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O'Really?
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September 1, 2010
05:17 AM
37 views

How Many Unique Papers Are There In Mendeley?

by Duncan Hull in O'Really?

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 why. At the time of writing Mendeley claims to have over 36 million papers, added by just under half a [...]... Read more »

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

July 27, 2010
11:17 AM
95 views

Twenty Million Papers in PubMed: A Triumph or a Tragedy?

by Duncan Hull in O'Really?

A 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 i... Read more »

Halevy, A., Norvig, P., & Pereira, F. (2009) The Unreasonable Effectiveness of Data. IEEE Intelligent Systems, 24(2), 8-12. DOI: 10.1109/MIS.2009.36

Torvik VI, & Smalheiser NR. (2009) Author Name Disambiguation in MEDLINE. ACM transactions on knowledge discovery from data, 3(3). PMID: 20072710

Islamaj Dogan R, Murray GC, Névéol A, & Lu Z. (2009) Understanding PubMed user search behavior through log analysis. Database : the journal of biological databases and curation. PMID: 20157491

July 15, 2010
07:00 AM
67 views

How many journal articles have been published (ever)?

by Duncan Hull in O'Really?

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?... Read more »

Oldenburg, H. (1665) Epistle Dedicatory. Philosophical Transactions of the Royal Society of London, 1(1-22). DOI: 10.1098/rstl.1665.0001

Jacsó, P. (2010) Metadata mega mess in Google Scholar. Online Information Review, 34(1), 175-191. DOI: 10.1108/14684521011024191

Jinha, A. (2010) Article 50 million: an estimate of the number of scholarly articles in existence. Learned Publishing, 23(3), 258-263. DOI: 10.1087/20100308

July 7, 2010
03:30 AM
159 views

Top Ten Excuses for World Cup Football Failures (with citations)

by Duncan Hull in O'Really?

Football 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 [...]... Read more »

Travis, K. (2010) Scoring a Career in Sports Science. Science. DOI: 10.1126/science.caredit.a1000067

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

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

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

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

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

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

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

June 22, 2010
02:39 AM
160 views

Impact Factor Boxing 2010

by Duncan Hull in O'Really?

Roll up, roll up, ladies and gentlemen, Impact Factor Boxing is here again. As with last year (2009), these metrics 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 value of [...]... Read more »

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

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

Van Noorden, R. (2010) Metrics: A profusion of measures. Nature, 465(7300), 864-866. DOI: 10.1038/465864a

Tibor Braun, Margit Osterloh, Jevin West, Jennifer Rohn, David Pendlebury, Carl Bergstrom, & Bruno Frey. (2010) How to improve the use of metrics. Nature, 465(7300), 870-872. DOI: 10.1038/465870a

Lane, J. (2010) Let's make science metrics more scientific. Nature, 464(7288), 488-489. DOI: 10.1038/464488a

June 3, 2010
02:47 AM
178 views

The smell of baking bread: Entity of the Month

by Duncan Hull in O'Really?

Release 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 baking bread, or more precisely 6-acetyl-2,3,4,5-tetrahydropyridine. The text below is reproduced from the ChEBI website where data is available [...]... Read more »

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 28, 2010
02:23 AM
252 views

The University of Twitter, UK: A Quick Survey

by Duncan Hull in O'Really?

Many people are still trying to work out exactly what twitter is good for but with more than 41 million users worldwide [1], 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 [...]... Read more »

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

Amy Maxmen. (2010) Science Networking Gets Serious. Cell, 141(3), 387-389. DOI: 10.1016/j.cell.2010.04.019

May 21, 2010
11:28 AM
176 views

myExperiment: The Videos

by Duncan Hull in O'Really?

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 [...]... Read more »

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

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

May 6, 2010
12:56 PM
228 views

Mephedrone: Entity of the Month

by Duncan Hull in O'Really?

Release 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 headlines lately and as wikipedia points out is “not to be confused with Methedrine, Methedrone, Methadone, or Methylone“. [...]... Read more »

Winstock, A., Marsden, J., & Mitcheson, L. (2010) What should be done about mephedrone?. BMJ, 340(mar23 1). DOI: 10.1136/bmj.c1605

April 30, 2010
02:12 AM
287 views

Daniel Cohen on the Social Life of Digital Libraries

by Duncan Hull in O'Really?

Daniel Cohen is giving a talk in Cambridge today on The Social Life of Digital Libraries, abstract below: The digitization of libraries had a clear initial goal: to permit anyone to read the contents of collections anywhere and anytime. But universal access is only the beginning of what may happen to libraries and researchers in [...]... Read more »

Hull, D., Pettifer, S., & Kell, D. (2008) Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Computational Biology, 4(10). DOI: 10.1371/journal.pcbi.1000204

April 28, 2010
01:28 AM
197 views

Philip Campbell on Science Facts and Frictions

by Duncan Hull in O'Really?

As part of the Gates Distinguished Lecture Series editor Philip Campbell is giving a public lecture at 6.30pm tonight titled Science – facts and frictions at Emmanuel College, Cambridge. The abstract and text below reproduced from talks.cam.ac.uk: ‘Climategate’, MMR vaccine, GM crops, stem cells – these are examples of public debates in which science and [...]... Read more »

Philip Campbell. (1995) Postscript from a new hand. Nature, 378(6558), 649-649. DOI: 10.1038/378649b0

April 8, 2010
06:04 AM
236 views

8-OHdG: Entity of the Month

by Duncan Hull in O'Really?

Chemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool. New in this release, the ChEBI ontology is now available in Web Ontology Language (OWL), which is part of an ongoing research project to automate [...]... Read more »

Wishart, D., Knox, C., Guo, A., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S.... (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn810

Kuchino, Y., Mori, F., Kasai, H., Inoue, H., Iwai, S., Miura, K., Ohtsuka, E., & Nishimura, S. (1987) Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues. Nature, 327(6117), 77-79. DOI: 10.1038/327077a0

Wu LL, Chiou CC, Chang PY, & Wu JT. (2004) Urinary 8-OHdG: a marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. Clinica chimica acta; international journal of clinical chemistry, 339(1-2), 1-9. PMID: 14687888

Schriner, S. (2005) Extension of Murine Life Span by Overexpression of Catalase Targeted to Mitochondria. Science, 308(5730), 1909-1911. DOI: 10.1126/science.1106653

Sumida S, Doi T, Sakurai M, Yoshioka Y, & Okamura K. (1997) Effect of a single bout of exercise and beta-carotene supplementation on the urinary excretion of 8-hydroxy-deoxyguanosine in humans. Free radical research, 27(6), 607-18. PMID: 9455696

Tarng DC, Huang TP, Wei YH, Liu TY, Chen HW, Wen Chen T, & Yang WC. (2000) 8-hydroxy-2'-deoxyguanosine of leukocyte DNA as a marker of oxidative stress in chronic hemodialysis patients. American journal of kidney diseases : the official journal of the National Kidney Foundation, 36(5), 934-44. PMID: 11054349

Fujihara, J., Agusa, T., Tanaka, J., Fujii, Y., Moritani, T., Hasegawa, M., Iwata, H., Tanabe, S., & Takeshita, H. (2009) 8-Hydroxy-2′-deoxyguanosine (8-OHdG) as a possible marker of arsenic poisoning: a clinical case study on the relationship between concentrations of 8-OHdG and each arsenic compound in urine of an acute promyelocytic leukemia patient being treated with a. Forensic Toxicology, 27(1), 41-44. DOI: 10.1007/s11419-008-0062-x

April 1, 2010
06:24 AM
375 views

Καλό Πάσχα: Happy Easter: Frohe Ostern

by Duncan Hull in O'Really?

Whatever your inclination, it’s difficult to ignore that sandwiched between the Vernal equinox and Beltane, it’s Easter time already. So Happy Easter, Frohe Ostern or Καλό Πάσχα, as they say down south, to all readers of this O’Really? blog.
If you’re gorging yourself on chocolate (see picture right), you might like to consider the food science [...]... Read more »

Stephen T. Beckett. (2000) The Science Of Chocolate. Royal Society of Chemistry Publihshing. DOI: 10.1039/9781847552143

March 17, 2010
06:27 AM
324 views

Hunkin’s Hypothesis: Technology Is What Makes Us Human

by Duncan Hull in O'Really?

Cartoonist and engineer Tim Hunkin is probably best known for his exhibits at the Science Museum in London and his Under The Pier Show “a mad arcade of home-made slot machines & simulator rides on Southwold Pier, Suffolk”. His website is a treasure trove of weird and wonderful things.
Tim has an interesting proposition, let’s call [...]... Read more »

Frances Evans. (1998) Two legs, thing using and talking: The origins of the creative engineering mind. AI , 12(3), 185-213. DOI: 10.1007/BF01206195

March 4, 2010
06:29 AM
336 views

Sildenafil citrate: Entity of the Month

by Duncan Hull in O'Really?

Release 66 of Chemical Entities of Biological Interest (ChEBI) is now available, containing 534,521 total entities, of which 20,151 are annotated entities and 698 were submitted via the ChEBI submission tool. This months entity of the month is Viagra, also known as Sildenafil citrate: (Text below reproduced from ChEBI website)
Few chemical compounds are better known [...]... Read more »

Dunn, P. (2005) Synthesis of Commercial Phosphodiesterase(V) Inhibitors. Organic Process Research , 9(1), 88-97. DOI: 10.1021/op040019c

Webb DJ, Freestone S, Allen MJ, & Muirhead GJ. (1999) Sildenafil citrate and blood-pressure-lowering drugs: results of drug interaction studies with an organic nitrate and a calcium antagonist. The American journal of cardiology, 83(5A). PMID: 10078539

Richalet, J. (2004) Sildenafil Inhibits Altitude-induced Hypoxemia and Pulmonary Hypertension. American Journal of Respiratory and Critical Care Medicine, 171(3), 275-281. DOI: 10.1164/rccm.200406-804OC

Agostino, P., Plano, S., & Golombek, D. (2007) Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules. Proceedings of the National Academy of Sciences, 104(23), 9834-9839. DOI: 10.1073/pnas.0703388104

February 25, 2010
05:00 AM
333 views

Apache Maven: A Misbehavin’ Build Tool?

by Duncan Hull in O'Really?

One of the many tools we use in our team to manage the development of ChEBI software is an automated build tool called Apache Maven. Opinions are often divided on whether Maven is a good or a bad thing. Most of them are very subjective, argumentative and often very extended. See why does maven have [...]... Read more »

Stroustrup, B. (2010) Viewpoint: What should we teach new software developers? Why?. Communications of the ACM, 53(1), 40. DOI: 10.1145/1629175.1629192

Bjarne Stroustrup. (2007) Evolving a language in and for the real world: C 1991-2006. Proceedings of the third ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/1238844.1238848

Bjarne Stroustrup. (1993) A history of C : 1979–1991. The second ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/154766.155375

February 12, 2010
10:12 AM
419 views

The 3rd OBO Foundry Workshop 2010, Cambridge, UK

by Duncan Hull in O'Really?

The Open Biomedical Ontologies (OBO) [1] are a set of reference ontologies for describing all kinds of biomedical data shared in a centralised OBO Foundry. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop two years [...]... Read more »

Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C.... (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. DOI: 10.1038/nbt1346

February 5, 2010
06:53 AM
468 views

Classic paper: Montagues and Capulets in Science

by Duncan Hull in O'Really?

In preparation for a joint seminar I’ll be doing with Midori Harris here at the EBI, here’s a classic paper [1,2] on the social problems of building biomedical ontologies. This paper is worth reading (or re-reading) because it makes lots of relevant points about the use and abuse of research and how people misunderstand each [...]... Read more »

Goble, C., & Wroe, C. (2004) The Montagues and the Capulets. Comparative and Functional Genomics, 5(8), 623-632. DOI: 10.1002/cfg.442

January 21, 2010
05:05 AM
411 views

Blogging a Book about Bio-Ontologies

by Duncan Hull in O'Really?

If you wanted to write a guide to Biomedical and Biological Ontologies [1], especially the what, why, when, how, where and who, there are at least three choices for publishing your work:

Journal publishing in your favourite scientific journal.
Book publishing with your favourite academic or technical publisher.
Self publishing on a web blog with your favourite blogging [...]... Read more »

Yu, A. (2006) Methods in biomedical ontology. Journal of Biomedical Informatics, 39(3), 252-266. DOI: 10.1016/j.jbi.2005.11.006

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