nodalpoint.org

I've been trying to come up with a nice way to mashup and process RSS feeds, mostly for the reason to be able to track articles from Journals that publish content that interests me. The best solution seems to be the workflows that can be constructed at Yahoo Pipes.

Steven Salzberg has an opinion piece in Genome Biology that talks about Wikis for managing genome annotation and the problem of bit rot in gene annotation (would that be annotation rot?).

I wrote a quick post about it. This harkens to the other gene wiki discussions on nodalpoint as well as some of the things Ian Holmes and his group are thinking about on the GbrowseAJAX mailing list.

Over at my little blog, I've been musing on how articles about web technology are entering the mainstream media. Examples include a recent SMH story on mash-ups (warning: fairly awful) and in the Guardian technology blog, a small piece on Google Trends.

Google Trends is quite addictive and informative. Try "bioinformatics" as a query - the trend for the past 2 years is rather interesting.

The newest release of the Structured Blogging plugins might be of interest to anyone using Wordpress or Movable Type for keeping a digital record of their work, as it includes a template for writing reviews of journal articles. This provides a form for filling in standard fields (article and journal titles, volume, issue and page numbers, that sort of thing) and produces nicely formatted output as well as auto-generating COinS links so that anyone reading the article review can get directly to the full text of the paper.

I've been wondering how difficult it would be to prescribe a standard format for entering the methods and results of scientific experiments into a weblog...

Liam Quin from W3C has given a few useful tips relating to processing documents (eg error-prone re-typed or scanned text) into XML.

Many of these practises are important for the sort of text processing tasks that seem to come up in bioinformatics.

Article summary: use lots of small one-off scripts to make small changes, continually validate your output, briefly document your steps, automate steps with a meta-script or Makefile and keep input and output text seperate (.. well duh!).

Well, its about time, Tim Berners-Lee finally has a blog.

Nature are really pushing this web technology angle - This week's issue contains an editorial and four news features on "science in the web age". Once again, quotes from popular blogger PZ Myers of Pharyngula and our very own Greg Tyrelle.

As the web was invented some 15 years ago by physicists, perhaps it should be "life science in the web age" - you can't help but form the impression that it's mostly biologists who have been slow to catch on.

CSIRO, Australia's governmental science organisation, is to host the local W3C office. There's a short, uninformed and generally poor summary at ABC News and an official press release at CSIRO.

It seems that the emperor has no clothes:

The utility of ontologies has been clearly demonstrated in several biological domains (e.g., Gene Ontology). However, within biology, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them.

This is from another Semantic Web related Nature article: Are the current ontologies in biology good ontologies?, via Julio Bonis. The point the authors are trying to make is that many of the current bio-ontologies are poorly designed and are therefor unsuitable for use in knowledge sharing applications and automated reasoning (i.e. Semantic Web). They put the MGED microarray ontology under the microscope, finding many inconsistencies.

Via the Semantic web life sciences list: A Nature Biotechnology Perspective disucssing the importance of Semantic Web Technologies and their impact on 'omic standards, is available online (I was able to access this from home ? But a subscription may be required, which is really starting to annoy me). I just don't understand how anyone is supposed to discuss science online if all the information is locked up in walled gardens ?

Anyway the article is good, it is long, but worth the read if you care about how you spend your time doing bioinformatics or if you want to see what the future has in store for biological standards development. So now that you've taken the trouble to read the article and attempted to digest the significance of it, you're probablly thinking "So what ?" it has no real practical benefite for me now ?

It is true that articles like this do not explain these technologies from the point of view of the "working bioinformatician" i.e. what is in it for me if I bother to investigate RDF now ? Read on for some working examples of RDF data integration and a few thoughts on the future of the semantic web and the life sciences (warning, this is an article not a post, so grab a beverage or something).