From GMOD

Contents 1 Introduction 1.1 Phenotypes at FlyBase 2 Tables 2.1 Table: feature_phenotype 2.2 Table: phenotype 2.3 Table: phenotype_cvterm 2.4 Table: phenotypeprop

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:

• feature_phenotype

• nd_experiment_phenotype

• phenotype_comparison

• phenotype_cvterm

• phenotypeprop

• phenstatement

---

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Deprecated and superceded by phenotypeprop.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

---