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Informatics

Duncan Hull
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March 17, 2010
06:27 AM
54 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
49 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
53 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
100 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
143 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
162 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
202 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
163 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 »

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

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
232 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 »

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

December 10, 2009
06:18 PM
287 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

December 4, 2009
06:27 PM
243 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

December 3, 2009
04:28 AM
255 views

It’s Snowing (JavaScript)!

by Duncan Hull in O'Really?

You know it’s December when it starts snowing in your web browser.
Let it snow, let it snow, let it snow!
Or programmatically:
snowStorm = new SnowStorm();
There was a time, not so very long ago when JavaScript snow would have been “best viewed in browser x”. Thankfully now its much more reliable, JBrowse [1] is a nice example [...]... Read more »

Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009) JBrowse: A next-generation genome browser. Genome Research, 19(9), 1630-1638. DOI: 10.1101/gr.094607.109

November 23, 2009
06:30 PM
289 views

Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2009, Amsterdam

by Duncan Hull in O'Really?

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 [1], 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 5, 2009
07:27 AM
290 views

Artemether: Entity of the Month

by Duncan Hull in O'Really?

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 [1] and ChEMBL [2]. 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

October 23, 2009
02:31 AM
376 views

Wellcome to the Genome Campus

by Duncan Hull in O'Really?

So, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus.
The Genome Campus owes its existence to the [...]... Read more »

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., & Ashburner, M. (2007) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research, 36(Database). DOI: 10.1093/nar/gkm791

September 18, 2009
06:50 AM
569 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

September 10, 2009
09:28 AM
489 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

September 4, 2009
11:13 AM
460 views

XML training in Oxford

by Duncan Hull in O'Really?

The XML Summer School returns this year at St. Edmund Hall, Oxford from 20th-25th September 2009. As always, it’s packed with high quality technical XML training for every level of expertise, from the Hands-on Introduction through to special classes devoted to XQuery and XSLT, Semantic Technologies, Open Source Applications, Web 2.0, Web Services and Identity. [...]... Read more »

Mike Hucka. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4), 524-531. DOI: 10.1093/bioinformatics/btg015

Bunduchi R, Williams R, Graham I, & Smart A. (2006) XML-based clinical data standardisation in the National Health Service Scotland. Informatics in primary care, 14(4), 227. PMID: 17504574

Sayers, E., Barrett, T., Benson, D., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Edgar, R., Federhen, S.... (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn741

August 24, 2009
01:07 PM
485 views

I bet you think this blog is about you, don’t you?

by Duncan Hull in O'Really?

Last Saturday, The Royal Institution of Great Britain hosted a conference called Science Online London (#solo09) co-organised by Mendeley.com and network.nature.com. The event, centred around the fantastic Faraday Theatre “this beautiful, historic theatre has deeply raked seating that creates an intimate atmosphere, even when full to capacity.” Just like last year, this event attracted delegates [...]... Read more »

Geoffrey Bilder. (2006) In Google We Trust?. Journal of Electronic Publishing, 9(1). DOI: 10.3998/3336451.0009.101

Matt Brown. (2008) Venerable institute gets a refit. Nature, 453(7195), 568-569. DOI: 10.1038/453568a

Matt Brown. (2008) Reimagining the Royal Institution. Nature, 453(7195), 595-595. DOI: 10.1038/453595a

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