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Saturday, December 17, 2005


 The BCNGroup Beadgames



Challenge Problem  ŕ



Lattice of ontologies



A review of this paper is suggested:




A philosophical position is defined and taken. 


Two scientific methodologies are identified.  The first is the use of what are called “systematic methods” to reconstruct evolutionary history of various gene expressions, ie phenotypes. 


The second also uses systematic methods to make an analysis of gene expression.


In cognitive science “systematic methods” means a characteristic of research studies that involves the careful and systematic use of research procedures.  In gene research the phrase often means the use of cluster techniques such as Kohonen self-organizing maps or some type of latent semantic indexing type similarity matrix – which also results in clusters of data – indicating some stable phenomenon.   (see {link} )


Systematic methods for organizing gene expression data require a means of measuring quantitatively if two expression profiles are similar to each other. In this regard it is useful to consider the values that make up the expression profile for a single gene as a series of coordinates, which define a vector, and to consider the data for a microarray experiment as a matrix, where the genes define the rows, and the arrays, or experiments define the columns. Once we consider these data as vectors, we can use standard mathematical techniques to measure their similarity. One distance metric that can thus be used is the Pearson Correlation, which is essentially a measure as to how similar the directions in which two expression vectors point are. The Pearson Correlation treats the vectors as if they were the same (unit) length, and is thus insensitive to the amplitude of changes that may be seen in the expression profiles. A second distance measure that can be used is the Euclidean distance, which measures the absolute distance between two points in space, which in this case are defined by two expression vectors. The Euclidean distance thus takes into account both the direction and the magnitude of the vectors.  {link}


The results of this analysis has to be placed into a formalism, and this formalism is often a tree like structure with relationships, properties, attributes and facets.