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Re: [ontolog-forum] Relating and Reconciling Ontologies

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Ali Hashemi <ali@xxxxxxxxx>
Date: Tue, 26 Apr 2011 14:25:24 -0400
Message-id: <BANLkTinh12+=Ps+4Rn8rd6r1KYZjQYZv=g@xxxxxxxxxxxxxx>
Heh, broadly related to the topics at hand,

This piece (http://blogs.forbes.com/alexknapp/2011/04/21/chess-art-robots-and-the-future-of-science/) in a forbes blog about the proposals in this article ( http://rsif.royalsocietypublishing.org/content/early/2011/04/08/rsif.2011.0029.full.pdf ).

Quote from the media article:

An ontology-based formalization makes it possible to keep an accurate track of all the result units used for different goals, while preserving the semantics of all the experimental entities involved in all the investigations. Therefore, it is possible to safely reuse information without fear that the meaning of the information will subtly depend on the context in an undocumented way. In addition, thanks to the comprehensive nature of the formalism, it is possible to safely re-use the information without fear that important information is missing. For example, it is possible to check if two yeast strains were grown under the same experimental conditions (temperature, medium, etc.), and if the same methods were used to calculate growth parameters, etc. Formalization makes it easier to compare like with like, and decreases the chance of the introduction of systematic error into a new investigation based on reusing information from another.

And the journal article abstract pasted below:

On the formalization and reuse of scientific research
Ross D. King, Maria Liakata, Chuan Lu, Stephen G. Oliver and Larisa N. Soldatova

Abstract The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [F] and reuse [R] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (Saccharomyces cerevisiae) functional genomics [ f1]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [r1 ¼ R( f1)]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [ f2 ¼ F(r1)]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [r2 ¼ R( f2 .[( This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [ f3 ¼ F(r2)]. These cycles of reuse are a model for the general reuse of scientific knowledge.

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