Chado Phenotype Module

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Introduction

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Chris Mungall's 2006 Chado for evolutionary science presentation discusses the Phenotype module.

Tables

Table: feature_phenotype

feature_phenotype Structure
F-Key Name Type Description
feature_phenotype_id serial PRIMARY KEY

feature

feature_id integer UNIQUE#1 NOT NULL

phenotype

phenotype_id integer UNIQUE#1 NOT NULL


Table: phenotype

A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.

phenotype Structure
F-Key Name Type Description
phenotype_id serial PRIMARY KEY
uniquename text UNIQUE NOT NULL

cvterm

observable_id integer

The entity: e.g. anatomy_part, biological_process.

cvterm

attr_id integer

Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.
value text

Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.

cvterm

cvalue_id integer

Phenotype attribute value (state).

cvterm

assay_id integer

Evidence type

Tables referencing this one via Foreign Key Constraints:



Table: phenotype_cvterm

phenotype_cvterm Structure
F-Key Name Type Description
phenotype_cvterm_id serial PRIMARY KEY

phenotype

phenotype_id integer UNIQUE#1 NOT NULL

cvterm

cvterm_id integer UNIQUE#1 NOT NULL