GMOD

Chado Phenotype Module

1 Introduction
2 Tables

Introduction

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

Tables

Table: feature_phenotype

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

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.

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