A thought experiment with lots of money The 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].

With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”? Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a couple of recent meetings, ChEBI is going

According to their website “The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain”. This week they are having a workshop in Cambridge, to bring myself up to speed, here is a quick name check of some of the

This thing called Science, whatever it is, who actually owns it? Scientists? Technology companies? Industrial Biotechnology and Pharmaceutical companies? Investors? Shareholders? Governments? Universities? Philanthropists? Charities? Publishers? Joe Public?

I’m not much of an evolutionary biologist, but Jonathan Eisen asked for help and I can’t resist. So, in the name of Science, here is some deserved Google Juice for various Trees of Life on the Web.

There is no shortage of bibliographic management tools out there, which ultimately aim to save your time managing the papers and books in your personal library. I’ve just been to a demo and sales pitch for one of them, a tool called RefWorks.

The School of Computer Science of the University of Manchester has up to 16 studentships to offer to highly motivated research students who wish to start a PhD in September 2008 (in exceptional circumstances the start date can be deferred until April 2009). The studentships pay tuition fees and a stipend to cover living expenses for 3 years.

What exactly is a drug? A project I’m currently working on requires a good solid definition, at the very least comprehensible to humans, and preferably understandable by more intelligent, semantically aware computers too.

Some rough and ready notes from day two of the first ChEBI workshop, 20th May 2008. There were two talks, one from Kirill Degtyarenko (European Patent Office) and the other from Janna Hastings (EBI), followed by a discussion. Kirill Degtyarenko: Good annotation practice for chemical data, ChEBI experience Kirill’s talk described how to give the most appropriate names, especially since “biologists don’t name things properly, if at all” (!).

Some notes from day one of the first ChEBI workshop, 19th May 2008. There were four talks from Colin Batchelor (Royal Society of Chemistry), Ulrike Witting (EML Research GmbH Hiedelberg), Giles Weaver (Unilever) and Paula de Matos (EBI). Christoph Steinbeck has already written some ChEBI notes, these just add a little more detail.

Chemical Entitites of Biological Interest, ChEBI, is a freely available dictionary [1] of molecular entities, especially small chemical compounds. Like all big dictionaries and ontologies, it has its own unique challenges. Fortunately, those nice people at the EBI are holding a workshop to discuss future developments in ChEBI. In preparation for the workshop, here are some brief notes on how ChEBI could be made better.