nodalpoint.org - The semantic web for life sciences now ! - Comments

I don't know of any system

Greg — Sun, 11 Dec 2005 03:06:22 -0500

I don't know of any system based on the semantic web technology stack (RDF/OWL/SPARQL/RULEML) that can do what you ask. However in my travels I have come across the following papers that attempt to discover new knowledge based on similar concepts (graphs, inferencing, ontologies etc.), these might provide a few pointers:

An architecture for biological information extraction and representation
HyBrow: a prototype system for computer-aided hypothesis evaluation
A graph-theoretic approach to testing associations between disparate sources of functional genomics data

When you originally posted this I couldn't remember these papers (shame on me for not keeping my citation database up to date). It was only during a recent paper "clean out" that I came across them again :)

Knowledge discovery with the Semantic Web

fjossinet — Fri, 28 Oct 2005 05:58:00 -0400

It's possible to query RDF but is it possible to discover new knowledge using RDF data and ontologies with some machine learning strategies ? Do you know any examples ? Can Jena or R/Rswub do that task ? Recently I was interested in the Weka framework, but it seems that there is nothing about RDF data mining. I have seen that RDF and OWL can be extended with probability informations. The semantic network can be extended as a Bayesian one. My problem is that representing knowledge and information with RDF is not enough. What i want is a framework to display, query and derive new information.Something like that. Any idea welcome ;)

Bunch of links here too.

alf — Mon, 03 Oct 2005 20:09:37 -0400

Bunch of links here too.

A nice introduction to RDF

Greg — Mon, 03 Oct 2005 19:01:03 -0400

A nice introduction to RDF was just posted on the semantic web interest group mailing list. It is a bit long, and not very gentle, but appropriate if you know your way around Perl/Python/Ruby/XML etc.

This article was mostly off

Greg — Mon, 26 Sep 2005 21:27:16 -0400

This article was mostly off the top of my head after reading the nature article (with a little bit of time messing with the RDF data). So I'm happy that it came out as a nice introduction, or at least an understandable introduction.

I have at no point in my investigation of the semantic web read any definitive books on the subject. The Explorers' Guide to the Semantic Web "looks good" although I can hardly recommend it, having not read it. The concept is so amorphous it is hard to get a real hold of, I think I got there the hard way, by just doing a lot of reading. I will try an put together a few resources for the semantic web on the wiki. For the moment you can try the official home page for The Semantic Web for Life Sciences W3C working group.

Or, since I have a lot of spare time a the moment I might even start writing a book on the subject...

Your favorite Semantic Web book

fjossinet — Mon, 26 Sep 2005 12:02:15 -0400

Nice introduction Greg. I'm exploring this direction for my own research. Do you have a book to suggest? I have seen this one that looks interesting: Explorer's Guide to the Semantic Web

Nature v Science

chris — Thu, 22 Sep 2005 00:47:40 -0400

I have to admit that I'd take Nature over Science in this respect: at least you can get to the content relatively easily. Science is an absolute nightmare. All that's missing is a row of blinking dots and an "under construction" sign...

The thing that floors me is that NPG are charging separate subscription rates for access to parts of their archives covering different periods. How extortionate is that? I'm sure it's been expensive to convert old back issues to pdf (which didn't exist in the 1880's), but really...

I'm beginning to get it

Neil — Wed, 21 Sep 2005 23:20:43 -0400

This is good stuff, I enjoyed it.

I used to think that the time I spend pre-processing and reformatting data before I can even use it for research was just part and parcel of bioinformatics. Now though, it just annoys me. I'm currently interested in retrieving intergenic regions from genomes (a fairly simple exercise in feature coordinate finding really) and I wish there were a web resource where I could simply type "NC_001234:1000..2000" or whatever and get that region in a fasta file. I posted a small piece over at one of my blogs on the challenges of parsing GenBank for this purpose.

Off-topic re: Nature - I hate their website for many reasons - bad design, flash ads, those useless careers editorials at the end - but mainly because of their nonsensical policy on what's premium content and what isn't. And they're not alone in that. The Science site is little better. You'd think the "big two" could get it together.

The semantic web for life sciences now !

Greg — Wed, 21 Sep 2005 16:32:56 -0400

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).