If you travel back in time, to around 2002, it isn’t difficult to find people claiming that Web services were going to be the new silver bullet technology to create world peace, eradicate global poverty and finally make some sense of all the data produced by the human genome project. Over hyped? Just a bit. One of the many reasons none of these things happened, is it turned out to be much harder than anticipated to build centralised registries, where people could go to find Web services to perform a given task. Can service registries ever be built? Critics like Tim Bray at Sun Microsystems for example, have suggested that (quote) “registries are a fantasy”, but some already exist and there are more in the pipeline. This article briefly introduces some of them: Seekda, BioMOBY, the Embrace service registry and the Biocatalogue project. (more…)
November 24, 2008
Embracing Registries of Web Services
November 17, 2008
Science blog meme: Why do we blog?
I have been virally infected by Martin Fenner’s “why do we blog” meme.
1. What is your blog about?
Science and technology, especially bioinformatics, systems biology and the Web. It is a personal laboratory notebook-cum-diary, with a few facts and many opinions that would be difficult to publish conventionally [1].
2. What will you never write about?
Banal personal trivia (“I went shopping today”), confidential work, collaborative projects before they have been published. If in doubt, I try to ask people, “is it OK if I blog this?”
3. Have you ever considered leaving science?
Already did, I left science after my undergraduate degree to work in industry, but came back after six years to do a PhD. I don’t think Science ever really leaves you, once a scientist, always a scientist. Can’t see myself “leaving” again, but you never know.
4. What would you do instead?
Tend olive trees in Greece. Sequence 10,000 + Olive tree genomes, do some olive tree systems biology [2]. Subsidise scientific research with money from olive oil export business.
5. What do you think will science blogging be like in 5 years?
Pretty much the same as it is now I reckon, maybe more senior scientists will start blogging, see big boffins with blogs.
6. What is the most extraordinary thing that happened to you because of blogging?
I’m pretty sure blogging was a significant factor in being invited to Science Foo Camp (scifoo)
7. Did you write a blog post or comment you later regretted?
Non, rien de rien. Non, je ne regrette rien. Some of the posts about semantic web and molecular biology I might come to regret in the future though, but life is too short. There is an ever present temptation to write controversial blog posts (that might be regretted later) to get more visitors to your blog. Sometimes I can’t resist. Also, there is no safety net of peer-review, so you can make mistakes very quickly, even faster than by drinking tequila. I often wonder what prospective employers and/or funding bodies would make of it all – by the time I find out, it might be too late 🙂
8. When did you first learn about science blogging?
Via nodalpoint which is run by Greg Tyrelle.
9. What do your colleagues at work say about your blogging?
So far, there have been five basic responses to my blog among colleagues.
a) Great idea, carry on (see picture, top right). Can you blog this for me?
b) Bad idea, why do you waste so much time blogging? When are you going to do some “real” work?
c) Teasing: “I’m drinking a coffee, are you blogging this?”
d) Head-in-the-sand, no acknowledgment, denial, look the other way.
e) Ignorance is bliss. What is a blog? Do you have one of those interweb things on your computer?
References
- Michael R. Seringhaus and Mark B. Gerstein (2007). Publishing perishing? towards tomorrow’s information architecture. BMC Bioinformatics 8, 17+. DOI:10.1186/1471-2105-8-17, pmid:17239245
- Royston Goodacre, Douglas B Kell, Giorgio Bianchi (1992). Neural networks and olive oil. Nature 359 (6396), 594. DOI:10.1038/359594a0
[Keep Calm and Carry On via AJC1]
October 31, 2008
Defrosting the Digital Library
Bibliographic Tools for the Next Generation Web
We started writing this paper [1] over a year ago, so it’s great to see it finally published today. Here is the abstract:
“Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.”
Thanks to Kevin Emamy, Richard Cameron, Martin Flack, and Ian Mulvany for answering questions on the CiteULike and Connotea mailing lists; and Greg Tyrelle for ongoing discussion about metadata and the semantic Web nodalpoint.org. Also thanks to Timo Hannay and Tim O’Reilly for an invitation to scifoo, where some of the issues described in this publication were discussed. Last but not least, thanks to Douglas Kell and Steve Pettifer for helping me write it and the BBSRC for funding it (grant code BB/E004431/1 REFINE project). We hope it is a useful review, and that you enjoy reading it as much as we enjoyed writing it.
References
- Duncan Hull, Steve Pettifer and Douglas B. Kell (2008). Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Computational Biology, 4(10):e1000204+. DOI:10.1371/journal.pcbi.1000204, pmid:18974831, pmcid:2568856, citeulike:3467077
- Also mentioned (in no particular order) by NCESS, Wowter, Twine, Stephen Abram, Rod Page, Digital Koans, Twitter, Bora Zivkovic, Digg, reddit, Library Intelligencer, OpenHelix, Delicious, friendfeed, Dr. Shock, GribbleLab, Nature Blogs, Ben Good, Rafael Sidi, Scholarship 2.0, Subio, up2date, SecondBrain, Hubmed, BusinessExchange, CiteGeist, Connotea and Google
[Sunrise Ice Sculptures picture from Mark K.]
October 30, 2008
Congratulations Matthew Horridge!
So, congratulations are due to Matthew Horridge, Bijan Parsia and Ulrike Sattler from The University of Manchester for winning the keenly fought best paper prize at the International Semantic Web Conference [ISWC 2008] in Karlsruhe for their paper “Laconic and Precise Justifications in OWL”. An abstract of the paper is reproduced below:
“A justification for an entailment in an OWL ontology is a minimal subset of the ontology that is sufficient for that entailment to hold. Since justifications respect the syntactic form of axioms in an ontology, they are usually neither syntactically nor semantically minimal. This paper presents two new subclasses of justifications—laconic justifications and precise justifications. Laconic justifications only consist of axioms that do not contain any superfluous “parts”. Precise justifications can be derived from laconic justifications and are characterised by the fact that they consist of flat, small axioms, which facilitate the generation of semantically minimal repairs. Formal definitions for both types of justification are presented. In contrast to previous work in this area, these definitions make it clear as to what exactly “parts of axioms” are. In order to demonstrate the practicability of computing laconic, and hence precise justifications, an algorithm is provided and results from an empirical evaluation carried out on several published ontologies are presented. The evaluation showed that laconic/precise justifications can be computed in a reasonable time for entailments in a range of ontologies that vary in size and complexity. It was found that in half of the ontologies sampled there were entailments that had more laconic/precise justifications than regular justifications. More surprisingly it was observed that for some ontologies there were fewer laconic justifications than regular justifications.”
But what does it all mean? One of the results of this research project has been an explanations plug-in for the Protégé ontology editor, see explanation in OWL at http://owl.cs.manchester.ac.uk. This helps users to understand when and why the reasoning goes all pear-shaped through better explanations than has previously been possible. So this is another step toward making building better ontologies with the Web Ontology Language (OWL) easier and less confusing. Yay!
References
- Matthew Horridge, Bijan Parsia and Ulrike Sattler (2008). Laconic and Precise Justifications in OWL Lecture Notes in Computer Science, LNCS Volume 5318/-1 The Semantic Web – ISWC 2008 DOI:10.1007/978-3-540-88564-1_21
[Picture of Manchester United player George Best by Sammy, Best paper prize picture by guitarfish]
October 27, 2008
OWL Experiences and Directions (OWLED) 2008
The Web Ontology Language (OWL) is a language for creating ontologies on the Web. It does exactly what it says on the tin. But what is an ontology? One way to think of it is as a better way of storing data and knowledge. Instead of just capturing and describing data in a databases, ontology languages like OWL provide ways to capture and describe knowledge in a knowledge base. Ontologies can allow more intelligent querying, integration and understanding of data than is possible using a plain old relational database.
Since 2003 developers and users of the Web Ontology Language, abbreviated to OWL (not WOL), have been gathering at a two-day workshop called OWLED (OWL Experiences and Directions). This year the workshop is in Karlsruhe in Germany. The full list of accepted papers is available, as with previous years, this years workshop has a distinctly biological flavour to the proceedings: (more…)
October 24, 2008
PNAS envy?
The United States National Academy of Sciences (NAS) is an “honorific society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare”. Set up by none other than Abraham Lincoln himself, the academy publishes a prestigious scientific journal, called the Proceedings of the National Academy of Sciences, better known as just “PNAS” and available at www.pnas.org. This publication is part of a supposedly elite club of high-profile journals – Nature, Science and PNAS (NSPNAS) – that many scientists from all around the world, strive to publish in. Now, there are those that think the world would be a better place if we concentrated on what scientists have to say, rather than where they say it. But currently, life doesn’t always work that way. Better journals, usually tend to have better reviewers and these are often the most important places to publish results. (more…)
October 14, 2008
Open Access Day: Why It Matters
Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view. According to the wikipedia article Open Access (OA) is “free, immediate, permanent, full-text, online access, for any user, web-wide, to digital scientific and scholarly material, primarily research articles published in peer-reviewed journals. OA means that any individual user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article. An OA article usually has limited copyright and licensing restrictions.” What does all this mean and why does it matter? Well, in four question-and-answer points, here goes… (more…)
October 10, 2008
PhD studentships at EMBL-EBI, UK
Any budding biomedical scientists out there, interested in doing a PhD, take note: The European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute (EBI) is having an open day on Monday 3rd November 2008. According to their website the EBI is “happy to welcome all Master students to this day”. Some talks at this open day include:
- Welcome and Introduction Cath Brooksbank
- PhD opportunities at the EBI Nick Goldman
- PhD experience at the EBI – computers, cells and cookies Heidi Dvinge
- 1000 genomes project Paul Flicek
- The truth about Systems Biology: Nicolas le Novère
- Small molecules: Christoph Steinbeck, see SteinBlog
- Extreme Informatics Matt Wood see homepage and Green is Good blog
The EMBL-EBI lies in the 55 acres of landscaped parkland in rural Cambridgeshire that make up the Wellcome Trust Genome Campus. The Campus also houses the Wellcome Trust Sanger Institute, making it one of the world’s largest concentrations of expertise in genomics and bioinformatics. See also PhD Studies in Bioinformatics at the EBI. If you are interested in attending, sign up at the registration page before the 20th October.
See also PhD Opportunities at the Wellcome Trust Sanger Institute, Cambridge.
October 9, 2008
While My Keyboard Gently Weeps
I look at the world and I notice it’s turning
While my keyboard gently weeps
With every mistake we must surely be learning
Still my keyboard gently weeps
Oh oh oh oh oh oh oh
oh oh, oh oh, oh oh
Yeah yeah yeah yeah
yeah yeah yeah yeah.
- George Harrison (1968) While My Guitar Gently Weeps
September 29, 2008
BBSRC UK Roadshow, Autumn 2008
The Biotechnology and Biological Sciences Research Council (BBSRC) is on the road this autumn in London, Manchester, Bristol, Glasgow and Cambridge. Potential applicants, grant holders and any other interested parties are strongly urged to attend and learn about BBSRC’s plans for the future including new procedures and new Committee structures. The road shows will also provide an opportunity to meet the new members of the BBSRC Senior Management team.
From an original email sent by Alf Game, Deputy Director of Science and Technology Group. See BBSRC Roadshows.
The BBSRC has revised its future strategic priorities and the way in which they will be delivered through responsive mode peer review and is holding a series of road shows “Enabling the Delivery of Excellence with Impact” at various locations across the UK. (more…)
O'Really? 