Ontology of Scientific Experiments

NewScientist of all places are talking about ontologies. Specifically An ontology for scientific experiments.

"Called EXPO, it can be used to translate scientific experiments into a format that can be interpreted by a computer."

Wow! translate experiments, that's impressive I would love to find out how the scrawny hand-writing, contained inside the standard lab notebook, dog-eared and drenched in all manner or reagents, gets translated into an ontology, that's more impressive than the ontology itself.

However on a more serious note, I agree with the concept, that something like this should exist. It would definately help in dissemination and analysis of data (providing the data is freely provided and in a standard structure of format), but this kind of process, an ontology for all of science, would have to have a major open development across all scientific disciplines, as FUGO (Functional Genomics Investigation Ontology) are doing, in order to be agreed upon and for the claim that it represents all scientific experiments.

Going by the article, and snooping around the EXPO site, a cross discipline development process doesn't appear to have taken place, or planned for the future (my apologies if this is not the case). And according to the article it has been tested on two use-cases, one on particle physics and one on evolutionary biology, this must be the only wet-lab science that exists these days. It would be interesting to see if the large scale collaboration effort of FUGO agrees with or already has a similar structure to EXPO
A quote at the bottom of the article says "Software to speed up this process could be a big boost ", I think he meant to say, "This would be impossible without software being available from the wet-lab bench, to data storage, to the publication process".

  1. #1 by Jean-Claude Bradley on June 9, 2006 - 11:32 am

    I have a wet lab also and I was trying to understand exactly what this software enabled. The title of the article may be misleading. I’ve asked my students to look into application to our own data. Since the article states that the software is open source we ought to be able to do that. We’ll post on our blog if we find out and hopefully you’ll do the same.

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