All I want for Christmas is a book about the semantic web, written by people who are actually building and using it, rather than “visionaries” who don’t have to. Maybe this year I’ll be lucky… A group of semantic webheads (aka HCLSIG the Health Care and Life Sciences Interest Group) led by Christopher J. Baker and Kei-Hoi Cheung and gathered together on public-semweb-lifesci@w3.org have written a book about the semantic web for life sciences.

Dear Santa, all I want for Christmas* is a better version of Connotea, please can you sort out it’s duplicated redundant links? In my book this particular bug is “buggotea” number one.

Have you recently built a bioinformatics web application useful to the wider community that you’d like to tell the world about? Are you also looking to score brownie points for a rigourously peer-reviewed publication that stands a reasonable chance of being well cited?

{please=““ dispose=““ thoughtfully=““ of=““ your=““ used=““ postdocs""=““ width=“240” height=“239”}{please=““ dispose=““ thoughtfully=““ of=““ your=““ used=““ postdocs"=““ by=““ dullhunk,=““ on=““ flickr"=““}Sometimes, being a PostDoctoral researcher is a tough life. Thankfully, help is at hand in Philip Bourne and Iddo Friedberg’s guide Ten Simple Rules for Selecting a Post-Doctoral Position published in PLOS Computational Biology.

This amusing picture-parody of the semantic web is worth a thousand words, was conceived of by Mark Butler for a presentation [1] and drawn by Rachel Murphy of Rude Girl Designs. References Mark Butler (2003) Is the semantic web hype?

UK news-rag The Grauniad has a series of interviews with some of the people behind the next generation web, so-called Web 2.0. After reading these interviews, I can’t help wondering, who are the equivalent pioneers in bioinformatics? The interviews include… Wikipedian Jimmy Wales WordPresser Matt Mullenweg Technorati’s Dave Sifry …and several others too.

There are all sorts of flaws with using impact factors for judging the quality of biomedical research. Love them or hate them, just getting hold of impact factors for journals in bioinformatics and related fields is much harder than it should be, so I thought I’d reproduce some statistics I gathered here.

MEDIE is an “intelligent” semantic search engine that retrieves biomedical correlations from over 14 million articles in MEDLINE. You can find abstracts and sentences in MEDLINE by specifying the semantics of correlations; for example, What activates tumour suppressor protein p53? So just how useful is MEDIE and is it at the cutting edge?

The Manchester Interdisciplinary Biocentre (MIB) is officially opening on 25/26th October 2006. The centre has been about a decade in the making, and aims to be a world-class research centre, with around £37 million (~$70 million) of initial funding from the Wellcome Trust charity, UK Research Councils and others.

Many computer scientists and software engineers are not familiar with basic biology or bioinformatics. Many biologists and bioinformaticians are not familiar with basic computer science or software engineering. This article points to some resources that can help with the former, and asks, what can be done about the latter?

The AAAI conference finished last Thursday, here are some highlights and papers that might be worth reading if you are interested in building and / or using a more “intelligent” (and possibly semantic) web in bioinformatics. Here are the papers or talks I enjoyed the most and hope you might also find them useful or inspiring. Unifying Logical and Statistical AI talk given by Pedro Domingos.