Chado Phenotype Module - Staging

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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.

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

public.feature_phenotype Structure
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


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.

Tables referencing this one via Foreign Key Constraints:



Table: phenotype_cvterm

Deprecated and superceded by phenotypeprop.

public.phenotype_cvterm Structure
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


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