May 27, 2010

The 2nd ChEBI workshop: Call for Participation

The NanoPutians:  Synthesis of Anthropomorphic MoleculesThe second Chemical Entities of Biological Interest (ChEBI) workshop will be held at the European Bioinformatics Institute (EBI) in Hinxton, Cambridgeshire, UK on the 23rd and 24th June 2010. The full provisional schedule (including registration page) for this workshop is now available. Speakers at the workshop include:

There will also be several discussion sessions on the future evolution of the ChEBI project. Training will be provided including using ChEBI for research purposes and submitting your chemicals to ChEBI for annotation. We (the ChEBI team) hope to welcome you to Hinxton in June.


  1. Image of The NanoPutians taken from: Chanteau, S., & Tour, J. (2003). Synthesis of Anthropomorphic Molecules: The NanoPutians The Journal of Organic Chemistry, 68 (23), 8750-8766 DOI: 10.1021/jo0349227

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]


  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

March 16, 2009

July 25, 2008

How to spend a £400 million Science budget

A thought experiment with lots of money

The Queens Ahead by canonsnapperThe Biotechnology and Biological Sciences Research Council (BBSRC) is the United Kingdom’s funding agency for academic research and training in the non-clinical life sciences. It supports a total of around 1600 scientists and 2000 research students in universities and institutes in the UK. The head of our laboratory, Douglas Kell, has recently been appointed Chief Executive of the BBSRC [1]. Congratulations Doug, we wish you the very best in your new job. Now, according to bbsrc.ac.uk, their annual budget is a cool £400 million (just short of $800 million or €500 million). This has left me wondering, how would you spend a £400 million Science budget for the life sciences? For the purposes of this article, imagine it was you that had been put in charge of said budget, and Prime Minister Gordon Brown (texture like sun) had given you, yes YOU, a big bag of cash to distribute as you see fit. A mouth-watering prospect, I think you’ll agree. Here, is my personal opinion of how, in my dreams, I would spend the money. (more…)

Blog at WordPress.com.