Duncan Hull

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O'Really?
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  • June 22, 2010
  • 02:39 AM
  • 1,256 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 As with last year (2009), these metrics are already a year out of date.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 »

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  

  • June 3, 2010
  • 02:47 AM
  • 1,325 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 »

  • May 28, 2010
  • 02:23 AM
  • 1,070 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  

  • May 21, 2010
  • 11:28 AM
  • 629 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
  • 1,120 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
  • 1,197 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 »

  • April 28, 2010
  • 01:28 AM
  • 1,596 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
  • 2,017 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  

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  

  • April 1, 2010
  • 06:24 AM
  • 2,370 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
  • 1,199 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 »

  • March 4, 2010
  • 06:29 AM
  • 2,008 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 »

  • February 25, 2010
  • 05:00 AM
  • 1,516 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 »

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
  • 1,637 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
  • 1,541 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
  • 1,341 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  

  • January 15, 2010
  • 08:11 AM
  • 1,704 views

Bio2RDF: Large Scale, Distributed Biological Knowledge Discovery

by Duncan Hull in O'Really?

Michel Dumontier was visiting the EBI this week, here’s the details of his seminar Bio2RDF and Beyond! Large Scale, Distributed Biological Knowledge Discovery (slides embedded below) for anyone interested who missed it:
Abstract: The Bio2RDF.org [1] project aims to transform silos of bioinformatics data into a distributed platform for biological knowledge discovery. Initial work focused on [...]... Read more »

BELLEAU, F., NOLIN, M., TOURIGNY, N., RIGAULT, P., & MORISSETTE, J. (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics, 41(5), 706-716. DOI: 10.1016/j.jbi.2008.03.004  

  • January 11, 2010
  • 04:59 AM
  • 1,264 views

Abscisic Acid: Entity of the Month

by Duncan Hull in O'Really?

Happy New Year from the ChEBI team where release 64 is now available, containing 534,142 total entities, of which 19,645 are annotated entities and 693 were submitted via the ChEBI submission tool. This month’s entity of the month is Abscisic acid.
(+)-Abscisic acid (CHEBI:2365), known commonly just as abscisic acid or ABA, is a ubiquitous isoprenoid [...]... Read more »

Sheard, L., & Zheng, N. (2009) Plant biology: Signal advance for abscisic acid. Nature, 462(7273), 575-576. DOI: 10.1038/462575a  

Melcher, K., Ng, L., Zhou, X., Soon, F., Xu, Y., Suino-Powell, K., Park, S., Weiner, J., Fujii, H., Chinnusamy, V.... (2009) A gate–latch–lock mechanism for hormone signalling by abscisic acid receptors. Nature, 462(7273), 602-608. DOI: 10.1038/nature08613  

  • December 21, 2009
  • 07:10 AM
  • 1,397 views

Happy Christmas Lectures 2009

by Duncan Hull in O'Really?

If you weren’t able to attend this years Christmas lectures in person, they are televised tonight in the UK on More4 from 7pm. This year, they are given by Professor Sue Hartley [1] (pictured right) from the University of Sussex. Here is some blurb on the series from the Royal Institution called “The 300 million [...]... Read more »

  • December 10, 2009
  • 06:18 PM
  • 1,679 views

The Semantic Biochemical Journal experiment

by Duncan Hull in O'Really?

There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and [...]... Read more »

Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009) Calling International Rescue: knowledge lost in literature and data landslide!. Biochemical Journal, 424(3), 317-333. DOI: 10.1042/BJ20091474  

Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008) BioLit: integrating biological literature with databases. Nucleic Acids Research, 36(Web Server). DOI: 10.1093/nar/gkn317  

Pafilis, E., O'Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009) Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27(6), 508-510. DOI: 10.1038/nbt0609-508  

Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009) Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10(Suppl 6). DOI: 10.1186/1471-2105-10-S6-S19  

  • December 4, 2009
  • 06:27 PM
  • 1,226 views

Adrenaline: Entity of the Month

by Duncan Hull in O'Really?

December’s entity of the month at ChEBI is Adrenaline, for all the adrenaline junkies out there. This accompanies ChEBI release 63, containing 536,978 total entities, of which 19,501 are annotated entities and 678 were submitted via the ChEBI submission tool. Text reproduced below from the ChEBI website:
Adrenaline (CHEBI:33568), also known as epinephrine, is a catecholamine [...]... Read more »

ANCHOR, J. (2004) Appropriate use of epinephrine in anaphylaxis. The American Journal of Emergency Medicine, 22(6), 488-490. DOI: 10.1016/j.ajem.2004.07.016  

Rainer TH, & Robertson CE. (1996) Adrenaline, cardiac arrest, and evidence based medicine. Journal of accident , 13(4), 234-7. PMID: 8832338  

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