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Thus, there is clear support for the contention that dynamic attractors represent phenotype in mammalian cells and that this has been inherited from more primitive organisms.
While character/character state definitions and EQ statements are both used to represent phenotype descriptions, there is not a one-to-one mapping between the two.
We propose a mathematical labeled graph to represent phenotype morphologies.
In the present work, we used patient data from a specific rare genetic disease (CTX) to formally represent phenotype descriptions using the ontological paradigm [ 15].
Phenotype searches using these modalities have already been developed; MaizeGDB has a sequence search mechanism called POPcorn available, and we have already explored in a previous work (20) how to represent phenotype images as feature vectors and perform image searches.
Interactions inferred by computational methods (37, 38) and genetic interactions, which represent phenotype alterations produced by the mutation/deletion of one gene in the background of a mutation/deletion of another gene (39 41), were not considered here mainly because only a small subset of the databases curate them.
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The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies.
Our study shows that the Semantic Web paradigm provides the technology required to represent phenotype-genotype relationships in diseases with complex and variable manifestations such as CTX.
Of these 259, 214 were determined to represent phenotypes or unmapped genes and not diseases.
These cutoffs represent phenotypes that were just large enough to see.
The expected mutant phenotypes, which represent phenotypes of double mutants in the absence of genetic interactions, are given by a matrix H.
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