloff, R., Park, J., Efremidze, L., Redwine, K., Morgan, K., & Matzner, W. (2009). Testosterone Administration Decreases Generosity in the Ultimatum Game PLoS ONE, 4 (12) DOI: 10.1371/journal.pone.0008330
  5. Elmar Bittner, Andreas Nussbaumer, Wolfhard Janke, & Martin Weigel (2006). Football fever: goal distributions and non-Gaussian statistics Eur. Phys. J. B 67, 459 (2009). arXiv: physics/0606016v1
  6. Lencioni, P. (2002). The Five Dysfunctions of a Team: A Leadership Fable (J-B Lencioni Series) (1 ed.). Jossey-Bass.
  7. Goff, J., & Carré, M. (2010). Soccer ball lift coefficients via trajectory analysis European Journal of Physics, 31 (4), 775-784 DOI: 10.1088/0143-0807/31/4/007
  8. Swanepoel de W, & Hall JW 3rd (2010). Football match spectator sound exposure and effect on hearing: a pretest-post-test study. South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde, 100 (4), 239-42 PMID: 20459971
  9. Kranjec, A., Lehet, M., Bromberger, B., & Chatterjee, A. (2010). A Sinister Bias for Calling Fouls in Soccer PLoS ONE, 5 (7) DOI: 10.1371/journal.pone.0011667
  10. Bärtsch P, Saltin B, Dvorak J, & Federation Internationale de Football Association (2008). Consensus statement on playing football at different altitude. Scandinavian journal of medicine & science in sports, 18 Suppl 1, 96-9 PMID: 18665957
  11. Schmied C, & Dvorak J (2010). Football is the most important unimportant thing in the world. European Heart Journal, 31 (12), 1425-7 PMID: 20556872
  12. Abell, J. (2010). ‘They seem to think “We’re better than you”’: Framing football support as a matter of ‘national identity’ in Scotland and England British Journal of Social Psychology DOI: 10.1348/014466610X514200
  13. Wayne C. Naidoo, & Jules R. Tapamo (2006). Soccer video analysis by ball, player and referee tracking SAICSIT ’06: Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries DOI: 10.1145/1216262.1216268

[Creative Commons licensed picture of Earth from the fantastic NASA Goddard Photo and Video collection on flickr]

June 22, 2010

Impact Factor Boxing 2010

Filed under: data mining,informatics,publishing — Duncan @ 7:39 am
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Golden Gloves Prelim Bouts by Kate GardinerRoll 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 http://isiknowledge.com/JCR Data 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?

Filed under: football — Duncan @ 5:13 pm
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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 @ 7:47 am
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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

Filed under: communication — Duncan @ 9:54 pm
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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

Filed under: web of science — Duncan @ 7:23 am
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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.]

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