From: Pankaj J. <pj...@co...> - 2008-07-28 20:46:17
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Samson Tu wrote: > Hi, > > Forgive me if this topic has been discussed and resolved before. (Can > someone points me to a searchable archive of this list?) > > My understanding of PATO is that it is an ontology of qualities that, > when combined with ontologies of quality-bearing entities, can be used > to post-coordinate a "phenotype" term such as "red eye." > > In this scheme, how does one talk about the characteristic (e.g., eye > color) of which "red" is a possible quality? Does one say that there is > no specific characteristic for which "red" is a possible quality? > Instead, one can talk about the "color", "chromatic property", "optical > quality," "full-spectrum EM radiation quality" (i.e., superclasses of > red color) of the eye as characteristics for which "red" is a quality. > > Is it fair to say that, in PATO, "phenotype" (e.g, red eye) is > synonymous with what some other people call "trait" (e.g., Wikipedia > "Phenotype" article says "The phenotype is composed of traits > <http://en.wikipedia.org/wiki/Trait_%28biology%29> or characteristics"? > Right In this case the trait = eye color value = red phenotype = trait+value Also trait = entity+attribute = eye+color Now there are two facets here. Depends on how the evaluation was done. Whether the phenotype value scored was any color. Which means ther various forms of color were scored like red/blue/green/purple etc. Where teh above scheme fits. The other option is scoring only for presence or absence of 'eye color red'. means trait = eye color red value = yes/no , +/-, present/absent In that case I think (OBO-phenotype people correct me), 'red' is part of the attribute because the quality scored was not the variation in any color but red only. Pankaj |