O'Really?

June 1, 2009

Scott Marshall on Interoperability

M. Scott MarshallScott Marshall is visiting Manchester this week, he will be doing a seminar on Friday 5th June, here are some details for anyone who is interested in attending:

Speaker: Dr. M. Scott Marshall, The University of Amsterdam

Date/Time: 5th June 2009, 11:00

Location: Room MLG.001 (Lecture Theatre), MIB building, (number 16 on campus map)

Title: Standards Enabled Interoperability: W3C Semantic Web for Health Care and Life Sciences Interest Group

Abstract: The W3C Semantic Web for Health Care and Life Sciences Interest Group (HCLS) has the mission of developing, advocating for, and supporting the use of Semantic Web technologies for biological science, translational medicine and health care. HCLS covers hot topics including data integration and federation, bridging commonly used domain standards such as CDISC and HL7, and the applications of medical terminologies. This talk will introduce the HCLS, as well as provide an overview of the activities that are currently ongoing within the task forces, as well as new developments and the recent Face2Face meeting. The role of information extraction and the current interest in Shared Identifiers will also be discussed.

References

  1. Ruttenberg, A., Rees, J., Samwald, M., & Marshall, M. (2009). Life sciences on the Semantic Web: the Neurocommons and beyond Briefings in Bioinformatics, 10 (2), 193-204 DOI: 10.1093/bib/bbp004

May 26, 2009

Subscribing to O’Really?

Filed under: technology — Duncan Hull @ 4:53 pm
Tags: , , , ,

Feed the WorldJust a quick note about subscribing: if you are a regular reader of this O’Really blog and you don’t already subscribe, there are two ways you can receive automatic notifications when new posts are published here:

  1. Point your feed reader at http://feeds2.feedburner.com/oreally, (the preferred method) or …
  2. Point your feed reader at https://duncan.hull.name/feed/ (the WordPress method) which unfortunately gives unreliable subscriber stats. This  feed is linked to by the blue or orange feed icon (pictured right) you should be able to see in your web browsers address bar.

The first feed, is just the second feed re-routed through the magic of FeedBurner, which gives more useful viewing statistics.

Grants on the Web: Transparent Scientific Funding?

Lord Drayson by DIUSGOVUKAll over the Britain, politicians are getting ready to publish their expenses on the Interweb. Why? Because they are trying to regain their lost credibility, after making some incredibly dodgy and embarrassing expense claims [1-7]. Scandals aside, this is all well and good since this money has come from the UK taxpayers pocket, and politicians are public servants, doing public work which is supposedly in the public good.

Scientists, like politicians, also provide a public service, spending public money, for the public good. Science is public knowledge after all and scientists spend quite a lot of public money. At least £3 billion was spent on scientific research in the UK during 2008 (see Who Funds Science in Britain?) and that was just research, not teaching. Wouldn’t it be great if anyone who was interested could see what all this money had been spent on, who spent it and what the outcomes were?

Thankfully you can already do this for some areas of research. The Engineering and Physical Sciences Research Council (EPSRC) which currently spends around £740 million a year on everything from “mathematics to materials science, and from information technology to structural engineering” has a system called Grants on the Web @ gow.epsrc.ac.uk. You can find out who spent the money and how much money was spent since the system was set up, see an EPSRC example here. Some of the original grant proposals are there too, which can be enlightening. The Biotechnology and Biological Sciences Research Council (BBSRC) also has a similar system (called oasis), though it is not as easy to use and link to – see a BBSRC example here. The trouble is, if you can’t easily link to it, it doesn’t get indexed by search engines. If it doesn’t get indexed by search engines, then it’s almost invisible. Fortunately, the BBSRC are working on improving this, with a new system due for release in the autumn of 2009.

Other organisations are putting grant information on the web too. Recently, thanks to the UK’s PubMed Central database you can also see the published results of publicly funded biomedical research. The funders pages at ukpmc.ac.uk/funders give a breakdown of published results from different funding bodies, as described in this article by Robert Kiley of the Wellcome Trust and this one by Alison Henning.

Now not all the research councils seem to publish their grants on the Web in a transparent manner*, and some of those that do, leave lots of room for improvement. But it is still useful to be able to see where some of that public money went and what the outcomes of the research were. More transparent spending of public money like this isn’t just a desirable extra, it should come as standard.

* (It is difficult to find the details of grants awarded by JISC, NERC, MRC and STFC, but please leave a comment below if you know where this information is published. More commentary on this post over at friendfeed.)

[Creative Commons licensed picture of Baron Paul Drayson, currently UK Science Minister from DIUSGOVUK.]

References

  1. The Daily Telegraph (2009) MPs’ expenses: all the gory details from the Daily Telegraph
  2. The Guardian (2009) Grauniad datablog: MP’s expenses as spreadsheet and Free Our Data: Make taxpayers’ data available to them
  3. Wikipedia (2009) MPs’ expenses in wikipedia
  4. BBC News (2009) MPs’ expenses: A triumph of journalism? A week after its opening salvo, the Daily Telegraph is still reaping great benefit from its exclusive expose of MPs’ expenses.
  5. BBC News (2009) Q&A: MP expenses row explained: Revelations in the Daily Telegraph about exactly what MPs have been claiming on expenses has prompted a public outcry and a pledge to reform the “gentlemen’s club” at Westminster
  6. BBC Newsnight (2009) Stephen Fry dismisses MPs’ expenses row, accusing journalists of hypocrisy
  7. The Guardian (2009) Censored version of MPs’ expenses will break the law, Hugh Tomlinson QC warns

May 21, 2009

Upcoming Gig: The Italian Job at NETTAB

NETTAB: Network Tools and Applications in BiologyNetwork Tools and Applications in Biology (NETTAB) is a series of workshops in Bioinformatics. It focuses on the most promising and innovative ICT tools and their utility in Bioinformatics. These workshops aim to introduce participants to the evolving network standards and technologies that are being applied to the field of biology.

Since 2001, the NETTAB workshops have being doing a Giro d’Italia or  Grand Tour of Italy; Genova, Bologna, Naples, Sardinia, Lake Como and Pisa have all played host to the workshop. This year, NETTAB 2009 is in Catania at the Università degli Studi di Catania in Sicily close to Mount Etna.

There is special theme for this years workshop, held on June 10-13, on Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development. So I’m very pleased that Paolo Romano asked me to do a keynote presentation (w00t!) on the work we have been doing in the REFINE project and myExperiment. Grazie Paolo, grazie. And thanks Carole Goble too for the recommendation.

If you’re going to NETTAB this year, see you there. If you’d like to come, today is the last day for the early bird discount, sign up at the registration page. The scientific programme looks interesting, it will be good to meet Alex Bateman and Tim Clark and the rest of this years speakers.

Now, if my keynote presentation is going to (as Michael Caine once famously said [1]) “blow the bl**dy doors off” [2], it needs loads more work. So I’d better get back to it. Ciao!

[Update: See reports from day one, day two and day three of NETTAB 2009.]

References

  1. Peter Collinson and Troy Kennedy-Martin (1969) The Italian Job
  2. Michael Caine (1969) “You’re only supposed to blow the bl**dy doors off!”
  3. Cannata, N., Schröder, M., Marangoni, R., & Romano, P. (2008). A Semantic Web for bioinformatics: goals, tools, systems, applications BMC Bioinformatics, 9 (Suppl 4) DOI: 10.1186/1471-2105-9-S4-S1

May 19, 2009

Defrosting the John Rylands University Library

Filed under: seminars — Duncan Hull @ 4:14 pm
Tags: , , , , , , , , , , , ,

http://www.flickr.com/photos/dpicker/3107856991/For anyone who missed the original bioinformatics seminar I’ll be doing a repeat of the “Defrosting the Digital Library” talk, this time for the staff in the John Rylands University Library (JRUL) . This is the main academic library in Manchester with (quote) “more than 4 million printed books and manuscripts, over 41,000 electronic journals and 500,000 electronic books, as well as several hundred databases, the John Rylands University Library is one of the best-resourced academic libraries in the country.” The journal subscription budget of the library is currently around £4 million per year, that’s before they’ve even bought any books! Here is the abstract for the talk:

After centuries with little change, scientific libraries have recently experienced massive upheaval. From being almost entirely paper-based, most libraries are now almost completely digital. This information revolution has all happened in less than 20 years and has created many novel opportunities and threats for scientists, publishers and libraries.

Today, we are struggling with an embarrassing wealth of digital knowledge on the Web. Most scientists access this knowledge through some kind of digital library, however these places can be cold, impersonal, isolated, and inaccessible places. Many libraries are still clinging to obsolete models of identity, attribution, contribution, citation and publication.

Based on a review published in PLoS Computational Biology, pubmed.gov/18974831 this talk will discuss the current chilly state of digital libraries for biologists, chemists and informaticians, including PubMed and Google Scholar. We highlight problems and solutions to the coupling and decoupling of publication data and metadata, with a tool called citeulike.org. This software tool (and many other tools just like it) exploit the Web to make digital libraries “warmer”: more personal, sociable, integrated, and accessible places.

Finally issues that will help or hinder the continued warming of libraries in the future, particularly the accurate identity of authors and their publications, are briefly introduced. These are discussed in the context of the BBSRC funded REFINE project, at the National Centre for Text Mining (NaCTeM.ac.uk), which is linking biochemical pathway data with evidence for pathways from the PubMed database.

Date: Thursday 21st May 2009, Time: 13.00, Location: John Rylands University (Main) Library Oxford Road, Parkinson Room (inside main entrance, first on right) University of Manchester (number 55 on google map of the Manchester campus). Please come along if you are interested…

References

  1. 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

[CC licensed picture above, the John Rylands Library on Deansgate by dpicker: David Picker]

May 15, 2009

Y.M.C.A. – Just a little bit of G.T.C.A.

OK, look I know that by posting the latest viral marketing video from Bio-Rad Laboratories, Inc. I’m just a pawn (or vector) in their advertising game. This particular video has been around for a couple of months now but it is probably poor internet hygiene to spread these pandemic viral videos. I should just catch it, kill it and bin it. However, I can’t resist this one any longer because, like the last one, it is pretty kitsch, pretty funny and in a strange way, it might just increase the public awareness of Science. Maybe.

And it’s Friday today too, so to the tune of Y.M.C.A. by the Village People, you are now infected with just a little bit of (altogether now…) G.T.C.A.!

The lyrics go a little something like this: (more…)

May 13, 2009

XML Summer School, Oxford

XML Summer School, Oxford, U.K.After a brief absence, it is good to see the XML Summer School is back again this September (20th-25th) at St. Edmund Hall, Oxford. This is  “a unique event for everyone using, designing or implementing solutions using XML and related technologies.” I’ve been both a delegate and a speaker here over the years; back in 2005, with Nick Drummond we presented the Protégé and OWL tutorial which was good fun.  So here is what I.M.H.O. makes the XML summer school worth a look: (more…)

May 6, 2009

Michel Dumontier on Representing Biochemistry

Michel Dumontier by Tom HeathMichel Dumontier is visiting Manchester this week, he will be doing a seminar on Monday 11th of May,  here are some details for anyone who is interested in attending:

Title: Increasingly Accurate Representation of Biochemistry

Speaker: Michel Dumontier, dumontierlab.com

Time: 14.00, Monday 11th May 2009
Venue: Atlas 1, Kilburn Building, University of Manchester, number 39 on the Google Campus Map

Abstract: Biochemical ontologies aim to capture and represent biochemical entities and the relations that exist between them in an accurate manner. A fundamental starting point is biochemical identity, but our current approach for generating identifiers is haphazard and consequently integrating data is error-prone. I will discuss plausible structure-based strategies for biochemical identity whether it be at molecular level or some part thereof (e.g. residues, collection of residues, atoms, collection of atoms, functional groups) such that identifiers may be generated in an automatic and curator/database independent manner. With structure-based identifiers in hand, we will be in a position to more accurately capture context-specific biochemical knowledge, such as how a set of residues in a binding site are involved in a chemical reaction including the fact that a key nitrogen atom must first be de-protonated. Thus, our current representation of biochemical knowledge may improve such that manual and automatic methods of biocuration are substantially more accurate.

Update: Slides are now available via SlideShare.

[Creative Commons licensed picture of Michel in action at ISWC 2008 from Tom Heath]

References

  1. Michel Dumontier and Natalia Villanueva-Rosales (2009) Towards pharmacogenomics knowledge discovery with the semantic web Briefings in Bioinformatics DOI:10.1093/bib/bbn056
  2. Doug Howe et al (2008) Big data: The future of biocuration Nature 455, 47-50 doi:10.1038/455047a

May 1, 2009

www2009: Twentieth Web Anniversary

www2009: Madrid, SpainThe 18th International World Wide Web Conference, www2009 finished last week in Madrid. In times of global economic, pandemic and ecologic crisis, the value of attending international conferences is questionable, so for armchair delegates like me, here are some www papers and www links that are www worth a look. Obviously, virtual conference attendance via the Web is no substitute for The Real Thing® in Real Time with Real People® , but it is cheaper and has a considerably smaller Carbon footprint than actual conference attendance. So, in no particular order, some www interesting www stuff: (more…)

April 17, 2009

The Unreasonable Effectiveness of Google

GoogleVia the Official Google Research Blog at the University of Google, Alon Halevy, Peter Norvig and Fernando Pereira have published an interesting expert opinion piece in the  March/April 2009 edition of IEEE Intelligent Systems: computer.org/intelligent. The paper talks about embracing complexity and making use of the “the unreasonable effectiveness of data” [1] drawing analogies with the “unreasonable effectiveness of mathematics” [2]. There is plenty to agree and disagree with in this provocative article which makes it an entertaining read. So what can we learn from those expert Googlers in the Googleplex? (more…)

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