81 posts · 81,584 views
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
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 »
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
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 »
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
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 »
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
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
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
The Open Biomedical Ontologies (OBO)  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
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 »
If you wanted to write a guide to Biomedical and Biological Ontologies , 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 »
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  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
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 »
Ohkuma, K., Lyon, J., Addicott, F., & Smith, O. (1963) Abscisin II, an Abscission-Accelerating Substance from Young Cotton Fruit. Science, 142(3599), 1592-1593. DOI: 10.1126/science.142.3599.1592
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
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  (pictured right) from the University of Sussex. Here is some blurb on the series from the Royal Institution called “The 300 million [...]... Read more »
Hartley, S., & Gange, A. (2009) Impacts of Plant Symbiotic Fungi on Insect Herbivores: Mutualism in a Multitrophic Context. Annual Review of Entomology, 54(1), 323-342. DOI: 10.1146/annurev.ento.54.110807.090614
There is an interesting review  (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
Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000361
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’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 »
Rainer TH, & Robertson CE. (1996) Adrenaline, cardiac arrest, and evidence based medicine. Journal of accident , 13(4), 234-7. PMID: 8832338
You know it’s December when it starts snowing in your web browser.
Let it snow, let it snow, let it snow!
snowStorm = new SnowStorm();
Last Friday, the Centrum Wiskunde & Informatica (CWI) in Amsterdam hosted a workshop Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2009.
Following on from last year , the workshop proceedings will be published at ceur-ws.org and in a special issue of the Journal of Biomedical Semantics, but if you want to find out [...]... Read more »
Burger, A., Romano, P., Paschke, A., & Splendiani, A. (2009) Semantic Web Applications and Tools for Life Sciences, 2008 – Introduction. BMC Bioinformatics, 10(Suppl 10). DOI: 10.1186/1471-2105-10-S10-S1
November’s entity of the month at ChEBI is the antimalarial drug Artemether. This accompanies release 62 of ChEBI, not just yet another incremental release but an increase of more than twentyfold in the number of entities in ChEBI, thanks to merging of data between an updated ChEBI  and ChEMBL . ChEBI now (as of [...]... Read more »
de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., & Steinbeck, C. (2009) Chemical Entities of Biological Interest: an update. Nucleic Acids Research. DOI: 10.1093/nar/gkp886
Warr, W. (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Journal of Computer-Aided Molecular Design, 23(4), 195-198. DOI: 10.1007/s10822-009-9260-9
Singh, N., & Panwar, V. (2006) Case Report of a Pituitary Macroadenoma Treated With Artemether. Integrative Cancer Therapies, 5(4), 391-394. DOI: 10.1177/1534735406295311
Wu, Z., Gao, C., Wu, Y., Zhu, Q., Yan Chen, ., Xin Liu, ., & Chuen Liu, . (2009) Inhibitive Effect of Artemether on Tumor Growth and Angiogenesis in the Rat C6 Orthotopic Brain Gliomas Model. Integrative Cancer Therapies, 8(1), 88-92. DOI: 10.1177/1534735408330714
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