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Informatics

Duncan Hull
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June 18, 2009
01:12 PM
1,531 views

Ooh aah Cantona! Welcome back Eric…

by Duncan Hull in O'Really?

It is great to see the eminent french football philosopher and scientist Eric Cantona back in his adopted hometown of Manchester. As well as visiting in person during production of the latest Ken Loach film (on the famous Keppel Road, Chorlton) and appearing at the premiere, Eric is currently gracing silver screens in cinemas all [...]... Read more »

Hopkin, M. (2006) Goal fever at the World Cup. Nature, 441(7095), 793-793. DOI: 10.1038/441793a

April 1, 2010
06:24 AM
1,382 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

July 20, 2009
06:40 PM
1,271 views

How to be a Rocket Scientist

by Duncan Hull in O'Really?

Today, the 20th July 2009, is the 40th anniversary of the first lunar landing. There has been plenty of global coverage, stargazing, astronautical analysis and heavenly commentary recently. But for me personally, the Apollo 11 anniversary brings back fond memories of rocket science lessons [1] – specifically, the things I learned in Chemistry at school. [...]... Read more »

Paul Smaglik. (2008) Beyond rocket science: Huntsville, Alabama, the original home of NASA and military weapons development, makes a move into biology . Nature, 453(7196), 818-820. DOI: 10.1038/nj7196-818a

June 10, 2009
03:24 AM
1,253 views

Kenjiro Taura on Parallel Workflows

by Duncan Hull in O'Really?

Kenjiro Taura is visting Manchester next week from the Department of Information and Communication Engineering at the University of Tokyo. He will be doing a seminar, the details of which are below:

Title: Large scale text processing made simple by GXP make: A Unixish way to parallel workflow processing

Date-time: Monday, 15 June 2009 at 11:00 AM

Location: [...]... Read more »

Miyao, Y., Sagae, K., Saetre, R., Matsuzaki, T., & Tsujii, J. (2008) Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics, 25(3), 394-400. DOI: 10.1093/bioinformatics/btn631

July 24, 2009
07:40 AM
1,211 views

Escape from the impact factor

by Duncan Hull in O'Really?

Quite by chance, I stumbled on this interesting paper [1] yesterday by Philip Campbell who is the Editor-in-Chief of Nature [2]. Here is the abstract:

As Editor-in-Chief of the journal Nature, I am concerned by the tendency within academic administrations to focus on a journal’s impact factor when judging the worth of scientific contributions by researchers, [...]... Read more »

Philip Campbell. (2008) Escape from the impact factor. Ethics in Science and Environmental Politics, 5-7. DOI: 10.3354/esep00078

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

September 18, 2009
06:50 AM
1,187 views

Popular, personal and public data at PLoS

by Duncan Hull in O'Really?

The Public Library of Science (PLoS) is a non-profit organisation committed to making the world’s scientific and medical literature freely accessible to everyone via open access publishing. As recently announced they have just published the first article-level metrics (e.g. web server logs and related information) for all articles in their library. This is novel, interesting [...]... Read more »

Ioannidis, J. (2005) Why Most Published Research Findings Are False. PLoS Medicine, 2(8). DOI: 10.1371/journal.pmed.0020124

Kirsch, I., Deacon, B., Huedo-Medina, T., Scoboria, A., Moore, T., & Johnson, B. (2008) Initial Severity and Antidepressant Benefits: A Meta-Analysis of Data Submitted to the Food and Drug Administration. PLoS Medicine, 5(2). DOI: 10.1371/journal.pmed.0050045

Lacasse, J., & Leo, J. (2005) Serotonin and Depression: A Disconnect between the Advertisements and the Scientific Literature. PLoS Medicine, 2(12). DOI: 10.1371/journal.pmed.0020392

Levy, S., Sutton, G., Ng, P., Feuk, L., Halpern, A., Walenz, B., Axelrod, N., Huang, J., Kirkness, E., Denisov, G.... (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biology, 5(10). DOI: 10.1371/journal.pbio.0050254

Holy, T., & Guo, Z. (2005) Ultrasonic Songs of Male Mice. PLoS Biology, 3(12). DOI: 10.1371/journal.pbio.0030386

Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005723

The PLoS Medicine Editors. (2006) The Impact Factor Game. PLoS Medicine, 3(6). DOI: 10.1371/journal.pmed.0030291

Voight, B., Kudaravalli, S., Wen, X., & Pritchard, J. (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biology, 4(3). DOI: 10.1371/journal.pbio.0040072

Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C., Wedeen, V., & Sporns, O. (2008) Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060159

Bourne, P. (2005) Ten Simple Rules for Getting Published. PLoS Computational Biology, 1(5). DOI: 10.1371/journal.pcbi.0010057

Lawrence, P. (2006) Men, Women, and Ghosts in Science. PLoS Biology, 4(1). DOI: 10.1371/journal.pbio.0040019

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

Beltrao, P., & Serrano, L. (2007) Specificity and Evolvability in Eukaryotic Protein Interaction Networks. PLoS Computational Biology, 3(2). DOI: 10.1371/journal.pcbi.0030025

Beltrao, P., & Serrano, L. (2005) Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions. PLoS Computational Biology, 1(3). DOI: 10.1371/journal.pcbi.0010026

Ho, B., & Dill, K. (2006) Folding Very Short Peptides Using Molecular Dynamics. PLoS Computational Biology, 2(4). DOI: 10.1371/journal.pcbi.0020027

Saunders, N., Beltrão, P., Jensen, L., Jurczak, D., Krause, R., Kuhn, M., & Wu, S. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Computational Biology, 5(1). DOI: 10.1371/journal.pcbi.1000263

Ho, B., & Agard, D. (2009) Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000343

Wolschin, F., & Gadau, J. (2009) Deciphering Proteomic Signatures of Early Diapause in Nasonia. PLoS ONE, 4(7). DOI: 10.1371/journal.pone.0006394

July 13, 2009
02:30 PM
1,174 views

Science Foo Camp 2009: Scifoo Day Two

by Duncan Hull in O'Really?

The fourth International Science Foo Camp (scifoo) 2009 has just concluded. Here are some very brief and incomplete notes and links from some of the sessions on the second day (Saturday), see the scholarly kitchen for a report on the first day. With seven parallel sessions, most people at this event miss most (six sevenths) [...]... Read more »

Kell, D., & Oliver, S. (2004) Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. BioEssays, 26(1), 99-105. DOI: 10.1002/bies.10385

September 10, 2009
09:28 AM
1,162 views

Why don’t scientists share data?

by Duncan Hull in O'Really?

As Vince Smith once put it [1] data are the fuel of Science:
“The fabric of science is changing, driven by a revolution in digital technologies that facilitate the acquisition and communication of massive amounts of data. This is changing the nature of collaboration and expanding opportunities to participate in science. If digital technologies are the [...]... Read more »

Vince Smith. (2009) Data publication: towards a database of everything. BMC Research Notes, 2(1), 113. DOI: 10.1186/1756-0500-2-113

Anonymous. (2009) Data's shameful neglect: Research cannot flourish if data are not preserved and made accessible. Nature, 461(7261), 145-145. DOI: 10.1038/461145a

Schofield, P., Bubela, T., Weaver, T., Portilla, L., Brown, S., Hancock, J., Einhorn, D., Tocchini-Valentini, G., Hrabe de Angelis, M., & Rosenthal, N. (2009) Post-publication sharing of data and tools. Nature, 461(7261), 171-173. DOI: 10.1038/461171a

Toronto International Data Release Workshop Authors. (2009) Prepublication data sharing. Nature, 461(7261), 168-170. DOI: 10.1038/461168a

Bryn Nelson. (2009) Data sharing: Empty archives. Nature, 461(7261), 160-163. DOI: 10.1038/461160a

Michael Seringhaus, & Mark Gerstein. (2007) Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics, 8(1), 17. DOI: 10.1186/1471-2105-8-17

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

June 23, 2009
08:59 AM
1,159 views

Impact Factor Boxing 2009

by Duncan Hull in O'Really?

The latest results from the world championship impact factor boxing are out. This year includes the first-ever update to the newly introduced Five Year Impact Factor and Eigenfactor™ Metrics [1,2] in JCR Web (See http://www.isiknowledge.com/JCR), presumably in response to widespread criticism of impact factors. The eigenfactor seems to correlate closely the impact factor scores, both [...]... Read more »

Fersht, A. (2009) The most influential journals: Impact Factor and Eigenfactor. Proceedings of the National Academy of Sciences, 106(17), 6883-6884. DOI: 10.1073/pnas.0903307106

Bergstrom, C., & West, J. (2008) Assessing citations with the EigenfactorTM Metrics. Neurology, 71(23), 1850-1851. DOI: 10.1212/01.wnl.0000338904.37585.66

Cockerill, M. (2004) Delayed impact: ISI's citation tracking choices are keeping scientists in the dark. BMC Bioinformatics, 5(1), 93. DOI: 10.1186/1471-2105-5-93

Allen, L., Jones, C., Dolby, K., Lynn, D., & Walport, M. (2009) Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs. PLoS ONE, 4(6). DOI: 10.1371/journal.pone.0005910

June 15, 2009
12:19 PM
1,132 views

Nettab 2009 Day One: Bio-wikis (and football)

by Duncan Hull in O'Really?

A brief wiki-report and some wiki-links from the first short and introductory day of Network Applications and Tools in Biology (NETTAB 2009) in Sicily where there was a tutorial on Technologies of wiki resources and bio-wikis delivered by Paolo Romano and Elda Rossi. This covered Gene Wiki, Wikiproteins, Wikigenes and Wikipathways [1-4].

There is already a [...]... Read more »

Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G., Musen, M., Cockerill, M., Hermjakob, H.... (2008) Calling on a million minds for community annotation in WikiProteins. Genome Biology, 9(5). DOI: 10.1186/gb-2008-9-5-r89

Hoffmann, R. (2008) A wiki for the life sciences where authorship matters. Nature Genetics, 40(9), 1047-1051. DOI: 10.1038/ng.f.217

Huss, J., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T., Valafar, F., & Su, A. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060175

Pico, A., Kelder, T., van Iersel, M., Hanspers, K., Conklin, B., & Evelo, C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060184

December 10, 2009
06:18 PM
1,044 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

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

June 19, 2009
07:26 AM
1,034 views

Nettab 2009 Day Three: Semantic Integration

by Duncan Hull in O'Really?

A brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applicatoins and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on Methods and Tools for RNA Structure and Functional Analysis. Disclaimer: RNA mania isn’t really my thing – so [...]... Read more »

Das, S., Girard, L., Green, T., Weitzman, L., Lewis-Bowen, A., & Clark, T. (2009) Building biomedical web communities using a semantically aware content management system. Briefings in Bioinformatics, 10(2), 129-138. DOI: 10.1093/bib/bbn052

January 15, 2010
08:11 AM
1,024 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

June 4, 2009
09:48 AM
1,013 views

Improving the OBO Foundry Principles

by Duncan Hull in O'Really?

The Open Biomedical Ontologies (OBO) are a set of reference ontologies for describing all kinds of biomedical data, see [1,2] for examples. Every year, users and developers of these ontologies gather from around the globe for a workshop. Following in from last year, the 2nd OBO workshop 2009 is fast approaching.

In preparation, I’ve been revisiting [...]... Read more »

Noy, N., Shah, N., Whetzel, P., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D., Storey, M., Chute, C.... (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research. DOI: 10.1093/nar/gkp440

Côté, R., Jones, P., Apweiler, R., & Hermjakob, H. (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7(1), 97. DOI: 10.1186/1471-2105-7-97

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

Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A., & Rosse, C. (2005) Relations in biomedical ontologies. Genome Biology, 6(5). DOI: 10.1186/gb-2005-6-5-r46

Bada, M., & Hunter, L. (2008) Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics, 24(12), 1448-1455. DOI: 10.1093/bioinformatics/btn194

February 5, 2010
06:53 AM
984 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

February 12, 2010
10:12 AM
957 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

April 8, 2010
06:04 AM
957 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

January 21, 2010
05:05 AM
945 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

March 4, 2010
06:29 AM
939 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

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