GMOD

Chado Phenotype Module - Staging

Under Construction

This page or section is under construction.

This page is a working area for updating the revised phenotype module that came out of the GMOD Evo Hackathon. Please edit the table and column descriptions below. These updates will be added to the PostgreSQL comments before the next Chado release.

Contents

Introduction

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

The phenotype tables are spread across the Phenotype and Genetic modules. Both modules originated at FlyBase. There were actually two versions of the Phenotype module that came out of FlyBase: An early one that included the feature_phenotype table; and a later one that included several new phenotype tables in the Genetic module, but did not make use of the feature_phenotype at all. The later release does not tie phenotypes to a single feature, but rather to a genotype, which is a collection of features.

Phenotypes at FlyBase

To try and understand the existing phenotype module during the GMOD Evo Hackathon, participants spent some time exploring the phenotype tables at FlyBase. The notes from that exploration are on the Chado Phenotype Module at FlyBase page.

Tables

Table: feature_phenotype

FK 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

public.feature_phenotype Structure

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.

public.phenotype Structure
FK Name Type Description
phenotype_id serial PRIMARY KEY
uniquename text

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

 units_id integer

Phenotype value units of measurement.

cvterm

 cvalue_id integer

Phenotype attribute value (state).

cvterm

 assay_id integer

Evidence type.

public.phenotype Structure

Tables referencing this one via Foreign Key Constraints:

Table: phenotype_cvterm

Deprecated and superceded by phenotypeprop.

FK 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
  rank integer UNIQUE#1 NOT NULL

public.phenotype_cvterm Structure

Table: phenotypeprop

A phenotype property should either have a value defined in phenotypeprop.value or in phenotypeprop.cvalue_id but not in both fields.

public.phenotypeprop Structure
FK Name Type Description
phenotypeprop_id serial PRIMARY KEY

phenotype

 phenotype_id integer UNIQUE#1 NOT NULL

cvterm

 type_id integer UNIQUE#1 NOT NULL
value text

Property value is free text.

cvterm

 cvalue_id integer

Property value is a cvterm.
rank integer UNIQUE#1 NOT NULL

public.phenotypeprop Structure

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