Storing Phenotypes.
Presentation: Naama Menda (BTI / SGN)Slides
What is a phenotype?
How can we store phenotypes?
Phenotypes include morphology, development, behavior, biochemical properies, molecular characteristics. Dependent on genotype and the environment.
Quantitative vs qualitative.
Metadata: weather information, who collected, how measured, etc.
Storing phenotypes: Chado phenotype modules. Problem: Chado tables too generic. One table captured all aspects of a phenotype (a cvterm for entity and a cvterm for the quality (etc), plus a value, cvalue_id (cvterm), and attribute_id. uniquename has a free text description that is basically for qualitative phenotypic information. This table is too limited.
Thinking not about phenotypes, but about natural diversity. Create Natural Diversity chado module, which can store lots of metadata about experiments and stocks.
Chado uses attribute/value, like PATO. Came from Flybase, old. Not
EQV, entity/quality/value (fruit/color/red). Flybase doesn't actually
use the id's, just text; and doesn't give the values, just names the
traits. But Sol can't change the Chado schema because it would affect
Flybase.
"Post-composed" phenotypes like fruit/color/red. Can it be reused for
different experiments?
Now the gmod.org/wiki/Chado_Natural_Diversity_Module.
Interactive QTL mapping in biparental populations. Want to add
association mapping and genomic selection.
Chado "property" tables, generic.
Storing post composed terms: work in progress. Who wants to help?
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